Calling all researchers in tuberculosis

By Christine Ferguson
Posted: March 11, 2013
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Editors are sometimes asked while out and about in the community, why it is that we attend conferences. Most folk presume we’re there to gather material, perhaps to write up a meeting report for the journal.  For conference-going PLOS Biology editors, meeting reports are not really on our agendas (since at PLOS Biology, we  don’t routinely publish these), but we’re certainly there to gather information: about the topic (what’s new, trending, old news) and about the community (who’s who; who would be well-placed to review articles in this field; who could write a fabulous Essay or Unsolved Mystery for our magazine section; and who could bring their wisdom and charisma to our editorial board – which, incidentally, we’re striving to diversify).

We’re also there to spread information about what we’re doing at PLOS and about what our journals can offer you. I’d like to start this conversation here, ahead of attending the joint Keystone symposia on tuberculosis, which are due to take place this week at the mountain resort of Whistler in Canada.

Since the last double-billed Keystone meeting on Tuberculosis (TB) in January 2011, PLOS has published 702 papers on tuberculosis – as copyright for these articles remains with the authors, and since they were published under the CC-BY licence, these articles are free to access and to reuse, as long as the authors are credited. While each of PLOS’ seven journals published a proportion of these, 608 papers appeared in PLOS ONE, which is now the largest journal in the world.

Below is a flavour of the breadth of PLOS Biology’s coverage in this field:

Metabolic Regulation of Mycobacterial Growth and Antibiotic Sensitivity by Seung-Hun Baek, Alice H. Li, Christopher M. Sassetti (2011)

Human Mucosal Associated Invariant T Cells Detect Bacterially Infected Cells by Marielle C. Gold, David M. Lewinsohn and colleagues (2010)

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography by Ruth Hershberg, Sebastien Gagneux and colleagues (2008)

You’ll notice that the wider range of articles at PLOS Biology reflects the reach of this month’s Keystone symposia to include host immune responses to bacterial pathogens,  disease ecology, bacterial genetics, bacterial physiology and systems biology.

 

SEM of Mycobacterium tuberculosis bacteria. Photo credit: Janice Haney Carr at the CDC

Tuberculosis research is a field we deem to be of particular importance and broad impact and is one that warrants publication in an open access journal, such as PLOS Biology. We’d like to publish more TB-related papers than we do currently, and as such we invite you to submit your best work to us.

What can we offer you in return?

We can offer you the combined strength of two successful editorial models: the services of a team of professional staff editors, who bring to the table an impressive number of collective years of scientific training, and editorial experience to support a consistent, thoughtful, ethical and collaborative editorial process. We work in partnership with practicing scientists on our Editorial Board, who have been selected for their standing and experience in their fields. Together, we screen submissions to identify those with potentially significant findings for the field and we work to pursue the best-placed reviewers to assess the impact and strength of these select studies. Our partnership with academic editors ensures that requested revisions are limited to the essential and that decisions are fast and fair.

Beyond ensuring that your paper is published with a license that accredits you as the author and provides every opportunity for reuse, every published manuscript is accompanied by an author summary that is written with the non-specialist scientist in mind and that is edited carefully by the editorial team.  We also select the most noteworthy papers to feature in a synopsis that is commissioned from a professional science writer, or in a primer written by an expert in the field. After publication, PLOS tracks the impact of your paper on the community and presents real-time article-level metrics that reflect downloads, social media interest and citations.

As one of the editorial team who handles TB-related submissions for the journal, I will be attending the forthcoming Keystone meeting on TB.  I’d be pleased to meet you there and to talk with you about work you are ready to submit, or if you are interested  in joining the PLOS Biology community as a reviewer, editorial board member or blogger.  Please contact me at the Biologue email address (biologue[at]plos.org). If you are planning to attend the meeting, be sure to pick up one of our few remaining 2013 PLOS Biology calendars featuring our favourite issue images.

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Molecular movements drive bacterial signaling

By Roli Roberts
Posted: February 28, 2013
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It’s a tough world out there, and just like us, bacteria need to be able to sense their environment in order to respond to it in a way that enhances their chances of survival. And because they’re cozily wrapped in a largely impermeable membrane, they need a system to transmit external information into the cell where it can be interpreted and acted upon.

One of the classic bacterial sensory systems is the so-called two-component system (TCS), where one protein (the sensor histidine kinase, SK) transmits chemical information across the membrane, and another (the response regulator, RR) turns that signal into the appropriate action (swimming, biofilm formation, spore formation, and so on). I’m not going to be talking about the RR here (it’s the arrow labeled “output” in the Figure), but we are going to take the SK apart because two papers published in PLOS Biology this month give us important insights into how it works.

The SK has several discernable modules to it. The first is an external domain that receives the input signal from the environment – this might be a nutrient in the case of chemotaxis, or a signal from one of its brethren in the case of quorum sensing. At the opposite end is a histidine kinase domain that generates the output information (in the form of a phosphate tag) to be passed to the RR. And between them lies a transmission system that connects the two. Somehow these all collaborate, enabling the recognition of a tasty morsel – or a bacterial party atmosphere – to trigger the marking of the RR with a phosphate flag.

Two papers in this month’s issue of PLOS Biology tackle the conformational changes involved in bacterial signal transduction (elements of Figure derived from Wang et al. and Airola et al., PLOS Biology 2013).

Just published in PLOS Biology is a paper by Chen Wang, Aidong Han and colleagues that gives us the detailed structure of almost the entire intracellular portion of a pair of SK molecules, namely the transmission and output modules (this is what I’ve used to make the left-hand part of the Figure). And although this is a static snapshot of the system, the authors have been able to use it as a starting point for mutating it to test how it responds to a signal.

The structural study shows the SK to be a long bundle of rods protruding into the cell from the membrane, and their data (including a pronounced asymmetry) suggest that in response to some sort of structural change triggered by the environmental input, a series of tightly coordinated movements occur within the SK molecule pair. A normally straight helix in the DHp region buckles, and the catalytic head of the molecule swings right round, gluing a phosphate onto the rod – this is the signal that’s then passed on to the RR as the output. The authors suggest that the two catalytic heads of the two molecules do this one after the other to fully activate the system (see bottom right of the Figure).

But what is the movement that triggers this pas de deux? This is where the second PLOS Biology paper, by Michael Airola, Brian Crane and colleagues, comes in (together with a Synopsis by Richard Robinson). They look in detail at the HAMP domain – the crucial part of the transmission system that lies closest to the membrane.

There’s been previous speculation that HAMP domains might be able to exist in two distinct conformations, one signalling “on” and one signalling “off”, and Airola and colleagues manage to demonstrate that this is indeed how they work. The presence of a signal outside the cell causes the HAMP domain just inside the cell to click from one state to the other (these are the blue and gold structures either side of the double-ended arrow in the Figure). Niftily, the authors were then able to use mutations to tweak the HAMP domain, changing its sensitivity and even flipping its logic to reverse the “on/off” response.

Together these papers contribute static and dynamic pictures to our understanding of how SKs work, and as the HAMP domain is a key component of tens of thousands of known signalling proteins across the tree of life, the clarification of how they work has potentially wide-ranging significance beyond SKs.

 

ResearchBlogging.org

Wang, C., Sang, J., Wang, J., Su, M., Downey, J., Wu, Q., Wang, S., Cai, Y., Xu, X., Wu, J., Senadheera, D., Cvitkovitch, D., Chen, L., Goodman, S., & Han, A. (2013). Mechanistic Insights Revealed by the Crystal Structure of a Histidine Kinase with Signal Transducer and Sensor Domains PLoS Biology, 11 (2) DOI: 10.1371/journal.pbio.1001493

ResearchBlogging.org

Airola, M., Sukomon, N., Samanta, D., Borbat, P., Freed, J., Watts, K., & Crane, B. (2013). HAMP Domain Conformers That Propagate Opposite Signals in Bacterial Chemoreceptors PLoS Biology, 11 (2) DOI: 10.1371/journal.pbio.1001479

Robinson R (2013) A Little Switch: Alternative Domain Conformations Control Bacterial Flagella Rotation Direction. PLoS Biol 11(2): e1001480. doi:10.1371/journal.pbio.1001480

 

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Bacterial Evolution – The Movie

By Roli Roberts
Posted: February 21, 2013
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Recent advances in sequencing technology have brought us the complexity of microbial metagenomes from oceans, soils and guts. These massive datasets of the combined genome sequences of hundreds or thousands of cohabiting bugs are presumably capturing a mere snapshot from an incredibly dynamic interplay between mutating, competing and adapting populations. How can we hope to tease apart these tangled banks?

A research article by Matthew Herron and Michael Doebeli just published in PLOS Biology steps back and gives us, instead of a snapshot, a set of three sixteen-frame high-definition movies of one of the simplest ecosystems conceivable. And the daunting complexity it reveals raises questions about our ability to comprehend, from metagenome data alone, what on earth is going on in wild bug populations.

As time pans from left to right, green glucose lovers and blue acetate addicts emerge from the gold ancestral population (Herron & Doebeli, PLOS Biology 2013).

The study uses frozen samples (the “fossil record”) from an old experiment in which Doebeli and colleagues allowed ten E. coli populations to evolve for 1200 generations in a mixture of two tasty nutrients – glucose and acetate (think sweet and sour sauce). Under these conditions it had been found that each initially uniform population reproducibly evolved into two separate communities, each adapted to its own niche – one that efficiently burns glucose, and another that’s less efficient but can switch to running on acetate. Here they take three of those ten experimental populations and throw next-generation sequencing technology at them, generating detailed metagenome sequences for each population over sixteen timepoints.

Many fascinating things emerge from this analysis, and in fact the best way into Herron and Doebeli’s study is probably to read the superb (and very accessible) accompanying Primer by Christopher Marx. But for me, the striking thing is that these three evolutionary movies are so similar (see the above images) – the actors are given only their starting positions, but in each case the action unfolds in a spookily stereotypic way. The same genes mutate in the same order, and often with the same mutations. Genotypes vie with each other, but no bug ever wins out, and a handful of crucial mutations can make a single species behave like two unrelated ones, each in its own niche. You’re left with the impression that despite the potential complexity, what emerges is a surprising degree of predictability or reproducibility in the evolutionary path – a triumph of determinism over happenstance?

So although it’s rather sobering to look at the complexity that can arise spontaneously from this simple experimental premise, and then to gaze helplessly on the slew of data from a single snapshot of a wild microbial ecosystem, the reproducibility does remind us that, like Hollywood, evolution has its motifs and tropes that may be replayed time and again. 

Marx, C. (2013) Can You Sequence Ecology? Metagenomics of Adaptive Diversification. PLOS Biology, 11 (2) DOI: 10.1371/journal.pbio.1001487

 

ResearchBlogging.org

Herron, M., & Doebeli, M. (2013). Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli PLoS Biology, 11 (2) DOI: 10.1371/journal.pbio.1001490

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Improving Data Access at PLOS

By John Chodacki
Posted: January 30, 2013
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In this guest post, John Chodacki, Director of Product Management at PLOS, shares PLOS’ recent advances in improving data access.

As part of our broader commitment to open access in scholarly communications, PLOS continues its efforts to drive towards openness in data use and re-use. Data access and sharing is paramount to the continued progress of research: replicating, refining, and building off previously established insights. Theo Bloom has shared this vision – the rationale, background, and overarching plan – in a previous piece, “Dealing with Data,” in PLOS Biologue.

PLOS continues its formal partnership with Dryad, an open access repository of data underlying peer-reviewed articles.  We established the integration of PLOS Biology with Dryad last July and are now extending it to PLOS Genetics.  Through this partnership, we can provide the research community seamless access to the underlying data alongside the final research output itself.  Dryad takes data “packages” associated with published articles and makes them freely available with a unique identifier (DOI).  Authors can also upload subsequent versions of their data (clearly indicated), as well as having download statistics for each data package.  To strengthen the review process, editors and reviewers are given confidential access to the data associated with articles under review.  The Dryad integration will launch soon in PLOS Genetics, and we plan to continue with other PLOS journals throughout the year. By providing an open access permanent repository for the data associated with publications, Dryad provides our journals with an important additional route to data sharing.

PLOS journals have always had a system to make it particularly easy for the figures and tables published in our articles to be re-used: we assign and register DOIs in a comprehensive manner for all figures across all PLOS articles. Now, we are pleased to say that all “Supporting Information” files are also included in the DOI registration effort and all such files in all our journals will receive a DOI at the time of publication.  Although the community’s ongoing critiques of data sharing through supplementary files are germane, this material currently remains an important part of the documentation that tells the research “story” to date.  As such, it remains important to ensure that such files have a reliable, persistent link online ensuring access to all parts of the content over time.

We have also established a new partnership with figshare to make the figures published in our articles more accessible and discoverable.  In the initial rollout, we will introduce a figshare widget that will display the contents of Supporting Information files, no matter the file type, directly in the article.  This encompasses dataset, text, documents, animated, video, and presentation files.  Our collaboration with figshare enhances usability by enabling users to manipulate the material in ways not supported before: search through the contents, magnify images for closer inspection, and download files singly or as a package.  “PLOS believes in making data as visible and useful as possible,” said Kristen Ratan, Chief Publishing and Product Officer. “Partnering with figshare is an important step in increasing the accessibility of the data associated with our research articles.”

We have many more plans in progress this year that will further realize our commitment to data access and sharing.  These developments include: continued integration of PLOS journals with Dryad, dedicated search support of figures with the introduction of a figshare portal for all PLOS figures, and expansion of partnerships with other entities that support open data. Watch this space for more from us, and please do let us know what you think of how we’re doing.

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Let’s Make Those Book Chapters Open Too!

By PLOS Computational Biology
Posted: January 23, 2013
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Following the launch of ‘Translational Bioinformatics’, a PLOS Computational Biology collection presented as an online book, in December 2012, PLOS Computational Biology Founding Editor-in-Chief Phil Bourne discusses how open access can boost the availability and prominence of book chapters.

As authors, many of us have had less than satisfactory experiences in writing book chapters as part of a themed volume, or textbook that, when published, are expensive, inaccessible and cited and used infrequently through lack of availability [1]. It could even be argued we write them from some sense of obligation and need, but do not put our best science and efforts into them because we know they won’t be read and hence cited. Putting that thought aside, let’s just say that a lot of good science goes underutilized. Some finds its way into journal reviews and journals that specialize in such content, for example the Elsevier Current Opinions series, but much languishes. I, many of the PLOS editors, and the PLOS management have long wanted this situation to change; well now it has.

Phil Bourne

The value of themed hardcover volumes and textbooks was understandable in a purely print era. An era during which we frequented the library more, which is where these volumes resided, being too expensive for individuals to purchase. These volumes make no sense today in a digital, open-access world. We are proud to report that PLOS Computational Biology has taken the first steps to address this nonsense. Translational Bioinformatics, edited by Guest Editor Maricel Kann and Education Editor Fran Lewitter, is the first complete PLOS “book” that can be accessed online as individual chapters or downloaded as a complete volume. An ePub version is now available too. The content is indexed, each chapter has a Digital Object Identifier (DOI) assigned and hence is resolvable (i.e., uniquely findable), and is indexed in PubMed and available as full text from PubMed Central, like all PLOS content.

Translational Bioinformatics can be used as a reference guide or textbook, and includes exercises. After review, the authors have had their hard work rewarded through a PLOS citation and greater accessibility to their work. The book uses the PLOS collection feature to bring the content together into a single entity while retaining the individuality of each article.  While we regard this as an important step forward it does raise some questions.

The first question is who pays? Obviously we are strong proponents of open access, but also the first to admit there must be a business model if open access content is to be persistent. Certainly most of us have never made any money from writing specialized book chapters contributed to a volume, but would we pay a modest amount to have them published open access? This remains an open question at this time. PLOS met the cost of publishing Translational Bioinformatics, but if this approach to book chapters were to take off, someone will have to foot the bill. At this time PLOS are interested in furthering this cause and, as with all front matter within the Education Section of the journal, book chapters are not subject to publishing fees. If the demand becomes too great we will need to revisit this. Support for chapter content would seem an opportunity for a wonderful contribution by an individual philanthropist or foundation in furthering scientific dissemination.

The second question is what quality of review do we require of chapter content? In general terms solicited book chapters do not undergo the level of review found in a research article.  Unless the content is terrible, the editors soliciting the material are hard pressed to reject it having persuaded the authors to write it in the first place. Good editors, as we have here, will provide the level of review found in a research article. Moreover, with greater exposure and article level metrics (ALMs) applied to each chapter, the content will rise or fall on its own merits and the end result will likely be higher quality content than we have traditionally seen from book chapters. With regard to PLOS Computational Biology specifically we regard this book content as front matter in the Education Section and as such it has had significant review. We will be revisiting the issue of review, and indeed all aspects of the scope of our support for chapters, as demand increases.

Image Credit: PLOS

The third question is what do we lose and gain in an online book? Of course there are the obvious issues, now long debated, regarding eBooks versus physical books and there is no need to revisit those issues here. What are worth visiting are the specific issues surrounding a book publication by PLOS, an organization which is currently set up to operate as a journal publisher.  PLOS have been wonderful in making this project happen and paving the way for more through the notion of collections. Collections do present challenges when used to represent a book. For example, the collection has no ISBN or other book-like identifier defining the citation; books have editions whereas there is no notion of versioning in a collection. On the positive side the collection can become a dynamic entity, such that new chapters (with their own journal-like citation) can be added to the collection at any time.

Open questions there might be, but an exciting time nevertheless, with PLOS continuing to push the envelope regarding scholarly communication. Over time we will sort this out, but in the meantime enjoy Translational Bioinformatics, a new innovation in open access publishing.

[1] http://blogs.lse.ac.uk/impactofsocialsciences/2012/08/29/how-to-bury-your-academic-writing/

Acknowledgments: Thanks to Maricel Kann and Fran Lewitter for editing a fine volume. To Editor-in-Chief Ruth Nussinov for useful input and to PLOS staff, Rosemary Dickin, Laura Taylor, Clare Weaver, Theo Bloom and Kristen Ratan for making it happen. This blog post will be published as an Editorial in the February issue of PLOS Computational Biology.

Philip E. Bourne is a professor of pharmacology and Associate Vice Chancellor for Innovation and Industrial Alliances at the University of California San Diego, the co-founder of SciVee.tv, and Founding Editor-in-Chief of PLOS Computational Biology.

If you’d like to share your feedback on this post, please add a comment below.

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PLOS Biology in the Media

By Bryan Ghosh
Posted: January 21, 2013
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The holiday period was a rather busy time at PLOS Biology, with a number of our published articles receiving significant attention both in the news and in social media.  Below you’ll find a quick summary of the three articles that people have found the most fascinating, along with a run-down of some of the reaction that they’ve received.

Sesame Street helps to reveal patterns of neural development

On January 3rd, PLOS Biology published this article by Jessica Cantlon and Rosa Li, detailing a study in which brain scans of children who watched Sesame Street proved to be better indicators of intellectual development than the standard, less naturalistic tests normally used in fMRI scans.  In the study, the authors used fMRI to create ‘neural maps’ of the thought processes of children and adults who watched a 20-minute Sesame Street video, and found that they could better predict IQ scores from these than from similar scans taken using the traditional tests.

The article was accompanied by a synopsis written by Janelle Weaver, and provoked a great deal of interest in the media, such as from TIME Magazine and CNN Blogs.  The Huffington Post featured both an article and a blog about the paper; the latter focusing on how the study can further our understanding of children’s varied rates or learning.

Although the study does not advocate television, it does show that “neural patterns during an everyday activity are related to a person’s intellectual maturity,” explains Professor Cantlon. “It’s not the case that if you put a child in front of an educational TV program that nothing is happening—that the brain just sort of zones out. Instead, what we see is that the patterns of neural activity that children are showing are meaningful and related to their intellectual abilities.”

The factor that could influence future breast cancer treatment

On December 27th, PLOS Biology published a research article by a team of scientists led by Chris Ormandy, in which the authors showed that the transcription factor ELF5, which is found in all breast cells, may be responsible for increasing breast cancer cells’ resistance to anti-estrogen therapy.  The obvious implications for health care and cancer treatment meant that this paper was very widely received, with a Reuters article being picked up by the Huffington Post and NBC News among many others. It also gained particularly extensive coverage in Australia, including this broadcast on ABC Radio.

Disease burden links ecology to economic growth

The Raja Ampat Islands in Indonesia are thought to have the greatest marine diversity on earth. Image: PLoS Biol 10(12): e1001457. doi:10.1371/journal.pbio.1001457

Another article published December 27th, by Matthew Bonds et al., showed how vector-borne and parasitic diseases have substantial effects on economic development across the globe, and are major drivers of the latitudinal gradient in income.  In addition, and perhaps counter-intuitively, the burden of these diseases is predicted to rise as biodiversity falls.  It was also accompanied by a synopsis written by Jon Chase, and featured in news outlets such as NPR and the LA Times as well as being discussed heavily in social media.

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Working to increase diversity of PLOS Biology Academic Editors and Advisory Board members

By Jonathan Eisen
Posted: January 16, 2013
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In the last few years I have spent a lot of time thinking about, and worrying about, the diversity of people involved in various aspects of the life sciences.  One area I have focused on extensively has been presenters at conferences (see some of my posts on this topic on my Tree of Life blog here).  In one recent online discussion about a conference I felt was heavily biased towards male speakers, a responder said something to the effect of “Oh yeah, well, what about the diversity of Editorial Board and Advisory Board members at PLOS Biology?”  And, well, they were right.  We do in fact have a less than ideal sampling of diversity there.  Two aspects of diversity in particular are, I think, in need of work – representation of women, and international coverage.  So as the new Chair of the PLOS Biology Advisory Board, I have decided that working on this diversity issue will be my main first task.

Fortunately for me, the PLOS Biology team has been not only very receptive to tackling the diversity issue, but has already been developing a plan to tackle it for some time.   Our goal for now is relatively simple – increase representation of women and people not from the US on the PLOS Biology Editorial Board and Advisory Board activities.  A key question however is – how do we achieve this goal?  To answer this it is necessary to figure out where the bottlenecks are in representing diversity in these groups.

Clearly, one possible bottleneck lies in invitations to join the Editorial Board and Advisory Board.  The path to becoming a member of the PLOS Biology Editorial Board is relatively simple – the PLOS Biology Editorial team invite new people to serve as Guest Academic Editors (so called Guest AEs) for a few papers.  If they do “well” then they can then be invited to be official Editorial Board Members.  So – we plan to do targeted Editorial Board recruitments to increase the diversity of people invited to be Guest AEs.   For the Advisory Board, the approach is somewhat similar – the PLOS Biology Editors identify what one could call “Super” AEs (labelled as such due to their workload and general commitment to the journal, often going beyond the normal call of duty of Editorial Board members), and these people are invited to join the Advisory Board.  We also plan to do targeted recruitments to increase the diversity of those invited to be on the Advisory Board.

But of course, just inviting people is not enough.  One needs to get people to (1) hear or see the invitations; (2) to consider the invitations seriously; and (3) to accept them.  In my experience in dealing with diversity issues at conferences, it seems that #1 and #2 are actually quite challenging.  People are overwhelmed with email and meetings and schedules and responsibilities.  So if you just send out a bunch of email invitations to a few extra people, if you only hear back from a small % of people you invite, this may not be too useful.  Same with the Editorial Board I suppose.  An email that says

“Dear Dr. So and So.  We are inviting you to take on a new responsibility that involves extra work for you.  In exchange we can offer you no payment and little recognition”

is probably not going to excite some of the key people you want to get involved.  So some more personal contact is almost certainly going to help.  This of course takes time, and some effort.  But it is probably worth it.  Fortunately, PLOS Biology is relatively unique in the biology journal world in that the Editorial Board members do little if any of the “grunt work” and can focus on the science.  The PLOS Biology Editors handle the main tasks of screening submissions, recruiting Editorial Board members to serve as Academic Editors, and making recommendations for reviewers.  The job of the Academic Editors is to advise the staff on whether a paper should be reviewed, and who good reviewers might be.  But the invitations to review and the chasing down of reviewers is done by the  journal staff.  Then, when reviews come back in the PLOS Biology Editorial team read through them, summarize them, and make a recommendation for what to do next.  They then consult with the Academic Editors to get their input on the reviews and the recommended course of action.  It is actually a relatively pleasant experience for AEs, to tell you the truth.  If more people knew how this worked, I have a feeling that more would say yes to invitations to be on the Editorial Board (some more detail on the process is available here: From Academic Editor in Chief to Chair of the Advisory Board: figuring out an official role for me (Jonathan Eisen) at PLoS Biology).

Plus of course another way to get people to say yes is to tell them that there are free to say no for specific requests whenever they are too busy.  What you want is for people to want to help you, not to feel they have to help you.  In the end, my goal as the Chair of the Advisory Board is to have PLOS Biology serve as a model for strong representation of diversity on its various Boards.  This may take some work, but it is important work.

And while I am at it, I think I would like to crowdsource this activity by asking for others to help.  Do you know strong open science advocates who are also good scientists who might be interested in getting more involved?  Are you perhaps such a person?  Send me / us the names and any other information by email or post comments here.

Finally, I want to add, that I realize that simply increasing the number of women and international representatives on the various PLOS Biology Boards is not the only aspect of diversity that we can or should tackle at PLOS Biology.  But it is a start.  And part of the start is to be more open about discussions of these issues.  In that regard, if any readers have experience with ways to increase diversity in STEM (science, technology, engineering, and mathematics) fields, or for that matter, other areas of academics,  it would be great to hear about it in comments.

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Translational Bioinformatics: PLOS Computational Biology presents an educational resource for an emerging field

By PLOS Computational Biology
Posted: December 28, 2012
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PLOS Computational Biology is pleased to announce the launch of a new collection of Education articles:  “Translational Bioinformatics”. This collection is presented as an online “book” which could serve as a reference tool for a graduate level introductory course, marking a step in an exciting new direction for the Education section of the journal.

Image Credit: PLOS

Translational bioinformatics is an emerging field that addresses the current challenges of integrating increasingly voluminous amounts of molecular and clinical data.  Its aim is to provide a better understanding of the molecular basis of disease, which in turn will inform clinical practice and ultimately improve human health. In the Introduction of the collection, Russ Altman highlights some of these challenges and the role of translational bioinformatics in resolving them, defining the field as “the development and application of informatics methods that connect molecular entities to clinical entities”.

As can be seen just by looking at the content of this collection, the field of translational bioinformatics encompasses a wide range of topics including pharmacogenomics, medical genomics and human microbiome analysis. In each of the 14 chapters, leading experts in the field focus on one of these key topics, providing a solid introduction for those new to translational bioinformatics. Like all other PLOS articles, chapters in this open-access collection are freely available to everyone for reuse and redistribution, for example as course materials. Notably, the authors have created exercise questions for each chapter, which could be used by students or other interested readers to test what they’ve learned. Answers to these exercises can be found in the supporting information. This is just the start though, as translational bioinformatics is a rapidly growing area, and publishing this resource as a PLOS Computational Biology collection will enable us to develop the content as the field develops.

The idea to create a collection in the format of a book was first conceived when Maricel Kann, Guest Editor of the collection, approached the journal earlier this year. Since then, Maricel, along with our Education Editor Fran Lewitter, has spearheaded the project and their hard work has created the resource you see today. A PDF of the full collection has been created, which you can download here. This has been an exciting new project to work on and Phil Bourne, Founding Editor-in-Chief of PLOS Computational Biology, keenly anticipates its role in marking a change in the accessibility of educational materials:

“The era of writing those time-consuming chapters that typically form mini-reviews in an expensive, little read book, are over. As PLOS Computational Biology publishes its first book in the form of an open-access collection, complete with exercises and answers, a new era begins: an era of wide distribution and access to important science for everyone. “Translational Bioinformatics” edited by Maricel Kann is a fitting beginning – an important “book” with excellent contributions from leading authors in a rapidly growing field. Thanks go to Maricel for her energy in pushing this, to Education Editor Fran Lewitter and the PLOS staff for making this happen, and to PLOS for continuing to push the envelope on making science accessible to all.”

By Laura Taylor

You can visit the collection at: www.ploscollections.org/translationalbioinformatics

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Category: Bioinformatics, Biology, Education, Open access, PLOS Computational Biology | 4 Comments

Algal Ancestor Shows How Deadly Pathogens Proliferate

By Rachel Jarmy
Posted: December 14, 2012
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Long ago, when life on our planet was in its infancy, a group of small single-celled algae floating in the vast prehistoric ocean swam freely by beating whip-like tails, or flagella. Now, over 800 million years later, these organisms have evolved into parasites called Apicomplexa, but are better known as the parasites that cause Malaria and Toxoplasmosis—serious diseases that infect millions of people every year, particularly in the developing world.

Now their algal past in the ocean may be the key to stopping the spread of these diseases, and is explored in the recent PLOS Biology article by Francia et al, and also in the accompanying synopsis by Stephanie Huang.

 

 

Parasite cell division depends on a fiber that once anchored the basal body of the flagellum in the algal ancestor. Here, you see the fiber (green), centrosomes (red), parasite daughter cells (blue), and nucleus (grey). The micrograph on the right depicts two Toxoplasma gondii parasites in division.
doi:10.1371/journal.pbio.1001445.g001

Professor Boris Striepen and colleagues from the University of Georgia explain in this paper how an important structure inside these parasitic cells, which evolved from the algal ancestor millions of years ago, allows the cells to replicate and spread inside their hosts. Their research may lead to new therapies to halt these deadly pathogens before they cause disease.

In their study, the researchers demonstrate that during the process of replication, and spreading the infection throughout the body, the parasite cell loads genetic material into its daughter cells via a strand of fiber that connects the two. By altering the genes for the components of this fiber in the laboratory, the researchers discovered that they could prevent parasite replication, rendering the parasite essentially harmless.

“These altered parasites can initially infect cells, but once we turn off the fiber genes, they cannot create new daughter cells and spread,” said Maria Francia, lead author of the study. “Since it cannot replicate, the parasite eventually dies without causing serious harm.”

This replication fiber appears to have evolved from the flagellum that enabled ancient algae to swim.

“This was a surprising finding,” said Boris Striepen. “These parasites no longer use flagella to swim, but they have apparently now repurposed this machinery to organize the assembly of an invasive cell”.

A blood smear showing red blood cells and two crescent- or sausage-shaped malaria parasites. Image from The Centers of Disease Control and Prevention as part of the United States Department of Health and Human Services.

The findings of this new research are also the topic of an accompanying PLOS Biology synopsis, by Stephanie Huang, which highlights the importance of the research with regards to the current difficulties in treating malaria and toxoplasmosis. First, the parasites are eukaryotic and thus more similar to human cells than bacterial pathogens, making it difficult to find treatments that kill the parasite without harming human host cells. Second, the parasite cells reside within human host cells for much of their life cycle, evading detection by the host’s immune system.

“It is extremely important to understand the evolution of different organisms, but especially the evolution of pathogens,” Striepen says. “The analysis of their evolution produces important opportunities to develop treatments, but it also helps us understand the basic structures of the pathogens that we must fight.”

 

Maria E. Francia,, Carly N. Jordan,, Jay D. Patel,, Lilach Sheiner,, Jessica L. Demerly,, Justin D. Fellows,, Jessica Cruz de Leon,, Naomi S. Morrissette,, Jean-François Dubremetz,, & Boris Striepen (2012). Cell Division in Apicomplexan Parasites Is Organized by a Homolog of the Striated Rootlet Fiber of Algal Flagella PLOS Biology : 10.1371/journal.pbio.1001444

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ASCB Annual Meeting 2012: An invitation from PLOS Biology

By Jane Alfred
Posted: December 12, 2012
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An evening with PLOS Biology and PLOS ONE

If you plan on attending the American Society for Cell Biology 2012 Annual Meeting in San Francisco, you are invited to a reception with PLOS Biology and PLOS ONE.

Join us for food and drinks, and for talks and discussion on an issue of core interest to the cell biology community – data.

Speakers:

Emma Ganley, Senior Editor, PLOS Biology
Data, Open Access All Areas

Jason Swedlow, Co-founder, Open Microscopy Environment (OME)
The Open Microscopy Environment: ‘Open Image Informatics for Data  Access, Sharing, Analysis, & Publication’

Venue:         The Box SF

Date:          Tuesday, December 18, 2012

Time:          6 PM — 8 PM

RSVP:        http://scibar.eventbrite.com

Register soon while we have availability!

Meet the Editors

If you are unable to attend the reception, please visit us at booth 1322 during exhibit hours and/or at our Meet the Editors event.

Event:        Meet the Editors
(Deputy Editor, Jane Alfred; Senior Editors, Emma Ganley and Ines Alvarez-Garcia)

Place:        Booth 1322

Date:          Sunday, December 16, 2012

Time:          Noon – 2 PM

We hope to see you there!

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