PLoS ONE Review of 2009

[By Peter Binfield, Managing Editor - PLoS ONE  |  originally posted at Everyone - PLoS ONE community blog]

'It was on Dec 20^th, 2006 that PLoS ONE launched, and 2009 (only our third full year of publication) has been packed full of exciting developments.  To note our birthday, I took the opportunity to round up the major events of the past 12 months. There have been an awful lot of them and it is a tribute to our staff and academic editors that we were able to achieve all of the following while increasing our publication volume from 2,726 articles published in 2008 to 4,400 expected in 2009 (something which, we believe, now makes us the third largest journal in the world, by publication volume).

The start of the year saw us developing new functionality, with the launch of Collections on PLoS ONE. This began with the publication of the ''Stress-Induced Depression and Comorbidities'' Collection in January, followed by our second in February – the  PLoS ONE Paleontology Collection. We subsequently launched the Prokaryotic Genome Collection in June and the Structural Genomics Consortium Collection in October (a collection which provides 'enhanced versions' of papers, incorporating advanced 3D interactive simulation software – an excellent example of the creative re-use of Open Access content).

In March, we launched everyONE, our community blog site; we announced our ability to accept LaTeX submissions; and we upgraded our site with a redesigned 'tabbed' user interface to accommodate our newly launched Article-Level Metrics functionality (of which more later).

In April, we announced our ''Blog Post of the Month Competition'' (in collaboration with researchblogging.org) which has since gone on to award a winner every month.

In May, we redesigned our email Table of Contents alerts so that recipients now receive an email categorized by subject area, and this was also the month in which we publicly thanked the 9,000 peer reviewers who gave us their expert opinions during 2008.

Our 2009 media coverage will be reviewed by Bex in a different post, but in May we published a paper that sparked our largest media story of the year – the Darwinius masillae (or 'Ida') paper – "Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology". The coverage of this paper was overviewed in three separate blog posts.  

May also saw a major event in the development of PLoS's technology platform – with the migration of PLoS Biology and PLoS Medicine, we were finally able to have all seven of our titles on Topaz, which is now our shared online platform.

In July, we began a partnership with DeepDyve to improve our search capabilities and we also launched the "Worth a Thousand Words" blog series (featuring a selected image from each week's publications). July also saw PLoS publicly express our opinion that there is more value in measuring impact at the article level than at the journal level – something which coincided with the announcement that we would no longer be promoting Impact Factors on our sites.

In August, PLoS ONE was featured in the popular internet comic, "PhD Comics" as part of their "Nature vs Science" series, and in the same month PLoS launched an important experiment in rapid publication – PLoS Currents: Influenza, a collaboration between PLoS, Google Knol and the NCBI

In September, PLoS ONE was immensely proud to win the ALPSP Award for Publishing Innovation, 2009 – this is a major industry award and a testament to the rapid pace of innovation that the journal has pioneered in the 3 years since launch.

September was also the month that saw our Article-Level Metrics program expand in a significant way, by displaying usage data on every article in the PLoS corpus. In December, we also added data from ResearchBlogging.org to the program.  We regard Article-Level Metrics as a significant new development in academic publishing and we  expect to significantly expand it in 2010. Several presentations were made through the year on the topic of Article-level Metrics, for example to NISO, to the ElPub Conference, and to UCSF/Berkeley and these are all archived with audio if you wanted to delve into the details.

In October, OASPA, the new association for Open Access Scholarly Publishers was launched and PLoS was proud to be a founding member. This coincided with Open Access Week, 2009. And in November, in response to many requests over the years, we launched our new PLoS store.

And finally, after a year of incredible developments, 2009 has culminated with what may yet turn out to be the most significant development of all – the request by the White House Office of Science and Technology Policy (OSTP) for public comments on the issue of broadening public access to publicly funded research. You still have time to provide your feedback and there would be no better New Year resolution than to make your voice heard in this forum.

Thank you to everyone who has supported us in 2009, and over the last three years – in particular thank you to our (almost) 1,000 Academic Editors, all of our peer reviewers and of course, all of our authors. We look forward to publishing more great science in 2010'.

Happy third birth day, PLoS ONE!

This is the time all supporters of OA should celebrate - for the great, unparallel success that PLoS ONE has achieved in three years: more than 8000 articles, an extended editorial force of 1000 Academic Editors, innovative article-level metrics, thematic collections, etc. We would like to thank all the reviewers who volunteered to review manuscripts within a very short time window of 10 days! The editorial staff deserve a big thank you for the hard work and readiness to help and solve problems. We must also thank our authors who have shown faith in PLoS ONE and submitted their high quality work to this journal. I hope next year will be even better.

New addition to Article-Level Metrics - blog posts from ResearchBlogging.org

(By Liz Allen, Thu 2009-12-17 12:19 | in syndication with PLoS Blog)

 

Throughout the course of 2009, PLoS has been adding a range of Metrics to each and every article that it has published. In addition to the many metrics already displayed (article pageviews and downloads, citations, social bookmarks, notes, comments and ratings), we are pleased to now add data relating to the blog coverage of any article, as measured by ResearchBlogging.org. You can find out more about the Article Level Metrics program here.

Every interested author and user can now see how many times an article has been downloaded (split into HTML Pageviews, PDF and XML downloads and displayed in a month-by-month format); how often an article has been cited (as measured by PubMed Central, Scopus and CrossRef); how many times it has been 'socially bookmarked' (at CiteULike and Connotea); how many times users have Commented, or left Notes, or provided Ratings; and how many blog articles have been written about it (as measured by the blog aggragators Postgenomic, Blog Lines, Nature Blogs and, from today, ResearchBlogging.org).

We've created a 2.4 minute screen shot video (with audio commentary) that you can watch to familiarize yourself with the blog aggregation functionality from ResearchBlogging.org so you can see for yourself the benefits of this part of the Article-Level Metrics program. 

On launching this new functionality, Pete Binfield, Publisher of PLoS ONE and the Community Journals said:

"We're delighted to add data from ResearchBlogging.org to the Article Level Metrics program because the blogs that they index are mainly written by practicing scientists, who are well versed at providing readable summaries of the research that we publish".

Bloggers who regularly write about scientific research are able to register with ResearchBlogging.org and (provided they qualify) they are then entitled to indicate that their blog entries refer to peer reviewed scientific research by adding an icon to their posts. As a result, the ResarchBlogging.org service represents a high quality source of highly relevant articles, typically written by practicing scientists, on the topic of peer reviewed research. Since all PLoS content is peer reviewed and free to read, PLoS articles tend to be regularly covered by their bloggers. You can find the current list of qualified ResearchBlogging.org bloggers here.

Dave Munger, the co-founder of ResearchBlogging.org, said:

"We're pleased to be working with PLoS to assess the impact of its articles. PLoS journals do a great job publishing and making research accessible to everyone, and we think coverage in thoughtful blog posts is an important component of the impact of a peer-reviewed journal article". You can read more in this blog post.

PLoS ONE and ResearchBlogging.org also collaborate on a monthly "Blog Pick of the Month" competition that we feature on everyONE, the PLoS ONE community blog. Every month, Bora Zivkovic, the Online Discussion Expert for PLoS, chooses the best blog about a PLoS ONE article that has appeared in ResearchBlogging.org and we feature it on our blog. The winning blogger and all the authors of the original PLoS ONE research article all win t-shirts. To enter, you simply need to be a ResearchBlogging.org blogger and start writing about PLoS ONE articles.

We welcome feedback and questions on any aspect of this program to alm@plos.org.

Open Access Workshop at the University of Hyderabad

One day Open Access Workshop was organized on November 18, 2009 at the University of Hyderabad at the initiative of the Indira Gandhi Memorial Library of the University. Professor Seyed E Hasnain, Vice-Chancellor, inaugurated the workshop and delivered his keynote speech. He stressed for the need to make the scientific literature open and free of cost. The university is planning to usher into green open access very soon.

Designer probiotics: the future or too much to stomach?

Although the benefits of probiotics have been postulated for more than 100 years, there has been an increasing interest in the effects of probiotics on ill health and general well being over recent years.
Studies have shown positive outcomes of probiotics in the treatment and prevention of gastrointestinal infections and disease. But are generic probiotics enough? In the review "Probiotics and gastrointestinal disease: successes, problems and future prospects" published in Gut Pathogens, Eamonn Culligan et al. review the treatment of various GI disorders with specific probiotic strains. They also discuss whether the future lies with designer probiotics, which are engineered to specifically target a particular toxin or pathogen, but raise concerns of a negative public reaction to the development of this possible course of treatment.
Will designer probiotics be the future treatment of GI disorders? Or will public resistance for genetically modified organisms hinder its progress? (Source: Biomed Central Blog)

 

Open Access, PLoS article level metrics part of syllabus for PhD course at Uni Hyderabad

Impressed by PLoS style, our university here decided to teach Open Access, creative reuse and article level metrics to entry level PhD students in Life Sciences. I am grateful to the university authorities for enabling us to direct such a timely and important course for the first time in the history of graduate teaching in India; see the course curriculum approved by the university below. I hope many other universities and institutes will be able to replicate this course:

 

Course name: Scientific writing; Course director: Dr Niyaz Ahmed; Course credits: 1 (12 lectures in a semester)

• 1. Documentation of scientific observations and maintenance of raw data in a biology lab
• 2. Primary research articles and secondary content - commentaries, reviews, book length evaluations
• 3. Creative re-use, semantic enhancements and reproduction of open access scientific material
• 4. Copyright and Creative Commons attribution licences
• 5. Publication ethics
• 6. Malpractices in scientific reporting - examples and case studies
• 7. Citations, evaluations, article-specific metrics and impact factors
• 8. Scientific deliberations

Coveted Industry Award to PLoS ONE for Publishing Innovation

PLoS ONE achieved yet another milestone yesterday by receiving an award from the ALPSP (the Association of Learned and Professional Society Publishers) for Publishing Innovation of the Year, 2009. The award is given in recognition of a truly innovative approach to any aspect of publication as adjudged from originality and innovative qualities, together with utility, benefit to the community and long term prospects. This prestigious industry award is therefore, a proof of the hard work of all the editors, managers, staff, authors, and reviewers! The award is a formal recognition of the fact that PLoS ONE has spearheaded a radical departure from traditional scientific publishing in a number of ways, from its pioneering editorial policies to its regular technical innovations, including the commentary and rating features available on all of its articles—in short, PLoS ONE now means 'new generation scientific publishing in a most innovative and interactive style'.

200th PLoS ONE article evaluated at Faculty of 1000

It is heartening to note that 200th article from PLoS ONE has now been evaluated at the Faculty of 1000 Biology. Last year on July 17, a report on the evaluation of 100th article from PLoS ONE was posted on this blog. It is about in a year's time that further one hundred articles were evaluated; a remarkable achievement despite a very high volume publishing in diverse areas. Since the number of articles almost tripled in a year (6000 in August 2009 versus 2600 in July 2008), the number of evaluations touched almost 10 per month (3.3% of total articles published). For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations serve as an important quality index for individual articles.

'Fine Reading: The Biocentric View of the Microbial World'

By - Elio  (Moselio Schaechter)

 

"How does anthropocentrism apply to microbiologists? In a current commentary in the new journal Gut Pathogens, Ramy Aziz reminds us that it shows up all over the place. Take the very term microbe, meaning small living thing. 'Small,' says who? Not the microbes. To them, other microbes would be of 'normal' size and we humans Rabelaisian gargantuas. This wouldn't much matter if it stopped there, with our choice of words alone. Aziz points out that anthropocentrism in microbiology can have serious consequences. For instance, 'pathogens' have been considered to be special group of microbes, separate from the rest. Nothing could be farther from the truth, and nothing could be more objectionable than to consider the human body to be anything but another habitat.

 

In recent years, it has been increasingly realized that pathogenic microbiology is merely another branch of microbial ecology. However, a gentle reminder in Aziz' well-turned words is welcomed. A truly integrated view of the microbial world, or of the biological world in general, cannot be anthropocentric but can only be, as Aziz says, biocentric".

 

[In syndication with ASM blog - 'Small things considered', original post here]. Ramy K Aziz is an Editorial Board Member of PLoS ONE.

 

The Journal of Biosciences, India: kicking and alive, or struggling to excel?

The Journal of Biosciences is the only 'high impact' journal of life sciences published from India under the aegis of the Indian Academy of Sciences. The journal has established an impressive rapport among life sciences communities in India and elsewhere. Sadly, however, it was flagged recently in a meeting (read ahead) that not many of its well-wishers themselves consider to publish their best of the best research in J Biosci. I attended the meeting of the Editors of the J Biosci recently wherein all interested to the cause of the journal were invited. I found morale of the associates of the journal and the authors quite upbeat, also in the aftermath of recently released 'journal impact factors' – JIF 2008; the J Biosci has recorded a 'comfortable' IF of 1.7! However, I think they need to be careful on the statistics part because the number of papers published by the journal has been traditionally very low; it published about 70 citable articles in a 2 year period. Given this, I thought it will not be appropriate to celebrate the jacked up IF, but to introspect as to why the acceptance rate is so low (just 7%) and why so many commentaries and secondary content being published and not much original research? I guess the board members, might consider to follow the example of PLoS journals wherein many of the PLoS advocates first published their high quality (the so called 'Nature, Cell, Science, PNAS quality' of stuff??) research in the journals they stood for. Well, this proposition didn't go well – there were arguments in favor and against and the excuses given were vivid. We can understand the hesitation, but as someone said, 'charity begins at home'! Other hindering things could be the extraordinarily long time taken by the journal, as told, for completing the peer review (somewhere near 3-4 months) and for eventual publication after acceptance (2 more months). Keeping aside these deficiencies, I think we are looking at an emerging journal coming up from a developing country domain and I am all in favor of publishing there as long as the journal follows an Open Access policy although Springer has already started selling the contents through paid views/downloads under an agreement with the journal/academy.

Failures of citation based rating - new analysis

Ramy Aziz, one of the most enthusiastic members of the PLoS ONE Editorial Board has very nicely commented on a recently published PLoS ONE article which highlights the failures of the so called 'impact factor' based rating of the value of science journals. The journal impact factors were released last week itself and thus the analysis presented in the article is very timely, indeed. Below are Ramy's comments to which I agree 100%:

"The presented results pertain to what we believe to be the largest and most thorough survey of usage- and citation based measures of scientific impact."

I agree with the above statement and I definitely like this thorough comparison of a large number of "impact measures." The article is also informative and has introduced in detail many methods for evaluation of scientific literature with which I was not familiar.

However, on reading the article, I had the following concerns regarding its reliability:

1) Most of the readers will only read the abstract, especially because the article is full of statistical and technical terms. The conclusion of the abstract is not so informative and poorly represents the insightful discussion at the end of the article.
In particular, I would have preferred a positive than a negative conclusion. I would have preferred a recommendation of which measures correlate better with each of the multiple dimensions of scientific attributes (e.g., quality, prestige, impact, immediacy, etc.) rather than the--rather obsolete--conclusion that JIF is not optimal and should be "used with caution." I have read more than 20 articles and editorials (including those in Science, JBC, JCI, PLoS) written in the past two years and stating that JIF should be used with caution.

2) I agree with the authors that JIF is misused; however, a value cannot be blamed for what it does not stand for. I believe the authors have given more importance to JIF (probably because of its "impact" on the scientific community), and I think that this has affected the objectiveness of the paper.

3) As the authors state in the introduction, until now I'm not sure whether how "scientific impact" is defined. Is it "journal impact", "article impact", or "scientist impact"? And which of these matters more? However, the authors seem to have committed the same unfair comparison that JIF and SJR do: measuring articles, scientists, and even "science" itself by the journals rather than by the articles. Journal-level metrics simply mean that an article is evaluated mostly prior to its publication. Once a scientist "makes it to Science or Nature," he or she celebrates even if the article will never be cited again!

4) Once more I declare my agreement with the authors that JIF is neither the most accurate nor the fairest way to measure scientists, articles, or even journals. However, this "conclusion" is clearly stated in the introduction (quoted below). Why the analysis then?

"The JIF is now commonly used to measure the impact of journals and by extension the impact of the articles they have published, and by even further extension the authors of these articles, their departments, their universities and even entire countries. However, the JIF has a number of undesirable properties which have been extensively discussed in the literature [2], [3], [4], [5], [6]. This had led to a situation in which most experts agree that the JIF is a far from perfect measure of scientific impact but it is still generally used because of the lack of accepted alternative"

5) One final concern/question.
Citation-based metrics take into consideration journals that are technologically behind (for many "non-science-related" reasons, including funding problems, poor management, being published in a developing country, etc.) and thus do not have well established web sites but are still citable and cited. Do the "usage-based metrics" just ignore those journals?

Need for qualitative assessment of biomedical research

Here comes a new PLoS ONE article describing one of the most authoritative analyses of the research impact - by none other than the Wellcome Trust. The research conducted by experts of the Trust summates that authoritative opinions about a published research finding constitute important benchmark of the quality of biomedical research. These data vindicate stand of the advocates of post publication peer review (and I am one humble volunteer) that modern day qualitative indicators are extremely necessary to judge the impact of biomedical research findings. Not only that this article supports and strengthens cause of the 'Faculty of 1000' but also that of PLoS ONE, although indirectly. The latter is no doubt the most successful forerunner of the idea of post-publication peer review and qualitative assessment while harnessing the web2.0 based semantic tools for such purposes. At this critical juncture, it is time for the concerned institutions to retrospect about their practices of evaluating research productivity of scientists based on bibliometric indices (such as the 'impact factor') alone.

New genome article added to 'PLoS ONE prokaryotic genome collection'

A new PLoS ONE article describing whole genome sequence of a contaminating mycobacterial species, Mycobacterium abscessus is the most recent addition to the 'PLoS ONE Prokaryotic Genome Collection'.

 

The article presents most important observations such as those related to the presence of several novel virulence determinants of non-mycobacterial origins and that these were perhaps acquired from other environmental organisms and pathogens including Rhodococcus sp., Streptomyces sp., pseudomonads and Burkholderia cepacia.

Standards for genome data reporting: should we go about it?

Within my overview article that accompanies the PLoS ONE Prokaryotic Genome Collection, one thing that I did not touch base with was the standards for genome data reporting. The Genome Standards Consortium (GSC) is now already in place (and I am one proud member of the same!) and they strongly advocate that certain standards be introduced (at the least) at the level of genome meta data. The consortium has recently published aims and objectives, prospective guidelines and envisaged benefits of such 'would be' mandatory standards (http://www.pubmedcentral....).

As a next critical step, the GSC are now starting to ask journals to require that new genome/metagenome publications be accompanied by completed 'Minumum Information about a Genome Sequence (MIGS/MIMS)' reports.

This sounds a wonderful proposition and I guess PLoS journals in this connection could lead headway as they already insist for adherence to certain other standards such as MIAME for reporting microarray data). Until this point, it is all OK. But some people feel that 'monopolizing' standards could be a kind of 'suffocation'. However, I am sure this will not lead to the kind of 'suffocating monopoly' created by certain 'nomenclature commissions' and their 'mouthpiece journals' in the area of taxonomy and systematics.

I discussed this with one of my friend, a genomic/bioinformatics expert and he says ".. my problem with standards is also not only the monopoly, but that it is also really hard to set a minimal role of meta data that need to be entered per genome. I suffer from the lack of organized meta data; but once the entry is enforced, people will just start putting anything to fill the tables and get their data out, which will lead to the opposite of what standards are supposed to achieve".

Given above, it is clear that some discussion and brainstorming is nevertheless required before journals start insisting for the MIGS/MIMS reports. I can not find a better place than PLoS ONE (sandbox) to discuss and resolve such issues.

New F1000 Evaluation of a PLoS ONE article

Yet another PLoS ONE article was evaluated by F1000 Biology, making the total number of evaluated articles to 180. At any given time, about 3-4% of PLoS ONE articles are evaluated at F1000. Below is a simplified version of the evaluation of the article by Myers et al. The article was evaluated by Felix Viana of the UMH Instituto de Neurociencias, Spain.

Evolution of thermal response properties in a cold-activated TRP channel.
Myers BR, Sigal YM, Julius D
PLoS ONE 2009 4(5):e5741 [abstract on PubMed] [citations on Google Scholar] [related articles] [FREE full text]

"This is an interesting study, comparing functional properties of ortholog thermosensitive TRPM8 channels in frogs and rats. It suggests that intrinsic thermosensitivity is tuned to the normal operating range of body temperature. Animals populate different ecological niches. Survival in these environments is strongly dependent on properly tuned sensory systems that allow the rapid detection of food and the avoidance of dangerous situations, like predators or exposure to extreme temperatures. TRPM8 is a transient receptor potential activated by cold temperatures and cooling compounds like menthol {1, 2}. In mice, TRPM8 is critical for the detection of mild cold temperatures, and perhaps for unpleasant or noxious cold. In this paper, the authors cloned and characterized the functional properties of frog, specifically Xenopus laevis and Xenopus tropicalis, TRPM8. These aquatic frogs are poikilotherms, their core body temperature fluctuates with environmental temperature, in a range clearly below the core body temperature of mammals and birds. While various properties (i.e. menthol sensitivity and voltage-dependence) of frog TRPM8 were similar to those described for rat and mice, there was a clear shift in the thermal response of the channel towards temperatures below their "normal" core temperature. The amino acid sequence of Xenopus TRPM8 displays 75% identity to the rat sequence. This result suggests that this thermo TRP is under strong evolutionary pressure, likely reflecting an important role in temperature sensing in species other than mammals. Besides the intrinsic interest of this novel information for thermosensory biology in general, a careful analysis of the differences in sequence between different species, and the construction of chimeras, may provide additional insights into the mechanism of temperature gating of TRPs, an important unsolved question".

References: {1} McKemy et al. Nature 2002, 416:52-8 [PMID:11882888]. {2} Peier et al. Cell 2002, 108:705-15 [PMID:11893340].

Single Cell Genomics: New PLoS ONE article evaluated at Faculty of 1000

I recently handled an interesting article at PLoS ONE [Assembling the marine metagenome, one cell at a time. Woyke T, et al., PLoS ONE 2009 4(4):e5299].

 

As for the other high ranking PLoS ONE articles, this article too was evaluated at the Faculty of 1000 Biology and was rated with a F1000 Factor of 6.0 (Must Read). A redacted version of the evaluation by Douglas Bartlett is here: 

 

'This work details the use of single cell genomics from two uncultured marine Flavobacteria to recruit considerable sequence data from the Global Ocean Survey (GOS) compared to genome sequences from cultured Flavobacteria isolates. The genome reconstruction and stringent quality control of the two SAGs (single amplified genomes) are well handled, considering contamination and chimeras associated with the amplification process. The analyses of the two SAGs indicate unique metabolic features such as hydrogen oxidation, proteorhodopsin photometabolism, and biopolymer hydrolysis. Also of interest is the genome streamlining in the ...' ..... Full evaluation of the article is available here (http://www.f1000biology.com/article/id/1160822).

 

 

BLoG ONE has moved to Word Press

A mirror of BLoG ONE now operates from WordPress. All contents from this site will be mirrored from there.

PLoS ONE Prokaryotic Genome Collection - now launched

I am excited to tell you of the latest collection of some of the high-impact articles, the PLoS ONE Prokaryotic Genome Collection. Liz Allen of PLoS, has some more things to say …read her full blog post here.

There is an editorial overview that accompanies the new collection; it’s written by me. Comments related to the collection and the ‘overview’ have started to trickle in, such as this one by Dr Ramy Aziz:

“This article lists very interesting challenges and questions that will be answered in the next decade of this millennium. With the revolution stirred by next-gen sequencing machines, sequencing/resequencing steps have become quick and cheap. Thus, data generation is the least part to worry about. However, as the article appropriately discusses, the problem is what to sequence and then how to make sense out of the piles.

We will very soon have 5,000 fully sequenced prokaryotic genomes, but, as quick annotation tools are being developed, we realize very well that more genomes annotated = more errors propagated.

In addition to high-speed and high-performance …” … Read more here.

Evidence of Leprosy in Ancient India

In a recent PLoS ONE article, Gwen Robbins and colleagues reported analysis of a 4000-year-old skeleton from India, which represents both the earliest archaeological evidence for human infection with Mycobacterium leprae in the world and the first evidence for the disease in prehistoric India. I think the authors need to have clear definitions of 'ancient origins' and 'historic presence'. Leprosy has clear origins from Africa as for tubeculosis (TB). After spreading from Africa the disease may have assumed endemic potentials in certain countries such as India. Therefore, the findings here should be consistent with our own research, published back in 2006 about TB, wherein we suggested that India was a historic cradle for mycobacterial infections and that she served as an ancient corridor for an early worldwide spread of TB. The authors did not cite our work; may be an oversight! But, I am more concerned that they as well forgot to refer to an important PLoS ONE paper which recently attempted to characterize about 9000 year old skeletons from submerged, ancient burials in Israel using paleopathology and DNA based evidence.

How to get cited one hundred times?

Exactly 2 years ago, PLoS ONE published this superb article (Fahlgren N, et al., 2007 High-throughput sequencing of Arabidopsis microRNAs: Evidence for frequent birth and death of MIRNA genes. PLoS ONE 2: e219), a citation classic. Thanks to its being published via Open Access, today it crossed the landmark of one hundred citations in Google Scholar. The paper thus became one of the star articles of PLoS series and the first one from PLoS ONE to log 3 digit citations in a record time of 2 years. The article was also evaluated in F1000 Biology and its corresponding author interviewed at PLoS blog.

Gut Pathogens: a new forum for enteric health at the interface of changing microbiology

Today is the special day for us and the ISOGEM; we launched Gut Pathogens, the 200th Open Access journal of the Biomed Central. Gut Pathogens is a new OA journal publishing articles on all aspects of the biology and pathogenesis of bacterial, parasitic and viral infections of the gut, including their diagnosis and clinical management.

Gut Pathogens shall be the official journal of The International Society for Genomic and Evolutionary Microbiology (ISOGEM) and is supported by a qualified Editorial Board of active scientists and clinicians. We have detailed in the launch Editorial how we hope that an open access journal in this field will provide a high-quality forum for research on enteric infections of humans and animals, facilitating the practice of preventive and social medicine for the benefit of the patients.

Novel ‘replication check mechanism’ key to dormant Tuberculosis

Tuberculosis is a major communicable disease expanding globally and is caused by Mycobacterium tuberculosis (M. tb). The disease is a main killer among infectious diseases in the world with the occurrence of 2 million deaths each year and 8 million cases of active disease. The biggest challenge of tuberculosis (TB) is its ability to survive in dormant form in apparently healthy individuals for decades. M.tb, the diehard pathogen that causes tuberculosis, is capable of staying asymptomatically in a latent form, persisting for years in very low replicating state, before getting reactivated to cause active infection.

M.tb is known to survive for extended periods during the latency phase without any replication. During this phase the bacterium senses the surrounding environmental conditions such as availability of nutrients, immune cell preponderance etc. and if needed puts its machinery back in action to grow and replicate. The regulation of chromosomal DNA replication therefore is a very important switch to maintain dormancy. While the bacterium is dormant replication is bare minimum.

A new study published by PLoS ONE (In-vitro helix opening of M. tuberculosis oriC by DnaA occurs at precise location and is inhibited by IciA like protein) provides some fresh insights into maintenance of dormancy by the pathogenic mycobacteria. Professor Seyed E. Hasnain (Distinguished Professor at the Institute of Life Sciences at the Hyderabad University campus, Hyderabad, India) who led the study said ‘the dormant state of the bacterium is maintained by a novel protein called as Inhibitor of Chromosomal initiation (IciA), which our group has rigorously characterized and which binds to the A+T rich region of the origin of replication’. ‘This binding blocks helix opening of the A+T rich region, a step critical for chromosomal replication initiation to occur’ says Hasnain. This represents the first evidence that chromosomal DNA replication control is a critical molecular switch in the form of IciA protein, which the TB bacteria over express to remain dormant.

Besides identification of the replication check phenomenon by the IciA, the study also generated an in vitro model of mycobacterial replication which will be a very important tool in the hands of infection biologists trying to understand intricacies of microbial acquisition, survival and adaptation under different stress conditions and in different hosts. Although the present study largely represents laboratory based observations, direct evidence for the role of the IciA like protein will come from M.tb iciA knockout experiments to be performed in an animal infection model. While such experiments are underway at Hasnain labs, it will be interesting to see if quantitative expression of IciA in tuberculosis patient’s material could effectively be harnessed as a molecular marker of M.tb activation.

Songs that thronged PLoS ONE through 2008

Well, we listened a lot to bird songs last year at PLoS ONE forums and journal clubs. After birds, mice arrived on the scene to sing and squeal, meaning that rodents could as well joyfully sing, and that their songs to prospective mates are as likely complex as those of birds. However, unlike birds, their vocalizations are discharged at ultrasonic frequencies, and that is why no one noticed them, nor was anyone motivated to celebrate them. But, as one of the many celebrated PLoS ONE stories (DOI: 10.1371/journal.pone.0001893) echoes in popular media and blogosphere, we may hope they will likely find a place in romantic poetry! The article was published by H. Wang and colleagues quite some time back (in April 2008), but was recently showcased in a recent news round-up by New Scientist of the top ten genetics stories of the year. Alison Motluk of New Scientist discussed this research and also provided recordings of the squeaks of male mice in a human audible format.

“Most musical, most melancholy bird,” said Samuel Taylor Coleridge of the nightingale ‘but whether birdsong can affect us in the same way as a beautiful sonata played by a human musician is another matter’ said Rebecca Walton in her blog post summating another celebrated article by Stefan Koelsch of the University of Sussex, wherein his team, investigated differential response to instrumental and computerised music. According to this research, volunteers who listened to recordings of professional pianists showed more emotional activity of the brain than did those who listened to recordings made by computer. This article was covered in different headlines by the Chronicle of Higher Education (Don't Cry For Me, R2D2), The Telegraph (Sweaty music find could help develop new treatments), The Guardian (Music that brings a tear to the eye), Wired (Study: Computer Musicians Ain't Got No Soul) and PsychCentral (Computer Music Not As Calming).

At the end of the year, one more article ("Practicing a musical instrument in childhood is associated with enhanced verbal ability and nonverbal reasoning" PLoS ONE, 2008) dominated the blogosphere, this time for another reason, to celebrate the second birthday of PLoS ONE! This was all about an excellent blog by SciCurious of the Neurotopia 2.0 (Einstein was smart, but Could He Play the Violin?) who won the PLoS ONE second birthday synchroblogging competition organized on December 20, 2008.

All content published in PLoS ONE, from dinosaurs to elephants to chimps to birds to bats and about mice to butterflies and bees is freely available online. Rate them and comment and discuss yourself to enjoy the full power of Web 2.0 technology that PLoS ONE harnesses. Here at PLoS ONE is certainly quite diverse food for thought and you can always join in the discussion by creating an account on the journal site and posting your comments for others to read.