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Research in the Biological and Life Sciences: A Guide for Cornell Researchers: Literature Reviews

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What is a Literature Review?

A literature review is a body of text that aims to review the critical points of current knowledge on a particular topic. Most often associated with science-oriented literature, such as a thesis, the literature review usually proceeds a research proposal, methodology and results section. Its ultimate goals is to bring the reader up to date with current literature on a topic and forms that basis for another goal, such as the justification for future research in the area. (retrieved from  http://en.wikipedia.org/wiki/Literature_review )

Writing a Literature Review

The literature review is the section of your paper in which you cite and briefly review the related research studies that have been conducted. In this space, you will describe the foundation on which  your  research will be/is built. You will:

• discuss the work of others
• evaluate their methods and findings
• identify any gaps in their research
• state how  your  research is different

The literature review should be selective and should group the cited studies in some logical fashion.

If you need some additional assistance writing your literature review, the Knight Institute for Writing in the Disciplines offers a  Graduate Writing Service .

Demystifying the Literature Review

For more information, visit our guide devoted to " Demystifying the Literature Review " which includes:

• guide to conducting a literature review,
• a recorded 1.5 hour workshop covering the steps of a literature review, a checklist for drafting your topic and search terms, citation management software for organizing your results, and database searching.

Online Resources

• A Guide to Library Research at Cornell University
• Literature Reviews: An Overview for Graduate Students North Carolina State University 
• The Literature Review: A Few Tips on Conducting Written by Dena Taylor, Director, Health Sciences Writing Centre, and Margaret Procter, Coordinator, Writing Support, University of Toronto
• How to Write a Literature Review University Library, University of California, Santa Cruz
• Review of Literature The Writing Center, University of Wisconsin-Madison

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Ten Simple Rules for Writing a Literature Review

Marco pautasso.

1 Centre for Functional and Evolutionary Ecology (CEFE), CNRS, Montpellier, France

2 Centre for Biodiversity Synthesis and Analysis (CESAB), FRB, Aix-en-Provence, France

Literature reviews are in great demand in most scientific fields. Their need stems from the ever-increasing output of scientific publications [1] . For example, compared to 1991, in 2008 three, eight, and forty times more papers were indexed in Web of Science on malaria, obesity, and biodiversity, respectively [2] . Given such mountains of papers, scientists cannot be expected to examine in detail every single new paper relevant to their interests [3] . Thus, it is both advantageous and necessary to rely on regular summaries of the recent literature. Although recognition for scientists mainly comes from primary research, timely literature reviews can lead to new synthetic insights and are often widely read [4] . For such summaries to be useful, however, they need to be compiled in a professional way [5] .

When starting from scratch, reviewing the literature can require a titanic amount of work. That is why researchers who have spent their career working on a certain research issue are in a perfect position to review that literature. Some graduate schools are now offering courses in reviewing the literature, given that most research students start their project by producing an overview of what has already been done on their research issue [6] . However, it is likely that most scientists have not thought in detail about how to approach and carry out a literature review.

Reviewing the literature requires the ability to juggle multiple tasks, from finding and evaluating relevant material to synthesising information from various sources, from critical thinking to paraphrasing, evaluating, and citation skills [7] . In this contribution, I share ten simple rules I learned working on about 25 literature reviews as a PhD and postdoctoral student. Ideas and insights also come from discussions with coauthors and colleagues, as well as feedback from reviewers and editors.

Rule 1: Define a Topic and Audience

How to choose which topic to review? There are so many issues in contemporary science that you could spend a lifetime of attending conferences and reading the literature just pondering what to review. On the one hand, if you take several years to choose, several other people may have had the same idea in the meantime. On the other hand, only a well-considered topic is likely to lead to a brilliant literature review [8] . The topic must at least be:

• interesting to you (ideally, you should have come across a series of recent papers related to your line of work that call for a critical summary),
• an important aspect of the field (so that many readers will be interested in the review and there will be enough material to write it), and
• a well-defined issue (otherwise you could potentially include thousands of publications, which would make the review unhelpful).

Ideas for potential reviews may come from papers providing lists of key research questions to be answered [9] , but also from serendipitous moments during desultory reading and discussions. In addition to choosing your topic, you should also select a target audience. In many cases, the topic (e.g., web services in computational biology) will automatically define an audience (e.g., computational biologists), but that same topic may also be of interest to neighbouring fields (e.g., computer science, biology, etc.).

Rule 2: Search and Re-search the Literature

After having chosen your topic and audience, start by checking the literature and downloading relevant papers. Five pieces of advice here:

• keep track of the search items you use (so that your search can be replicated [10] ),
• keep a list of papers whose pdfs you cannot access immediately (so as to retrieve them later with alternative strategies),
• use a paper management system (e.g., Mendeley, Papers, Qiqqa, Sente),
• define early in the process some criteria for exclusion of irrelevant papers (these criteria can then be described in the review to help define its scope), and
• do not just look for research papers in the area you wish to review, but also seek previous reviews.

The chances are high that someone will already have published a literature review ( Figure 1 ), if not exactly on the issue you are planning to tackle, at least on a related topic. If there are already a few or several reviews of the literature on your issue, my advice is not to give up, but to carry on with your own literature review,

The bottom-right situation (many literature reviews but few research papers) is not just a theoretical situation; it applies, for example, to the study of the impacts of climate change on plant diseases, where there appear to be more literature reviews than research studies [33] .

• discussing in your review the approaches, limitations, and conclusions of past reviews,
• trying to find a new angle that has not been covered adequately in the previous reviews, and
• incorporating new material that has inevitably accumulated since their appearance.

When searching the literature for pertinent papers and reviews, the usual rules apply:

• be thorough,
• use different keywords and database sources (e.g., DBLP, Google Scholar, ISI Proceedings, JSTOR Search, Medline, Scopus, Web of Science), and
• look at who has cited past relevant papers and book chapters.

Rule 3: Take Notes While Reading

If you read the papers first, and only afterwards start writing the review, you will need a very good memory to remember who wrote what, and what your impressions and associations were while reading each single paper. My advice is, while reading, to start writing down interesting pieces of information, insights about how to organize the review, and thoughts on what to write. This way, by the time you have read the literature you selected, you will already have a rough draft of the review.

Of course, this draft will still need much rewriting, restructuring, and rethinking to obtain a text with a coherent argument [11] , but you will have avoided the danger posed by staring at a blank document. Be careful when taking notes to use quotation marks if you are provisionally copying verbatim from the literature. It is advisable then to reformulate such quotes with your own words in the final draft. It is important to be careful in noting the references already at this stage, so as to avoid misattributions. Using referencing software from the very beginning of your endeavour will save you time.

Rule 4: Choose the Type of Review You Wish to Write

After having taken notes while reading the literature, you will have a rough idea of the amount of material available for the review. This is probably a good time to decide whether to go for a mini- or a full review. Some journals are now favouring the publication of rather short reviews focusing on the last few years, with a limit on the number of words and citations. A mini-review is not necessarily a minor review: it may well attract more attention from busy readers, although it will inevitably simplify some issues and leave out some relevant material due to space limitations. A full review will have the advantage of more freedom to cover in detail the complexities of a particular scientific development, but may then be left in the pile of the very important papers “to be read” by readers with little time to spare for major monographs.

There is probably a continuum between mini- and full reviews. The same point applies to the dichotomy of descriptive vs. integrative reviews. While descriptive reviews focus on the methodology, findings, and interpretation of each reviewed study, integrative reviews attempt to find common ideas and concepts from the reviewed material [12] . A similar distinction exists between narrative and systematic reviews: while narrative reviews are qualitative, systematic reviews attempt to test a hypothesis based on the published evidence, which is gathered using a predefined protocol to reduce bias [13] , [14] . When systematic reviews analyse quantitative results in a quantitative way, they become meta-analyses. The choice between different review types will have to be made on a case-by-case basis, depending not just on the nature of the material found and the preferences of the target journal(s), but also on the time available to write the review and the number of coauthors [15] .

Rule 5: Keep the Review Focused, but Make It of Broad Interest

Whether your plan is to write a mini- or a full review, it is good advice to keep it focused 16 , 17 . Including material just for the sake of it can easily lead to reviews that are trying to do too many things at once. The need to keep a review focused can be problematic for interdisciplinary reviews, where the aim is to bridge the gap between fields [18] . If you are writing a review on, for example, how epidemiological approaches are used in modelling the spread of ideas, you may be inclined to include material from both parent fields, epidemiology and the study of cultural diffusion. This may be necessary to some extent, but in this case a focused review would only deal in detail with those studies at the interface between epidemiology and the spread of ideas.

While focus is an important feature of a successful review, this requirement has to be balanced with the need to make the review relevant to a broad audience. This square may be circled by discussing the wider implications of the reviewed topic for other disciplines.

Rule 6: Be Critical and Consistent

Reviewing the literature is not stamp collecting. A good review does not just summarize the literature, but discusses it critically, identifies methodological problems, and points out research gaps [19] . After having read a review of the literature, a reader should have a rough idea of:

• the major achievements in the reviewed field,
• the main areas of debate, and
• the outstanding research questions.

It is challenging to achieve a successful review on all these fronts. A solution can be to involve a set of complementary coauthors: some people are excellent at mapping what has been achieved, some others are very good at identifying dark clouds on the horizon, and some have instead a knack at predicting where solutions are going to come from. If your journal club has exactly this sort of team, then you should definitely write a review of the literature! In addition to critical thinking, a literature review needs consistency, for example in the choice of passive vs. active voice and present vs. past tense.

Rule 7: Find a Logical Structure

Like a well-baked cake, a good review has a number of telling features: it is worth the reader's time, timely, systematic, well written, focused, and critical. It also needs a good structure. With reviews, the usual subdivision of research papers into introduction, methods, results, and discussion does not work or is rarely used. However, a general introduction of the context and, toward the end, a recapitulation of the main points covered and take-home messages make sense also in the case of reviews. For systematic reviews, there is a trend towards including information about how the literature was searched (database, keywords, time limits) [20] .

How can you organize the flow of the main body of the review so that the reader will be drawn into and guided through it? It is generally helpful to draw a conceptual scheme of the review, e.g., with mind-mapping techniques. Such diagrams can help recognize a logical way to order and link the various sections of a review [21] . This is the case not just at the writing stage, but also for readers if the diagram is included in the review as a figure. A careful selection of diagrams and figures relevant to the reviewed topic can be very helpful to structure the text too [22] .

Rule 8: Make Use of Feedback

Reviews of the literature are normally peer-reviewed in the same way as research papers, and rightly so [23] . As a rule, incorporating feedback from reviewers greatly helps improve a review draft. Having read the review with a fresh mind, reviewers may spot inaccuracies, inconsistencies, and ambiguities that had not been noticed by the writers due to rereading the typescript too many times. It is however advisable to reread the draft one more time before submission, as a last-minute correction of typos, leaps, and muddled sentences may enable the reviewers to focus on providing advice on the content rather than the form.

Feedback is vital to writing a good review, and should be sought from a variety of colleagues, so as to obtain a diversity of views on the draft. This may lead in some cases to conflicting views on the merits of the paper, and on how to improve it, but such a situation is better than the absence of feedback. A diversity of feedback perspectives on a literature review can help identify where the consensus view stands in the landscape of the current scientific understanding of an issue [24] .

Rule 9: Include Your Own Relevant Research, but Be Objective

In many cases, reviewers of the literature will have published studies relevant to the review they are writing. This could create a conflict of interest: how can reviewers report objectively on their own work [25] ? Some scientists may be overly enthusiastic about what they have published, and thus risk giving too much importance to their own findings in the review. However, bias could also occur in the other direction: some scientists may be unduly dismissive of their own achievements, so that they will tend to downplay their contribution (if any) to a field when reviewing it.

In general, a review of the literature should neither be a public relations brochure nor an exercise in competitive self-denial. If a reviewer is up to the job of producing a well-organized and methodical review, which flows well and provides a service to the readership, then it should be possible to be objective in reviewing one's own relevant findings. In reviews written by multiple authors, this may be achieved by assigning the review of the results of a coauthor to different coauthors.

Rule 10: Be Up-to-Date, but Do Not Forget Older Studies

Given the progressive acceleration in the publication of scientific papers, today's reviews of the literature need awareness not just of the overall direction and achievements of a field of inquiry, but also of the latest studies, so as not to become out-of-date before they have been published. Ideally, a literature review should not identify as a major research gap an issue that has just been addressed in a series of papers in press (the same applies, of course, to older, overlooked studies (“sleeping beauties” [26] )). This implies that literature reviewers would do well to keep an eye on electronic lists of papers in press, given that it can take months before these appear in scientific databases. Some reviews declare that they have scanned the literature up to a certain point in time, but given that peer review can be a rather lengthy process, a full search for newly appeared literature at the revision stage may be worthwhile. Assessing the contribution of papers that have just appeared is particularly challenging, because there is little perspective with which to gauge their significance and impact on further research and society.

Inevitably, new papers on the reviewed topic (including independently written literature reviews) will appear from all quarters after the review has been published, so that there may soon be the need for an updated review. But this is the nature of science [27] – [32] . I wish everybody good luck with writing a review of the literature.

Acknowledgments

Many thanks to M. Barbosa, K. Dehnen-Schmutz, T. Döring, D. Fontaneto, M. Garbelotto, O. Holdenrieder, M. Jeger, D. Lonsdale, A. MacLeod, P. Mills, M. Moslonka-Lefebvre, G. Stancanelli, P. Weisberg, and X. Xu for insights and discussions, and to P. Bourne, T. Matoni, and D. Smith for helpful comments on a previous draft.

Funding Statement

This work was funded by the French Foundation for Research on Biodiversity (FRB) through its Centre for Synthesis and Analysis of Biodiversity data (CESAB), as part of the NETSEED research project. The funders had no role in the preparation of the manuscript.

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• CAREER FEATURE
• 04 December 2020
• Correction 09 December 2020

How to write a superb literature review

Andy Tay is a freelance writer based in Singapore.

You can also search for this author in PubMed   Google Scholar

Literature reviews are important resources for scientists. They provide historical context for a field while offering opinions on its future trajectory. Creating them can provide inspiration for one’s own research, as well as some practice in writing. But few scientists are trained in how to write a review — or in what constitutes an excellent one. Even picking the appropriate software to use can be an involved decision (see ‘Tools and techniques’). So Nature asked editors and working scientists with well-cited reviews for their tips.

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doi: https://doi.org/10.1038/d41586-020-03422-x

Interviews have been edited for length and clarity.

Updates & Corrections

Correction 09 December 2020 : An earlier version of the tables in this article included some incorrect details about the programs Zotero, Endnote and Manubot. These have now been corrected.

Hsing, I.-M., Xu, Y. & Zhao, W. Electroanalysis 19 , 755–768 (2007).

Article   Google Scholar  

Ledesma, H. A. et al. Nature Nanotechnol. 14 , 645–657 (2019).

Article   PubMed   Google Scholar  

Brahlek, M., Koirala, N., Bansal, N. & Oh, S. Solid State Commun. 215–216 , 54–62 (2015).

Choi, Y. & Lee, S. Y. Nature Rev. Chem . https://doi.org/10.1038/s41570-020-00221-w (2020).

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Literature Review Basics

• Literature Review Step-by-Step
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This video will provide a short introduction to literature reviews.

Steps For Writing a Literature Review

Recommended steps for writing a literature review:

• Review what a literature review is, and is not 
• Review your assignment and seek clarification from your instructor if needed
• Narrow your topic
• Search and gather literature resources. 
• Read and analyze literature resources
• Write the literature review
• Review appropriate  Citation and Documentation Style  for your assignment and literature review

Common Questions

What is a literature review?

A literature review is a type of scholarly, researched writing that discusses the already published information on a narrow topic . 

What is the purpose of a writing literature review?

Writing a literature review improves your personal understanding of a topic, and demonstrates your knowledge and ability to make connections between concepts and ideas. The literature review is a service to your reader, summarizing past ideas about a topic, bringing them up to date on the latest research, and making sure they have all any background information they need to understand the topic.  

What is "the literature"?

This already published information- called the literature- can be from primary information sources such as speeches, interviews, and reports, or from secondary information sources such as peer-reviewed journal articles, dissertations, and books. These type of sources are probably familiar to you from previous research projects you’ve done in your classes.

Is a literature review it's own paper?

You can write a literature review as a standalone paper , or as part of a larger research paper . When a standalone paper, the literature review acts as a summary, or snapshot, of what has been said and done about a topic in the field so far. When part of the a larger paper, a literature review still acts as a snapshot, but the prior information it provides can also support the new information, research, or arguments presented later in the paper.

Does a literature review contain an argument?

No, a literature review does NOT present an argument or new information. The literature review is a foundation that summarizes and synthesizes the existing literature in order for you and your readers to understand what has already been said and done about your topic.

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University Library

Using the Biological Literature: A Practical Guide

Schmidt, D. (2014). Using the biological literature: A practical guide. Boca Raton : CRC Press.

The fourth edition of the guide includes numerous Web sites. These were chosen on the basis of their importance and presumed stability. Of course Web sites change frequently, so the author has extracted all of the Web resources listed in the book and presents them here. This site will be kept up to date, with annotations changing as sites change their focus or their URLs. New sites will not be added so that this Web site is kept in sync with the print book.

To see a list of important resources for biologists, click on the links below.

Table of Contents

• Chapter 1     Introduction to the Electronic Biological Literature
• Chapter 3     General Sources
• Chapter 4     Abstracts and Indexes
• Chapter 5     Biochemistry and Biophysics
• Chapter 6     Molecular and Cellular Biology
• Chapter 7    Genetics, Biotechnology, and Developmental Biology
• Chapter 8    Microbiology and Immunology
• Chapter 9    Ecology, Evolution, and Animal Behavior
• Chapter 10  Plant Biology
• Chapter 11  Anatomy and Physiology
• Chapter 12  Entomology
• Chapter 13  Zoology

Chapter 1: Introduction

Electronic biological literature.

The vast proliferation of the biological literature has made the computer an indispensable part of any biologist’s toolkit. Abstracts and indexes have been computerized since the early 1970s and were originally searched by trained intermediaries such as librarians and information specialists (see the introduction to Chapter 4 for more information). Beginning in the mid-1980s, these tools have been available for end users, and their availability has only expanded in the years since then. The next wave of computerization improved access to journals, and electronic books trailed behind their periodical siblings by a couple of decades but are beginning to come into their own.

Electronic journals have become commonplace today; only 15 years ago they were a novelty, eliciting a great deal of discussion concerning utility, availability, cost, archival storage, ownership, intellectual property rights, peer review, and copyright compliance. These controversial issues are still relevant but the electronic age is proceeding apace. All of the major commercial publishers and society publishers currently make their journals available electronically, and several initiatives in the biological sciences assisted smaller society publishers to move to full text. Stanford University Library has been offering electronic publishing assistance since 1995 through its HighWire Press (http://www.highwire.org). They currently provide access over 1,500 journals published by societies and university presses. A more recent initiative made by the Scholarly Publishing and Academic Resources Coalition (SPARC), called BioOne (http://www.bioone.org), created a single database containing articles from journals published by member societies from the American Institute of Biological Sciences (AIBS). It was launched in April 2001 with about 30 journals participating, and is now up to more than 175 titles in 3 collections.

Most of the e-journals presently available are electronic versions of existing print journals. In the heady early days of electronic publishing a number of new paradigms were envisioned, including abolishing or drastically modifying the present system of peer review. Preprint archives such as the physics service arXiv (http://arxiv.org/‎) were seen as a way of providing speedy access to research. Partly due to the concerns about peer review mentioned earlier, the beginning of the electronic journal age in the life sciences got off to a much more sedate start than in physics. The earliest e-journals in the mid to late 1990s were simply electronic versions of standard print journals, usually in bundled subscriptions with both print and online versions for one price. New journals published in electronic format only, without a print equivalent but after undergoing the usual peer review process, were launched but faced numerous hurdles. The first well-funded online journal in the life sciences was the Online Journal of Current Clinical Trials (OJCCT) , which was founded in July 1992. Despite extensive efforts, it was initially difficult to find authors willing to publish in the journal, even after 1994 when it gained an official stamp of approval by becoming the first online journal indexed in Index Medicus . It ceased publication in 1996, but it was only the first of many online-only journals. Now in the mid-2010s, many standard journals have ceased publication in print and are only available online and many newly created journals are only available online.

The issue of how to archive electronic journal backfiles is one that publishers and librarians have wrestled with extensively. We know how to preserve copies of print books and journals: publishers print them on acid-free paper and librarians place copies of them in climate-controlled facilities in multiple locations around the world. The situation is profoundly different in the case of electronic journals. Initially, publishers kept control of the electronic backfiles for their journals, causing librarians and users to be concerned about what would happen when keeping the files was no longer economically advantageous to the publishers, or if they went out of business. Also, given all the changes in electronic media (magnetic tapes to thumb drives) and standard software programs (remember WordPerfect?), there are concerns about migrating all the masses of data from one standard platform to another. Librarians and publishers have worked on this issue, so robust and redundant standards and systems are in place that should allow seamless updates and transfers in the future. These systems have yet to be significantly tested in real life, but having them in existence is a relief to everyone involved. Portico ( http://www.portico.org/ ), LOCKSS (Lots Of Copies Keeps Stuff Safe, http://www.lockss.org/ ), and CLOCKSS (Controlled LOCKSS, http://www.clockss.org ) are among the most important initiatives.

Another series of initiatives that have revolutionized the biological literature focuses on Open Access (OA). The genesis of the OA movement goes back to the beginning of the Internet age, with its mantra that “Information wants to be free.” In addition, the subscription price crisis in the 1980s and 1990s encouraged authors and librarians to explore alternatives to the traditional modes of publishing. The final outcome of the tension between traditional publishing and OA is yet to be determined, but among other things governmental policies such as the NIH Public Access Policy discussed below guarantee that there will be a place for OA in the future of scientific communication.

There are many “flavors” of Open Access, but the basic definition provided by advocate Peter Suber (2013) is that “Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions.” The two types of OA found in the life sciences include Author Pays (also known as “gold” OA) and Open Access repositories (“green” OA). The Author Pays model has attracted most of the attention, both positive and negative. In this model, authors of scientific publications pay a fee to the journal publisher to make their articles available for free immediately upon publication. Some journals are completely OA, such as the PLoS journals, but there are many other mixed journals in which some authors choose to pay for Open Access and some do not. These OA articles receive the same peer review that other articles receive and many grants provide funds for OA publications. This model is rather similar to the system found in many society publications, in which authors are expected to pay page charges. This helps keep subscription prices low. Two major resources for OA information are the Directory of Open Access Journals (DOAJ), which lists OA journals ( http://www.doaj.org/‎ ), and the SHERPA/Romeo Web site ( http://www.sherpa.ac.uk/romeo/ ), which lists publisher OA policies.

The biological and medical sciences have been in the vanguard of the Open Access movement. More than half of the substantial journals listed in the DOAJ are biomedical; biomedical journals also publish more articles than the journals in other fields and charge higher author fees. The three largest OA publishers, PLoS, Biomed Central, and Oxford University Press, all publish in the biomedical field (Walters and Linville, 2011). More recently, in August 2013 a series of reports commissioned for the European Commission’s Directorate-General for Research and Innovation showed that 40% of articles published worldwide from 2004-2011 were available as Open Access (Archambault et al, 2013). Biology had achieved 57% OA, while 61% of biomedical research articles were available as OA. The NIH and NSF Public Access policies discussed below have also had a significant effect on the OA cause in the biomedical fields.

Some of the early concern with the Author Pays model focused on the possibility of abuse. While the major OA publishers such as PLoS and BioMed Central have strict peer review processes that are equal to those in the best standard journals, the fear has always been that unscrupulous publishers would see this model as a cash cow, publishing any kind of dreck as long as authors were willing to cough up the money. While the vast majority of OA publishers are focused more on the ideal of making information available for free and breaking even rather than making money, some unscrupulous publishers have been identified. Authors looking for OA journals to publish in should ask many of the same questions that they would for any journal. Who publishes the journal? Are the author fees in line with other OA journals in your field? Have you or your mentors ever heard of it? Is the journal indexed in any of the major indexes? Have authors you know and respect published in it, or are on the editorial board?

The OA Repository or Green OA model is different from the Author Pays model. In this model, after publishing in a journal authors make their articles available for free in some kind of repository, such as the author’s personal Web site or an institutional or disciplinary repository. In some cases publishers only allow copyedited word processor versions of the final article rather than a PDF of the actual article to be available in a repository. Many journals now follow this Green model by making all of the content of their journals available for free after an embargo period, which is usually between 6 months to a year or even longer. The assumption in this model is that most of the use of articles comes in a fairly short period following their publication so publishers are not risking the loss of subscriptions by making older content available for free. This is the model followed by the NIH and NSF policies discussed below.

Like other initiatives that seek to change the publication model for scientists, OA has been controversial from the start. The history of PubMed Central illustrates this. The original PubMed Central proposal, first publicized in March 1999, was for a single all-inclusive database containing all biomedical research papers from traditional journals as well as preprints, all available for free. Both parts of the proposal proved to be controversial, and when the PubMed Central project went online in February of 2000, it was with a far more limited scope than originally planned. It consisted of only a few journals and the preprint server idea was completely dropped. As of February 2001, only about 10 journals were available on PubMed Central but by 2013 over a thousand journals were included. Despite the early setbacks OA supporters soldiered on, and in April 2008 the Public Access Policy was implemented. It required that all research funded by NIH grants must be made publicly available within 12 months of publication, and in February 2013 a similar policy was passed affecting the NSF and all the other Federal agencies that spend over $100 million per year supporting research. Authors must either publish in journals following the green OA system or deposit their articles in PubMed Central or another repository. The US is not the only country interested in OA repositories. At the same time PubMed Central was proposed, the E-BioSci OA portal was implemented.

One of the potential benefits of the OA model that has been extensively touted by OA advocates is that greater availability of free articles would lead to increased visibility and use of those articles. Research studying citation rates for OA and non OA articles has been mixed, with most recent studies showing only a modest increase of citation rates for OA articles (Davis and Walters, 2011; Archambault et al, 2013). That includes comparisons of OA and non OA articles within the same mixed-model journals (Davis, 2009).

Non-European and small European countries have been quick to find value in the OA model as a mechanism to promote the research performed in their own countries. One good example is Brazil’s SciELO ( http://www.scielo.org ), a platform that publishes over 1,000 OA journals from several South and Central American countries. Waters and Linville (2011) found that 27% of the OA journals they studied published articles in languages other than English, and that the percentage of OA journals published outside of Europe and North America had increased from 10% in 2005 to 31% in 2009. While it isn’t a completely valid comparison, compare this to the 19% of non-European and North American journals indexed in BIOSIS Previews mentioned above.

Researchers in the biological sciences create massive amounts of data that must be accessible to be useful. The data may include ecological data from long-term studies, the holdings of museum collections, neuroscience images, or molecular or genetic sequences. Formerly, the data were published in articles or books and rarely updated but with the development of electronic journals and databases this material is far more accessible and easier to manipulate.  Molecular biology is a good example of a discipline that uses electronic publishing to share new data with a multi-disciplinary research community through electronic productions like GenBank, PDB (the Protein Data Bank), the Human Genome Project, and so on. What is unique about these databases is that data is accepted before being published in the journal literature, and in fact most journals require that sequences be added to GenBank prior to their publication in print.

As a result of the availability of all this data, techniques for finding and interconnecting data have become one of the fastest growth areas in biology and information science. Bioinformatics, the use of computer and information science to analyze biological data, has exploded in use. While the term is often used to refer just to the analysis of genomic or molecular biology information, all areas of biology that create large amounts of data have their own bioinformatics needs and practitioners. The Open Access movement has made some areas of bioinformatics such as text mining possible. Articles that are locked away behind a paywall are not available for text mining sweeps, but abstracts in PubMed and full text from OA journals are. The next step is to combine the journal literature with the huge molecular biology databases in new and interesting ways.

All of the above discussion of the electronic biological literature focuses on electronic journals and databases, a measure of their importance to the biological sciences. Electronic books have been slower in coming. The earliest e-books included encyclopedias, dictionaries, and textbooks. While some implementations of electronic textbooks have not been popular with students, their promise is obvious. More recently, monographs that mimic journals in that they consist of individual chapters acting like separate articles rather than a cohesive whole have been successful online, and most publishers produce electronic versions of their books. One complication is the multiplicity of incompatible e-book readers, although one way around this problem is to publish scientific books as PDF files of individual chapters. Libraries can subscribe to individual titles or large or small book packages, much like the infamous Big Deals that journal publishers offer.

There are relatively few OA books, but out of copyright books could be seen as the e-book equivalent of OA although the two issues are only tangentially related. At this point, according to US copyright law all books published before 1923 are out of copyright (also known as in the public domain) and can be used and republished as desired; books published between 1923 and 1989 may or may not be out of copyright and materials published after 1989 are almost certainly in copyright. Other countries’ copyright laws vary, so the issue is extremely complicated and can slow scientific advancement. Probably the most famous digitization project is Google’s Google Book project (http://books.google.com), which aims to digitize all the world’s literature, ran into many issues related to copyright but has made public domain books much more accessible. The Internet Archive at http://archive.org (also home to the Wayback Machine, which archives Web pages) is another digitization project, although it focuses on material in the public domain.

Of even greater interest to biologists, especially taxonomists, is the Biodiversity Heritage Library (BHL), which has the goal of digitizing all the biodiversity literature in the world. This project began in 2005 and was created by a coalition of major botanical gardens, natural history museums, and universities in the US and the UK. One major benefit of this project is to make the historical taxonomic literature (which can go back to Linnaeus’s publications) more widely available to local taxonomists who do not have easy access to the major American and European institutional libraries, which may hold the only copies of rare taxonomic works. The BHL records feed into the Encyclopedia of Life , a project aimed at producing a Web page for each of the approximately 1.8 million species of organisms (see Chapter 3).

While no one can read the future of the biological literature, it is safe to say that it will continue to grow apace, and that while peer review will continue, new formats merging the best of the print world and the new electronic world will emerge. Publishers, authors, and librarians will continue to wrestle with issues related to Open Access and journal prices.

Bibliography

Archambault, Eric, et al. (2013). Proportion of Open Access Peer-Reviewed Papers at the European and World Levels—2004-2011. http://www.science-metrix.com/pdf/SM_EC_OA_Availability_2004-2011.pdf.

Davis, P. M. (2009). Author-choice open access publishing in the biological and medical literature: A citation analysis. Journal of the American Society for Information Science and Technology 60(1):3-8.

Davis, P. M. and W. H. Walters. (2011). The impact of free access to the scientific literature: a review of recent research. Journal of the Medical Library Association 99(3): 208-217.

Suber, P. (2013). Open Access Overview . http://legacy.earlham.edu/~peters/fos/overview.htm .

Walters, W. H. and A. C. Linvill. (2011). Characteristics of Open Access journals in six subject areas. College and Research Libraries 72(4): 372-392.

Chapter 3: General Sources

Introduction.

This chapter describes selected sources that are relevant to biology in general, with no attempt to be comprehensive.  These titles were chosen as especially appropriate for undergraduates needing an introduction to the field, or for anyone requiring sources covering the broad spectrum of the biological sciences.  In addition, there are a number of resources that are useful for new graduate students, including books on how to fit in to a lab, how to publish a paper, and so on.  Knowledge of most of the publications annotated in this chapter is helpful in effectively utilizing the more specialized chapters that follow.  Arrangement is by topic, presenting publications that acquaint readers to the field of biology from the viewpoint of the history of the life sciences, mathematical and statistical sources, and pertinent techniques, just to name a few of the sections that follow.  These general sources may be used as a base upon which to expand or define more specific subjects, to open up the literature as a beginning, not an end.

Jump to Section:

Associations, bibliographies, classification, nomenclature, and systematics, dictionaries and encyclopedias, directories, field guides, full text sources, general works, guides for young scientists, guides to the literature, methods and techniques, writing guides, periodicals, reviews of the literature.

• American Association for the Advancement of Science (AAAS) . 1200 New York Ave., NW, Washington, DC 20005. E-Mail: [email protected] . URL: http://www.aaas.org Founded 1848. This the largest general scientific organization representing all fields of science. Membership includes 10 million individuals and 261 affiliated societies and academies of science. Objectives are to further the work of scientists to facilitate cooperation among them, to foster scientific freedom and responsibility, to improve the effectiveness of science in the promotion of human welfare, to advance education in science, and to increase public understanding and appreciation of the importance and promise of the methods of science in human progress. Publications include Science , Science Signaling , Science Translational Medicine , Science Books and Films , Science Careers Web site, and EurekAlert! news service. The Web site provides information about AAAS, news about science and society, science education, careers, media, awards, science books and films, and more.
• American Institute of Biological Sciences (AIBS) . 1444 I St. NW, Ste. 200 Washington, DC 20005. E-Mail: [email protected] . URL: http://www.aibs.org Founded 1947. 6,000 members. This is a professional member organization and federation of biological associations, laboratories and museums whose members have an interest in the life sciences. Publications: BioScience and ActionBioscience.org, an English-Spanish science education resource. The Web site includes information about AIBS, publications, outreach and education, and public policy. AIBS member societies are participating in the electronic publishing venture, BioOne (see Chapter 1 ).
• Association for Tropical Biology and Conservation (ATBC) . PO Box 37012. Washington, DC 20013-7012. E-Mail: [email protected] . URL: http://www.tropicalbio.org Founded 1963. 1,350 members. An international organization of persons who are interested in tropical biology, seeking to coordinate existing information and provide new information about the plants and animals (including humans) of the tropics. Affiliated with AIBS. Publications: Biotropica. The Web page provides information about the association. Formerly: Association for Tropical Biology (ATB).
• Association of Applied Biologists (AAB) . Warwick Enterprise Park. Warwick CV35 9EF, UK. E-Mail: [email protected] . URL: http://www.aab.org.uk Founded 1904. 1,200 members. Research scientists in private and state applied biology institutes and universities in 60 countries interested in furthering development in the field of applied biology. Publications: Annals of Applied Biology, Plant Biotechnology Journal, and Food and Energy Security . Web site includes membership information and links to other resources.
• Council of Science Editors (CSE) . 10200 W 44th Ave., Ste. 304. Wheat Ridge, CO 80033. E-Mail: [email protected] . URL: http://www.councilscienceeditors.org
• Founded 1957. 1,289 members. Active and former editors of primary and secondary journals in the life sciences and those in scientific publishing and editing who consider all aspects of communication in the life sciences with emphasis on publication, especially in primary journals and retrieval in secondary media. Publications: Science Editor and Scientific Style and Format . Formerly: Council of Biology Editors.
• European Molecular Biology Organization (EMBO) . Meyerhofstrasse 1, D-69117 Heidelberg, Germany. E-Mail: [email protected] . URL: http://www.embo.org
• Promotes the advancement of molecular biology in Europe and neighboring countries, administers programs funded by the Europe­an Molecular Biology Conference consisting of fellowships and courses. The organization holds courses and workshops, and presents an annual award. Publications: EMBO Journal, EMBO Reports, Molecular Systems Biology, and EMBO Molecular Medicine . They hold periodic general assemblies and an annual symposium.
• Federation of American Societies for Experimental Biology (FASEB) . 9650 Rockville Pike. Bethesda, MD 20814. E-mail: [email protected] . URL: http://www.faseb.org Founded 1912. 110,000 members in 27 member societies. Member societies include American Physiological Society, American Society for Biochemistry and Molecular Biology, American Society for Pharmacology and Experimental Therapeutics, American Society for Investigative Pathology, American Society for Nutritional Sciences, American Association of Immunologists, American Society for Cell Biology, Biophysical Society, American Association of Anatomists, and The Protein Society among others. Publishes the FASEB Journal , Breakthroughs in Bioscience , and Horizons in Bioscience . The Web page has links to the member societies, public affairs, career resources, meetings and conferences, membership directories, publications, and employment opportunities.
• International Union of Biological Sciences (IUBS); Union Internationale des Sciences Biologiques . Bat 442 Universite Paris-Sud 11. 91 405 Orsay Cedex, France. E-Mail: [email protected] . URL: http://www.iubs.org Founded 1919. 117 member societies. This is an organization of national societies and international associations and commissions engaged in the study of biological sciences. Their aims are to promote the study of biological sciences; to initiate, facilitate, and coordinate research and other scientific activities; to ensure the discussion and dissemination of the results of cooperative research; to promote the organization of international conferences; and to assist in the publication of their reports. Publications: Biology International ; Monograph Series, Methodology Series , and the proceedings of the IUBS General Assembly. The Web page has primarily society information.
• Marine Biological Association of the United Kingdom (MBAUK) . The Laboratory, Citadel Hill, Devon, Plymouth PL1 2PB, UK. E-Mail: [email protected] . URL: http://www.mba.ac.uk
• Founded 1884. 1,500 members. Marine biologists, botanists, and scientists encourage cooperation among members; disseminates information on latest research; studies living resources of the seas. Publishes Journal of the Marine Biological Association . The Web page provides access to MBA information, research, biodiversity initiatives, education, communication, membership, and knowledge exchange.
• National Academy of Sciences (NAS) . 500 5th St. NW, Washington, DC 20001. URL: http://www.nasonline.org Founded 1741. 2,200 members. Honorary organization dedicated to the furtherance of science and engineering. Members are elected in recognition of their distinguished and continuing contributions. Founded by an act of Congress to serve as official adviser to the federal government on scientific and technical matters. Publishes Proceedings of the National Academy of Sciences, Biographical Memoirs and Issues in Science and Technology . The very extensive Web site provides information on the Academy, news bulletins, numerous online reports created by the Academy, and links to the National Academy Press. Thousands of books published by the press can be viewed for free on their Web site.
• Society for Experimental Biology (SEB); Societe de Biologie Experimentale (SBE) . Charles Darwin House, 12 Roger St., London WC1N 2JU, UK. E-Mail: [email protected] . URL: http://www.sebiology.org Founded 1923. 2,150 members. Experimental biologists, students, universities, scientific institutions involved in disseminating information on recent advances in experimental biological research. Publications: Journal of Experimental Botany, The Plant Journal, Plant Biotechnology Journal and the book series Essential Reviews in Experimental Biology . The Web page is primarily for society information.
• Society for Experimental Biology and Medicine (SEBM) . 130 W Pleasant Ave., No. 334, Maywood, NJ 07607. E-Mail: [email protected] . URL: http://www.sebm.org Founded 1903. 1,500 members and 3 regional groups actively engaged in research in experimental biology and experimental medicine. Publication: Experimental Biology and Medicine . The Web site has membership information.
• Society of Biology . Charles Darwin House 12 Roger St. London WC1N 2JU, UK. E-Mail: [email protected] . URL: http://www.societyofbiology.org
• Founded 1950. 17,000 members. The purpose of this group is to advance education and research in biology. Conducts educational programs and presents awards. Publications: Biologist , the Journal of Biological Education , and occasional publications. The Web page provides links to information about the society, education and training, news, publications, membership, affiliated societies, and UK branches. Formerly: Institute of Biology; Bioscience Federations.
• Society of Systematic Biologists (SSB) . c/o David Hibbett, Exec. VP, Clark University, 15 Maywood St., Worcester, MA 01603. E-Mail: [email protected] . URL: http://systbiol.org Founded 1948. The society represents 1,550 scientists interested in classification of animals or other aspects of taxonomy or systematics. They promote the study of animals, invertebrate and vertebrate, living and fossilized, and all aspects of systematic zoology. Publishes Systematic Biology . Formerly Society of Systematic Zoology. The Web page provides information about the Society, their journal, and news.
• Tropical Biology Association (TBA) . Dept. of Zoology, Downing St., Cambridge CB2 3EJ, UK. E-Mail: [email protected] . URL: http://www.tropical-biology.org Founded 1994. 37 members. The Association aims to meet the challenge of biodiversity conservation by establishing an informed, well-motivated community of tropical biologists based both in Europe and in tropical countries. The Web site contains information about the association and resources for funding, skill building, and much more.

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• BIOSIS Serial Sources. Philadelphia, PA: BIOSIS, 1995-2005. ISBN 1086-2951.Has always been the go-to resource for biology journal titles and abbreviations, but it is no longer produced in print and the online version lacks abbreviations. Previous titles include Serial Sources for the BIOSIS Data Base (1978-1988) and Serial Sources for the BIOSIS Previews Database (1989-1994). Online version at http://science.thomsonreuters.com/cgi-bin/jrnlst/jloptions.cgi?PC=BA .
• CAB International Serials Checklist. New York: CAB International, 1996. $85.00. ISBN 0851989713; 9780851989716.This list contains references to over 11,000 journals, annual reports, technical reports, working papers and newsletters regularly screened for CAB Abstracts . While not updated very often (the previous edition was done in 1988), this is the best directory for information on agricultural journals. The list of journals covered in CABI can also be found at the CAB Web site at http://www.cabi.org/publishing-products/online-information-resources/cab-abstracts/ .
• Chemical Abstracts Service Source Index: 1907-2004 Cumulative. Columbus, OH: Chemical Abstracts Service, 2005. $731.00.This serial list for the Chemical Abstracts database has about 155,000 entries covering over 80,000 scientific journals and non-serial publications. CASSI , as it is universally known, cumulates every five years. It is particularly useful since it covers a vast number of journals in all fields of science and technology back to 1907 and is thus valuable for its coverage of obscure foreign journals or journals that have ceased publication. CASSI is also available for free online at http://cassi.cas.org and can be searched by journal title, abbreviation, and ISSN.
• Directory of Open Access Journals: DOAJ. Lund, Sweden: Lund University Libraries, 2003- . http://www.doaj.org/ .As the site states, this directory “covers free, full text, quality controlled scientific and scholarly journals”. Viewers can search for specific titles or browse by subject area. The number of Open Access journals is increasing rapidly so this site provides a valuable service.
• Genamics JournalSeek. Genamics, 2000s- . http://journalseek.net/ .This useful database contains information on nearly 100,000 periodicals from over 5,500 publishers, with ISSNs, links to publisher web sites and online content, and subject descriptors. It is supported by OCLC as part of the WorldCat Knowledge Base .
• Hough, Lloyd and Geoff Patton. Biological Journals and Abbreviations . Lloyd Hough, 1996- . http://home.ncifcrf.gov/research/bja/ .
• A very extensive list of biological journals, arranged alphabetically by abbreviation with full title spelled out. It includes journals in multiple languages. It is not comprehensive but is a very good resource for abbreviations and full titles for current serials.A very extensive list of biological journals, arranged alphabetically by abbreviation with full title spelled out. It includes journals in multiple languages. It is not comprehensive but is a very good resource for abbreviations and full titles for current serials.
• NLM Catalog: Journals Referenced in the NCBI Databases. Bethesda, MD: National Center for Biotechnology Information, US National Library of Medicine, 2000s- . http://www.ncbi.nlm.nih.gov/nlmcatalog/journals .
• This database provides information on all journals indexed by PubMed and other NCBI databases. The journal database can be searched by title, title abbreviation, or ISSN and includes basic publication information such as dates, title changes, publisher, and more. A very useful tool to verify journal titles and publication information. Replaces List of Journals Indexed for MEDLINE.
• Zoological Record Serial Sources. v. 1987/88-v. 11 (2004), 1988-2004. Philadelphia, PA: BIOSIS. ISSN 1041-4657.
• This journal list is similar to the BIOSIS Serial Sources , above, and is equally useful for verifying journals. It covers 4,500 current titles and 5,500 archival titles. The list of current titles is also available at http://science.thomsonreuters.com/cgi-bin/jrnlst/jloptions.cgi?PC=B7. The online version does not include abbreviations.
• The Barcode of Life Data Systems (BOLD) is an informatics workbench aiding the acquisition, storage, analysis, and publication of DNA barcode records. By assembling molecular, morphological, and distributional data, it bridges a traditional bioinformatics chasm. BOLD is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances.
• Cantino, Philip D. and Kevin de Queiroz, eds. The Phylocode . 2010. http://www.ohio.edu/phylocode/ .“The PhyloCode is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny.” The site allows users to download PDF and HTML versions of the draft code.
• Hedges, S. Blair and Sudhir Kumar, eds. The Timetree of Life. New York: Oxford University Press, 2009. 551 p. (Oxford biology). $200.00. ISBN 0199535035; 9780199535033.This book provides a timeline of evolution for the major taxa of organisms. Each section summarizes the taxa (order or family), its phylogenetic relationships, the time of divergence, and usually concludes with a brief discussion of geological events at the time. A companion Web site at http://www.timetree.org allows users to discover the estimated time of divergence for any two taxa (dogs and cats or oaks and pines, for instance). The data is also available for mobile Web devices, and chapters of the book are available at the site for free download for non-commercial use.
• Integrated Taxonomic Information System: ITIS. Washington, DC: Integrated Taxonomic Information System, 1996- . http://www.itis.gov .ITIS provides authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. It is a partnership of US, Canadian, and Mexican agencies (ITIS-North America), other organizations, and taxonomic specialists. ITIS is also a partner of Species 2000, the Global Biodiversity Information Facility (GBIF), and Encyclopedia of Life (see under Dictionaries and Encyclopedias, below).
• Maddison, David R. and K. -S Schulz. The Tree of Life Web Project. Tucson, AZ: D. R. Maddison and W. P. Maddison, 2007- . http://tolweb.org/ .Intended to provide a means for finding information on all taxa of living organisms, especially their evolutionary relationships.

D ictionaries and Encyclopedias

• The Encyclopedia of Life: EOL. 2008- . http://www.eol.org/ .”Ultimately, the Encyclopedia of Life will provide an online database for all 1.8 million species now known to live on Earth.” (from the Web site) A speech by E.O. Wilson was the impetus for this site, which is supported by a consortium of major research institutions. Each species page will contain summary information on biology, systematics, and distribution; images; maps; Web resources and links to the literature. The literature page also provides links to digitized books from the Biodiversity Heritage Library (see full description in Full Text section, below).
• Directory of Field Stations . Organization of Biological Field Stations. http://www.obfs.org/directories .
• Lists about 250 biological field stations in North and Central America. Information includes address, contact information, and link to Web sites.
• Ostriker, J. P., Charlotte V. Kuh and James A. Voytuk. A Data-Based Assessment of Research-Doctorate Programs in the United States. Washington, DC: National Academies Press, 2011. 304 p. $99.95 (pa). ISBN 0309160308 (pa); 9780309160308 (pa).The data for this assessment was collected in the 2005-2006 academic year from 212 universities. It includes both faculty and student characteristics as well as size of program and time to degree. The print volume comes with a CD containing an Excel spreadsheet with all the data for users to manipulate. The full text and spreadsheet are also available for free at the NAP site at http://www.nap.edu/rdp/. The most respected assessment of doctoral programs.
• Schmidt, Diane. International Field Guides . Urbana, IL: University of Illinois, 1999-  . http://www.library.illinois.edu/bix/fieldguides/index.html .Companion to the print guide to North American field guides listed above.  Over 6,000 field guides from all parts of the world, including North America, are described.  Most are in English, though many other languages are also represented.
• Biodiversity Heritage Library. Biodiversity Heritage Library Consortium, 2007- . http://www.biodiversitylibrary.org/ .Created by a consortium of major natural history libraries and institutions, this online library has digitized thousands of rare books dealing with taxonomy and natural history. Most of the books are out of copyright, but several of the participating institutions have digitized all of their own publications regardless of copyright status. The BHL is a partner in the Internet Archive and its records feed into the Encyclopedia of Life (both discussed in this chapter).
• Google Books. 2004- . http://books.google.com/ .Probably the best known source for digital books. Google has digitized millions of both in-copyright and out-of-copyright books. Books that are out of copyright may be viewed in their entirety while in copyright books can be searched but only viewed in short “snippets”. Many libraries and publishers have provided Google with material to digitize. Some serial volumes are also included although the focus is on books.
• Highwire Press . Stanford, CA: Board of Trustees of the Leland Stanford Junior University, 1995- . http://highwire.stanford.edu/ .Highwire Press is a digital publishing endeavor of Stanford University that provided one of the earliest e-journal publishing platforms. As of May 2013 the press published 1775 journals, books, proceedings, and other publications. This included over 2.25 million free articles, usually available after an embargo period of 6 months to a year or more.
• Internet Archive . 1996- . http://archive.org/index.php .This site provides access to millions of books, videos, and music recordings, as well as the Wayback Machine (archived Web pages). The majority of the digitized books are out of copyright although some are more recent and available through Creative Commons licenses. The Internet Archive is home to many other projects, including Project Gutenberg and the Biodiversity Heritage Library , above. Books can be downloaded or read online in PDF, EPUB, Kindle, Daisy, Fulltext, and DjVu formats.
• PubMed Central: An Archive of Life Science Journals . Bethesda, MD: National Library of Medicine, 2000- . http://www.pubmedcentral.nih.gov/ .A free, full-text repository for biomedical and life science journal articles. Some of the content comes from participating publishers wanting to make their content available, usually after an embargo period, while much of the content is from authors depositing their manuscripts in accordance with the NIH Public Access Policy (see Chapter 1). As of May 2013, over 2.7 million articles had been deposited.
• Committee on Science, Engineering, and Public Policy (US). Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age. Washington, DC: National Academies Press, 2009. 162 p. $34.95 (pa). ISBN 0309136849 (pa); 9780309136846 (pa).This report explores issues related to research data across the scientific and engineering fields. The full text is also freely available at http://www.nap.edu/catalog.php?record_id=12615
• Dee, Phil. Building a Successful Career in Scientific Research: A Guide for Ph.D. Students and Post-Docs. New York: Cambridge University Press, 2006. 130 p. $96.00; $31.00 (pa). ISBN 0521851912; 9780521851916; 0521617405 (pa); 9780521617406 (pa).This guide is based on columns from Science magazine’s Next Wave site (now part of http://sciencecareers.sciencemag.org/). The advice is aimed at graduate students and post-docs and covers topics such as choosing an advisor, how to write well, the transition to a post-doc, writing grants, and succeeding as a scientist.
• INFOMINE Scholarly Internet Resource Collections. Biological, Agricultural and Medical Sciences. Riverside, CA: Regents of the University of California, 1994- . http://infomine.ucr.edu/cgi-bin/search?bioag .
• This site links to both free and fee-based Internet resources in the life sciences and has very extensive coverage.
• The Scout Report: A Publication of the Internet Scout Project: A Project of the InterNIC. Madison, WI: Internet Scout Research Project, 1994- . https://scout.wisc.edu/scout-report .This weekly report lists the best free Internet resources in a variety of subjects, including science and technology. The reports are available from the Internet Scout Web site and also by email subscription.
• IUCN Red List of Threatened Species .  http://www.iucnredlist.org/ .This site provides detailed information on endangered, threatened, or vulnerable species of plants and animals from around the world. It is the most comprehensive source of information on the conservation status of species, and the Web site provides conservation and taxonomic notes on individual species as well as statistics, maps, and other resources for conservation groups. The IUCN has been publishing the list (formerly printed in red volumes, hence the title) since the 1960s. Formerly: Red Data Book .
• National Research Council (US). Guide for the Care and use of Laboratory Animals. 8th ed. Washington, DC: National Academies Press, 2011. 220 p. $19.95 (pa). ISBN 0309154006 (pa); 9780309154000 (pa).This guide is designed to assist institutions and individual researchers in the scientific and humane use of animals in research. Its use is required by the Public Health Service Policy in the US and is also used internationally. The full text of the guide is also freely available at http://www.nap.edu/catalog.php?record_id=12910
• Biographical Memoirs. v. 1- , 1877- . Washington, DC: National Academy of Sciences. Annual. $88.50. ISSN 0077-2933.Provides biographical and publication information about deceased National Academy of Sciences members.The full text of all 1,500 memoirs is available at the NAS web site at http://www.nasonline.org/publications/biographical-memoirs/.
• Biographical Memoirs of Fellows of the Royal Society. v. 1- , 1955- . London: Royal Society (Great Britain). Annual. $321.00 (print). ISSN 0080-4606 (print); 1748-8494 (online).Each annual volume of this publication contains 20-25 obituaries of eminent members of this major society. Volumes from 2001 are available online for free, with a one year embargo, at http://rsbm.royalsocietypublishing.org/. The Memoirs were formerly titled Obituary Notices of Fellows of the Royal Society from 1932 to 1954.
• Journal of Visualized Experiments: JoVE. v. 1- , 2006- . Boston, MA: MYJoVE Corp. Price varies. ISSN 1940-087X.A Web-based video journal providing video demonstrations of scientific procedures and methods. There are currently several sections, including neuroscience, immunology, clinical and translational medicine, bioengineering, applied physics, and chemistry. Subscriptions are available only to institutions, and may be purchased for the entire collection or individual sections. Some articles are available for free at http://www.jove.com/.
• World Health Organization. Laboratory Biosafety Manual. 3rd ed. Geneva, Switzerland: World Health Organization, 2004. 178 p. $60.00 (pa). ISBN 9241546506 (pa); 9789241546508 (pa).Designed to help countries and individual laboratories in the safe handling of microorganisms. It covers biosecurity, lab equipment, safety training, and checklists. Also available as a free PDF file at http://www.who.int/csr/resources/publications/biosafety/en/Biosafety7.pdf
• The Chicago Manual of Style. 16th ed. Chicago, IL: The University of Chicago Press, 2010. $65.00. ISBN 0226104206; 9780226104201.One of the standard style manuals. Most of the advice in this manual is aimed at authors in the humanities and social sciences, though the manual provides information on scientific citation style. The manual’s Web page at http://www.chicagomanualofstyle.org contains some free content, but most of the site is available only to subscribers.
• ICMJE: International Committee of Medical Journal Editors. International Committee of Medical Journal Editors, 2009- . http://www.icmje.org/index.html .This committee is composed of editors of general medical journals. Its purpose is to prepare the Uniform Requirements for Manuscripts. This annually updated document outlines requirements such as parts of an article, standards for references and tables, abbreviations, and information that should be included with article submission. The document is available at the committee’s web site in PDF.
• Iverson, Cheryl, et al., eds. AMA Manual of Style: A Guide for Authors and Editors. 10th ed. New York: Oxford University Press, 2007. 1010 p. $43.85. ISBN 0195176332; 9780195176339.This standard style guide for the medical field contains updated information on citing electronic resources, new nomenclature, and much more. Updates to the manual are available at the manual’s web site at http://www.amamanualofstyle.com/ to subscribers only.
• Purdue University Writing Lab. The Purdue Online Writing Lab (OWL). West Lafayette, IN: Purdue University, 1990s- . http://owl.english.purdue.edu/ .
• This website links to many sites dealing with writing, including academic writing, professional writing in several different areas, the job search, English as a Second Language, grammar and punctuation, and much more. The site also provides links to information on the APA and Chicago Manual of Style citation formats.
• Biology Direct. v. 1- , 2006- . London: BioMed Central. Continually updated. Open Access. ISSN 1745-6150.” Biology Direct considers original research articles, hypotheses, comments, discovery notes and reviews in subject areas currently identified as those most conducive to the open review approach, primarily those with a significant non-experimental component. Subsequently, new sections will be added.” Authors select reviewers from the BMC board and reviewer comments are publicly available. To date, the subjects covered by this new model focus on molecular biology and ‘omics. The journal’s website is at http://www.biology-direct.com/.
• Biology Open: BiO. v. 1- , 2011- . Cambridge, UK: Company of Biologists. Monthly. Open Access. ISSN 2046-6390 (online).” Biology Open is an online-only Open Access journal that publishes original research across all aspects of biological science, including cell science, developmental biology and experimental biology.” Many of the articles in this journal were originally submitted to the other Company of Biologists periodicals. The journal is available at http://bio.biologists.org .

BMC Biology. v. 1- , 2003- . London: BioMed Central. Continually updated. Open Access. ISSN 1741-7007.” BMC Biology is the flagship biology journal of the BMC series, publishing peer-reviewed research and methodology articles of special importance and broad interest in any area of biology, as well as reviews, opinion pieces, comment and Q&As on topics of special or topical interest.” Articles are available at http://www.biomedcentral.com/bmcbiol

• Database: The Journal of Biological Databases and Curation. v. 1- , 2009- . New York: Oxford University Press. Irregular. Open Access. ISSN 1758-0463 (online).Provides an Open Access platform for the presentation of novel ideas in database research and biocuration, and aims to help strengthen the bridge between database developers, curators, and users.” Articles available at http://database.oxfordjournals.org/.
• F1000 Biology Reports. 2009- . London: Faculty of 1000. Open Access. ISSN 1757-594X.”Publishes short commentaries by the world’s top scientists in which the hottest biology papers/clusters of papers identified by Faculty of 1000 are put into a broader context.” Articles are available at http://f1000.com/prime/reports/biology .
• Genome Biology. v. 1- , 2001- . London: BioMed Central. Monthly. Price varies. ISSN 1474-7596.” Genome Biology publishes research articles, new methods and software tools, in addition to reviews and opinions, from the full spectrum of biology, including molecular, cellular, organism or population biology studied from a genomic perspective, as well as sequence analysis, bioinformatics, proteomics, comparative biology and evolution.” Research articles are Open Access, while access to reviews, opinion pieces, and meeting reports requires a subscription. Free content available at http://genomebiology.com/.
• New Scientist. v. 52- , 1971- . London: New Science Publications. Weekly. $99.00 (personal, p+e). ISSN 0262-4079.General science British periodical publishing science and technology news, commentary, feature articles, and book reviews. Selected news and feature articles are available for free at the magazine’s Web site at http://www.newscientist.com/. Formerly New Scientist and Science Journal .
• PLoS Biology. v. 1- , 2003- . San Francisco, CA: Public Library of Science. Weekly. Open Access. ISSN 1545-7885 (print); 1544-9173 (online).The first of the PLoS journals, publishing “works of exceptional significance, originality, and relevance in all areas of biological science, from molecules to ecosystems, including works at the interface of other disciplines, such as chemistry, medicine, and mathematics.” Articles available at http://www.plosbiology.org/ .
• PLoS Computational Biology. v. 1- , 2005- . San Francisco, CA: Public Library of Science. Weekly. Open Access. ISSN 1553-7358 (print); 1553-734X (online).The journal “features works of exceptional significance that further our understanding of living systems at all scales—from molecules and cells, to patient populations and ecosystems—through the application of computational methods.” Articles available at http://www.ploscompbiol.org/ .
• PLoS Medicine. v. 1- , 2004- . San Francisco, CA: Public Library of Science. Weekly. Open Access. ISSN 1549-1277 (pirnt); 1549-1676 (online).Publishes articles on a wide range of medical topics, focusing on the conditions and risk factors that cause the greatest problems worldwide. Articles available at http://www.plosmedicine.org/ .
• PLoS One. v. 1- , 2006- . San Francisco, CA: Public Library of Science. Continually updated. Open Access. ISSN 1932-6203. aPLoS One provides rapid publication of articles in all fields of biology and medicine. Articles are peer-reviewed only for technical soundness rather than for importance or appropriateness for the journal’s subject area. Articles available at http://www.plosone.org/ .
• Science. v. 1- , 1880- . New York: American Association for the Advancement of Science. Weekly. Price varies. ISSN 0036-8075.Prestigious general scientific journal with a majority of biological articles reporting original research, news, comments, book reviews, and special sections for grants, laboratory aids, etc. At http://www.sciencemag.org/ there is access to content highlights.
• Science News. v.1- , 1921- . Washington, DC: Science Service. Biweekly. $49.95 (print); $39.95 (online). ISSN 0036-8423 (print); 1943-0930 (online).A weekly news magazine which covers the entire spectrum of sciences. Selected articles are available for free at http://www.sciencenews.org/. Formerly Science News Letter.
• The Scientist. v. 1- , 1986- . Midland, ONT: LabX Media Group. Monthly. Price varies. ISSN 0890-3670.” The Scientist is the magazine for life science professionals—publication dedicated to covering a wide range of topics central to the study of cell and molecular biology, genetics, and other life-science fields.” Available at no charge on the Web at http://www.the-scientist.com , although there is an institutional subscription as well.
• Scientific American. v. 1- , 1845- . New York: Nature. Monthly. $317.00 (print). ISSN 0036-8733 (print).Scholarly review articles written for the educated layperson; also includes news, comments, games, and book reviews. Selected articles and news items are available for free at http://www.scientificamerican.com/ .

Chapter 4: Abstracts and Indexes

This chapter can be seen as a companion to Chapter 2, “Searching the Biological Literature”. Abstracts and indexes are used to locate articles, proceedings, patents, dissertations, books, and book chapters in various subjects. Because the literature of biology is so vast it should come as no surprise to find that there are many indexes offering access to that literature. This chapter annotates the major indexes and abstracts that cover general science and/or multiple subjects in biology. Those indexes that deal with narrower fields such as entomology or plant taxonomy will be covered in the appropriate subject chapter.

Jump to Section

Current awareness, retrospective tools.

• AGRICOLA. Washington, DC: National Agricultural Library, 1970- . http://agricola.nal.usda.gov .Covers the worldwide literature of agriculture, including journal articles, monographs, government documents, technical reports, and proceedings; from the Nation­al Agriculture Library (NAL). This database is valuable for life sciences students and researchers who are interested in plants or animals of economic importance. Available for free from NAL or through several other vendors by subscription. The ceased print version of AGRICOLA was the Bibliography of Agriculture . The list of serial titles indexed in AGRICOLA is available at http://www.nal.usda.gov/nal-catalog/journals-indexed-agricola-jia .
• Embase. 1974- . New York: Elsevier Science. Daily. Price varies. ISSN 0929-3302.This biomedical database is a competitor to MEDLINE , and contains records from the 41 sections of the print Excerpta Medica indexes plus MEDLINE records. EMBASE covers more than 7,600 journals and 2,000 conferences, including many not covered by MEDLINE . EMBASE focuses on the European literature, especially in pharmacology and related fields. An EMBASE Classic version is also available, searchable back to 1947. The list of journals covered can be found at http://www.embase.com/info/what-is-embase/coverage. EMBASE is available directly through Elsevier or via several other vendors.
• Google Scholar. Mountain View, CA: Google, 2004- . http://scholar.google.com/ .Indexes scholarly articles, theses, books, white papers, court opinions, and Web sites harvested from academic publishers, professional societies, scholarly repositories, and universities in all areas of scholarly endeavor. Libraries can link their holdings and subscriptions to Google Scholar , allowing users to connect directly to subscription-based resources. The index also indicates who has cited indexed works, and users with Google accounts can create alerts to keep up to date.
• Official Gazette of the United States Patent and Trademark Office. Patents. Washington, DC: US Dept. of Commerce, US Patent and Trademark Office, Information Products Division, 2000s- . http://www.uspto.gov/news/og/patent_og/index.jsp .Listing of patents; includes abstract and sketches. The USPTO site includes PatFT , a searchable database containing the full text of all US patents issued since January 1, 1976, and full-page images of each page of every US patent issued since 1790. AppFT lists patent applications since 2001.
• Open WorldCat. OCLC Online Computer Library Center. http://www.worldcat.org/ .This is a freely searchable database that corresponds to the subscription WorldCat database, the largest library catalog in the world. Users can search for books and journals and find out which libraries hold the material. The majority of the participating libraries are in the United States, but most of the large national and academic libraries from around the world are also included.
• PubMed. Bethesda, MD: NCBI, 1949- . http://www.ncbi.nlm.nih.gov/pubmed . PubMed is another version of the MEDLINE database and offers a number of useful services aimed at the biological research community. It is available for free at the National Center for Biotechnology Information’s (NCBI) site. The PubMed database indexes articles that are not included in the main MEDLINE database, including all articles from journals that are indexed selectively in MEDLINE . Citations show up earlier in PubMed than in MEDLINE as well. PubMed also provides links to articles from over 700 full text journals and to the molecular biology databases of DNA/protein sequences and 3-D structure data that have been developed by NCBI. Researchers can set up Current Awareness searches through the “MyNCBI” account. There are also a number of other useful services such as browseable databases for journal titles and MeSH headings, and citation matching services.
• This site was retired in 2014, statement from Elsevier: “We are sad to say goodbye. Scirus is set to retire in early 2014. An official retirement date will be posted here as soon as it is determined. To ensure a smooth transition, we are informing you now so that you have sufficient time to find an alternative search solution for science-specific content. Thank you for being a devoted user of Scirus. We have enjoyed serving you.”
• Index-Catalogue of the Library of the Surgeon-General’s Office. 1st-5th series, 1880-1961. Washington, DC: GPO.This series indexes the publications held in the library of the Army’s Surgeon-General and predates Index Medicus . The articles and transactions are indexed in a mixed author and subject list. The Index-Catalogue was the most comprehensive biomedical index of its time. The full text of the Index-Catalogue is freely available at NLM’s site at http://indexcat.nlm.nih.gov/.

Chapter 5: Biochemistry and Biophysics

Biochemistry and biophysics have been grouped together in this chapter.  Biochemistry is “the study of the chemistry of living organisms, especially the structure and function of their chemical components”, while biophysics is “the study of physical aspects of biology” ( Oxford Dictionary of Biology , 4 th ed., 2000). Both are integral parts of biology, and their interdisciplinary relationship with basic biological sciences often blurs subject area lines.  Frequently, the materials and literature for one discipline will satisfy the demands or questions posed by the other.

There will be substantial overlap, also, between biochemis­try/biophysics with molecular and cellular biology which have been placed in Chapter 6. Toxicology is also included in this chapter.

Abstracts and Indexes

• This has become a subset in PubMed: https://pubmed.ncbi.nlm.nih.gov/?term=tox%20%5Bsubset%5D%20AND%20 .
• American Chemical Society (ACS) . 1155 16th St. NW, Washington, DC 20036. E-Mail: [email protected] . URL: http://portal.acs.org/portal/acs/corg/content .Founded 1876, 151,000 members. Scientific and educational society of chemists and chemical engineers. Publishes 50 journals includ­ing ACS Chemical Biology , ACS Chemical Neuroscience , Biochemistry , Journal of Agricultural and Food Chemistry , Journal of Natural Products , Journal of the American Chemical Society , and Journal of Physical and Chemical Refer­ence Data , as well as numerous books.  CAS (Chemical Abstract Service), a division of ACS, publishes Chemical Abstracts (see Chapter 4). The ACS Web site is a major source of information for chemists.
• American Institute of Physics (AIP) . 1 Physics Ellipse, College Park, MD 20740. E-Mail: [email protected] . URL: http://www.aip.org. Founded 1931. Ten national member societies, including 135,000 members in the fields of physics, astronomy and related disciplines. Seeks to assist in the advancement and diffusion of the knowledge of physics and its application to human welfare. Publishes several scientific journals, including Review of Scientific Instruments . Web site contains extensive information for physicists.
• American Society for Biochemistry and Molecular Biology (ASBMB) . 11200 Rockville Pike, Ste. 302, Rockville, MD 20852-3110. E-Mail: [email protected] . URL: http://www.asbmb.org Founded 1906, 9,300 members. Biochemists and molecular biologists who have conducted and published original investiga­tions in biological chemistry and/or molecular biology. Publishes Journal of Biological Chemistry , Journal of Lipid Research , and Molecular and Cellular Proteomics . Formerly American Society of Biological Chemists. Web site primarily for society information.
• Biochemical Society (BS) . 3rd Fl., Eagle House, 16 Procter St., London WC1V 6NX, UK. E-Mail: [email protected] . URL: http://www.biochemistry.org .Founded 1911. 9,000 members. Objectives are to promote biochemistry and to provide a forum for information exchange and discussion of various aspects of teaching and research in biochemistry. Publishes Biochemi­cal Journal , Biochemical Society Transac­tions , The Biochemist , Essays in Biochemistry , Journal of Lipid Research , Molecular and Cellular Proteomics, and more. Web site contains membership information and links to education resources.
• Biophysical Society (BPS) . 9650 Rockville Pike, Bethesda, MD 20814. E-Mail: [email protected] . URL: http://www.biophysics.org Founded 1957. 5,600 members. Biophysicists, physical bio­chem­ists, and physical and biological scientists interested in the application of physical laws and techniques to the analysis of biological or living phenomena. Publishes Biophysical Journal and Biophysi­cal Society Newsletter . Web site provides career information, membership information, and a product guide.
• Canadian Society for Chemistry (CSC) Societe Canadienne de Chimie . The Chemical Institute of Canada, 130 Slater St., Ste. 550, Ottawa, ONT, Canada K1P 6E2. E-Mail: [email protected] . URL: http://www.chemistry.ca Founded 1985, 3,500 members. Scientific association of chemists in education, government, and industry. Covers chemical research, development, management, and education. Publishes Canadian Chemical News . Web site primarily for society information, but has links to other chemical resources.
• Federation of European Biochemical Societies (FEBS) . The Weizmann Institute of Science, Department of Immunology, PO Box 2676100 Rehovot, Israel. E-Mail: [email protected] . URL: http://www.febs.org. Founded 1964. 39,000 members. Purpose is to further re­search and education in the field of biochemistry and to dissemi­nate research findings. Publishes FEBS Journal , FEBS Letters, FEBS Open Bio , and Molecular Oncology . Web site primarily for society information.
• International Union for Pure and Applied Biophysics (IUPAB) Organisation Internationale de Biophysique Pure et Appliquee . c/o Prof. Chris dos Remedios, Sec. Gen., University of Sydney, Bosch Institute Anderson Stuart F13, Sydney, New South Wales 2006, Australia. E-Mail: [email protected] . URL: http://iupab.org. Founded 1966. National committees appointed by academies and research councils representing 50 countries. Purposes are to organize international cooperation in biophysics and to promote communication between the various branches of biophysics and allied subjects; to encour­age cooperation between the societies that represent the interests of biophysics; and to contribute to the advancement of biophysics. Publishes Biophysical Reviews and IUBG Report . Web site primarily for membership information.
• International Union of Biochemistry and Molecular Biology (IUBMB) . University of Calgary, Faculty of Medicine, Dept. of Biochemistry and Molecular Biology, 3330 Hospital Dr. NW, Calgary, AB, Canada T2N 4N1. E-Mail: [email protected] . URL: http://www.iubmb.org. Founded 1955. 65 member societies. National academies, research councils, or biochemical societies; associated bodies represent national biochemical and molecular biology societies; special members are organizations representing industrial and other groups.­­ Publishes Biochemistry and Molecular Biology Education , Biotechnolo­gy and Applied Biochemistry , IUBMB Life , Molecular Aspects of Medicine , and Trends in Biochemical Sciences . Web site primarily for society information.
• Protein Society . 9650 Rockville Pike, Bethesda, MD 20814-3999. E-Mail: [email protected] . URL: http://www.proteinsociety.org.
• Founded 1986. To promote international interactions among investigators in order to explore all aspects of the “building blocks of life: protein molecules.” Membership is open to scholars and researchers interested in the analysis, chemistry, folding, structure, function, and regulation of proteins. Publishes Protein Science . Web site provides membership information and educational resources.
• Wiggins, Gary. Chemical Information Sources. New York: McGraw-Hill, 1991. 352 p. (McGraw-Hill series in advanced chemistry). ISBN 0079099394; 9780079099396.A well-known comprehensive guide to the literature of chemistry, covering both print and online resources. Updated on the Web at the Chemical Information Sources site at http://en.wikibooks.org/wiki/Chemical_Information_Sources .
• This has been folder into PubChem: https://pubchem.ncbi.nlm.nih.gov/.
• Moss, Gerard P. and Edwin C. Webb. Enzyme Nomenclature. London: Queen Mary and Westfield College, 2001. http://www.chem.qmw.ac.uk/iubmb/enzyme/ .The Web version of Enzyme Nomenclature 1992 , including all of the supplements. The Web site provides general information on enzyme nomenclature, links to information about pathways, and suggestions on how to propose new enzymes and changes in the nomenclature.
• Center for History of Physics . American Institute for Physics, 2000s-. http://www.aip.org/history/ .The American Institute of Physics maintains this site for information about the history of physics. It provides documentation and educational programs, and its library has extensive exhibits, visual archives, oral histories, and publications.
• FEBS Open Bio. v. 1- , 2011- . Cambridge, UK: Elsevier on behalf of the Federation of European Biochemical Societies. Continually updated. Open Access. ISSN 2211-5463.”As a charity whose objectives are to promote research and education in the Life Sciences, FEBS aims to meet the growing interest in open access publishing and therefore has established FEBS OPEN BIO for the rapid publication of articles in the molecular and cellular life sciences in both health and disease.” Articles available at http://www.journals.elsevier.com/febs-open-bio/ .

Chapter 6: Molecular and Cellular Biology

Molecular biology is defined as “The study of the structure and function of large molecules associated with living organisms, in particular proteins and the nucleic acids DNA and RNA” ( Oxford Dictionary of Biology, 4 th ed., 2000), while cellular biology is the study of cells, “the structural and functional unit of most living organisms” ( Oxford Dictionary of Biology, 4 th ed., 2000).

Molecular biology is among the most rapidly growing fields within biology with recent success stories such as the sequencing of the entire human genome (reported in Science and Nature ). Molecular biology is unusual in that the major information source for molecular biologists is not journal articles, but public databases such as GenBank, PDB, and DDBJ (annotated below in the database section). This is one reason why there are relatively fewer handbooks and treatises for molecular biology than there are for other biological subjects.

There is a natural affinity between this chapter and the ones discussing reference materials for biochemistry (Chapter 5) and genetics (Chapter 7). Given this very substantial overlap, it is essential to review the sources annotated in these chapters for a more complete understanding of the literature of molecular biology.

Textbooks and Treatises

• American Society for Cell Biology (ASCB) . 8120 Woodmont Ave., Ste. 750, Bethesda, MD 20814-2762. E-Mail: [email protected] . URL: http://www.ascb.org. Founded in 1960. 9,000 members. Includes scientists with educational or re­search experience in cell biology or an allied field. Placement service is offered. Publications: ASCB Newsletter, Molecular Biology of the Cell , and CBE—Life Sciences Education. Web site provides membership information and access to the Society’s products and services, meetings, news, publications, public policy, and careers.
• European Molecular Biology Laboratory (EMBL) . Meyerhofstrasse 1, D-69117 Heidelberg, Germany. E-Mail: [email protected] . URL: http://www.embl.de. Founded 1975. 16 member countries. Conducts molecular biological research in a wide array of areas. Their Website lists their outstation locations and provides access to information about each site. Formerly European Laboratory for Molecular Biology.
• International Federation of Cell Biology (IFCB) . c/o Dr. W. Elaine Hardman, Treas., Marshall University School of Medicine, 1542 Spring Valley Dr., Huntington, WV 25704-9388. URL: http://www.ifcbiol.org. Founded 1972. 21 member associations. National and regional associations of cell biologists promoting international cooperation among scientists working in cell biology and related fields, and contributing to the advancement of cell biology in all of its branches. Publishes Cell Biology International and Cell Biology International Reports . Formerly: International Society for Cell Biology and International Society for Experimental Cytology.
• RNA Society (RNA) . 9650 Rockville Pike, Bethesda, MD 20814-3998. E-Mail: [email protected] . URL: http://www.rnasociety.org. Founded 1993. 1000 members. Professionals working in molecular, evolutionary, and structural biology, biochemistry, biomedical sciences, chemistry, genetics, virology, and related disciplines with an interest in the structure and functions of ribonucleic acid (RNA). Publishes RNA . Web site provides membership and conference information.
• Society for in Vitro Biology (SIVB) . 514 Daniels St., Ste. 411, Raleigh, NC 27605-1317. E-Mail: [email protected] . URL: http://www.sivb.org. Founded 1946. 2,500 members. Professional society of individuals using mammalian, invertebrate, plant cell tissue, and organ cultures as research tools in chemistry, physics, radiation, medicine, physiology, nutrition, and cytogenetics. Publications: In Vitro-Animal , In Vitro-Plant , and In-Vitro Report . Their Web site provides access to society information and links to educational material.

Molecular biology information is available extensively on the Web.  Many of the databases discussed here provide access to gene or protein sequences.  Each time a researcher sequences a gene or protein, he or she is expected not only to publish the sequence in a research journal, but also to submit the sequence to a sequence database.  Sometimes journals will not accept articles until the sequences have appeared in a database, which is one of the few cases in which journals will accept data previously published elsewhere. The annual Nucleic Acids Research Database Issue is the best source for information on the major databases (currently volume 42, issue D1 or at http://nar.oxfordjournals.org/content/42/D1.toc).  The associated 2013 Molecular Biology Database (http://www.oxfordjournals.org/nar/database/a/) lists 1,512 databases, and there are many others as well.

• DDBJ (DNA Data Bank of Japan). Mishima, Japan: National Institute of Genetics, 1986- . http://www.ddbj.nig.ac.jp/ .Collaborates with GenBank and EMBL (both below) to collect nucleotide sequences, which are compiled to form the INSD: International Nucleotide Sequence Database .
• Entrez. Bethesda, MD: National Center for Biotechnology Information, 1990s- . http://www.ncbi.nlm.nih.gov/sites/gquery .Entrez “is a search and retrieval system that integrates information from databases at NCBI. These databases include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE , through PubMed .”
• European Nucleotide Archive. Heidelberg, Germany: EMBL Data Library, 1980- . http://www.ebi.ac.uk/ena/ .A nucleotide sequence database, created by EMBL in collaboration with GenBank and DDBJ .
• Genbank. Bethesda, MD: National Center for Biotechnology Information, 1982- . http://www.ncbi.nlm.nih.gov/genbank/ .NIH’s “annotated collection of all publicly available DNA sequences”. Contained over 165 million sequence records from 260,000 species in July 2013. Accessible via ENTREZ , above.
• Protein Data Bank (PDB). Research Collaboratory for Structural Bioinformatics (RCSB), 1993- . http:// www.rcsb.org/pdb/home/home.do .“The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.” (from the Web page). It was established at Brookhaven National Laboratories in 1971 and contained just 7 structures; by June 2000, there were over 12,500 structures and by December 2013, there were 96,250 structures. The PDB Web site provides links to many molecular biology databases and other resources. There are three other mirror sites in Europe, Japan, and the US.
• National Center for Biotechnology Information (NCBI). Bethesda, MD: National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/ .The NCBI is one of the primary resources for molecular biology worldwide. Its Web site provides access to dozens of databases, software products, projects, tutorials and training opportunities, and literature.
• Guidelines for Human Embryonic Stem Cell Research. Washington, DC: National Academies Press, 2005. 166 p. $34.95 (pa). ISBN 0309096537 (pa); 9780309096539 (pa).Provides recommendations for safe and ethical research on human stem cells. Also available as a free PDF download at the NAP web site ( http://www.nap.edu/catalog.php?record_id=11278 ).
• OpenHelix. http://www.openhelix.com/ . Bellevue, WA: OpenHelix, 2010. Price varies.”The OpenHelix Search Portal provides a mechanism to search for, and evaluate, online bioinformatics and genomics resources by providing contextual displays of search results.” Individual and institutional subscriptions are available, although some tutorials are free.
• DNA Learning Center. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, Dolan DNA Learning Center, 1993- . http://www.dnalc.org/ .”The DNA Learning Center (DNALC) is the world’s first science center devoted entirely to genetics education and is an operating unit of Cold Spring Harbor Laboratory, an important center for molecular genetics research.” The learning center offers on-site courses but also provides numerous Web sites and tools for educators and students.
• Mount, David W. Bioinformatics: Sequence and Genome Analysis. 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2004. 692 p. $95.00 (pa). ISBN 0879696877; 9780879696870; 0879697121 (pa); 9780879697129 (pa).This guide is a comprehensive introduction to bioinformatics at both the undergraduate and graduate level. Unlike most bioinformatics texts, it includes information on collecting and storing sequences, not just analyzing them. It also discusses programming using Perl and analysis of genomes and microarrays. The text is augmented by a Web site, http://www.bioinformaticsonline.org/.
• Bioscience Reports. v. 1- , 1981- . London: Portland Press. Bimonthly. Open Access. ISSN 0144-8463.”Bioscience Reports publishes articles in the cellular and molecular life sciences.” Starting in mid-2012 the journal became fully Open Access; articles are available at http://www.bioscirep.org/bsr/toc.htm.
• BMC Genomics. v. 1- , 2000- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2164.Publishes “articles on all aspects of genome-scale analysis, functional genomics, and proteomics.” Articles available at http://www.biomedcentral.com/bmcgenomics.
• BMC Molecular Biology. v. 1- , 2000- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2199.Publishes “articles on all aspects of DNA and RNA in a cellular context, encompassing investigations of chromatin, replication, recombination, mutation, repair, transcription, translation and RNA processing and function.” Articles available at http://www.biomedcentral.com/bmcmolbiol.

Chapter 7: Genetics, Biotechnology, and Developmental Biology

Genetics is “the branch of biology concerned with the study of heredity and variation”. Biotechnology is “the development of techniques for the application of biological processes to the production of materials of use in medicine and industry.” Development is “the complex process of growth and maturation that occurs in living organisms.” ( Oxford Dictionary of Biology , 4 th ed., 2000). This chapter also includes the study of “omics”, a suffix used to indicate studies in several fields performed on a genome-wide scale, such as proteomics or metabolomics. The more applied aspects of biotechnology and genetics such as plant or animal breeding and industrial biotechnology are not included.

All of the subjects covered in this chapter overlap with other chapters.  For instance, molecular biologists study DNA while geneticists study genes so Chapter 6, “Molecular and Cellular Biology”, should also be checked for information sources.  Research in development may be done by geneticists, cell biologists, or physiologists, so other related resources are found in Chapter 11, “Anatomy and Physiology”.

• American Genetic Association (AGA) . 2030 SE Marine Science Dr., Newport, OR 97365. E-Mail: [email protected] . URL: http://www.theaga.org .Founded in 1903, 750 members. Emphasis on applied areas of genetics. Publishes Journal of Heredity . Formerly American Breeders Association.
• American Society of Human Genetics (ASHG) . 9650 Rockville Pike, Bethesda, MD 20814-3998. E-Mail: [email protected] . URL: http://www.ashg.org .Founded in 1948, 6,361members in 1999. Physicians, genetic counselors, researchers interested in human genetics. Publishes American Journal of Human Genetics . Web site primarily for society information.
• British Society for Developmental Biology (BSDB) . MRC Brain Development Programme, Centre for Developmental Neurobiology, King’s College London, New Hunt’s House (4 th Floor), Grey’s Hospital Campus, London SE1 9RT. URL: http://bsdb.org/ .1,000 members. Aims “to represent developmental biology to external organizations in the UK and Europe.” Organizes meetings and publishes newsletter. Web site contains society information and list of useful links for developmental biologists and teachers.
• Canadian Society for Molecular Biosciences (CSMB) . c/o Mrs. Wafaa H. Antonious, Canadian Society for Molecular Biosciences, 17 Dossetter Way, Ottawa, ONT, Canada K1G 4S3. E-Mail: [email protected] . URL: http://www.csmb-scbm.ca/. Society for professional biochemists, molecular biologists, and geneticists in Canada. Publishes quarterly Bulletin . Holds annual meeting. Originally called the Canadian Biochemical Society; merged with the Canadian Society of Cellular and Molecular Biology in 1992 and with the Genetics Society of Canada in 2010.
• European Society of Human Genetics (ESHG) . c/o Vienna Medical Academy, Alser Strasse 4, 1090 Vienna, Austria. E-Mail: [email protected] . URL: http://www.eshg.org. Founded 1967. “Promotes research in basic and applied human and medical genetics and facilitates contact between all persons who share these aims.” Publishes European Journal of Human Genetics .
• Genetics Society (GS) . Roslin BioCentre, Wallace Bldg., Roslin, Midlothian EH25 9PS, UK. Phone: 44 131 2006392. Fax: 44 131 2006394. E-Mail: [email protected] . URL: http://www.genetics.org.uk .Founded in 1919. Approximately 2000 members. The “world’s first society devoted to the study of mechanisms of inheritance.” For all active geneticists in the U.K. interested in research or teaching. Publishes Heredity and Genes and Development . Formerly: Genetical Society. Web site includes information on careers as well as society information.
• Genetics Society of America (GSA). 9650 Rockville Pike, Bethesda, MD 20814-3998. E-Mail: [email protected] . URL: http://www.genetics-gsa.org. Founded in 1931, 4,100 members. Includes all areas of genetics. Publishes Genetics and G3 , an Open Access journal. Awards GSA medal and Thomas Hunt Morgan Medal. Annual conference. Web site has education resources and policy statements as well as society information.
• International Society of Developmental Biologists (ISDB). c/o Douglas Sipp, Business Mgr., RIKEN Center for Developmental Biology, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan. E-Mail: [email protected] . URL: http://www.developmental-biology.org. Founded 1911. 900 members, both individual and corporate. Scientists from 31 countries. Promotes the study of developmental biology by encouraging research and communication in the field. Organizes conferences and workshops. Publishes Mechanisms of Development and Gene Expression Patterns. Web site has links to other societies and developmental biology databases as well as membership information. Formerly called the International Institute of Embryology. Absorbed the Developmental Biology Section, International Union of Biological Sciences.
• Japanese Society of Developmental Biologists (JSDB). Center for Developmental Biology, RIKIEN Kobe, 2-2-3 Minatojima-minami Chuo-ku, Kobe 650-0047, Japan. E-Mail: [email protected] . URL: http://www.jsdb.jp/english/index.html. Founded in 1968. 1,300 members. Professional society for developmental biologists, researchers and educators. Publishes Development, and Growth and Differentiation (DGD) . Web site primarily for membership information.
• Society for Developmental Biology (SDB). 9650 Rockville Pike, Bethesda, MD 20814-3998. E-Mail: [email protected] . URL: http://www.sdbonline.org. Founded 1939. 2,100 members. Professional society of biologists interested in problems of development and growth of organisms. Publishes Developmental Biology . Web site contains membership information and conference information, and links to developmental biology sites. Formerly Society for the Study of Development and Growth.
• Mouse Genome Informatics. Bar Harbor, ME: Jackson Laboratory, 1980s- . www.informatics.jax.org .Maintained by the Jackson Laboratory, a major mouse mutant repository and center for mouse research, this site “is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.” (from the Web site). Includes the Mouse Genome Database , the Gene Expression Database and the Mouse Tumor Database projects, among others.
• Xenbase: Xenopus laevis and Xenopus tropicalis Biology and Genomics Resource. http://www.xenbase.org/common/ .A “database of information pertaining to the cell and developmental biology of the frog, Xenopus ”. Also contains genetic and genomic information, as well as directories, methods, links to databases and electronic journals, announcements of conferences and more.
• Davidson, Duncan and Richard Baldock. The e-Mouse Atlas Project. www.emouseatlas.org .This site contains two projects, EMA, the e-Mouse Atlas (3-D anatomical atlas of mouse embryo development and histology) and EMAGE, the e-Mouse Atlas of Gene Expression , a “database of mouse gene expression where, uniquely, the gene expression is mapped into the EMA 3-D space and can be queried spatially”. The site includes tutorials and a glossary of terms to aid new users.
• McKusick, Victor A. OMIM–Online Mendelian Inheritance in Man. Bethesda, MD: National Center for Biotechnology Information, 2005- . http://www.ncbi.nlm.nih.gov/omim .The online, freely-accessible version of Mendelian Inheritance in Man , a handbook that features catalogs of human genes, phenotypes, and genetic disorders. For physicians and advanced students, although it is accessible to the general public.
• Society for Developmental Biology. The Interactive Fly. http://www.sdbonline.org/fly/aimain/1aahome.htm .”A cyberspace guide to Drosophila development and metazoan evolution” (from the Web site). This portal provides links to genes, tissue and organ development, and study aids for Drosophila . The site is hosted by the Society for Developmental Biology.
• WormBase Consortium. Wormbase. 2000- . http://www.wormbase.org/ .”WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.” (from the Web site). Includes news, resouces, and tools for researchers.
• The Zebrafish Model Organism Database. Eugene, OR: University of Oregon. http://zfin.org.Provides access to a wealth of information for researchers on this fish which is a major model organism for developmental studies. Database includes developmental atlases and dictionaries, genetic mutants and maps, nomenclature, publications, resources, conference information and directories of people in the field.
• Talking Glossary of Genetic Terms. Bethesda, MD: National Human Genome Research Institute, National Institutes of Health, 2001- . https://www.genome.gov/genetics-glossary .This free online dictionary provides audio definitions, illustrations, animations, and other resources for more than 200 terms. A text-only version is also available at the site. Also available as an iTunes app.
• Sturtevant, A. H. A History of Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2001. 174 p. $21.00. ISBN 0879696079 (pa); 9780879696078 (pa).A classic work on the early history of genetics first published in 1965. This new reprint edition has an accompanying Web site at http://www.esp.org/books/sturt/history.
• BMC Bioinformatics. v. 1- , 2000- . London: BioMed Central. Frequently updated. Open Access. ISSN 1471-2105.”An open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.” Articles available at http://www.biomedcentral.com/bmcbioinformatics .
• BMC Biotechnology. v. 1- , 2001- . London: BioMed Central. Frequently updated. Open Access. ISSN 1472-6750.Publishes “articles on the manipulation of biological macromolecules or organisms for use in experimental procedures, cellular and tissue engineering or in the pharmaceutical, agricultural biotechnology and allied industries.” Articles available at http://www.biomedcentral.com/bmcbiotechnol .
• Nucleic Acids Research. v. 1- , 1974- . New York: Oxford University Press. Biweekly. Open Access. ISSN 0305-1048 (print).”Publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. ” The first issue each year covers genetic, protein, and the July issue is devoted to genome databases. An Open Access journal. Articles are available at http://nar.oxfordjournals.org/ .
• PLOS Genetics. v. 1- , 2005- . San Francisco, CA: Public Library of Science. Weekly. Open Access. ISSN 1553-7390 (print); 1553-7404 (online).Publishes articles on genetics and genomics using human subjects and model organisms. In addition to research articles, the journal also publishes editorials, viewpoints, interviews, special reports, and review articles. Articles are available at http://www.plosgenetics.org/ .

Chapter 8: Microbiology and Immunology

This chapter includes reference sources useful for microbio­logy and immunology.  Microbiology is “the scientific study of microorganisms (e.g. bacteria, viruses and fungi).” For purposes of this discussion, however, fungi such as yeasts are included with plant biology in Chapter 10, “Plant Biology”. Immunology is the study of immunity, “the state of relative insusceptibility of an animal to infection by disease-producing organisms”. ( Oxford Dictionary of Biology , 4 th ed, 2000) Because microbial systems are convenient and effective for studying a whole range of life processes, there is a significant overlap between this chapter and Chapters 5-7, covering biochemistry and biophysics, molecular and cell biology, and genetics, respectively.  Although medical microbiology and immunology are not comprehensively discussed in this chapter, some basic materials are included that pertain to the study of pathogenic microbiology and diagnostic immunology.

• American Type Culture Collection (ATCC) . PO Box 1549, Manassas, VA 20108. E-Mail: [email protected] . URL: http://www.atcc.org. Founded 1925. 225 staff. A private organization seeking to collect, propagate, preserve, and distribute authentic cultures of microorganisms and genetic materials for reference purposes for use in educational, research, and other scientific and industrial activities. Conducts research, maintains depository for cultures, aids in processing and packaging biohazardous materials, and identifies cultures. Web site provides access to catalogs, news, and information about the ATCC.
• American Academy of Microbiology (AAM) . 1752 N St. NW, Washington, DC 20036-2804. E-Mail: [email protected] . URL: https://www.asm.org/Academy/Academy. Founded in 1955, 1,500 members. Honorific leadership component of American Society for Microbiology (see below) concerned with microscopic and submicro­scopic organisms. Encourages exchange of information among members. Publishes ­­­Academy News and Views . Web site provides links to Colloquium Reports, membership information, and more.
• American Association of Immunologists (AAI) . 9650 Rockville Pike, Bethesda, MD 20814-3998. E-Mail: [email protected] . URL: http://www.aai.org. Founded 1913, 5,500 members. Scientists engaged in immunological research including aspects of virology, bacteriology, biochemis­try, genetics, and related disciplines. Goals are to advance knowledge of immunology and related disciplines and to facilitate the interchange of information among investigators in various fields. Promotes interaction between laboratory investigators and clinicians; conducts training courses, symposia, workshops, and lectures; bestows awards; compiles statistics. Publishes quarterly AAI Newsletter and Journal of Immunology . Web site contains membership information, and information on educational and policy programs.
• American Society for Microbiology (ASM) . 1752 N St. NW, Washington, DC 20036. E-Mail: [email protected] . URL: http://www.asm.org. Founded in 1899, 42,000 members with 36 local groups. Scientific society of microbiologists promoting advancement of scientific knowledge in order to improve education in microbi­ology. Encou­rages the highest professional and ethical standards and the adoption of sound legislative and regulatory policies affecting the disci­pline of microbiology at all levels. Affiliat­ed with the Interna­tional Union of Microbiological Societies. Publishes over twenty scientific journals and many books. Formerly: the Society of American Bacteriologists. Web site includes membership information, news, and educational materials for K12 and the general public.
• Canadian Society for Immunology (CSI) Societe Canadienne d’Immunologie . University of Saskatchewan, Dept. of Veterinary Microbiology, 52 Campus Dr., Saskatoon, SK, Canada S7N 5B4. URL: http://www.csi-sci.ca/ .Immunologists and other health care professionals and scientists with an interest in immunology. Seeks to advance immunological study, research, and practice. Promotes ongoing professional development of members. Serves as a network linking members; sponsors research and educational programs. Web site contains membership information, links to other societies and immunology journals.
• European Culture Collections’ Organisation (ECCO) . DSMZ-Deutsche Sammlung,von Mikroorganismen, und Zellkulturen GMBHMascheroder Weg 1b, 38124 Braunschweig, Germany. E-Mail: [email protected] . URL: http://www.eccosite.org. Founded 1981. 61 members. Members of European organizations in 22 countries participating in the maintenance of biological material. Encourages communication and collaborative research among members. Informs members of current developments concerning taxonomy, culture identification, and patent information. Web site has links to other societies, transport regulations, and more.
• European Federation of Immunological Societies (EFIS) . c/o Astrid Hahner, Coor., PO Box 42 08 07, D-12068 Berlin, Germany. E-Mail: [email protected] . URL: http://www.efis.org. Founded 1975, 16,000 members. Immunological societies from around the world focusing on Europe. Promotes the advancement of research and education in immunology. Publishes European Journal of Immunology and Immunology Letters . Web site includes links to databases and organizations of interest to immunologists.
• International Committee on Systematics of Prokaryotes (ICSP) . http://www.the-icsp.org/ .Founded 1930. 140 members. Multinational. A committee of the International Union of Microbiological Societies. Sponsors international collaboration and research in systematic bacteriology. Publishes quarterly International Journal of Systematic and Evolutionary Microbiology­ ; International Code of Nomenclature of Bacteria .
• International Committee on Taxonomy of Viruses (ICTV) . URL: http://ictvonline.org/ Founded 1966. 120 members. Multinational. A committee of the Virology Division of the International Union of Microbiological Societies. Seeks to develop a standard, internationally accepted system of virus classification and nomenclature. Publishes triennial ICTV Reports . Web site provides extensive information on viral taxonomy.
• International Union of Immunological Societies (IUIS) . c/o Mag. Gerlinde M. Jahn, Vienna Academy of Postgraduate Medical Education and Research, Alser Strasse 4, A-1090 Vienna, Austria. E-Mail: [email protected] . URL: http://www.iuisonline.org. Founded 1969, 51 members. National professional societies of basic and applied immunologists. Encourages the orderly development and utilization of the science of immunology; promotes the applica­tion of new developments to clinical and veterinary problems and standardizes reagents and nomenclature; conducts educational symposia and scientific meetings. Publishes Frontiers in Immunology . Web site for membership information.
• International Union of Microbiological Societies (IUMS) Union Internationale des Societes de Microbiologie . c/o Robert A. Samson, Sec. Gen., PO Box 85167, 3508 AD Utrecht, Netherlands. E-Mail: [email protected] . URL: http://www.iums.org. Founded 1930. 106 members. Multinational. National microbiological societies in 62 countries representing 100,000 microbiologists. Publishes International Journal of Systematic and Evolutionary Microbiology and International Journal of Food Microbiology . Web site lists affiliated groups.
• Society for Applied Microbiology (SFAM) . Bedford Heights, Brickhill Dr., Bedford MK41 7PH, UK. E-Mail: [email protected] . URL: http://www.sfam.org.uk. Founded 1931, 1,800 members. Multinational. Individuals in­volved in the study of microbiology whose purpose is to promote and advance the study of microbiology, particularly bacteriology, in its application to agriculture, industry, and the environment. Publishes Microbiologist , Journal of Applied Microbiology , Letters in Applied Microbiology , Microbial Biotechnology , Environmental Microbiology , and Environmental Microbiology Reports . Holds three meetings each year. Formerly: Society for Applied Bacteriology.
• Society for General Microbiology (SGM) . Marlborough House, Basingstoke Rd., Spencers Wood, Reading RG7 1AG, United Kingdom. E-Mail: [email protected] . URL: http://www.sgm.ac.uk. Founded 1945, 5,500 members. Multinational. Works to advance the study of general microbiology. Bestows awards and grants. Affiliated with the International Union of Microbiological Societies, and the Federation of the European Microbiological Societies. Publishes International Journal of Systematic and Evolutionary Microbiology , Journal of General Virology , Journal of Medical Microbiology , Microbiology , Microbiology Today , and an annual symposium series. Web site contains membership information, news, and links.
• Society for Industrial Microbiology and Biotechnology (SIMB) . 3929 Old Lee Hwy., Ste. 92A, Fairfax, VA 22030-2421. E-Mail: [email protected] . URL: http://www.simhq.org. Founded 1948, 2,122 members and 2 local groups. Mycologists, bacteriologists, biologists, chemists, engineers, zoologists, and others interested in biological processes as applied to industri­al materials and processes of microorganisms. Affiliated with the American Institute of Biological Sciences. Publishes Journal of Industrial Microbiology and Biotechnology and SIMB News. Web site includes career information.
• Lapage, S. P., et al., eds. International Code of Nomenclature of Bacteria. Washington, DC: Published for the International Union of Microbiological Societies by American Society for Microbiology, 2006- . http://www.ncbi.nlm.nih.gov/books/NBK8817/ .Covers the rules and procedures for correct bacterial nomenclature based on the 1990 revision. Also provides a summary of the history of the Code and lists of conserved and rejected names.
• Linscott, William D. Linscott’s Directory of Immunological and Biological Reagents. Mill Valley, CA: Linscott’s Directory, 1990s- . http://www.linscottsdirectory.com/ .Catalog for nearly a million biological products, reagents, and immune serums. ­ The directory has been published since 1980 in print but is now only available online.

Two publishers that should be especially acknowledged are the American Society for Microbiology in Washington, DC ( http://estore.asm.org/ ) and the Cold Spring Harbor Laboratory Press in Plainview, NY ( http://www.cshlpress.com/ ).  Both of these publishers issue authoritative laboratory methods manuals and handbooks of importance to microbiologists, immunologists, and molecular biologists.

Consult Chapter 5, “Biochemistry and Biophysics”, Chapter 6, “Molecular and Cellular Biology”, and Chapter 7, “Genetics, Biotechnology, and Developmental Biology” for other handbooks relevant to microbiology and immu­nology.

• Converted into online journal in 2013: EcoSal Plus

Techniques useful for microbiology may be found, also, in the “Handbooks” section, or in the biochemistry, genetics, and molecular biology chapters.

• Chosewood, L. Casey and Deborah E. Wilson, eds. Biosafety in Microbiological and Biomedical Laboratories. 5th ed. Washington DC: National Institutes of Health, 2009. 415 p. (HHS publication, no. (CDC) 21-1112). $39.00.Standards and safety best practices for microbiological and medical laboratories. Available for free at http://www.cdc.gov/biosafety/publications/bmbl5/index.htm.
• Todar, Kenneth. Todar’s Online Textbook of Bacteriology. Madison, WI: Kenneth Todar, University of Wisconsin-Madison Dept. of Bacteriology, 2003. http://www.textbookofbacteriology.net/ .This freely accessible online textbook is aimed at high school students and undergraduates.
• BMC Microbiology. v. 1- , 2001- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2180.Publishes “articles on analytical and functional studies of prokaryotic and eukaryotic microorganisms, viruses and small parasites, as well as host and therapeutic responses to them and their interaction with the environment.” Articles available at http://www.biomedcentral.com/bmcmicrobiol.
• mBio. v. 1- , 2010- . Washington, DC: American Society for Microbiology. Bimonthly. Open Access. ISSN 2150-7511 (online).”The scope of mBio reflects the enormity of the microbial world, a highly interconnected biosphere where microbes interact with living and nonliving matter to produce outcomes that range from symbiosis to pathogenesis, energy acquisition and conversion, climate change, geologic change, food and drug production, and even animal behavioral change.” Articles available at http://mbio.asm.org/ .
• PLOS Pathogens. v. 1- , 2005- . San Francisco, CA: Public Library of Science. Monthly. Open Access. ISSN 1553-7366 (print); 1553-7374 (online).Publishes “articles that significantly advance the understanding of pathogens and how they interact with their host organisms.” Articles are available at http://www.plospathogens.org/ .

Chapter 9: Ecology, Evolution, and Animal Behavior

This chapter covers materials for the allied fields of ecology, evolu­tion, and animal behavior.  Ecology is “the study of the interrelationships between organ­isms and their natural environment, both living and nonliving.”  Conservation biology and environ­mentalism are closely related, but not extensively covered in this chapter.  Evolution is “the gradual process by which the present diversity of plant and animal life arose from the earliest and most primitive organisms.”  See also Chapter 7, “Genetics”, for related materials. Animal behavior, “the activities that constitute an animal’s response to its external environment”, here encompasses all biological sub-disci­plines includ­ing ethology, socio­biology and behavioral ecology. Human behavior and comparative psychology are largely excluded from consideration, and neurobiology is covered in Chapter 11.

• American Society of Naturalists (ASN) . University of Chicago Press, 1427 E 60th St., Chicago, IL 60637. E-Mail: [email protected] . URL: http://www.amnat.org. Founded 1883, 700 members. Professional naturalists. Affiliated with the American Association for the Advancement of Science. Sponsors The American Naturalist . Web site primarily for membership information; includes online directory. Offers Young Investigator’s Prizes, Sewall Wright Award, and E.O. Wilson Naturalist Award.
• Animal Behavior Society (ABS) . Indiana University, 402 N Park Ave., Bloomington, IN 47408. E-Mail: [email protected] . URL: http://animalbehaviorsociety.org. Founded in 1964, 3,000 members. Professional society for the study of animal behavior. Closely associated with the Division of Animal Behavior of the American Society of Zoolo­gists. Affiliated with the Association for the Study of Animal Behaviour (see below). Publishes Graduate Programs in Animal Behavior and the Newsletter , and co-publishes Animal Behaviour .
• Association for the Study of Animal Behaviour (ASAB) . University of St. Andrews, Saint Mary’s College, South St. St. Andrews KY16 9JP, United Kingdom. E-Mail: [email protected] . URL: http://asab.nottingham.ac.uk. Founded in 1936, 1,000 members. A multinational associa­tion for the study of animal behavior. Affiliated with the Animal Behavior Society. Publishes the Newsletter and co-pub­lishes Animal Behaviour . Web site primarily for membership information.
• British Ecological Society (BES) . 12 Roger St., London WC1N 2JU, United Kingdom. E-Mail: [email protected] . URL: http://www.britishecologicalsociety.org. Founded in 1913, 5,000 members. Publishes Functional Ecology , Journal of Animal Ecology , Journal of Applied Ecology , and Journal of Ecology . Web site primarily for members, but does include international list of ecological societies.
• Ecological Society of America (ESA) . 1990 M St. NW, Ste. 700, Washington, DC 20036. E-Mail: [email protected] . URL: http://www.esa.org. Founded in 1915, 10,000 members. The largest ecological association in the United States. Affiliated with the American Institute of Biological Sciences. Publishes the Bulletin , Ecological Applications , Ecological Monographs , Ecology , Frontiers in Ecology and the Environment , and Ecosphere . The middle four journals are available full text from volume 1 on JSTOR while Ecosphere is Open Access. Web site includes educational resources created by the society, links to ecological resources on the Web (mostly other associations), and public policy information.
• International Astrobiology Society (ISSOL) . Osservatorio Astrofisico di Arcetri, Largo Enrico Fermi 5, 50125 Florence, Italy. E-Mail: [email protected] . URL: http://www.issol.org. For scientists of all disciplines interested in studying the origin of life. Bestows the A. I. Oparin medal. Publishes Origins of Life and Evolution of the Biosphere.  Formerly : International Society for the Study of the Origin of Life.
• International Society for Behavioral Ecology . URL: http://www.behavecol.com/pages/society/welcome.html. Founded in 1986 to promote the field of behavioral ecology, 1000 members, Web site primarily for membership information. Publishes Behavioral Ecology .
• International Society of Chemical Ecology (ISCE) . URL: http://www.chemecol.org. Founded in 1983, 750 members. Promotes understanding of the origin, function, and importance of natural chemicals that mediate interactions within and among organisms. Publishes Journal of Chemical Ecology.
• Society for the Study of Evolution (SSE) . c/o Judy Stone, Sec., Colby College, 5720 Mayflower Hill Dr., Waterville, ME 04901. E-Mail: [email protected] . URL: http://www.evolutionsociety.org. Founded in 1946, 3,000 members. Biologists working in the area of organic evolution. Publishes Evolution . Web site primarily for the journal.
• The Wildlife Society (TWS) . 5410 Grosvenor Ln., Ste. 200, Bethesda, MD 20814-2144. E-Mail: [email protected] . URL: http://www.wildlife.org. Founded 1937, 9,600 members. Society for wildlife biolo­gists and conservationists. Publishes Journal of Wildlife Management , Wildlife Monographs , Wildlife Society Bulletin , and the newsletter Wildlifer . Web site primarily for membership information.
• Invasive Species Compendium. Wallingford, UK: CABI, 2011- . http://www.cabi.org/isc/ .This freely available compendium provides datasheets on over 1,500 invasive species and diseases from around the world. Each entry provides scientific and common name, original and invasive distributions, summary of invasiveness, biology, description, taxonomy, and references. The compendium also includes an extensive glossary.
• Darwin, Charles. The Origin of Species by Means of Natural Selection, Or, the Preservation of Favored Races in the Struggle for Life. New York: Modern Library, 1993. 689 p. $23.00. ISBN 0679600701; 9780679600701. On the Origin of Species was first published in 1859, and hasn’t been out of print since. There are several versions available to modern readers, including multiple electronic versions. The first edition is available from the Talk.Origins Web site at http://www.talkorigins.org/faqs/origin.html and several other Web sites including van Wyhe’s Darwin Online , below.
• van Wyhe, John, ed. Darwin Online. 2002- . http://darwin-online.org.uk/ .This site provides access to all of Darwin’s publications, manuscripts, and some letters, including translations in other languages. An excellent resource for information about Darwin and his writings.
• BMC Evolutionary Biology. v. 1- , 2001- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2148.Publishes articles “articles on all aspects of molecular and non-molecular evolution of all organisms, as well as phylogenetics and palaeontology.” Articles available at http://www.biomedcentral.com/bmcevolbiol.
• Ecology and Evolution. v. 1- , 2011- . Hoboken, NJ: Wiley-Blackwell. Monthly. Open Access. ISSN 2045-7758 (online).” Ecology and Evolution is the peer reviewed journal for rapid dissemination of research in all areas of ecology, evolution and conservation science. The journal gives priority to quality research reports, theoretical or empirical, that develop our understanding of organisms and their diversity, interactions between them, and the natural environment.” All articles are published under a Creative Commons License agreement. A journal of the British Ecological Society. Articles are available at http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292045-7758 .
• Ecosphere. v. 1- , 2010- . Ithaca, NY: Ecological Society of America. Irregular. Open Access. ISSN 2150-8925. Ecosphere “is an online-only, open-access alternative with a scope as broad as the science of ecology itself. The journal publishes submissions from all subdisciplines of ecological science, including theoretical, empirical, and applied ecology.” Articles are available at https://esajournals.onlinelibrary.wiley.com/journal/21508925/ .

Chapter 10: Plant Biology

Botany is “the scientific study of plants, including their anatomy, morphology, physiology, biochemistry, taxonomy, cytology, genetics, evolution, and geographical distribution ( Oxford Dictionary of Biology , 4 th ed., 2000).”  In this chapter, the terms “botany” and “plant biology” will be used interchangeably.  In practice, botany may carry the connotation of taxonomic studies, while plant biology is often the preferred “modern” term for the entire field.

The study of botany has a long and distinguished history.  This fact, coupled with the complexi­ty of the subject as it has grown from descriptive botany to the molecular plant sciences, is reflected in its literature, producing a complicated and often confusing array of resources. For the purposes of this book, plant biology encompasses the literature of botany and the plant kingdom, including fungi.  This chapter does not include agricul­ture, forestry, horti­culture, or any of the applied areas of plant science, except biotechnology and medicinal plants.

The field of plant biology overlaps significantly with other areas of biology, so also check Chapter 3, “General Sources”; Chapter 5, “Biochemistry and Biophysics”; Chapter 7, “Genet­ics, Biotechnology, and Developmental Biology”; and Chapter 8, “Micro­biolo­gy and Immunology” for more useful resources.

Checklists and Identification Manuals

• Bibliography of Systematic Mycology. v. 1 – , 1947- . Kew, UK: CAB International. Biannual. Price varies. ISSN 0006-1573.Lists papers and books on all aspects of the taxonomy of fungi compiled from world literature. Each issue has an author and classified index, and book reviews of interests to botanists. Freely available online as part of Index Fungorum at http://www.indexfungorum.org/BSM/bsm.asp .
• Index of Fungi. v. 1 – , 1940 – . Oxfordshire, UK: CAB International. Biannual. Price varies. ISSN 0019-3895.Lists of names of new genera, species and varieties of fungi, new combinations and new names, compiled from world literature. Supersedes Petrak’s Lists (in Retrospective Sources, below). Fungal names from the Index and other sources are listed in the online Index Fungorum at http://www.indexfungorum.org/ .
• Hooker, Sir Joseph Dalton, et. al. Index Kewensis Plantarum Phanerogamarum Nomina et Synonyma Omnium Generum et Specierum a Linnaeo usque ad Annum MDCCCLXXXV Complectens Nomine Recepto Auctore Patria Unicuique Plantae Subjectis. Oxfordshire, UK: E prelo Clarendoniano, 1893-1895. 4 v. Supplementum v. 1-21, 1886-1996. Continued by Kew Index for… compiled by R. A. Davies and K. M. Lloyd. New York: Oxford University Press, 1987-1989.This indispensable index is an alphabetical listing of plant names with bibliographic references to the place of first publi­cation. Some print volumes, including supplements, are available from Kew Publishing at present. The index was also published on CD-ROM from Oxford University Press in 1993. The data from Index Kewensis forms the backbone of the International Plant Names Index , freely available at http://www.ipni.org/ .
• Index to American Botanical Literature, 1886-1966. Boston, MA: G.K. Hall, 1969. 4 v.Invaluable card index in book form arranged by author. Continued as a section in the Bulletin of the Torrey Botanical Club and later in Brittonia . The data is now searchable at the New York Botanical Garden’s site, http://sweetgum.nybg.org/iabl/.
• The Kew Record of Taxonomic Literature. London: H.M. Stationery Office, 1971-2007. ISSN 0307-2835.Comprehensive publication of worldwide taxonomic literature of flowering plants, gymnosperms, and ferns. Systematic arrange­ment; also includes citations to phytogeography, floristics, nomencla­ture, chromosome surveys, chemotaxonomy, anatomy, repro­ductive biology, personnalia, etc. The bibliography has ceased publication, but records are available on the Web at http://kbd.kew.org/kbd/searchpage.do , along with the databases Economic Botany and Plant Micromorphology .
• American Bryological and Lichenological Society (ABLS) . c/o James Bennett, Sec.-Treas., University of Wisconsin, Dept. of Botany430 Lincoln Dr., Madison, WI 53706. E-Mail: [email protected] . URL: http://www.abls.org .Founded 1898, 500 members. Professional botanists, botany teachers, and hobbyists interested in the study of mosses, liverworts, and lichens. Publishes Bryologist and Evansia .
• American Phytopathological Society (APS) . 3340 Pilot Knob Rd., St. Paul, MN 55121. E-Mail: [email protected] . URL: http://www.apsnet.org .Founded 1908, 5000 members. Professional educators, research­ers, and other interested in the study and control of plant diseases. Publishes Molecular Plant-Microbe Interactions, Phyto­pathology, Plant Disease, Plant Health Report, Plant Disease Management Reports, and many books. Web site includes membership information, educational resources, and career materials.
• American Society of Plant Biologists (ASPB) . 15501 Monona Dr., Rockville, MD 20855. E-Mail: [email protected] . URL: http://www.aspb.org .Founded 1924, 5200 members. Professional international society of plant physi­ologists, plant biochemists, plant molecular and cellular biologists and other plant scientists engaged in research and teaching. Publishes ASPB News, Plant Cell, and Plant Physiology . Formerly: American Society of Plant Physiologists (ASPP). Web site has membership, career, and educational resources.
• American Society of Plant Taxonomists (ASPT) . University of Wyoming, Dept. of Botany 3165, 1000 E University Ave. Laramie, WY 82071-2000. E-Mail: [email protected] . URL: http://www.aspt.net .Founded 1935, 1300 members. Botanists and others interested in all phases of plant taxonomy. Publications: Systematic Botany, Systematic Botany Monographs , and a newsletter. Web site includes membership information and links to plant systematics resources.
• Bioversity International . Via dei Tre Denari 472-A, Maccarese, I-00057 Rome, Italy. E-Mail: [email protected] . URL: http://www.bioversityinternational.org .Founded 1974. An international research institute with a mandate to advance the conservation and use of genetic diversity for the well-being of present and future generations. Publishes Geneflow, Plant Genetic Resources Abstracts, and a newsletter. Formerly: International Plant Genetic Resources Institute (IPGRI).
• Botanical Society of America (BSA) . PO Box 299, St. Louis, MO 63166. E-Mail: [email protected] . URL: http://www.botany.org .Founded 1906, 3000 members. Professional society of botanists. Publishes American Journal of Botany, Applications in Plant Sciences, and Plant Science Bulletin . Web site includes membership information, links to useful Web sites, and more.
• Council on Botanical and Horticultural Libraries (CBHL) . Auraria Library, 1100 Lawrence St., Denver, CO 80204-2095. E-Mail: [email protected] . URL: http://www.cbhl.net .Founded 1970, 250 members. Libraries and collections in botani­cal or horticultural materials; librarians, bibliog­raphers, booksellers, publishers, researchers, and administra­tors.
• International Association for Plant Taxonomy (IAPT) . University of Vienna, Institute of Botany, Rennweg 14, A-1030 Vienna, Austria. E-Mail: [email protected] . URL:  http://www.iapt-taxon.org/.Founded 1950, 2900 members. Coordinates work related to plant taxonomy and international codification of plant names. Formerly Commission on the Nomenclature of Plants. Publishes Regnum Vegetabile book series and Taxon .
• International Association for Vegetation Science (IAVS) . Wes Beekhuizenweg 3, NL-6871 VJ Renkum, Netherlands. E-Mail: [email protected] . URL: http://www.iavs.org .Founded 1930. 1568 members. Vegetation scientists in 83 coun­tries including botanists and ecologists. Formerly: Inter­national Society for Vegetation Science. Publishes Applied Vegetation Science, Journal of Vegetation Science , and IAVS Bulletin . Web site includes links to useful resources.
• International Mycological Association (IMA) . c/o Prof. J. Taylor, Pres., University of California, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, CA 94720. E-Mail: [email protected] . URL: http://www.ima-mycology.org .Founded 1971, 2500 members. International society representing 20,000 mycologists from 80 countries. Promotes the study of mycology in all its aspects.
• International Phycological Society (IPS) . P.O. Box 1897, Lawrence, KS 66044. URL: http://www.intphycsoc.org/ .Founded 1960, 900 members. Scientists working to develop phycology. Publishes Phycologia .
• International Society of Plant Morphologists (ISPM) . University of Delhi, Department of Botany, New Delhi 110 007, Delhi, India. E-Mail: [email protected] . URL: http://phytomorphology.tripod.com .Founded 1950, 805 members. Individuals in 26 countries inter­ested in plant morphology and its allied sciences. Purpose is to promote international cooperation among botanists. Publishes Phytomorphology .
• Mycological Society of America (MSA) . PO Box 7065, Lawrence, KS 66044. E-Mail: [email protected] . URL: http://www.msafungi.org .Founded 1931, 1300 members. Researchers, industrial and medical mycologists, plant pathologists, students, and others interested in the study of fungi through research, teaching, and industrial applications. Annual meeting. Publishes Mycologia, Mycologia Memoirs, and Inoculum .
• North American Mycological Association (NAMA) . PO Box 64, Christiansburg, VA 24068. E-Mail: [email protected] . URL: http://www.namyco.org .Founded 1959, 2200 members consisting of regional, state, and local groups. Amateur and professional mycologists, students, and botanists. Publishes McIlvain­ea and Mycophile . Web site includes information on mushroom cultivation, photography, and poisoning.

Phycological Society of America (PSA) . Virginia Tech., University Libraries, Special Collections Library, PO Box 90001, Blackburg, VA 24062 USA. E-Mail: [email protected] . URL: http://www.psaalgae.org .Founded 1946, 1,100 members. Educators, researchers, and others interested in the pure, applied, or avocational study and utili­zation of algae. Publishes Algaezine, Journal of Phycology, Phycologi­cal Newsletter .

• Phytochemical Society of Europe (PSE) . Centre for Pharmacognosy and Phytotherapy, 29-39 Brunswick Sq., London WC1N 1AX, UK. c/o Dr. Deniz Tasdemir, Membership Sec., University of London, School of Pharmacy. E-Mail: [email protected] . URL: http://www.phytochemicalsociety.org .Founded 1957, 500 members. Scientists in 17 countries working in the field of plant chemistry. Publishes Proceedings of the Phytochemical Society of Europe, Phytochemistry, Phytochemistry Letters, and Phytochemistry Reviews .
• Phytochemical Society of North America (PSNA) . E-mail: [email protected] . URL: http://www.psna-online.org/ .Founded 1960. 405 members. Membership comprises primarily research scientists interested in all aspects of the chemistry of plants. Publishes newsletter and Recent Advances in Phytochemistry .
• Plant Growth Regulation Society of America (PGRSA) . 1018 Duke St., Alexandria, VA 22314. E-Mail: [email protected] . URL: http://www.pgrsa.org .Founded 1973, 850 members. Scientists concerned with plant growth regulation. Publishes PGRSA Quarterly and books on techniques.
• Society for Economic Botany (SEB) . PO Box 299, St. Louis, MO 63166-0299. E-Mail: [email protected] . URL: http://cms.gogrid.econbot.org/ .Founded 1959, 1,200 members. Botanists, anthropologists, pharma­cologists, and others interested in scientific studies of useful plants. Publishes Economic Botany and Plants and People .
• Society for Medicinal Plant Research (Gesellschaft für Arzneipflanzenforschung) . Society of Medicinal Plant and Natural Product Research, Uttenreuther Strasse 1 D-91077 Neunkirchen am Brand, Germany. E-Mail: [email protected] . URL: http://www.ga-online.org .Founded 1953. 1300 members. Scientists in 70 countries who promote medicinal plant research. Publishes Newsletter and Planta Medica .
• The Torrey Botanical Society . URL: http://www.torreybotanical.org/ .Founded 1860. Botanists and others interested in botany and in collecting and disseminating information on all phases of plant science. Publishes Journal of the Torrey Botanical Society, Memoirs of the Torrey Botanical Society . Formerly: The Torrey Botanical Club.
• Flora of North America: North of Mexico. New York: Oxford University Press, 1993-. v. $95.00 (per volume). ISBN varies.This projected 30 volume monumental work aims to survey and classify all the more than 20,000 plant species known to grow spontaneously from the Florida Keys to the Aleutian Islands. This authoritative set provides identification keys; distribution maps; summaries of habitat and geographical ranges; precise descriptions for families, genera, and species; chromosome numbers; pertinent synonymies; line drawings; endangered and threatened plants; selected references. The set will be updated by a computer database for taxonomic information housed at the Missou­ri Botanical Garden in St. Louis, MO. See their Web site at http://floranorthamerica.org/ . To date, v. 1-8, 19-27 have been published.
• Brummitt, R. K. Vascular Plant Families and Genera: A Listing of the Genera of Vascular Plants of the World According to their Families, as Recognised in the Kew Herbarium, with an Analysis of Relationships of the Flowering Plant Families According to Eight Systems of Classification. Kew, England: Royal Botanic Gardens, 1992. $82.00. ISBN 0947643435; 9780947643430.The standard reference for generic names. In three parts: an alphabetic list of 14,000 accepted generic names, a list of genera by family, and an analysis of plant families following the eight systems of classification mentioned in the title. Also freely available on the Web at http://www.rbgkew.org.uk/data/vascplnt.html .
• Harvard University Herbaria Databases. http://kiki.huh.harvard.edu/databases/ . Includes the Gray Herbarium Index of New World Plants (now incorporated into the International Plant Names Index ), the Harvard University Herbaria Type Specimen Database, Botanical Authors database, and Botanical Publications database.
• Index of Mosses Database. St. Louis, MO: Missouri Botanical Garden, 1995- . http://www.mobot.org/MOBOT/tropicos/most/iom.shtml .The Index of Mosses Database, also known as W3MOST, provides current information on bryophyte names from the TROPICOS MOST database compiled by the Index of Mosses project at the Missouri Botanical Garden.
• Kartesz, John T., Hugh D. Wilson, and Erich Schneider. A Synonymized Checklist of the Vascular Flora of the United States, Puerto Rico, and the Virgin Islands. Chapel Hill, NC; College Station, TX: BONAP; TAMU-BWG, 1998. http://www.csdl.tamu.edu/FLORA/b98/check98.htm .An updated Web version of the authors’ print checklist of the same name.
• McNeill, John. International Code of Nomenclature for Algae, Fungi and Plants (Melbourne Code). Königstein, Germany: Koeltz Scientific Books, 2012. 208 p. (Regnum vegetabile, v. 154). $90.00. ISBN 3874294250; 9783874294256.The standard code for botanical nomenclature. The name of this edition was changed from the International Code of Botanical Nomenclature (ICBN) to reflect the fact that the code covers algae and fungi as well. The full text is available for free at http://www.iapt-taxon.org/nomen/main.php .
• Names in Current use of Extant Plant Genera (NCU-3e). International Association for Plant Taxonomy: 1997-. https://archive.bgbm.org/iapt/ncu/genera/Default.htm . This online database is based on the print NCU-3 volume published in 1993 as v. 129 of Regnum Vegetabile , which attempted to establish official names for the genera of algae, bryophytes, ferns, flowering plants, and fungi. For each genus, the original citation, date, type species, and family and order are included. The database is continuously updated.
• Plants Database. Greensboro, NC: National Plant Data Team, 1996- . http://plants.usda.gov/ .”The Plants database provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories.” (from the web site) For each species viewers can find the common and scientific names plus synonyms, classification, distribution, related taxa, and links to more information. The site also provides information on invasive or threatened plant species, cover crops, culturally significant plants, and much more.
• The Plant List. St. Louis, MO: Missouri Botanical Garden, 2010- . http://www.theplantlist.org/ .”The Plant List is a working list of all known plant species; it provides the accepted Latin name for most species, with links to all synonyms by which that species has been known.” (from the Web site) Currently, the database includes vascular plants and bryophytes.
• Stevens, P. F. Angiosperm Phylogeny Website . St. Louis, MO: Missouri Botanical Garden, 2001- . http://www.mobot.org/MOBOT/research/APweb/ .“This series of pages is a set of characterizations of all orders and families of extant angiosperms (flowering plants) and gymnosperms, i.e. all seed plants…” It is designed as a teaching tool and is frequently updated.
• Holmgren, Patricia K., Noel H. Holmgren, and Lisa C. Barnett. Index Herbariorum. Part I, the Herbaria of the World. 8th ed. Bronx, NY: New York Botanical Garden, 1990. 693 p. (Regnum vegetabile, vol. 120). ISBN 0893273589; 9780893273583.Directory of the public herbaria of the world. For Part II: Collectors , see annotation in the History section. Also available on the Web at http://sweetgum.nybg.org/science/ih/ .
• Internet Directory for Botany . http://www.botany.net/IDB/ .An index to botanical information found on the Internet. Divided into an alphabetical directory and a subject directory.
• Metz Library. Web Resources . New York Botanical Garden. http://www.nybg.org/library/WebResources.php .A useful list of recommended botany resources from the New York Botanical Garden. Includes botany libraries, online catalogs (some subscription), general botany resources, plant pictures, plant information, and archival resources.
• The Arabidopsis Book. Rockville, MD: American Society of Plant Biologists, 2002- http://aspb.org/publications/other-aspb-publications/the-arabidopsis-book/ . This open access book provides over 100 frequently updated articles about the biology of Arabidopsis , one of the most common model organisms for plant biology and genetics.
• The Arabidopsis Information Resources (TAIR). Stanford, CA: Carnegie Institution for Science Department of Plant Biology, 1999- . http://www.arabidopsis.org/ .TAIR replaces the Arabidopsis thaliana Database Project (AtDB) that ended in 1999. It is a collaborative effort between the Carnegie Institution of Washington Department of Plant Biology and the National Center for Genome Resources and contains genetic and molecular biology information for the popular model organism, Arabidopsis . Beginning in mid-2014 TAIR will only be available by subscription.
• Brunt, Alan, et al., eds. Plant Viruses Online: Descriptions and Lists from the VIDE Database. 1996- . http://www1.biologie.uni-hamburg.de/b-online/e35/35tmv.htm .Includes information on most species of virus known to infect plants, including data on host range; transmission and control; geographical distribution; physical, chemical and genomic properties; taxonomy and relationships; and selected literature references. Data from this resource have also been published in 1996 as Viruses of Plants: Descriptions and Lists from the VIDE Database .
• Moerman, Daniel E. Native American Ethnobotany Database–Foods, Drugs, Dyes, and Fibers of Native North American Peoples. 2003- . http://naeb.brit.org/ .Database of plant uses “by 291 Native American groups of 4,029 species from 243 different plant families.” (from the Web site) This is the third version of the database. It supersedes the 1977 publication, American Medical Ethnobotany and the 1986 database, Medicinal Plants of Native America .
• Walker, Rick. Carnivorous Plant Database. 2010- . http://www.omnisterra.com/bot/cp_home.cgi .Database of over 3,000 carnivorous plants. Each entry consists of the scientific name, date and place of discovery, and name of discoverer. International in coverage. Includes photographs and illustrations.
• Brummitt, R. K. and C. E. Powell. Authors of Plant Names: A List of Authors of Scientific Names of Plants, with Recommended Standard Forms of their Names, Including Abbreviations. London: Royal Botanic Gardens, 2002. 732 p. $82.00. ISBN 1842460854; 9781842460856.A standard index of the authors of plant names, including birth and death dates, recommended abbreviations, and notes on the plant taxa authored for each individual. The index can be searched as part of the International Plant Names Index (see Classification and Nomenclature, above), at https://www.ipni.org/ .
• Vegter, I. Hettie. Index Herbariorum: A Guide to the Location and Contents of the World’s Public Herbaria. Part 2, Collectors. Boston, MA: Kluwer Academic, 1986. (Regnum vegetabile, v. 114). ISBN 9031305855; 9789031305858.A list of plant collectors including dates active, collection specialty, location of voucher specimens, and sources. Now searchable as part of the online Index Herbariorum at http://sweetgum.nybg.org/science/ih/ .
• BMC Plant Biology. v. 1- , 2001- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2229.Covers all aspects of plant biology including cellular, tissue-level, organismal, functional and developmental aspects. Articles can be found at http://www.biomedcentral.com/bmcplantbiol .
• Studies in Mycology. v. 1- , 1972- . Baarn, Netherlands: Centraalbureau voor Schimmelcultures. 3 issues per year. Open Access. ISSN 0166-0616 (print); 1872-9797 (online).”Publishes systematic monographs of filamentous fungi and yeasts, and at occasions the proceedings of special meetings related to all fields of mycology”. Articles are available at http://studiesinmycology.org/ .

Chapter 11: Anatomy and Physiology

This chapter covers neurobiology and endocrinology as well as anatomy and physiology.  Anatomy is a “the study of the structure of living organisms, especially of their internal parts by means of dissection and microscopical examination.”  The same source interprets “physiology” as the “branch of biology concerned with the vital functions of plants and animals, such as nutrition, respiration, reproduction and excretion.” ( Oxford Dictionary of Biology , 4 th ed, 2000). Neurobiology is the study of the nervous system.  This chapter includes primarily human anatomy and physiology: plants and animals are discussed in Chapters 10, “Plant Biology” and 13, “Zoology.”  Although a few medical titles are included, emphasis in this chapter is on the biological sciences rather than the behavioral or clinical.

As usual, there is overlap between this chapter and Chapters 5, “Biochemistry and Biophysics,” and 6, “Molecular and Cellular Biology,” so don’t neglect to broaden the search to these other chapters. Developmental biology is covered in Chapter 7.

• American Association of Anatomists (AAA) . 9650 Rockville Pike, Bethesda, MD 20814-3998. E-Mail: [email protected] . URL: https://www.anatomy.org/. Founded in 1888. Over 2,500 members. Professional society of anatomists and scientists in related fields. Publishes Anatomical News , Anatomical Record , Developmental Dynamics, and Anatomical Sciences Education . Their Web site includes extensive links as well as membership information.
• American Physiological Society (APS) . 9650 Rockville Pike, Bethesda, MD 20814-3991. E-Mail: [email protected] . URL: http://www.the-aps.org .Founded 1887. 9,100 members. Professional society of physiologists. Publishes: Advances in Physiology Education , American Journal of Physiology and all of the sections, Comprehensive Physiology , Journal of Applied Physiology , Journal of Neurophysiology , News in Physiological Sciences , Physiological Genomics , Physiological Reports , Physiological Reviews , The Physiologist, Physiology . Web site primarily for membership information. Also, publishes Methods in Physiology , Clinical Physiology , and People and Ideas book series.
• American Society for Neurochemistry (ASN) . 9037 Ron Den Ln., Windermere, FL 34786. E-Mail: [email protected] . URL: http://www.asneurochem.org .Founded 1969. Over 1,000 members. Investigators in the field of neurochemistry and scientists who are qualified specialists in other disciplines and are interested in the activities of the Society. Publishes ASN Newsletter , ASN Neuro and the book Basic Neurochemistry. The Web site includes membership information and links to resources.
• Anatomical Society (AS) . c/o Ms. Mary-Anne Piggott, BSc, Exec. Admin., King’s College, Dept. of Anatomy Hodgkin Building, Rm. HB 4.1, London SE1 1UL, UK. E-Mail: [email protected] . URL: http://www.anatsoc.org.uk .Founded 1887. 650 members. Individuals involved in anatomical science. Promotes development and advancement in anatomy and related science through research and education. Offers program for graduate students. Publishes Aging Cell and Journal of Anatomy . The Web site provides links to educational sites. Formerly: Anatomical Society of Great Britain and Ireland.
• Endocrine Society . 8401 Connecticut Ave., Ste. 900, Chevy Chase, MD 20815-5817. E-Mail: [email protected] . URL: http://www.endo-society.org .Founded 1918. 8,000 members. Promotes excellence in research, education, and clinical practice in endocrinology and related disciplines. Publishes Endocrine News , Endocrine Reviews , Endocrinology , Hormones and Cancer , Journal of Clinical Endocrinology and Metabolism , Molecular Endocrinology, Translational Research in Endocrinology and Metabolism, and Translational Research in Endocrinology and Metabolism Monographs . Formerly: Association for Study of Internal Secretions. Web site provides news bulletins and links clinical guidelines as well as membership information.
• International Brain Research Organization (IBRO) Organisation Internationale de Recherche sur le Cerveau . c/o Stephanie de la Rochefoucauld, Exec. Dir., 255 rue St. Honore, F-75001 Paris, France. E-Mail: [email protected] . URL: http://ibro.info .Founded 1960. 55,000 members. Scientists working in neuroanatomy, neuroendocrinology, the behavioral sciences, neurocommunications and biophysics, brain pathology, and clinical and health-related sciences. Works to promote international cooperation in research on the nervous system. Web site primarily for membership information.
• International Society for Developmental Neuroscience (ISDN) . c/o John Steeves, Sec. Gen., University of British Columbia, 2469-6270 University Blvd., Vancouver, BC, Canada V6T 1Z4. E-Mail: [email protected] . URL: http://www.developmental-neuroscience.org .Founded 1978. 850 members. Aims to advance research and knowledge concerning the development of the nervous system and to support the effective application of this information for the improvement of human health. Publishes International Journal of Developmental Neurosciences , ISDN Newsletter . Web site provides membership information and newsletter.
• International Society for Endocrinology (ISE) . c/o Hannah van Oudheusden, Exec. Off., University of Birmingham, Institute of Biomedical Research, Wolfson Dr., Edgbaston, Birmingham B15 2TT, UK. E-Mail: [email protected] . URL: http://www.endosociety.com .Founded 1966. 53 member societies. Federation of national endocrinology societies with 15,000 individual members. Disseminates information on endocrinology and facilitates collaboration between national endocrinological societies and persons interested in the field. Publishes Abstracts of Congresses and Symposia Abstracts . Web site primarily for meeting and membership information.
• Physiological Society-UK . Peer House, Verulam St., London WC1X 8LZ, UK. E-Mail: [email protected] . URL: http://www.physoc.org .Founded 1876, 1,775 members. Multinational physiologists at senior levels in universities, research institutions, hospitals, and relevant industries and government departments, about a third of whom are resident overseas. Promotes the advancement of physiology in all areas. Publishes Experimental Physiology , The Journal of Physiology , and Physiology News . Web site provides membership information and educational resources. Formerly: Physiological Society-England.
• Society for Endocrinology . 22 Apex Ct., Woodlands, Bradley Stoke, Bristol BS32 4JT, UK. URL: http://www.endocrinology.org .Founded 1939, 1,700 members. Clinicians and scientists working within the field of hormones and hormone related disease. Publishes Clinical Endocrinology , Endocrine-Related Cancer , Endocrine Connections , Endocrine Abstracts, Journal of Endocrinology , and Journal of Molecular Endocrinology .
• Society for Neuroscience (SfN) . 1121 14th St. NW, Ste. 1010, Washington, DC 20005. E-Mail: [email protected] . URL: http://www.sfn.org .Founded 1969, 28,000 members. Scientists engaged in research relating to the nervous system. Seeks to advance understanding of nervous systems, including their relation to behavior, by bringing together scientists of various backgrounds and by facilitating integration of research all levels of biological organizations. Produces nontechnical reports on the results and implications of current research. Publishes Brain Facts , and Journal of Neuroscience . The Web site includes membership directory, links to related sites.
• Society of General Physiologists (SGP) . PO Box 257, Woods Hole, MA 02543-0257. E-Mail: [email protected] . URL: http://www.sgpweb.org .Founded 1946, 1,000 members. Biologists interested in fundamental physiological principles and phenomena. Publishes Journal of General Physiology and Proceedings of Annual Symposium . Web site limited to membership information.

A wide variety of atlases are listed, from the classic to the recently published, in an effort to provide examples of illustrations of the human body geared to a wide group of student, medical, or lay person audiences. Animal atlases and dissection manuals are found in Chapter 13.

• Allen Institute for Brain Science. Allen Brain Atlas. Seattle, WA: Allen Institute for Brain Science, 2004- . http://www.brainatlas.org/ .”The Allen Brain Atlas resources are a growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools (from the website).” At the time of viewing, the site contained several interactive atlases for mouse, human, and non-human primate brains plus data on glioblastoma and sleep.
• Braininfo. Seattle, WA National Primate Research Center, University of Washington, 1991- . http://braininfo.rprc.washington.edu/ .A portal to neuroscience on the Web with 3 main components: NeuroNames, a database of definitions of neuroanatomic structures in four species, NeuroMaps, a digital stereotaxic atlas of rhesus macaque and mouse brains, and the Template Atlas of the Primate Brain, a stereotaxic atlas of the macaque brain.
• Visible Human Project. Bethesda, MD: National Library of Medicine, 2003- . http://www.nlm.nih.gov/research/visible/visible_human.html .Excellent access to anatomy is provided by the Visible Human Project and the related Visible Embryo Project with the goal of creating complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies.
• Busis, Neil A. Neurosciences on the Internet <Neuroguide.com>. 1995- . http://www.neuroguide.com/ .This site is designed to “List the best neuroscience resources on the Web in one location [and] present original neuroscience content not available elsewhere.” The Best Bets page lists about 25 top sites, including associations, institutes, and Web accessible projects. At the time of writing, the original content was restricted to a chart of the “Cutaneous Fields of Peripheral Nerves”.
• MIT Cognet. Cambridge, MA: Massachusetts Institute of Technology, 2000- . http://cognet.mit.edu .This site “provides a unique electronic community for researchers in cognitive and brain sciences, with in-depth current and classic text resources, and a dynamic interactive forum for today’s scholars, students, and professionals.” For an annual fee of between $15.00 and $195.00, individuals can subscribe to the service and gain access to neuroscience books, journals, and reference works published by MIT, job listings, virtual poster sessions, and other resources. A library or institutional subscription is also available.
• BMC Neuroscience. v. 1- , 2000- . London: BioMed Central. Continually updated. Open Access. ISSN 1471-2202.Publishes “articles on all aspects of the nervous system, including molecular, cellular, developmental and animal model studies, as well as cognitive and behavioral research, and computational modeling.” Articles available at http://www.biomedcentral.com/bmcneurosci .

Chapter 12: Entomology

Entomology is “the study of insects,” according to the Oxford Dictionary of Biology , 4 th ed, 2000.  Strictly speaking, the true insects are only those belonging to the class Insecta, which does not include the spiders and other animals often thought of as insects such as millipedes or ticks.  However, this chapter includes material on both insects and their close relatives since many resources treat these related groups together.  Applied entomology is largely excluded, although some basic tools are mentioned. Resources about Drosophila used as a model organism for genetics or developmental biology are included in Chapter 7, “Genetics, Biotechnology, and Developmental Biology”.

• American Entomological Society . The American Entomological Society at The Academy of Natural Sciences 1900 Benjamin Franklin Parkway Philadelphia, PA 19103-1195. E-Mail: [email protected] . URL: http://darwin.ansp.org/hosted/aes/ .Founded in 1859, 430 members. For professionals and amateurs. Publishes Entomological News , Memoirs of the American Entomological Society , and Transactions of the American Entomological Society . The Web site is primarily for membership information.
• American Mosquito Control Association (AMCA) . 15000 Commerce Pkwy., Ste. C, Mount Laurel, NJ 08054. E-Mail: [email protected] . URL: http://www.mosquito.org .Founded in 1935, 2,000 members. Web site includes membership information, “Mosquito Links” (primarily links to mosquito control districts and other technical resources), and a nice set of pages with general information on mosquitos and their control. Publishes Journal of the American Mosquito Control Association , AMCA Newsletter , and Wing Beats .
• Coleopterists Society (CS) . 3294 Meadowview Rd., Sacramento, CA 95832-1448. E-Mail: [email protected] . URL: http://www.coleopsoc.org .Founded in 1969, 775 members. “An international organization devoted to the study of all aspects of systematics and biology of beetles of the world.” Publishes The Coleopterists Bulletin . Web site includes resource links and membership information.
• Entomological Society of America (ESA) . 10001 Derekwood Ln., Ste. 100, Lanham, MD 20706-4876. E-Mail: [email protected] . URL: http://www.entsoc.org .Founded 1953, 8,500 members. The largest US entomological society; publishes American Entomologist , Annals of the Entomological Society of America , Arthropod Management Tests, Entomological Society of America-Newsletter , Environmental Entomology,   Insecticide and Acaricide Tests , Journal of Economic Entomology , Journal of Medical Entomology , and Journal of Integrated Pest Management . Also publishes many monographic works. Formed by the merger of the American Association of Economic Entomologists and the former Entomological Society of America. Absorbed the American Registry of Professional Entomologists. Site includes membership information, publications, job information, educational information, links to other entomological sites, and much more. The Web site is a good source for general information on entomology.
• Entomological Society of Canada (ESC); Societe d’Entomologie du Canada . 393 Winston Ave., Ottawa, ON, Canada K2A 1Y8. E-Mail: [email protected] . URL: http://www.esc-sec.ca .Founded 1868, 550 members. Publishes The Canadian Entomologist , Bulletin of the Entomological Society of Canada , Memoirs of the Entomological Society of Canada , Occasional Publications. Web site includes downloadable version of Common Names of Insects in Canada (zip file), information on entomology in Canada, and entomological links as well as membership information.
• International Bee Research Association (IBRA); Association Internationale de Recherche Apicole . 16 N Rd., Cardiff CF10 3DY, UK. E-Mail: [email protected] . URL: http://www.ibra.org.uk .Founded 1949, 800 members. Publishes Apicultural Abstracts , Bee World , Journal of Apicultural Research . The extensive Web site lists publications, library services, and bee links in addition to membership information.
• International Centre of Insect Physiology and Ecology (ICIPE) . PO Box 30772-00100, Nairobi, Kenya. E-Mail: [email protected] . URL: http://www.icipe.org .Founded 1970, 310 members. Publishes International Journal of Tropical Insect Science . Web site has extensive information on ICIPE’s programs and services.
• The International Society of Hymenopterists . URL: http://hymenopterists.org/index.php .Founded in 1982. Publishes Journal of Hymenoptera Research and Hamuli: The Newsletter of the International Society of Hymenopterists . Web site primarily for membership information.
• International Union for the Study of Social Insects (IUSSI) . 105 Northway Rd., Greenbelt, MD 20770. E-Mail: [email protected] . URL: http://iussi.bees.net .Founded in 1952, 800 members. There are several country-specific chapters. Publishes Insectes Sociaux/Social Insects . Web site includes links to information about social insects and links to various chapters.
• Lepidopterists’ Society . Michael E. Toliver Science and Mathematics Division Eureka College 300 East College Street Eureka, IL 61530. E-Mail: [email protected] . URL: http://www.lepsoc.org/ .Founded 1947, 1,600 members. “Open to all persons interested in any aspect of Lepidopterology.” Publishes Journal of the Lepidopterists’ Society , News of the Lepidopterists’ Society , and Memoirs of the Lepidopterists’ Society . Also makes available Catalogue/Checklist of the Butterflies of America North of Mexico . Web site includes extensive list of lepidoptera and other entomology links and a statement on collecting butterflies and moths.
• Royal Entomological Society (RES) . The Mansion House, Chriswell Green Ln., St. Albans AL2 3NS, UK. E-Mail: [email protected] . URL: http://www.royensoc.co.uk .Founded 1833, 2,000 members. Publishes Agricultural and Forest Entomology , Antenna, Ecological Entomology , Insect Conservation and Diversity , Insect Molecular Entomology, Medical and Veterinary Entomology , Physiological Entomology , and Systematic Entomology . Web site has entomological links and membership information.
• Michener, Charles Duncan. The Bees of the World. 2nd ed. Baltimore, MD: Johns Hopkins University Press, 2007. 953 p. $185.00. ISBN 0801885736; 9780801885730.A comprehensive treatment of all bees world wide. There is an extensive introduction covering the evolution, systematics, anatomy, and behavior of bees. This is followed by keys to bee families and accounts of each family, subfamily, and tribe. There are a number of black and white illustrations and photographs, plus a few color photos. This new edition includes extensive updates to bee taxonomy.
• Common Names Database. Entomological Society of Canada: 2006- http://www.entsoc.org/common-names . This website provides access to the approved common names of Canadian insects and other arthropods, both in English and French. It can be browsed or searched, and the full database can be downloaded in Excel format. A PDF version of the list is available at http://www.entsoc.org/sites/default/files/files/common_name.pdf .
• Common Names of Insects and Related Organisms. Lanham, MD: Entomological Society of America, 2003- . http://www.entsoc.org./pubs/common_names .”Now exclusively online in a database format, this resource is an essential reference for anyone who works with insects. It includes more than 2,000 common names and is searchable by common name, scientific name, author, order, family, genus, and species.” (from the Website) The Website also includes PDFs of the list sorted by common name, scientific name, and taxa as well as information on how to submit new common names.
• Opler, Paul A., Harry Pavulaan and Ray E. Stanford. Butterflies and Moths of North America: Collecting and Sharing Data about Lepidoptera. Bozeman, MT: Big Sky Institute at Montana State University and the NBII Mountain Prairie Information Node: 2006- . http://www.butterfliesandmoths.org .Provides maps, photographs, species accounts, and species checklists for Lepidoptera in the United States and Mexico. The site also has identification tools and citizen science information.
• Arnett, Ross H., G. Allan Samuelson, and Gordon M. Nishida. The Insect and Spider Collections of the World. 2nd ed. Gainesville, FL: Sandhill Crane Press, 1993. (Flora and fauna handbook, no. 11). 310 p. ISBN 1877743151; 9781877743153.This guide lists entomological collections by country, with brief information on each country (population, size, biogeographical region) as well as detailed information on each major insect collection in the country. An updated version is available at Bernice Pauahi Bishop Museum Web site at http://hbs.bishopmuseum.org/codens/ . All collections that have a Web site are linked.
• This site has been archived and is no longer available.
• This resource is no longer maintained online.
• Systematic Entomology Laboratory (U.S.). Collecting and Preserving Insects and Mites: Techniques and Tools. Beltsville, MD: Systematic Entomology Laboratory, USDA, 2005- . http://www.ars.usda.gov/Main/site_main.htm .This site is an updated version of the 1986 USDA publication Insects and Mites: Techniques for Collection and Preservation and covers all topics in collecting, rearing, preserving, and labeling specimens.
• Florida Entomologist. v. 1- , 1917- . Gainesville, FL: Florida Entomological Society. Quarterly. Open Access. ISSN 0015-4040.Published by the Florida Entomological Society. “Manuscripts from all areas of the discipline of entomology are accepted for consideration. At least one author must be a member of the Florida Entomological Society.” Available as part of BioOne.1 and JSTOR. Free full text access is available at http://www.fcla.edu/FlaEnt/ . This was the first journal to provide electronic access to its content and was a very early Open Access advocate.
• Journal of Insect Science. v. 1- , 2001- . Madison, WI: University of Wisconsin Library. Irregular. Open Access. ISSN 1536-2442.”The Journal of Insect Science publishes papers in all aspects of the biology of insects and other arthropods from the molecular to the ecological.” One of the earliest Open Access journals, available freely from BioOne at http://www.bioone.org/loi/insc .

Chapter 13: Zoology

Zoology is “the scientific study of animals,” according to the Oxford Dictionary of Biology , 4 th ed, 2000.  Entomology is treated separately in Chapter 12 since it has traditionally been treated as a separate discipline.  The other branches of zoology such as ornithology or nematology are not separated in this chapter; rather, the arrangement is by type of material following the pattern established earlier.

Anatomical atlases and dissection manuals for non-human animals are found in this chapter; for human anatomy see Chapter 11, although some of the atlases and manuals in that chapter also briefly mention non-human animal anatomy.

• Ornithological Worldwide Literature: OWL. Oxford, UK: Edward Grey Institute of Field Ornithology, 2002- . http://www.birdlit.org/OWL/ .This resource grew out of Recent Ornithological Literature , a publication that was a joint supplement to The Auk , The Emu , and Ibis from 1983 to 1999 but is now available only online. It attempts to provide comprehensive coverage of the world literature in ornithology, scanning about 1,500 titles and at the time of writing went back to about 1980.
• Index-Catalogue of Medical and Veterinary Zoology: Authors. v. 1-18, 1932-1952. Washington, DC: Animal Parasitology Institute. Supplement . v. 1-24, 1953-1983. Index to the literature of animal parasites of humans and animals. Indispensable source for parasitologists. The first series was in alphabetical order by authors names. Issued as series of supplements. Digitized at the Texas A&M University Library site at http://tamu.libguides.com/c.php?g=524644&p=3587162 .
• American Association for Zoological Nomenclature (AAZN) . URL: http://aazn.org/ .Founded 1983, 250 members. For those interested in the systematics of both living and extinct animals. Publishes AAZN Newsletter .
• American Fisheries Society (AFS) . 5410 Grosvenor Ln., Ste. 110, Bethesda, MD 20814-2199. E-Mail: [email protected] . URL: http://www.fisheries.org .Founded in 1870, 9000 members. International organization for aquatic sciences and fisheries professionals. Publishes Fisheries: Bulletin of the American Fisheries Society , Journal of Aquatic Animal Health , Marine and Coastal Fisheries , North American Journal of Aquaculture , North American Journal of Fisheries Management, and Transactions of the American Fisheries Society . The Web site contains membership information, job postings, and links to other fisheries pages.
• American Malacological Society (AMS) . Tunison Laboratory of Aquatic Science, 3075 Gracie Rd., Cortland, NY 13045. E-Mail: [email protected] . URL: http://www.malacological.org/index.php .Founded in 1931. 600 members. For professionals and hobbyists interested in mollusks. Publishes American Malacological Bulletin and supplements and AMS Newsletter . Formerly American Malacological Union. Web site includes membership information and links to other resources.
• American Ornithologists’ Union (AOU) . 5405 Villa View Dr., Farmington, NM 87402. E-Mail: [email protected] . URL: http://www.aou.org .Founded 1883, 4,000 members. Publishes The Auk , Check-List of North American Birds , Handbook of North American Birds , Ornithological Monographs , and Ornithological Newsletter . Web site has membership information, bird-related links, and links to checklists for North and South America.
• American Society of Ichthyologists and Herpetologists (ASIH) . Florida International University, College of Arts and Science, Dept. of Biological Sciences, 11200 SW 8th St., Miami, FL 33199. E-Mail: [email protected] . URL: http://www.asih.org .Founded 1913, 3,600 members. For scientists and students interested in fish, amphibians, and reptiles. Publishes Copeia . Web site includes membership information.
• American Society of Mammalogists (ASM) . PO Box 1897, Lawrence, KS 66044. E-Mail: [email protected] . URL: http://www.mammalsociety.org .Founded in 1919, 3600 members. Publishes Journal of Mammalogy , Mammalian Species , and special publications. Web site includes membership information.
• Association of Field Ornithologists (AFO) . c/o Kathryn Purcell, VP, Sierra Nevada Research Center, 2081 E Sierra Ave., Fresno, CA 93710. E-Mail: [email protected] . URL: http://www.afonet.org .Founded 1924, 2,400 members. Formerly Northeastern Bird-Banding Association. Publishes Journal of Field Ornithology . Web site primarily for membership information.
• Cooper Ornithological Society (COS) . c/o Abby N. Powell, Sec., University of Alaska, Department of Biology and Wildlife Fairbanks, AK 99775-7020. E-Mail: [email protected] . URL: http://www.cooper.org .Founded 1893, 2200 members. Professional ornithological society. Publishes Condor and Studies in Avian Biology . Web site primarily for publication and membership information.
• The Crustacean Society (TCS) . PO Box 7065, Lawrence, KS 66044-7065. E-Mail: [email protected] . URL: http://www.thecrustaceansociety.org/ .Founded 1980, 850 members. Publishes The Ecdysiast and The Journal of Crustacean Biology . Web site includes membership information, journal information, and related links.
• Herpetologists’ League (HL) . c/o Meredith Mahoney, Treas., ISM Research and Collections Center, 1011 E Ash St., Springfield, IL 62703. URL: http://www.herpetologistsleague.org .Founded 1936, 2,000 members. Publishes Herpetologica and Herpetological Monographs . Web site includes information on membership and links to other herpetological societies.
• International Society of Protistologists (ISOP) . c/o David Montagnes, VP, University of Liverpool, School of Biological ScienceCrown St., Liverpool L69 7ZB, UK. E-Mail: [email protected] . URL: https://protistologists.org/ .Founded 1947, 1125 members. Publishes Journal of Eukaryotic Microbiology , Newsletter , Illustrated Guide to the Protozoa . Web site includes membership information. Formerly: Society of Protozoologists.
• Society for Integrative and Comparative Biology (SICB) . 1313 Dolley Madison Blvd., Ste. 402, McLean, VA 22101-3926. E-Mail: [email protected] . URL: http://www.sicb.org .Founded in 1890, 2300 members. For professional zoologists. Publishes Integrative and Comparative Biology . Formerly American Society of Zoologists; absorbed American Morphological Society. Web site primarily for membership information, but also includes searchable database of educational resources.
• Society for the Study of Amphibians and Reptiles (SSAR) . Zoo Atlanta, 800 Cherokee Ave. SE, Atlanta, GA 30315. E-Mail: [email protected] . URL: http://www.ssarherps.org .Founded 1958, 2,700 members. Formerly: Ohio Herpetological Society. Publishes Herpetological Circulars , Herpetological Review , Journal of Herpetology . Web site includes membership information.
• Society of Nematologists (SON) . PO Box 311, Marceline, MO 64658. E-Mail: [email protected] . URL: http://www.nematologists.org .Founded in 1961, 650 members. For people interested in basic and applied nematology. Publishes Journal of Nematology , and Nematology Newsletter . Web site provides membership information, related links, and information on publications and discussion groups.
• Wilson Ornithological Society (WOS) . c/o OSNA Business Office, 400 Bosque Blvd., Ste. 680, Waco, TX 76710. E-Mail: [email protected] . URL: http://www.wilsonsociety.org .Founded 1888. 2,500 members. For professional ornithologists and hobbyists interested in the scientific study of birds. Publishes Wilson Journal of Ornithology .
• Hall, David H. and Zeynep F. Altun. C. elegans Atlas. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2008. 348 p. $179.00; $128.00 (spiralbound). ISBN 0879697946; 9780879697945; 0879697156 (spiralbound); 9780879697150 (spiralbound).This atlas provides detailed images and descriptions of internal and external structures of adult specimens of this important model organism. The images are from the online site WormBase , http://www.wormbase.org/ , home to the C. elegans research community.
• Check-List of North American Birds: The Species of Birds of North America from the Arctic through Panama, Including the West Indies and Hawaiian Islands. 7th ed. Washington, DC: The Union, 1998. 829 p. ISBN 189127600X; 9781891276002.The checklist is prepared by the Committee on Classification and Nomenclature of the American Ornithologists’ Union and is updated irregularly. Each species is listed with scientific and English name, original citation, habitat, distribution (summer and winter), and notes. The list and its supplements may also be found at https://americanornithology.org/publications/north-and-middle-american-checklist/ .
• Clements, James F. The Clements Checklist of Birds of the World. 6th ed. Ithaca, NY: Comstock. Associates/Cornell University Press, 2007. 843 p. $62.95. ISBN 0801445019; 9780801445019.For dedicated birders, this checklist lists more than 9,800 species of birds and can serve as a lifelist. Each entry has a checkbox to use as a lifelist, common and scientific names, and distribution. A separate section lists extinct birds, and two appendixes outline the distribution of birds. The checklist is updated regularly at the Cornell Laboratory of Ornithology’s Web site at http://www.birds.cornell.edu/clementschecklist .
• Gill, F. and D. Donsker, eds. IOC World Bird List . 2013- . http://www.worldbirdnames.org .Provides lists of accepted common names for all bird species from around the world plus spelling guidelines for English common names. The site provides the avian taxonomy information used in the Tree of Life project (see Chapter 3).
• Monroe, Burt L. and Charles Gald Sibley. A World Checklist of Birds. New Haven, CT: Yale University Press, 1993. 393 p. $75.00. ISBN 0300055471; 9780300055474.This checklist is based on the taxonomic system of Sibley and Monroe (see below). As well as the usual Latin and English names and distribution of each species, the checklist provides a column for the dedicated birder to check off which of the 9,702 species he/she has seen. The list is also available for download at http://home.planet.nl/~by000012/SM/SMorg/sibley4.html .
• Amphibiaweb: Information on Amphibian Biology and Conservation. Berkeley, CA: Amphibiaweb, 2000- . http://amphibiaweb.org/ .This database provides taxonomic information on all species of amphibians taken from Frost’s Amphibian Species of the World (below). The intent is to provide detailed taxonomic and ecological information on all species of amphibians of the world, currently over 7,000 species. The site also includes information on the decline in amphibian populations worldwide.
• Avibase . 2003- . http://avibase.bsc-eoc.org .Contains over ten million records about 10,000 species of birds world-wide. Each account includes a recording of songs, taxonomy, common names in multiple languages, authorities accepting the name, and links to range maps and other ornithological Web sites.
• Collins, Joseph T. and Travis William Taggart. Standard Common and Current Scientific Names for North American Amphibians, Turtles, Reptiles and Crocodilians. 6th ed. Lawrence, KS: Center for North American Herpetology, 2009. 44 p. ISBN 0972193715; 9780972193719.Provides approved common names for the reptiles of North America. The guide is available at the Center for North American Herpetology’s web site at http://www.cnah.org/ . The first through fourth editions were published under the title Standard Common and Current Scientific Names for North American Amphibians and Reptiles . The 7th edition is expected in early 2014.
• Eschmeyer, William N. Catalog of Fishes. San Francisco, CA: California Academy of Sciences, 1998. (Special publication of the Center for Biodiversity Research and Information, California Academy of Sciences, no. 1). ISBN 0940228475; 9780940228474.Lists genera in alphabetical order with name, author, date, type specimen, remarks, and status. Separate sections list names by class and literature cited. Updates the author’s Catalog of the Genera of Recent Fishes , published in 1990. Available on the Web at http://researcharchive.calacademy.org/research/Ichthyology/catalog/fishcatmain.asp .
• Frost, Darrel R. Amphibian Species of the World: An Online Reference. New York: American Museum of Natural History, 2013- . Version 5.6. http://research.amnh.org/herpetology/amphibia/index.html .Provides scientific name, authority, year of publication, type species, specimen, and location, distribution, and status. Updates the author’s Amphibian Species of the World: A Taxonomic and Geographical Reference , published in 1985.
• Index to Organism Names (ION). Philadelphia, PA: Thomson Scientific, 2007- . http://www.organismnames.com/ .This list of organismal names is taken from Zoological Record and contains information on millions of fossil and current species. Records include approved scientific name, source of the original description, and links to outside resources such as the Encyclopedia of Life , GBIF, and NCBI data. At the time of writing, only protozoa and animals were included, but the site plans on adding bacterial, plant, and fungal names from Biological Abstracts .
• Martin, Joel W. and George E. Davis. An Updated Classification of the Recent Crustacea. Los Angeles, CA: Natural History Museum of Los Angeles County, 2001. 124 p. (Science series, no. 39). ISBN 1891276271; 9781891276279.Provides general notes about the relationship of crustacean taxa plus a detailed classification system. Also freely available as a PDF at http://web.vims.edu/tcs/LACM-39-01-final.pdf .
• Pyle, Richard. Zoobank. International Commission for Zoological Nomenclature: 2008- . http://zoobank.org/ .According to the Web site, “ZooBank is the official registry of Zoological Nomenclature, according to the International Commission on Zoological Nomenclature (ICZN).” The database contains lists of “nomenclatural acts” (usually descriptions of new species), and will eventually include registration of type specimens.
• Wilson, Don E. and DeeAnn M. Reeder. Mammal Species of the World: A Taxonomic and Geographic Reference. 3rd ed. Baltimore, MD: Johns Hopkins University Press, 2005. 2 v. $134.00 (set). ISBN 0801882214 (set); 9780801882210 (set).A checklist, providing common name, original citation, type locality, distribution, status, synonyms, and comments for 5,416 species. The full text is also freely available at the Smithsonian Institute’s site at   https://www.departments.bucknell.edu/biology/resources/msw3/ for non-commercial use.
• NatureServe Explorer: An Online Encyclopedia of Life. Arlington, VA: NatureServe, 2000- . http://www.natureserve.org/explorer/ .Authoritative conservation information on more than 70,000 plants, animals, and ecological communities of the United States and Canada. Provides detailed information on rare and endangered species but includes common plants and animals as well.
• Crawford, Richard L. Information Resources on Amphibians. Beltsville, MD: U.S. Dept. of Agriculture, National Agricultural Library, Animal Welfare Information Center, 2008. (AWIC resource series, no. 42).”The citations in this bibliography pertain to the health, care and housing of amphibians and reptiles owned as pets, exhibited in zoos and aquariums, or used for research.’ (from the website) Freely available at http://www.nal.usda.gov/awic/pubs/Amphibians/amphibians.shtml . Updates Information Resources on Amphibians, Fish and Reptiles Used in Biomedical Research .
• Crawford, Richard L. Information Resources on Reptiles. Beltsville, MD: U.S. Dept. of Agriculture, National Agricultural Library, Animal Welfare Information Center, 2008. (AWIC Resource Series, no. 43).”The citations in this bibliography pertain to the health, care and housing of reptiles owned as pets, exhibited in zoos and aquariums, or used for research.” (from the website) Freely available at http://www.nal.usda.gov/awic/pubs/Reptiles/reptiles.shtml .
• Taggart, Travis William. The Center for North American Herpetology CNAH: Home Page. Lawrence, KS: Center for North American Herpetology, 1994- . http://www.cnah.org/ .This Web portal provides links to information on amphibians and reptiles of the United States and Canada, including links to nomenclature, societies, news, meetings, forums, announcements, and much more. There is also a searchable database of over 2,000 literature references from 1586 on.
• American Society of Ichthyologists and Herpetologists and Herpetological Animal Care and Use Committee. Guidelines for use of Live Amphibians and Reptiles in Field and Laboratory Research. Lawrence, KS: American Society of Ichthyologists and Herpetologists, 2004. http://www.asih.org/files/hacc-final.pdf .This handbook provides guidelines for the ethical use of amphibians and reptiles in scientific studies.
• The Auk: A Quarterly Journal of Ornithology. v. 1- , 1884- . Washington, DC: American Ornithologists’ Union. Quarterly. Price varies. ISSN 0004-8038 (print); 1938-4254 (online).The journal of the American Ornithologists’ Union. “Topics of articles appearing in The Auk include the documentation, analysis, and interpretation of laboratory and field studies, theoretical or methodological developments, and reviews of information or ideas.” Also publishes perspectives, comments, letters, and book reviews. Available as part of BioOne.1 and JSTOR. Backfiles available from JSTOR (subscription) or SORA (free, https://sora.unm.edu/node/183 ).
• The Condor: An International Journal of Avian Biology. v. 1- , 1899- . Los Angeles, CA: Cooper Ornithological Society. Quarterly. Price varies. ISSN 0010-5422 (print); 1938-5129 (online).The journal of the Cooper Ornithological Society. “ The Condor is an international journal that publishes (quarterly) original research reports, review articles, and commentary pertaining to the biology of wild bird species.” Backfiles are available online from JSTOR (subscription) or SORA (free, https://sora.unm.edu/node/194 ).
• Journal of Field Ornithology. v. 51- , 1980- . New Ipswich, NH: Northeastern Bird-Banding Association. Quarterly. Price varies. ISSN 0273-8570 (print); 1557-9263 (online).The journal “publishes original empirical and methodological papers dealing with the ecology, behavior, taxonomy, life history, and zoogeography of birds in their natural habitats.” Also publishes bibliography of current foreign ornithological literature. The abstracts are in English and Spanish. Available as part of BioOne.1 and JSTOR. Backfiles available from JSTOR (subscription) or SORA (free, https://sora.unm.edu/node/196 ). Formerly: Bird-Banding .
• The Wilson Journal of Ornithology. v. 118- , 2006- . Lawrence, KS: Wilson Ornithological Society. Quarterly. Price varies. ISSN 1559-4491 (print); 1938-5447 (online).The journal of the Wilson Ornithological Society. “The principal focus of the Journal is the study of living birds, their behavior, ecology, adaptive physiology and conservation.” Also publishes book reviews. Available as part of BioOne.1 and JSTOR. Backfiles available from JSTOR (subscription) or SORA (free, https://wjoonline.org/ ). Formerly: The Wilson Bulletin.

Literature Reviews

• Getting started

What is a literature review?

Why conduct a literature review, stages of a literature review, lit reviews: an overview (video), check out these books.

• Types of reviews
• 1. Define your research question
• 2. Plan your search
• 3. Search the literature
• 4. Organize your results
• 5. Synthesize your findings
• 6. Write the review
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Definition: A literature review is a systematic examination and synthesis of existing scholarly research on a specific topic or subject.

Purpose: It serves to provide a comprehensive overview of the current state of knowledge within a particular field.

Analysis: Involves critically evaluating and summarizing key findings, methodologies, and debates found in academic literature.

Identifying Gaps: Aims to pinpoint areas where there is a lack of research or unresolved questions, highlighting opportunities for further investigation.

Contextualization: Enables researchers to understand how their work fits into the broader academic conversation and contributes to the existing body of knowledge.

tl;dr  A literature review critically examines and synthesizes existing scholarly research and publications on a specific topic to provide a comprehensive understanding of the current state of knowledge in the field.

What is a literature review NOT?

❌ An annotated bibliography

❌ Original research

❌ A summary

❌ Something to be conducted at the end of your research

❌ An opinion piece

❌ A chronological compilation of studies

The reason for conducting a literature review is to:

Literature Reviews: An Overview for Graduate Students

While this 9-minute video from NCSU is geared toward graduate students, it is useful for anyone conducting a literature review.

Writing the literature review: A practical guide

Available 3rd floor of Perkins

Writing literature reviews: A guide for students of the social and behavioral sciences

Available online!

So, you have to write a literature review: A guided workbook for engineers

Telling a research story: Writing a literature review

The literature review: Six steps to success

Systematic approaches to a successful literature review

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Effectiveness of Virtual Laboratories in Teaching and Learning Biology: A Review of Literature

Scholars have debated whether virtual laboratories are educationally effective tools and if they should be continuously developed. In this paper, we comprehensively review literature about the effectiveness of virtual labs in teaching and learning biology to identify the topics often taught and the linked learning outcomes. We used Google Scholar, ERIC, and Web of Science electronic databases to access journal articles and conference proceeding papers. Through a systematic analysis, we obtained 26 articles solely related to virtual lab use in biology education. The overall findings from the reviewed literature indicated that virtual laboratories are often used on topics that seem abstract. These include cell and molecular biology topics, followed by microbiology, genetics, and other practical topics such as dissection and biotechnology. This review study revealed that virtual labs are effective as they improve students’ conceptual understanding, laboratory or practical skills, and motivation and attitudes towards biology. We recommend the use of virtual labs in teaching as a means of actively involving students in safer and more cost-effective scientific inquiry.

https://doi.org/10.26803/ijlter.21.6.1

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Flowers, L. O. (2011). Investigating the effectiveness of virtual laboratories in an undergraduate biology course. Journal of Human Resources & Adult Learning, 7(2), 110 116. http://www.hraljournal.com/Page/12%20Lawrence%20O.%20Flowers-1.pdf

Gallagher, A. G., Ritter, E. M., Champion, H., Higgins, G., Fried, M. P., Moses, G., Smith, C. D., & Satava, R. M. (2005). Virtual reality simulation for the operating room: Proficiency-based training as a paradigm shift in surgical skills training. Annals of Surgery, 241(2), 364-372. https://doi.org/10.1097/01.sla.0000151982.85062.80

Griffin, J. D. (2003). Technology in the teaching of neuroscience: Enhanced student learning. American Journal of Physiology – Advances in Physiology Education, 27(1-4), 146-155. https://doi.org/10.1152/advan.00059.2002

Havlícková, V., Šorgo, A., & Bílek, M. (2018). Can virtual dissection replace traditional hands-on dissection in school biology laboratory work? Eurasia Journal of Mathematics, Science and Technology Education, 14(4), 1415-1429. https://doi.org/10.29333/ejmste/83679

Hofstein, A., & Mamlok-Naaman, R. (2007). The laboratory in science education: The state of the art. Chemistry Education Research and Practice, 8(2l), 105-107. https://doi.org/10.1039/B7RP90003A

Huppert, J., Lomask, S. M., & Lazarowitz, R. (2002). Computer simulations in the high school: Students’ cognitive stages, science process skills and academic achievement in microbiology. International Journal of Science Education, 22(8), 803 821. https://doi.org/10.1080/09500690110049150

Ismail, I., Permanasari, A., & Setiawan, W. (2016). STEM virtual lab: An alternative practical media to enhance student’s scientific literacy. Jurnal Pendidikan IPA Indonesia, 5(2), 239-246. https://journal.unnes.ac.id/nju/index.php/jpii/article/view/5492/5457

Johnstone, A. H., & Al-Shuaili, A. (2001). Conversion of bench demonstration using the overhead projector/Conversión de demostraciones en el aula utilizando retroproyector. Journal of Science Education, 2(2), 78-80. https://www.proquest.com/openview/0051fa7d17702e76f72edcb34c0eab0c/1?pq-origsite=gscholar&cbl=28899

Jones, S. M., * Edwards, A. (2010). Online pre-laboratory exercises enhance student preparedness for first year biology practical classes. International Journal of Innovation in Science and Mathematics Education, 18(2), 1-9.

Keller, H., & Keller, E. (2005). Making real virtual labs. The Science Education Review, 4(1), 2 11. https://files.eric.ed.gov/fulltext/EJ1049733.pdf

Kiboss, J., Wekesa, E., & Ndirangu, M. (2006). Improving students’ understanding and perception of cell theory in school biology using a computer-based instruction simulation program. Journal of Educational Multimedia and Hypermedia, 15(4), 397 410. https://eric.ed.gov/?id=EJ742381

Kolb, A. Y., & Kolb, D. A. (2005). Learning styles and learning spaces: Enhancing experiential learning in higher education. Academy of Management Learning & Education, 4(2), 193 212. https://doi.org/10.1007/978-1-4419-1428-6

Krist, A. C., & Showsh, S. A. (2007). Experimental evolution of antibiotic resistance in bacteria. The American Biology Teacher, 69(2), 94-97. https://doi.org/10.1662/0002-7685(2007)69[94:EEOARI]2.0.CO;2

Ma, J., & Nickerson, J. V. (2006). Hands-on, simulated, and remote laboratories: A comparative literature review. ACM Computing Surveys, 38(3), 7-es. https://doi.org/10.1145/1132960.1132961

Makransky, G., Mayer, R. E., Veitch, N., Hood, M., Christensen, K. B., & Gadegaard, H. (2019). Equivalence of using a desktop virtual reality science simulation at home and in class. PLoS ONE, 14(4), 1-14. https://doi.org/10.1371/journal.pone.0214944

Makransky, G., Thisgaard, M. W., & Gadegaard, H. (2016). Virtual simulations as preparation for lab exercises: Assessing learning of key laboratory skills in microbiology and improvement of essential non-cognitive skills. PLoS ONE, 11(6), 1 11. https://doi.org/10.1371/journal.pone.0155895

Maldarelli, G. A., Hartmann, E. M., Cummings, P. J., Horner, R. D., Obom, K. M., Shingles, R., & Pearlman, R. S. (2009). Virtual lab demonstrations improve students’ mastery of basic biology laboratory techniques. Journal of Microbiology & Biology Education, 10(1), 51-57. https://doi.org/https://doi.org/10.1128/jmbe.v10.99

Marbach-Ad, G., Rotbain, Y., & Stavy, R. (2008). Using computer animation and illustration activities to improve high school students’ achievement in molecular genetics. Journal of Research in Science Teaching, 45(3), 273 292. https://doi.org/10.1002/tea.20222

Marchevsky, A. M., Relan, A., & Baillie, S. (2003). Self-instructional “virtual pathology” laboratories using web-based technology enhance medical school teaching of pathology. Human Pathology, 34(5), 423-429. https://doi.org/10.1016/S0046-8177(03)00089-3

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Moher, D., Liberati, A., Tetzlaff, J., Altman, D. G., Altman, D., Antes, G., & Tugwell, P. (2009). Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement (Chinese edition). Journal of Chinese Integrative Medicine, 7(9), 889-896. https://doi.org/10.3736/jcim20090918

Muhamad, M., Zaman, H. B., & Ahmad, A. (2010). Virtual laboratory for learning biology: A preliminary investigation. World Academy of Science, Engineering and Technology, 71, 572-575.

Muhamad, M., Zaman, H. B., & Ahmad, A. (2012). Virtual biology laboratory (VLab-Bio): Scenario-based learning approach. Procedia – Social and Behavioral Sciences, 69, 162 168. https://doi.org/10.1016/j.sbspro.2012.11.395

Nehm, R. H., & Schonfeld, I. S. (2008). Measuring knowledge of natural selection: A comparison of the CINS, an open?response instrument, and an oral interview. Journal of Research in Science Teaching, 45(10), 1131-1160. https://doi.org/10.1002/tea.20251

Olympiou, G., Zacharias, Z., & DeJong, T. (2013). Making the invisible visible: Enhancing students’ conceptual understanding by introducing representations of abstract objects in a simulation. Instructional Science, 41(3), 575 596. https://doi.org/10.1007/s11251-012-9245-2

Oser, R., & Fraser, B. J. (2015). Effectiveness of virtual laboratories in terms of learning environment, attitudes and achievement among high-school genetics students. Curriculum and Teaching, 30(2), 65-80. https://doi.org/10.7459/ct/30.2.05

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Assessing the effects of Biology Practical Activities on Academic Performance of Senior Secondary School Students, Zambia

2019, Journal of Education and Practice

Related Papers

ABDULAZEEZ UMAR ADAMU

This project work was carried out to determine the effect of biology practical activities on academic achievement of students Adamu Tafawa Balewa College of Education Kangere. Chapter one and two is the background of the study and the review of related literature respectively. The background of the study emphasized the use of practical activities in biology as stimulates learner’s interest in the science subject they are studying. In the review of literature, the need for the teaching and learning of biology in secondary schools were discussed. The factors which affect the achievement of biology students were also reviewed which include: inadequate laboratory facilities, teacher factors, student factors and environmental factors. In chapter three, the area of the study, population for study, data collection and analysis were presented. The study was carried out in the department of Biology College of Adamu Tafawa Balewa Education Kangere; the target population includes all the NCE I, II, and III students in Biology Department. The students were given tests and the test was marked and they were scored according to their performances using simple frequency and percentage counts. The discussion of the results, educational implications, recommendation, and conclusion were also treated in chapter five.

Emmanuel Achor

The study examined the effect of frequency of practical work on achievement of senior secondary two (SS2) students in Biology. A sample of 228 SS2 Students from three government-approved schools in Konshisha Local Government Area of Benue State Nigeria was used. Biology Achievement Test (BAT) with reliability coefficients of 0.89 was used to collect data from students in Biology. Mean and standard deviations were used to answer research questions while analysis of covariance was used to test the hypotheses at 0.05 level of significance. ANCOVA with the P-value of less than 0.05 for achievement (F 2 , 221 = 240.521, p<0.05) among the harmonized, intermediate and the control groups showed that there was significant difference in achievement. No significant difference was observed between boys and girls in the intermediate (F 1 , 278 =0.015, p>0.05) and the harmonized (F 1 , 65 = 3.248, p>0.05) groups. It is recommended that teachers should endeavour to organize practical work for students as frequently as possible (at least once a week) so as to develop in the students the practical skills required of them for final examination. Also students should be advised to take every biology practical work very seriously. Finally laboratory technicians should be employed by school authorities to assist biology teacher(s) in the area of practical work so that workload, time management and frequent practical are realistic to enhance students' achievement.

Jeffrey M Torgby

This study was carried out to investigate the performance of senior high school students in biology practical work in the Cape Coast Municipality of the Central Region of Ghana. The mixed method approach was used and the design used was sequential explanatory design. A sample of 90 senior high school form 2 (SHS2) elective biology students randomly drawn from three public senior high schools were used for the study. The study was guided by three research questions. The Biology Practical Performance Test (BPPT) developed by the researcher and semi-structured interview guide were used for the data collection. The data collected were analyzed using mean, standard deviation and Analysis of Variance (ANOVA) at 0.05 level of significance. The results of interview were transcribed and analyzed thematically. The results showed that majority of the elective biology students performed averagely in biology practical test. The study also showed that there is significant difference in the performance of males and females in biology practical work as measured by the Biology Practical Performance Test (BPPT). Also, the study showed that there was no significant difference in the performance of the various age groups involved in the study and hence age has no effect on performance. It was recommended that biology teachers should take students through a lot of practical activities to help improve students’ performance in practical work.

KIBOGORA POLYTECHNIC

Thadee NSABIMANA

This action research entitled “Relevance of practical works on teaching and learning biology in ordinary level, secondary education, was carried out at G.S NYAKINAMA I” with the purpose of exploring the relevance of practical work on teaching and learning biology. The total population of this study was 328 persons which make a sample of 81 participants using Yamane formula. The latter wase composed by 76 students, 3 staff members and 2 biology teachers. The sample was selected using purposive sampling, probability and non-probability sampling methods based on the information for the study. The primary data for this research was collected using structured interviews and questionnaires. Class tests were also used to evaluate student’s performance. The data was collected by using Microsoft excel and presented in tables. In our study, we found that teachers do not use practical work as it should. All respondents agreed that they gain many skills from practical works at 100%. Teachers’ views indicated that 38.75% of the respondent confirm that insufficient time for practical works in biology is a barrier while 61.25% disagree. However, 48.75% agree that class size is not a challenge while 51.25% disagree. This study indicates that too long syllabus is a challenge agreed 27.5% and disagreed at 72.5%. For implementation of laboratories, results show that 75% agree that it is a challenge while 25% disagree. Therefore, practical works influenced learner’s understanding ability of lesson and retention of factual knowledge. Learning through theory good performance for 13 students (17.105%) and 63 students (82.8947%) failed while learners’ performance in biology through. Practically, the learner’s performance was increased where 62 students (81.579%) from ordinary level succeed and 14 students (18.4211%). Finally, the recommendations were given. The science teachers have to look at specific experiments and give them to students and let them be responsible for themselves in order to know that they should do even in the absence of a teachers. School administration should advice all teachers to use surrounding environment to create teaching aids to use in teaching and learning process. MINEDUC should provide materials to schools and advise teachers to adapt themselves on the use of improvisations.

Global Journal of Guidance and Counseling in Schools: Current Perspectives

Chekula Sitotaw

The aim of this study was to investigate the effects of practical work enriching instruction of biology lessons on ninth grade students’ attitudes towards biology lessons and their achievement based on students’ success. Attitude pre-test, attitude post-test, achievement pre-test and achievement post-test are employed for all participants in addition to interviewing four students randomly selected from the total participants. The test was applied to students in two different times. According to the research results, it was found that the experimental teaching method was more effective in the attitude and achievement level of students in some biology lessons, and attitude and achievement have a positive correlation. Therefore, the study recommends that high school biology teachers should plan their lessons in a more practical way to boost (enhance) learners&#39; attitude as well as achievement. All stakeholders including curriculum planners should take part in the planning process. K...

KP Student. THADEE NSABIMANA

Thadée NSABIMANA

Lara mae Mendoza

European Journal of Health and Biology Education

Florence Omosholape

The study investigated the effect of Laboratory practical on senior secondary school students’ performance in Biology in Ilorin South LGA, Kwara State. Three research questions and two hypotheses guided the study. Descriptive survey was adopted for this study. The population comprised SS1 to SS3 Biology students in Ilorin South LGA, Kwara state. Questionnaires were designed for one hundred and eighty (180) Biology students and the data collected were analyzed using descriptive mean, t-test and analysis of variance ANOVA. The findings revealed that the impact of Laboratory practical was significant to the students’ performance. There was no significant difference in students&#39; opinion towards the impact of Laboratory practical on the performance of students based on gender and school type. The following recommendations are made: Adequate laboratory equipment should be provided for senior secondary school students to ease the learning difficulty experienced in learning Biology prac...

muriu wagura

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Effect of cytoplasmic fragmentation on embryo development, quality, and pregnancy outcome: a systematic review of the literature

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• Iman Halvaei 2 ,
• Catherine Boniface 1 &
• Navid Esfandiari   ORCID: orcid.org/0000-0003-0979-5236 1 , 4  

Reproductive Biology and Endocrinology volume  22 , Article number:  55 ( 2024 ) Cite this article

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The role of cytoplasmic fragmentation in human embryo development and reproductive potential is widely recognized, albeit without standard definition nor agreed upon implication. While fragmentation is best understood to be a natural process across species, the origin of fragmentation remains incompletely understood and likely multifactorial. Several factors including embryo culture condition, gamete quality, aneuploidy, and abnormal cytokinesis seem to have important role in the etiology of cytoplasmic fragmentation. Fragmentation reduces the volume of cytoplasm and depletes embryo of essential organelles and regulatory proteins, compromising the developmental potential of the embryo. While it has been shown that degree of fragmentation and embryo implantation potential are inversely proportional, the degree, pattern, and distribution of fragmentation as it relates to pregnancy outcome is debated in the literature. This review highlights some of the challenges in analysis of fragmentation, while revealing trends in our evolving knowledge of how fragmentation may relate to functional development of the human embryos, implantation, and pregnancy outcome.

Introduction

Human preimplantation embryo scoring systems have been widely used to predict blastocyst development and implantation rate after in-vitro fertilization (IVF). The grading of embryos on day-2 and -3 after fertilization is largely subjective and interpretation varies across IVF laboratories, as it is commonly based on morphological appearance. Characteristics in early embryo grading schema include the amount of cytoplasmic fragmentation (CF) during early cleavage, speed of cellular division, number, size, and symmetry of cells (blastomeres). As defined by the Istanbul consensus workshop on embryo assessment, a fragment is “an extracellular membrane-bound cytoplasmic structure that is < 45 µm diameter in a day-2 embryo and < 40 µm diameter in a day-3 embryo” [ 1 ]. There are several different systems to evaluate embryo morphology including Hill’s scoring system [ 2 ] Cummins' grading system [ 3 ] ASEBIR grading system [ 1 ], the UK/ACE grading scheme [ 4 ]; each system has its own classification for degree of fragmentation as well as embryo grade. This heterogeneity further complicates analysis of fragmentation in relation to outcomes.

CF has been shown to occur early in embryonic division and is a common phenomenon seen in embryos cultured in vitro. CF has traditionally been used as a metric of embryo implantation potential [ 3 , 5 , 6 , 7 ]. The amount and pattern of fragments are analyzed in early development, incorporated into the embryo grade depending on grading system, and used to help select the most developmentally competent embryo to be transferred during an IVF cycle. This classification system is important as a proportion of embryos within a single cohort will not successfully develop to the blastocyst stage in vitro. Although there are various contributing factors to an embryo’s developmental capacity and viability, it is largely agreed upon that fragmentation plays an important role. It seems that the etiology of embryo fragmentation is not fully understood but it may be related to several factors like gamete quality, culture condition, and genetic abnormalities in the embryo [ 8 ]. It is difficult to directly compare and quantify relative degrees of fragmentation across studies. However, it has been repeatedly shown that the extent of fragmentation and implantation potential are inversely proportional [ 5 , 7 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ]. While a low degree of fragmentation does not seem to significantly impact embryo viability, severe fragmentation does [ 7 , 22 , 23 ]. Alongside the cell to cytoplasmic ratio, the pattern and distribution of fragmentation influence the developmental quality of the embryo [ 7 , 24 ]. There are two main patterns of embryo cytoplasmic fragments: scattered and concentrated. The former is characterized by fragment contact within several blastomeres and is related to aneuploidy [ 25 ]. Time-lapse studies have shown that fragmentation is thought to be a dynamic process, where some fragments can be expelled or reintroduced into the cells as the embryo continues to divide [ 25 , 26 ]. Fragments can also easily move or rotate around the associated blastomere and change their position in the embryo [ 27 ].

Current grading systems used to evaluate cleavage-stage embryos are largely based on day-2 or -3 morphology. This can be problematic, as developmental growth of an embryo is variable and the grade of a developing embryo at one point in time is not guaranteed to persist. For example, studies have suggested that embryo selection on day-2 or -3 based on morphological grade can be unreliable and lead to negative pregnancy outcomes [ 28 , 29 , 30 ]. Accordingly, new parameters for predicting implantation success have been proposed including extended embryo culture to the blastocyst stage to day-5, -6 or -7 [ 31 ]. Delaying embryo transfer to the blastocyst stage is advantageous as it can limit the number of unsuccessful embryo transfers and biochemical pregnancies or clinical pregnancy losses in IVF. While there are multiple reports on the impact of cleavage-stage embryo quality on blastocyst formation and blastocyst quality [ 32 , 33 ], few have specifically looked at the degree of fragmentation as a predictive variable.

In this systematic review, we comprehensively reviewed the available literature on the origin and characteristics of CF, factors affecting CF, and the effect of CF and fragment removal on embryo development and pregnancy rate.

Materials and methods

A search was conducted on October 10, 2023, using PubMed and Google Scholar databases in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines [ 34 ]. In PubMed, the search terms “embryo*[tw] OR cleavage stage [tw] OR "Embryonic Structures"[Mesh] OR "Embryonic Development"[Mesh] OR "Embryo, Mammalian"[Mesh] OR "Cleavage Stage, Ovum"[Mesh]” AND “cytoplasm*[tw] AND fragment*[tw] AND “(Blastocyst*[tw] OR "Blastocyst"[Mesh]) AND (form* OR develop* OR quality*)” were used. A title search in Google Scholar using search terms as above and “embryo cytoplasm fragmentation”, “blastocyst quality”, “blastocyst development” was performed. Only full-text publications in English were included. Full-text articles which did not have any mention of cytoplasmic or embryo fragmentation were excluded, however articles which mentioned both DNA fragmentation and CF were included. Since most of the studies discussing CF also discussed other morphologic features of the embryo, studies that mention embryo morphology, grade or quality were also included. Articles that looked at non-human embryo fragmentation, case reports, case series, book chapters and review papers were excluded. Titles and abstracts were screened, and study quality and bias were assessed. The primary outcomes of interest were embryo quality, blastocyst formation, and pregnancy outcome.

Figure 1 provides details of study screening and inclusion. There were 206 studies screened between the two search engines PubMed ( n =106) and Google Scholar ( n =100). There were 18 duplicates giving a total of 188 articles. Due to the small number of studies from the search criteria, no filter of time was placed. After removal of non-full text articles, articles that used non-human embryos, and articles not relevant to the topic, 20 articles were eligible for inclusion. Forty relevant references from the articles were also extracted, reviewed, and included in this review. These additional articles were reviewed with the same inclusion and exclusion criteria as mentioned above. A total of 60 articles were included in the qualitative synthesis of this review.

Article Identification and Screening

Origin and etiology of CF

The etiology of CF is not completely understood. There are several proposed theories as to why embryos display variable degrees of fragmentation. Fragmentation has been shown to be a natural, unpredictable process both in vitro and in vivo and is documented in various species [ 35 , 36 ]. This suggests that embryo fragmentation is neither species-specific nor solely a byproduct of in vitro culture. Assisted reproductive technology (ART) and IVF techniques, such as time-lapse microscopy (TLM) and transmission electron microscopic (TEM) analyses, have recently allowed for further understanding of embryo developmental potential and fragmentation (Figs.  2 and 3 ). Seven of the included studies in this review propose potential hypotheses as to the origin of CF (Table 1 ). Three of the articles evaluated gamete quality as related to fragmentation in a developing embryo [ 37 , 38 , 39 ].

Human cleavage stage embryos a) Day-2 embryo at 4-cell stage with no fragmentation, b) fragmented Day-2 embryo, c) Day-3 embryo at 8-cell stage with no fragmentation, d) fragmented Day-3 embryo, e) Day-5 cavitating Morula with no fragmentation, f) fragmented Day-5 cavitating Morula

Ultrastructure and organelle microtopography of an embryo fragment by transmission electron microscopy. Ly: primary lysosome, M: mitochondrion, rM: remnant of regressing mitochondrion, MV: mitochondria-vesicle complex, V: vesicle; scale bar: 1 µM

An early study showed that sperm DNA oxidation has been associated with embryo development and quality, and therefore linked to CF [ 37 ]. Nucleolar asynchrony in the zygote from sperm DNA fragmentation has previously been shown to predict future low-quality blastocyst development. A positive correlation has also been found between the percentage of sperm OxiDNA-stained cells with embryo fragmentation on day-2 and -3 of development. Sperm DNA oxidation may therefore be associated with fragmented, nonviable, poor-quality embryos [ 37 ] . A recent study also showed the negative correlation between sperm DNA fragmentation and blastomere DNA fragmentation and blastulation rate [ 40 ]. Further studies are needed to confirm the impact of sperm DNA oxidation on embryo fragmentation.

An observational study documented the degree of fragmentation of human embryos as they progressed through mitotic cell cycles [ 38 ]. In this study, the authors analyzed nearly 2,000 oocytes and 372 embryos, and found that increased embryo fragmentation (>50%) was associated with a specific pattern of development: delayed first division (oocyte spindle detected at 36.2 hours after hCG injection vs. 35.5 hours in low fragmentation), a significantly earlier start of the second mitosis (8.9 hours vs. 10.8 hours after the first mitosis), and a significant delay of the third mitosis after the second mitosis (2.2. hours vs. 0.6 hours). The authors did not comment on whether fragmentation could be a result of the cell dividing before proper chromosome alignment, or if existing aneuploidy resulted in erroneous cleavage patterns [ 38 ].

Polar body (PB) fragmentation has also been investigated in relation to cytoplasmic fragmentation. Ebner et al., in a prospective study analyzed the relationship between a fragmented first PB and embryo quality in patients undergoing ICSI. Two groups of oocytes were analyzed according to PB fragmentation: intact first PBs and those with fragmented PBs. Forty-two hours after ICSI, embryo morphology (i.e., number of blastomeres and degree of fragmentation) was recorded. Overall, a significantly higher percentage of cytoplasmic fragmentation was seen in day-2 embryos that originated from oocytes with fragmented first PBs than those with intact PBs ( P < 0.05). This study further supports the concept that oocyte quality contributes to overall embryo fragmentation and provides evidence that preselection of oocytes may contribute to the prognosis of embryo quality and blastocyst development [ 39 ]. The role of PB fragmentation on embryo quality was confirmed in other studies [ 41 , 42 ], however, a recent study has not recommended considering PB status as a tool for embryo selection [ 43 ].

Beyond analysis of gamete quality, other studies have shown a biochemical relationship between embryo competence and fragmentation. One study showed that disturbances in E-cadherin, a cell adhesion protein that plays a critical role in morphogenesis, occur in embryos with cleavage abnormalities and extensive cytoplasmic fragmentation, suggesting a possible mechanism to the loss of embryonic viability [ 44 ]. Further, by using mitochondrial fluorescence techniques, Van Blerkom et al., found that mitochondrial distribution at the pronuclear stage may be an epigenetic factor related to the organization of the embryo and further embryonic development [ 45 ]. Blastomeres that were deficient in mitochondria and thus ATP at the first or second cell division remained undivided and often died during subsequent culture. Although this study examined morphologically normal (unfragmented) cleavage-stage embryos, it may support the idea that perinuclear mitochondrial distribution and microtubular organization influence developmental capacity of early cleavage-stage embryos [ 45 ]. Higher numbers of mitochondria reported in fragmented compared to the normal blastomeres show the rapid depletion of ATP in the fragmented embryos [ 21 ]. There have also been reports of increased gene transcription of mitochondrial factors like OXPHOS complexes, ATP synthase, and mtDNA content in highly fragmented embryos compared to controls [ 46 ]. Mitochondrial activity is lower and more centralized in fragmented embryos compared to good quality embryos on day-3 [ 47 ]. Mitochondria are the main source of ATP for embryo mitosis, and their proper function is essential for embryo development. More research is needed to elucidate the morphology and role of mitochondria in embryo development, especially in relation to fragmentation.

A subsequent study by Van Blerkom et al., analyzed the temporal and spatial aspects of fragmentation through TLM and TEM analyses from the pronuclear to the 10-12-cell stage. Through TLM, the authors visualized the non-discrete, dynamic nature of fragments and noted that many were “bleb-elaborations” of the plasma membrane and cytoplasm. They characterized two patterns of fragmentation: definitive and pseudo-fragmentation. Definitive fragmentation was described as fragments detached from a blastomere, and pseudo-fragmentation was assigned when the fragments were no longer detectable during subsequent development. Often one developing embryo would show both fragmentation patterns at different stages of development, suggesting that these patterns may have different etiologies and effects on embryo development competence [ 47 ]. Hardarson et al., similarly used TLM to document that fragments are dynamic and can be internalized throughout cleavage during culture periods. The contents of the fragments were noted to be internalized and released into the cytoplasm of the blastomere and seen on multiple time-lapse photographs as a cytoplasmic turbulence. This is the first reported evidence that cellular fragments can “disappear” during the culture period in human IVF [ 26 ]. It seems that in mild to moderate CF, the timing of embryo evaluation and grading can affect the reported percent of fragmentation.

Lastly, we have included a preliminary study performed by Sermondade et al., that suggests a specific subgroup of patients who have had repeated IVF failures (presumably due to a recurring high rate of fragmented embryos) may benefit from early intrauterine embryo transfer at the zygote stage (2PN) [ 48 ]. Data showed a delivery rate per oocyte retrieval of 18.9%, which was significantly higher than the delivery rate of 7.5% in the matched control group. The results were encouraging and suggestive of a safe, non-invasive rescue strategy for patients who experience recurrent highly fragmented embryos and failed IVF attempts. The data further suggests that fertilized oocytes of this subgroup may have deficiencies in certain maternal factors (i.e., stress-response factors) that do not allow normal embryo development in culture environments [ 48 ]. Another study was also confirmed application of zygote transfer in patients with history of low-quality embryos [ 49 ]. However, further studies are required to verify the impact of this technique for patients with history of fragmented embryos.

Apoptosis is another proposed etiology of fragmentation. Apoptosis may occur in blastomeres with defective cytoplasm or abnormal chromosomes, leading to embryo fragmentation [ 50 ]. There are several studies reporting apoptosis in both fragments and neighboring blastomeres in a fragmented embryo [ 24 , 50 ]. Chi et al., showed that fragments are associated with both apoptosis and necrosis [ 21 ]. One of the factors that appears to induce apoptosis in blastomeres is suboptimal culture conditions such as hypoxia [ 51 ]. In addition, there are controversial reports on the role of reactive oxygen species (ROS) in embryo fragmentation [ 52 , 53 ]. It has been shown that ROS are present at high levels in the culture media of fragmented embryos [ 52 , 54 ]. Chen et al., recently showed that embryo culture in 5% oxygen, from days 1 to 3, is associated with higher embryo quality and live birth rate compared to 20% oxygen [ 55 ]. The effects of culture condition modifications, such as hypoxia and ROS, on embryo fragmentation need to be clarified to understand the importance of culture condition in this process.

Membrane compartmentalization of DNA, abnormal cytokinesis, and extra vesicular formation are other proposed theories for embryo fragmentation [ 8 ]. Defects or damages in mitochondria are associated with low ATP and high ROS production leading to a compromised cell division and cytokinesis [ 27 ]. In addition, there is a correlation between embryo fragmentation and ploidy status. Chavez et al., showed that CF was seen in a high proportion of aneuploid embryos, and that meiotic and mitotic errors may cause fragmentation in different cell development stages. Meiotic errors were associated with fragmentation at one-cell stage while mitotic errors were associated with fragmentation at interphase or after first cytokinesis [ 56 ]. Chromosomally abnormal embryos often have severe fragmentation, which may be another cause of CF [ 55 , 57 ].

Overall, the precise cause of CF has yet to be clearly defined. The above investigations have elucidated potential sources and associations of what is likely a complex and multifactorial process and represent our current understanding of CF origin.

What is contained in CF?

Four of the included studies used various technological advances to study the contents of CF in human embryos (Table 2 ). Two studies used TEM methods to evaluate fragment ultrastructure (Fig.  3 ) [ 21 , 58 ]. Fragments were extracted from embryos with 10-50% fragmentation and the ultrastructure evaluated by TEM. Micrographs showed that the fragments had a distinct membrane containing cytoplasmic organelles including mitochondria, mitochondria-vesicle complexes, Golgi apparatus, primary lysosomes, and vacuoles. Mitochondria were the most abundant structure.

In an additional evaluation of CF contents, Johansson et al., analyzed DNA content of fragments to define a cutoff diameter for an anucleate fragment or blastomere. Findings showed that 98% of fragments <45 µm on day-2 and 97% of those <40 µm on day-3 contained no DNA and, if not reabsorbed into a blastomere, showed a loss of cytoplasm. Presence of essential blastomere organelles such as mitochondria, mRNA, and proteins within cytoplasmic fragments were related to embryo development arrest [ 59 ]. Lastly, Chi et al., also used TEM to examine ultrastructure of the human fragmented embryos and found that blastomeres with anucleate fragments contained fewer mitochondria in their cytoplasm compared to normal blastomeres [ 21 ].

Cell death and CF

Eight of the included studies analyzed the relationship between cell death and embryo fragmentation (Table 3 ). Five studies analyzed the status of chromatin in arrested fragmented embryos through a combined technique for simultaneous nuclear and terminal transferase-mediated DNA end labelling (TUNEL) [ 24 , 60 , 61 , 62 , 63 ]. Two studies used a comet assay to analyze DNA fragmentation [ 21 , 63 ]. Four of the eight studies used Annexin V staining [ 21 , 61 , 62 , 63 ] with three including the presence of propidium iodide (PI) to compare apoptosis to necrosis [ 21 , 61 , 63 ].

Jurisicova et al., used a combined nuclear and fragmented DNA labeling approach which allowed distinction between chromatin status and DNA fragmentation, which serve as markers of apoptosis versus necrosis respectively [ 60 ]. After fertilization, embryos were stained with 4,6-diamidino-2-phenylindole (DAPI). In cases of compromised cell membrane integrity, DAPI stain was observed in the cytoplasm as a sign of necrosis. Concomitant use of TUNEL labeling reflected the integrity of the DNA and allowed distinction between necrotic and apoptotic cells. Through combined techniques of DAPI/TUNEL, TEM, scanning electron microscopy (SEM) and stereomicroscopic observations, 153 of 203 (75.4%) fragmented early cleavage-stage embryos displayed signs of apoptosis (i.e., chromatin condensation, cellular shrinkage, DNA fragmentation, presence of cell corpses) with or without normal nuclei [ 60 ].

Similarly, Levy et al., analyzed early arrested or fragmented preimplantation embryos and the pattern of DNA fragmentation using TUNEL assay and the presence of phosphatidylserine through Fluorescein isothiocyanate (FITC)-labelled Annexin V, a phosphatidylserine binding protein. The authors observed TUNEL staining in one or more nuclei of 15 out of 50 (30%) arrested embryos from the 2-cell stage to uncompacted morulae, all of which had high degrees of CF. Furthermore, embryos with regular-sized blastomeres without fragmentation were all TUNEL negative [ 50 ].

A separate prospective study by Antczak et al., explored the possible association between fragmentation and apoptosis using PI and Annexin V staining of plasma membrane phosphatidylserine and TUNEL analysis of blastomere DNA [ 24 ]. In contradistinction to prior studies, these authors found no direct correlation between fragmentation and apoptosis. Virtually all blastomeres that were PI negative, intact or fragmented, showed no TUNEL or annexin V fluorescence, suggesting no signs of apoptosis [ 24 ].

Liu et al., used a similar methodology of TUNEL labeling and Annexin V staining to detect markers of apoptosis in fragmented human embryos derived from IVF [ 61 ]. Overall, highly fragmented embryos had apoptotic features including bright fluorescence (positive TUNEL labeling signifying DNA fragmentation) on the cell corpses and in intact blastomeres [ 61 ]. By staining cells with both annexin V and PI, this study was able to demonstrate that apoptosis occurs frequently in fragmented human embryos and the coexistence of apoptotic, necrotic and viable sibling blastomeres can occur. Sibling blastomeres within an embryo often showed apoptotic features that led to secondary necrosis while others did not initiate apoptosis. The authors did not find a significant difference in the expression frequency of apoptotic genes between viable and nonviable or arrested embryos [ 61 ].

Chi et al., stained human embryos ( n =10) with annexin V and PI and found that human fragmented embryos exhibited characteristics of both necrosis and apoptosis [ 20 ]. Rather than TUNEL assay, these authors used a modified sperm comet assay to investigate DNA fragmentation of human fragmented embryos. They found that 6/7 human fragmented embryos (85.1%) stained positively for PI with the intensity of staining increasing with the degree of fragmentation. Of note, DNA fragmentation was observed in fragmented human embryos but not in the normal embryo [ 21 ].

Metcalfe et al., analyzed the expression of 11 BCL-2 family genes in normally developing embryos and in severely fragmented embryos [ 64 ]. They found that the expression of BCL-2 family genes was highest in the pronuclear stage and eight-cell stages, and lowest at the two-cell, four-cell, and blastocyst stages in developmentally intact embryos. Furthermore, the expression did not change in fragmented embryos, suggesting that embryo fragmentation does not likely compromise mRNA integrity and gene detection [ 64 ]. However, like Liu et al., [ 61 ] these authors did detect far fewer pro-apoptotic BCL-2 genes in fragmented embryos at the eight-cell stage. The authors noted that these findings do not distinguish between iatrogenic apoptosis from suboptimal in-vitro culture conditions [ 64 ]. A separate study by Jurisicova et al. similarly analyzed gene expression at the 2-, 4- and 8-cell stage of fragmented embryos. Embryos that had 30-50% fragmentation showed a significant increase in Hrk mRNA levels, a BCL-2 protein encoding gene ( P = 0.016). Further, these authors found an increase in Caspase-3 mRNA in fragmented embryos, as well as induction of Caspase-3-like enzyme activity in nucleated fragments, although this finding was not statistically significant [ 65 ].

Van Blerkom et al., also used TUNEL assay in conjunction with the comet assay as a method of identifying the specific pattern of cell death (necrosis, lysis or apoptosis) and the extent of DNA damage in developing embryos [ 47 ]. They analyzed the integrity of the plasma membrane through annexin V staining with PI. They examined both transient and persistent fragment clusters at day-3 and 3.5 embryos for evidence of programed cell death using time-lapse video and TEM. In contrast to previous studies, they found no indication of nuclear DNA damage or loss of membrane integrity. These results, led the authors to hypothesize that the fragmentation observed was not characteristic of programed cell death, but rather resembled features of oncosis. The culture in this study was not severely oxygen-deprived and thus the authors concluded that this oncosis-like process was potentially a result of disproportionate mitochondrial segregation during the first cleavage division. Without sufficient mitochondria, the early blastomeres did not maintain adequate ATP for normal cell function which may have precipitated an ATP-driven oncosis-like process [ 47 ].

Lastly, a study by Bencomo et al., found correlations between the degree of apoptosis in human granulosa-lutein (GL) cells, the outcome of IVF-ET cycle, the percentage of embryo fragmentation, and patient’s age [ 66 ]. Human GL cells were collected from follicular fluid, cultured for 48 hours, and marked with caspACE FITC-VAD-FMK, a fluorescent marker for activated caspases. Results showed that GL cells of older women (>38 years old) were significantly more susceptible to apoptosis at 43.2 ± 18.0% compared to the younger group (<38 years old) with a mean percentage of apoptotic cells 33 ± 17.2%. Women who had a positive pregnancy had a lower level of apoptosis in GL cultures than those who did not get pregnant (30.2 ± 14% vs. 40.4 ± 19.5%). There was a positive correlation between embryo fragmentation and GL cell apoptosis ( r = 0.214). Overall, the level of apoptosis of cultured GL cells was correlated with IVF outcome [ 66 ].

These studies demonstrate the diversity among techniques to evaluate cell death in the developing embryo. TUNEL labeling, sperm comet assay, annexin V staining or some combination of these techniques have been described. Furthermore, there are discrepancies between the stage at which apoptosis might occur, with majority of studies cited here suggesting that cell death occurs in early stages of development before blastocyst formation. While some studies suggest that fragmented embryos display signs of apoptosis, these findings are still disputed and the distinction between apoptosis and necrosis is not clearly defined in the literature.

Patient age and CF

There are inconsistencies within the literature regarding the relationship between maternal age and CF. A total of six studies in this review focused on this relationship (Table 4 ). Three of the studies found a positive correlation between patient age and degree of embryo fragmentation [ 67 , 68 , 69 ]. The other three studies found no age-related correlation between embryo fragmentation or quality [ 7 , 70 , 71 ].

A retrospective study by Ziebe et al., compared the relationship between age of women undergoing IVF and the proportion of anucleate fragmentation in cleavage-stage embryos. Using a logistic regression analysis, the authors compared the percentage of transfers using fragmented embryos with age; the odds of fragmentation increased by 3% per year (OR 1.033 [95% CI 0.996, 1.071]). There was a linear relationship between age and embryo fragmentation rate, with an increase in fragmentation of 0.76% per year (95% CI -0.09%, 1.61%) [ 68 ].

Keltz et al., assessed various predictors of embryo fragmentation in IVF and found that increased maternal age and lower number of oocytes and embryos were associated with increased embryo fragmentation. There was a significant difference between cycles with fragmented embryos ( n =74) at a mean age of 36.9 ± 4.24 years as compared to cycles with no fragmented embryos ( n =234) at a mean age of 35.4 ± 4.74 years. Overall, this retrospective analysis of fresh IVF cycles found that embryo fragmentation is indeed associated with older age and ultimately poor cycle outcome [ 67 ].

Contrary to these findings, an early study by Alikani et al., showed no relationship between maternal age and CF [ 7 ]. In a retrospective analysis of degree and pattern of embryo fragmentation on days 2 and 3, they defined five patterns of fragmentation. Both the degree and pattern of fragmentation impacted pregnancy and implantation rate, but the authors found no correlation between appearance of any CF pattern and maternal age. The average maternal age in their population was 35.7 ± 4.25 years [ 7 ]. Another study by Stensen et al., analyzed the effect of chronological age on oocyte quality (assessed by maturity) and embryo quality (assessed by cleavage-stage, blastomere size and embryo fragmentation). Women were divided into five age groups: ≤25, 26–30, 31–35, 36–40 and ≥41 years. The embryo morphological score was based on fragmentation and blastomere size with score of 0-4 where score of 4 being equally sized blastomeres and no fragmentation and score of 0 being cleavage arrest or morphologically abnormal embryo. The mean oocyte score and embryo morphology score were not found to be significantly different across the age groups [ 70 ]. Wu et al., also showed that age does not influence embryo fragmentation. Patient ages ranged from 20 to 44 years with a mean age of 30.6 ± 4.6 years and were divided into age groups of ≤29, 30–34, 35–37, 38–40, and ≥41 years of age. Analysis of embryos with similar degrees of fragmentation was used to assess whether maternal age was associated with embryo fragmentation and blastocyst development. There was no correlation between age and embryo fragmentation as a continuous variable ( r = 0.02; P = 0.25) nor was there a correlation when age was divided into the groups ( P = 0.2). They also found that neither age ( r = -0.08; P =0.16) nor degree of fragmentation ( r = -0.01; P = 0.81) had a significant impact on blastocyst development [ 71 ].

Recently, a retrospective time-lapse study evaluated the implantation rate of 379 fragmented embryos. The results showed that there was an association between advanced maternal age and fragmentation. Fragmentation rate was higher in patients ˃35 compared to patients ≤35 years old. It seems that the lower quality of oocytes in older patients results in increasing fragmentation [ 69 ]. Overall, the included studies have differing conclusions on the effect of maternal age and CF; varying definitions and analysis of CF remain a limitation.

IVF vs ICSI procedures and CF

Five of the included studies compared embryo quality between conventional IVF and intracytoplasmic sperm injection (ICSI) procedures (Table 5 ). Two of these studies found that ICSI was associated with impaired embryo morphology compared to IVF [ 72 , 73 ], while the other three showed no difference in embryo quality between the two fertilization modalities [ 74 , 75 , 76 ]. There were no studies within our search that identified embryos created by ICSI having greater morphology grade, or less embryo fragmentation, than IVF.

Frattarelli et al., directly examined the effect of ICSI on embryo fragmentation and implantation rate compared to IVF. There was a significant difference in mean embryo grade between IVF and ICSI. IVF patients had significantly more grade I, or non-fragmented, embryos compared to the ICSI group ( P < 0.01). However, there was no significant difference in mean number of embryos per embryo grade II – IV [ 72 ].

Similarly, Hsu et al., compared embryo quality, morphology, and cleavage after ICSI with standard IVF patients. They defined the grading system from 1 – 5, ranging from no fragments (grade 1) to severe or complete fragmentation (grade 5). They found that for the overall population, when comparing ICSI and IVF patients after matching for age and number of embryos transferred, the number of embryos with good morphology was significantly greater in the IVF group compared to ICSI ( P < 0.006). The average morphology scores, similar to the results of Frattarelli et al., were significantly different between the ICSI group and the IVF group. They also found IVF patients’ embryos to have significantly better cleavage rate than those from ICSI patients ( P < 0.001) [ 73 ].

Garello et al., evaluated if fertilization via ICSI influences pronuclear orientation, PB placement, and embryo quality when compared to IVF. Embryos were assessed using morphology, and grouped as good (grades 1-2), average (grades 3-4), or poor (grades 5-6). Embryos were also assessed for cleavage regularity and proportion of fragmentation (0, <20%, 20–50%, >50%). There was no statistically significant difference in mean morphology (good, average, poor) between the groups, although they did note an apparent increase in grade 4 versus grade 3 embryos after ICSI procedure. The two groups had similar proportions of fragmentation [ 74 ].

Two other studies took a unique approach in comparing embryo quality in ICSI and IVF patients by using randomized sibling oocytes [ 75 , 76 ]. Yoeli et al., studied oocytes retrieved from patients with a less than 40% fertilization rate in a previous standard IVF cycle and divided these oocytes into a conventional insemination group and an ICSI group. Each group had over 1400 oocytes. Overall, there was no significant difference between the IVF and ICSI groups in terms of cleavage rate or rate of high-quality embryos (both Grade A embryos with ≤10% fragmentation and embryos with ≤20% fragmentation) [ 75 ]. Ruiz et al., also analyzed sibling oocytes in patients who had failed intrauterine insemination attempts. The authors similarly found no significant difference in fertilization rates and degree of fragmentation between ICSI and standard IVF groups [ 76 ]. Most studies included in the search criteria showed that ART techniques such as ICSI do not significantly impact fragmentation rate in developing embryos, suggesting that ICSI is not a significant contributor to poorer outcomes by way of embryo fragmentation. Of note, the timing of cumulus cell denudation after conventional IVF is a matter of debate; none of the included studies in this review performed short-time insemination. In a meta-analysis reviewing denudation times, the number of good quality embryos produced after retaining cumulus cells was similar to those produced after early removal of these cells, suggesting that brief insemination has no impact on CF [ 77 ]. Liu et al. also showed that short insemination time is not associated with different outcomes in terms of embryo development [ 78 ].

Effect of CF on embryo development

It is commonly believed that CF has detrimental effects on embryo development. Thirteen of the included studies found a negative effect of CF on embryo development (Table 6 ). Various approaches have been used to propose a hypothesis as to how increased fragmentation impedes embryo development.

Van Blerkom et al., showed through time-lapse video and TEM that fragments physically impede cell-cell interactions, interfering with compaction, cavitation, and blastocyst formation [ 63 ]. In an ultrastructural observational study by Sathananthan et al., 15 embryos were cultured with human ampullary cell lines and TEM used to evaluate embryo development. They noted degeneration of blastomeres, including incomplete incorporation of chromatin into nuclei and formation of micronuclei, which was possibly a consequence of being adjacent to blastomere fragments [ 79 ]. A much larger prospective study by Antczak and Van Blerkom analyzed 2293 fertilized eggs from 257 IVF cycles to examine the effect of fragmentation on the distribution of eight regulatory proteins. Fragmentation reduced the volume of cytoplasm and depleted embryos of essential organelles or regulatory proteins, compromising the embryo developmental potential. They also found that specific fragmentation patterns during various stages of embryo development, i.e., 2- and 4-cell stages, were associated with embryo viability and therefore could have clinical application in the selection of embryos for transfer [ 24 ]. As previously mentioned, fragmentation may affect compacted/morula and blastocyst quality [ 80 ]. Cell exclusion at this stage is due to failure or abnormal expression of proteins involved in compaction [ 44 , 81 ]. Blastomeres may also irregularly divide, resulting in fragmentation and exclusion from compaction [ 82 ], and excluded cells have a high rate of aneuploidy [ 83 ]. Blastocyst quality from fully compacted embryos has been reported to be higher than blastocysts with partial compaction [ 84 ].

The hypothesis that fragmentation reflects inherent embryogenetic abnormalities, such as aneuploidy, increased mosaicism, or polyploidy, is supported by multiple studies in this review [ 55 , 57 , 85 ]. Morphologically poor-quality embryos, defined by amount of fragmentation, were often found to have concomitant chromosomal abnormalities [ 57 , 85 ]. Culture environment has also been implicated in presence and degree of fragmentation. For example, Morgan et al., using video-cinematography found that embryos cultured on a monolayer of feeder cells had fewer fragments than did embryos cultured alone [ 86 ]. In addition to aneuploidy and external environment, degree of fragmentation also appears to be related to embryo quality. Both Alikani et al., and Hardy et al., have shown that a small degree of fragmentation (<15%) on day-2 embryos did not affect blastocyst formation but increased (> 15%) fragmentation was associated with significantly reduced blastocyst development [ 23 , 87 ]. Similarly, a prospective study of over 4000 embryos by Guerif et al., showed that the rate of blastocyst formation increased significantly with decreased fragmentation (<20%) on day-2 embryos [ 32 ].

A separate study by Ivec et al., graded day-4 and -5 morulae based on the degree of fragmentation (<5%, 5%–20%, or >20%) and compared their blastocyst development rate. They found a negative correlation between degree of fragmentation and clinically usable blastocysts, optimal blastocysts, and those with a hatching zona pellucida. Through logistic regression analysis, they found that with each increase in percentage of fragmentation in morulae, there was a 4% decrease in the odds of hatching (OR: 0.96, 95% CI: 0.95–0.98;  P < 0.001) and optimal blastocyst formation (OR: 0.96, 95% CI: 0.94–0.97;  P < 0.001) [ 88 ]. It is important to point out that the degree of embryo fragmentation, no matter at what stage of development, is measured subjectively without standardized methods. One study from Hnida et al., included here recognized this limitation and used a computer-controlled system for multilevel embryo morphology analysis [ 89 ]. The degree of fragmentation was evaluated based on digital image sequences and correlated to the blastomere size. Fragments were defined to be anucleate with an average diameter of <40 µm. Not surprisingly, the mean blastomere volume decreased significantly with increasing degree of fragmentation ( P < 0.001). In addition, average blastomere size was significantly affected by the degree of fragmentation and multinuclearity which may function as a biomarker for embryo quality [ 89 ]. Furthermore, Sjöblom et al., analyzed the relationship of morphological characteristics to the developmental potential of embryos [ 90 ]. These authors, similar to Hnida et al., found that a large cytoplasmic deficit, i.e., blastomeres not filling the space under the zona, was detrimental to blastocyst development (P < 0.044). However, this is the only study in which the extent of CF observed was not significantly associated with blastocyst development [ 90 ]. Another study using time-lapse imaging showed an association between cytoplasmic fragments at the two-cell stage and perivitelline threads. Perivitelline threads can be observed as the cytoplasmic membrane withdraws from the zona pellucida during embryo cleavage. Ultimately, the presence of these threads, despite the level of fragmentation, did not affect embryo development [ 91 ]. As demonstrated by the studies described here, the degree of CF has a largely negative effect on embryo development.

Effect of CF on embryo implantation and pregnancy

In addition to evaluating the effect of CF on preimplantation embryo development, it is important to assess the effect of CF on implantation and pregnancy outcomes. Five of the included studies have shown a negative effect of CF on implantation or pregnancy outcome (Table 7 ). Assuming that increased fragmentation is detrimental to embryo development, implantation, and pregnancy outcome, it is important to understand the embryo scoring system that determines the best embryo for transfer. Giorgetti et al., used single embryo transfers to devise an embryo scoring pattern to best predict successful implantation. Not surprisingly, higher pregnancy rates were observed with embryos that displayed no fragmentation. The authors found that both pregnancy rate and live birth rate were significantly correlated with a 4-point score based on cleavage rate, fragmentation, irregularities displayed, and presence of a 4-cell embryo on day-2 [ 12 ].

Racowsky et al., assessed if multiple evaluations of an embryo improve selection quality and thus implantation and pregnancy success. They noted that an increased level of fragmentation on both day-2 and -3 was associated with a significant reduction in the number of fetuses that developed to 12 weeks. They also noted that severe fragmentation (>50%) impaired overall embryo viability and may be related to low pregnancy rates and high risk of congenital malformations. The authors ultimately concluded that single day morphological evaluation on day-2 or day-3 has the same predictive value to a multi-day scoring system [ 22 ].

Another retrospective analysis of 460 fresh embryo transfers by Ebner et al., sought to determine the impact of embryo fragmentation on not just pregnancy, but also obstetric and perinatal outcomes. There was a significant relationship between fragmentation and implantation and clinical pregnancy rate, but not with multiple pregnancy rate or ongoing pregnancy rate [ 10 ]. Alikani et al., also studied embryo fragmentation and its implications for implantation and pregnancy rate and included fragmentation pattern into their discussion. They too found a significant decrease in implantation and pregnancy rate as the degree of fragmentation increased. They identified an effect on pregnancy rate when the degree of fragmentation was greater than 35%. The authors went on to discuss that not all fragmentations are detrimental to the embryo development and that the pattern of fragmentation matters. They found that fragmentation pattern type IV, defined as having large fragments distributed randomly and associated with uneven cells, had significantly lower implantation and clinical pregnancy rates when compared to types I-III. They concluded that detaching blastomere cytoplasm as large fragments is most detrimental to embryo development and implantation rate. In contrast, small, scattered fragments (type III) did not seem to appreciably affect the cell number or pose a serious threat to further development [ 7 ].

Lastly, Paternot et al., used sequential imaging techniques and a computer-assisted scoring system to study blastocyst development and the effect of fragmentation on clinical pregnancy. The authors reviewed the volume reduction over time as a measure of embryo fragmentation. They analyzed volumes on day-1 to -3 and found a significant association between total embryo volume and pregnancy rate on both day-2 ( P = 0.003) and day-3 ( P = 0.0003), with the total volume measured on day-3 being the best predictor of pregnancy outcome [ 92 ]. In contrast, Lahav-Baratz recently showed that there was no association between fragmentation rate and abortion or live birth rate. It was concluded that fragmented embryos still have implantation potential and could be considered for transfer when applicable [ 69 ].

Effect of CF removal on embryo development

The effect of fragment removal on IVF outcomes has been controversial. Six of the studies included in this review discussed the impact of removing fragments on embryo development (Table 8 ) [ 7 , 67 , 93 , 94 , 95 , 96 ]. The literature is mixed, with some studies showing improvement in embryo development quality after fragmentation removal [ 7 , 93 ], and others showing no difference at all [ 70 , 94 , 95 ].

Alikani et al., were one of the first investigators to define various patterns of fragmentation and perform microsurgical fragment removal to improve implantation potential [ 7 ]. The authors found that the pattern and degree of fragmentation, and not merely the presence of fragmentation, was significant. When assisted hatching and microsurgical fragment removal was performed, there was an overall 4% increase in implantation rate. They concluded that the removal of the fragments possibly restored the spatial relationship of the cells and limited the interference of cell-cell contact. Further, their preliminary data showed that blastocysts formed after fragment removal were better organized than their unmanipulated counterparts [ 7 ].

Eftekhari-Yazdi et al., similarly studied the effect of fragment removal on blastocyst formation and quality of embryos [ 93 ]. They compared day-2 embryos without removal of fragments to those that fragments were microsurgically removed. There were significantly higher quality embryos in defragmented group compared to the control. Furthermore, fragment removal improved the blastocyst quality compared to the control group. There was also a reduction of apoptotic and necrotic cells in experimental group when compared with the control group [ 93 ].

Two separate studies by Keltz et al., assessed implantation, clinical pregnancy, and birth outcomes after defragmentation [ 67 ], as well as embryo development and fragmentation rate after day-3 embryo defragmentation [ 94 ]. The authors first compared cycle outcomes between low-grade embryos that underwent micromanipulation for fragment removal (>10% fragmentation) and high-grade embryos that did not undergo defragmentation but were hatched on day 3. When compared, the defragmented group showed no difference in rates of implantation, clinical pregnancy, live birth, spontaneous abortion, or fetal defects as compared to the cycles that included all top-grade embryos. Factors associated with poor IVF prognosis and formation of embryo fragments included advanced age, decreased number of oocytes and embryos, and embryo grade [ 67 ].

A separate prospective randomized study by Keltz et al., looked more specifically at day-5 fragmentation, compaction, morulation and blastulation rates after low grade day-3 embryo defragmentation [ 94 ]. Paired embryos from the same patient, not intended to be transferred, were randomly placed in either the experimental group, assisted hatching and embryo defragmentation, or control group (assisted hatching alone). Paired embryos had no difference in mean cell number, percent fragmentation, and grade before randomization. Results showed that on day-5, embryos in the defragmentation group had significantly diminished fragmentation when compared with controls; however, there was no difference in compaction rate, morula formation rate or blastocyst formation rate. Embryo grade generally improved in the treatment group, but this was not statistically significant. Overall, in both groups, improved embryo development was significantly associated with lower levels of fragmentation in the day-3 embryos, supporting the idea that defragmented embryos maintain their reduced fragmented state throughout preimplantation development. Of note, this study had 35 embryos in each group and was limited to lower grade embryos not intended for transfer [ 94 ].

Another, larger prospective randomized study by Halvaei et al., compared the effect of microsurgical removal of fragments on ART outcomes. The authors divided 150 embryos with 10-50% fragmentation into three groups, case ( n =50), sham ( n =50), and control ( n =50). They found no significant difference in rates of clinical pregnancy, miscarriage, live birth, multiple pregnancies, or congenital anomalies between these groups, ultimately showing that cosmetic microsurgery on preimplantation embryos to remove CFs had no beneficial effect [ 95 ].

Lastly, a pilot study by Yumoto et al., aimed to decrease CF in developing embryos by removing the zona pellucida of abnormally fertilized (3PN) donated oocytes [ 96 ]. Although they did not attempt to remove fragments themselves, this study is included as ZP-free oocytes are sometimes encountered in or because of ART procedures, i.e., ICSI. The results suggest that the rate of fragmentation is decreased after mechanical ZP removal. The authors concluded that ZP is not always necessary for normal embryo development since the ZP-free embryos developed normally, maintained their cell adhesions, and had a decreased rate of fragmentation [ 96 ]. It seems that defragmentation of an aneuploid or severely fragmented embryo, only improves the embryo morphology grade but the quality and fate of embryo is not changed [ 97 ].

CF and chromosomal abnormalities in embryo

Although the relationship between DNA fragmentation and chromosomal abnormalities has been more commonly explored in the literature, CF may also be related to intrinsic chromosomal abnormalities in developing embryos. Fourteen studies included in this review explored this relationship (Table 9 ) [ 55 , 56 , 85 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 ].

CF was rarely seen in embryos with normal chromosomal content. Findikli et al., studied DNA fragmentation and aneuploidy in poor quality embryos by TUNEL and fluorescent in situ hybridization (FISH) techniques. Within seven chromosomally abnormal embryos, each had variable degrees of CF [ 98 ]. This study suggests that DNA fragmentation, being a sign of chromosomal abnormalities, may exist together with CF.

An earlier study by Munne et al., examined 524 embryos using FISH analysis for three to five chromosomes. While controlling for age, they divided the embryos into three groups: arrested, slow and/or fragmented, or morphologically and developmentally normal. They found that polyploidy was the most common chromosomal abnormality in the arrested embryo group and decreased with increasing embryonic competence, with 44.5% polyploidy in arrested compared to 2.1% in morphologically normal embryos. Maternal age was not associated with polyploidy rates, but aneuploidy significantly increased with maternal age in morphologically normal human embryos [ 57 ]. Another early study by Almeida and Bolton also examined the relationship between chromosomal abnormalities and embryonic developmental potential. They found that cleavage-stage embryos with poor morphology, defined as irregular shaped blastomeres with severe fragmentation, showed a higher incidence of chromosomal abnormalities than those with good morphology [ 100 ]. Magli et al., found a more direct relationship between chromosomal abnormalities and embryo fragmentation in a larger retrospective study of nearly 1600 embryos. There was a strong association between percentage of fragmentation and chromosomal abnormalities (monosomies and trisomies), where 90% of chromosomal abnormalities were found in embryos with greater than 40% fragmentation [ 101 ].

Another retrospective study comparing maternal age to embryo morphology and chromosomal abnormalities was conducted by Moayeri et al., By examining nine chromosomes in day-3 embryos, they found that morphology predicted chromosomal status in the advanced maternal age group (≥38 years old), but not in younger patients. Fragmentation alone predicted euploidy in both the advanced maternal age and younger groups. This suggests that cellular fragmentation may be a predictor of chromosomal competence and thus embryo developmental potential [ 102 ].

In contrast, Baltaci et al., examined 1,000 embryos and concluded that embryo morphology was not predictive of euploidy and that a considerable number of chromosomally abnormal embryos with good development potential may be selected for embryo transfer. They used FISH for five chromosomes and found that a large proportion of both normal and aneuploid embryos were evaluated as top quality (grade I). For example, 66% of chromosomally abnormal embryos were of good quality (grade I and II). They found no significant difference among aneuploid embryos when distributed by age. However, a higher embryo quality found in normal compared to aneuploid embryos [ 103 ].

In addition, Pellestor et al., compared the relationship between morphology and chromosomal abnormalities in two separate studies. The first study found that aneuploidy was the most frequently observed abnormality after cytogenetic analysis of preimplantation embryos [ 55 ]. They defined the quality of embryos as good (grade I and II) and poor (grades III and IV). There was an increased chromosomal abnormality in poor quality embryos (84.3%) when compared to embryos with good quality (33.9%). Both aneuploidy and fragmentation were shown to be predominant in poor quality embryos, whereas mosaicism and polyploidy were the most frequent abnormalities in good quality embryos [ 55 ]. Pellestor et al., also performed cytogenetic analysis on 411 poor-quality embryos (grade IV) [ 85 ]. Ninety percent of the successfully analyzed cases showed abnormal chromosome complements, with aneuploidy being the most frequently observed. These results further support that a large majority of poor grade embryos are chromosomally abnormal and ultimately offer low chance of reproductive success for either embryo transfer or cryopreservation [ 85 ].

A separate study by Chavez et al., combined time-lapse imaging with karyotypic status of blastomeres in the 4-cell embryo to test whether blastomere behavior may reflect chromosomal abnormalities, using array comparative genomic hybridization (aCGH), during early cleavage [ 56 ]. In time-lapse observations, a large proportion of aneuploid and triploid, but not euploid embryos, exhibited cellular fragmentation. They showed that the probability of aneuploidy increased with higher fragmentation and only 65% of the fragmented embryo would be expected to form blastocyst. Furthermore, all the aneuploid embryos with additional unbalanced sub-chromosomal errors exhibited CF. The authors concluded that although fragmentation alone at a single point in time does not predict embryo developmental potential, time-lapse imaging with dynamic fragmentation screening may help detect embryonic aneuploidy [ 56 ].

Two more recent studies also used aCGH to evaluate the association between embryo ploidy and fragmentation. Vera-Rodriguez et al., in a retrospective study, compared the rate of embryo aneuploidy between two groups of high (≥25%) and low (˂25%) fragmentation. They found that the rate of aneuploidy in high and low fragmentation was 62.5 and 46.3%, respectively. However, the difference was not statistically significant concluding that using degree of fragmentation alone is not suggested to predict the embryo ploidy status [ 107 ]. Minasi et al., in a case series evaluated 1730 blastocyst ploidy with aCGH. They showed that there is no significant difference between day-3 embryo morphology and embryo ploidy. However, the quality of blastocyst (inner cell mass grade, trophectoderm grade, degree of expansion) was associated with embryo ploidy [ 106 ].

In a recent meta-analysis, it was shown there is trend between degree of fragmentation and rate of aneuploidy [ 109 ]. A major source of controversy in both early and recent studies on aneuploidy and fragmentation is the variation in the methods and criteria used to evaluate these factors. One of the aspects that differ across studies include the technique for detecting aneuploidy; FISH vs aCGH. Recent studies have used aCGH to detect aneuploidy and found no clear relationship in this regard. Also, the quality of the matching between groups, the design of the study (retrospective vs prospective), the timing of the fragmentation assessment, the use of time-lapse imaging to monitor the fate of fragments are the other reasons for this discrepancy. There is still the lack of a clear cut-off point for the percentage of fragmentation to predict aneuploidy. Further powerful studies using new methods like next gene sequencing and tile-lapse systems are recommended to shed light on the relationship between fragmentation and aneuploidy.

The literature highlights that poor quality embryos have a higher incidence of chromosomal abnormalities. Notably, CF is rarely observed in embryos with normal chromosomal content. Technological advancements, such as TLM, offer promising avenues to enhance our understanding and detection of embryonic aneuploidy. Overall, these studies underscore the complexity of the relationship between fragmentation and chromosomal abnormalities, emphasizing the need for continued research to refine embryo selection strategies and improve reproductive outcomes.

Discussion and conclusion

The role of fragmentation in human embryo development and reproductive potential is widely recognized, albeit without standard definition nor agreed upon implication. While it has been shown that degree of fragmentation and embryo implantation potential are inversely proportional [ 5 , 7 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ], the degree, pattern, and distribution of fragmentation as it relates to pregnancy outcome is debated in the literature. Our qualitative synthesis of 60 articles related to the study of embryo fragmentation and reproductive outcomes highlighted some of the challenges in analysis of fragmentation, while revealing trends in our evolving knowledge of how fragmentation may relate to functional development of the human embryo.

While fragmentation is best understood to be a natural process across species, the origin of fragmentation remains incompletely understood and likely multifactorial. Degree of fragmentation has been plausibly correlated to sperm DNA oxidation [ 37 ], errors in division [ 37 ], mitochondrial distribution [ 45 ], and overall embryo quality [ 39 ]. However, some causes of fragmentation are based on outdated studies and require validation in future research with higher quality and more advanced techniques. While cause of fragmentation remains a focus of investigation, advances in technology have allowed for more detailed analysis of its effect on embryo development and reproductive outcome. At the cellular level, increased fragmentation has been shown to be associated with higher rates of apoptosis, necrosis, and programmed cell death of cleavage-stage embryos [ 60 , 61 , 62 ]. Given the recognized significance of fragmentation on embryo development, it follows that many studies have been focused on IVF and ART impacts on fragmentation, as well as determining quantitative reproductive outcomes. In terms of other influences on degree of fragmentation, patient age was not universally found to be significantly associated with fragmentation [ 7 , 70 , 71 ] although age is certainly known to influence embryo quality. Most studies included in the search criteria showed that ART such as ICSI do not significantly impact fragmentation rate in developing embryos [ 74 , 75 , 76 ]. Those studies that found significant differences in embryo grading either between conventional fertilization and ICSI either did not find a difference in implantation or pregnancy rate or did not study it, suggesting that ICSI is not a significant contributor to poorer ART outcomes by way of embryo fragmentation.

In synthesizing the available data on ART and pregnancy outcomes with varying degrees of embryo fragmentation, most included studies did find a negative impact of increasing fragmentation on reproductive success while severe fragmentation does appear to be associated with poorer implantation rate and clinical pregnancy rate. This association may be related to the observation that increased fragmentation at the cleavage-stage embryo is related to chromosomal abnormalities incompatible with ongoing development or pregnancy.

The reviewed studies have several limitations. There are different grading systems in use that may impact detecting and reporting the degree of CF. Different criteria and terminology used in different studies may in turn make the comparison of outcome measures difficult. Another factor is the distribution pattern of CF. There are two types of scattered and concentrated fragments with different prognoses that is not considered in grading systems. Therefore, due to the lack of a standard cleavage-stage embryo grading system, comparing different studies should be done with caution. In addition, evaluation of embryo fragmentation is mostly based on individual observation which is subjective and has inter- and intra-observer subjectivity leading to high variable results even if performed by an experienced embryologist [ 110 ]. TLM is considered as a non-invasive tool and evaluates the embryo quality continuously and without the need to remove the embryo from the incubator [ 111 ]. The use of this technology allows for the analysis of embryo morphokinetics and has advanced knowledge of the developing embryo. Recently, artificial intelligence (AI) including machine learning and neural network has gained popularity in various fields of medicine including IVF and embryology. Accuracy of AI in prediction of fragmentation has been studied with encouraging results [ 112 ]. Further advances in technology will promote the use of AI as a tool in defining the effect of fragmentation on human embryo development and reproductive potential.

Although the precise origin and the importance of external or iatrogenic factors on fragmentation of cleavage-stage embryos varies in the literature, there is more consensus regarding severe fragmentation worsening reproductive outcomes. Given this important pattern, and the availability of increasingly sophisticated embryologic technology, further research is warranted to characterize more completely preventative or rescue techniques to improve reproductive outcomes.

Availability of data and materials

No datasets were generated or analysed during the current study.

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Yazdani, A., Halvaei, I., Boniface, C. et al. Effect of cytoplasmic fragmentation on embryo development, quality, and pregnancy outcome: a systematic review of the literature. Reprod Biol Endocrinol 22 , 55 (2024). https://doi.org/10.1186/s12958-024-01217-7

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• Fragmentation
• Embryo development
• Implantation
• In vitro fertilization
• Pregnancy outcome

Reproductive Biology and Endocrinology

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Summer REU position with COASST (Coastal Observation and Seabird Survey Team)

The Coastal Observation and Seabird Survey Team has an open REU position for the summer, helping us assemble the elements for our new beached marine mammal guide. This position will work as part of an in-office team, completing duties related to the preparation and development of a new COASST marine mammal guide.

The position will begin on June 17 and last until September 13th, with some flexibility for time off or vacation. The REU project stiped is a total of $10,000, dispersed over the summer quarter. Expected working hours are ~40 hours/week (full time), in person at the Fisheries Building (COASST offices, FSH 254).

Major projects:

• Query COASST marine mammal photo database for carcasses of all target species in a variety of conditions. Sort them according to the Level A carcass condition scale. Index and organize for easy retrieval. Train interns to support this ongoing task.
• Determine which National Stranding Network photos are needed to “fill gaps.”
• Search the web for photos of all target species as beachcast carcasses, and “fill gaps” with finds as appropriate.
• Create a database (e.g., Zotero) of all publications.
• Create a flat file (e.g., Excel file) of all measurements and identification characters, with one sheet per species. This work will build upon previous work by COASST.
• Stranding Network Data: assemble measurements data from stranding network database for target species carcasses found in “COASST relevant” locations.
• Experts: from the literature review gather names/contact information for local experts (West Coast and Alaska) from across multiple sectors (tribal, government, academic, stranding network) who should be invited to participate in co-design workshops.
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• Use library search tools to find existing research
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• Present results of research to other members of the team

Position Requirements: in-progress undergraduate degree; experience with Microsoft Office Suite including Excel/Spreadsheets.

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