Wednesday, April 30, 2008

The ‘Omic’ revolution, Science 2.0 and PLoS ONE: Are they synonymous?

With the new developments in sequencing technology, more and more species and varieties of organisms are being sequenced more faster than never before, possibly within weeks now. Revolutionary new algorithms for genome analyses have enabled fast and reliable predictions as regards to evolution, physiology, lifestyles and fitness of the sequenced organisms. The scientific journals showcasing such studies have a greater role as regards to access and ease of access to the data and information.

As the new community genomics era dawns ahead, the Open Access journal PLoS ONE has suddenly become a preferred home for genomic and metagenomic studies. This can be gauged from the fact that a whopping 25% of its 2000 papers published until April 2008 was flagged under Genetics and Genomics. Out of this about 50 of the landmark papers addressed the whole genome inferred biology of multiple species of organisms. The most important have been for instance the genome sequences of grape-wine, the Group A Streptococci, Actinobacillus spp., Yersinia spp., Deinococcus geothermalis, Francisella tularensis, Shewanella piezotolerans, Acinetobacters, Leptospira biflexa, Arcobacter butzleri, Bacillus pumilus, Fusobacterium nucleatum, Staphylococcus aureus, Burkholderia mallei and so on.

In addition, six largescale metagenomic studies have been published there in the last few months and it continues to attract submissions in this area and the newly emerging field of ‘Microbiomics’. The Mediterranean metagenomics, coral reef microbial metagenomics and the ocean viral metagenomics projects published at PLoS ONE have been widely discussed both in media and the blogosphere.

No wonder this is truly the magic of web 2.0 based science communication that has transformed PLoS ONE to be the most cutting edge platform for the dissemination of the message of ‘omic’ sciences. So good, the journal is now TOPAZ enabled for community based review, rating and dialogue. It makes a terrific resource when genome data access is enabled through such channels with functionality for community engagement through forums such as Journal Clubs (JC) on PLoS ONE articles. Such JCs involve groups of scientists who volunteer to discuss PLoS ONE articles and to post their discussions as a series of comments, annotations, and ratings eventually triggering discussions within a broader scientific community.

Competing interest: I serve as Section Editor for PLoS ONE.

Tuesday, April 22, 2008

New PLoS ONE evaluations at Faculty of 1000 Biology

On April 21, Michael Symonds from the University of Nottingham evaluated at the F1000Biology a very recent article published in PLoS ONE (Unique environmental effects on physical activity participation: a twin study. Duncan GE, Goldberg J, Noonan C, Moudon AV, Hurvitz P, Buchwald D PLoS ONE 2008 3(4):e2019). He rated this article with the F1000 factor of 3.00; this value denotes that the article is of interest to community in the corresponding research area and that he recommends it to be referred to.

Here are the evaluator's specific remarks:

"As with all aspects of human health and behaviour, the relative influence of genes versus environment looms large. This novel twin study strongly suggests that environmental, rather than genetic, factors are the main determinants of physical activity participation. One way in which this study differs from others in the field is the threshold level of physical activity, which may explain its apparently surprising results."

Another PLoS ONE article (The Cayman crab fly revisited--phylogeny and biology of Drosophila endobranchia. Stensmyr MC, Stieber R, Hansson BS. PLoS ONE 2008 3(4):e1942) was evaluated by Artyom Kopp of University of California. The faculty has recommended this article to be read by the community members in the corresponding research area and has rated the article with the F1000 factor of 3.00.

This article reports rediscovery of Drosophila endobranchia, a fruit fly that lives in the mouth of land crabs on the Caribbean Island of Grand Cayman and that was last sighted in 1966. The evaluators’ specific comments on the article are here:

“This paper will revive the interest in a very unusual species of Drosophila that feeds on the secretions of land crabs - D. endobranchia from the Grand Cayman Island. Following up on Hampton Carson's work, the authors describe the ecology and behavior of this species and determine its phylogenetic position. Drosophila, while commonly known as "fruit flies", exploit a wide variety of food sources, and crab feeding in particular has evolved at least three times in different Drosophila lineages”.

Separate to this, the article has enjoyed a lot of media attention in the last few days.

Roughly about 5% of PLoSONE articles are evaluated on the Faculty of 1000 at a given time, which coincides to fourth position in terms of number of evaluations, after Science (~17% of the published articles evaluated), Nature (~15% of the published articles evaluated) and PNAS (~15% of the published articles evaluated).

PS: F1000Biology is available to subscribers only. All major research institutions across the world already subscribe to the service. All contents at F1000 are usable through the creative commons attribution license unless otherwise stated.

Thursday, April 17, 2008

Genomes of scientific hubris multiply: After Venter's, here is Watson's

Nature today published genome of James Watson. Well it sounds good news more for Watson after going through one of the major controversies of his life. Otherwise the article perhaps appears much like a ‘closed access’ version of a previous PLoS Biology article detailing Craig Venter’s genome.

These mighty projects denote a competition between the ‘genome giants’ although Venter managed to be ahead of Jim Watson. While the new genome finding is more or less confirmatory of the previous individual's genome biology, the only difference what I can see is that the latter study employed new generation sequencing strategy; massively parallel sequencing.

Perhaps the most practical outcome of these studies shall be the decipherment of chunks of new single nucleotide and copy number polymorphisms and the construction of long-range haplotypes.

From a genetic health perspective, however, it is difficult to foresee how these data will be informative about or indicative of the future health of these two 'old men'. This casts shadows of uncertainty over the practical implications of such studies and it will be interesting to look if or not they will pave the way for 'personalized genomics' to usher in a new challenging discipline. If it does, there shall be much of a great biotechnology ahead, as well as community genomics in the microbial world, individual genomics in the human world and the amalgamation of the two, for example - we should be ready in a few years to see their individualized microbiomes and microbial-human interactomes !

Wednesday, April 16, 2008

This Week's Evaluations at Faculty of 1000 Medicine

The following important articles were evaluated this week at the Faculty of 1000 Medicine:

1) Genetics of gene expression and its effect on disease. Emilsson V, Thorleifsson G, ..., Schadt EE, Stefansson K Nature 2008 Mar 27 452 (7186):423-8 Section Epidemiology Recommended by Dominique Langin "This study is the first large-scale attempt to combine gene expression with DNA and complex trait..." [F1000 Factor 6.0 - Must Read]

2) Increased risk of recurrence after hormone replacement therapy in breast cancer survivors. Holmberg L, Iversen OE, ..., Maenpa J, HABITS Study Group J Natl Cancer Inst 2008 Apr 2 100 (7):475-82 Section Epidemiology Recommended by Pagona Lagiou "In my opinion, and according to this study, clinicians following up breast cancer survivors shoul..." [F1000 Factor 6.0 - Must Read]

3) Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Fraser C, Hollingsworth TD, ..., de Wolf F, Hanage WP Proc Natl Acad Sci U S A 2007 Oct 30 104 (44):17441-6 Section Global health Recommended by Isaac Zulu with Kayvon Modjarrad "This study models the optimal transmission dynamics of HIV-1 virus. Its conclusions may have publ..." [F1000 Factor 3.0 - Recommended]

4) Survival among patients with kidney failure in Jalisco, Mexico. Garcia-Garcia G, Briseño-Rentería G, ..., Gill J, Tonelli M J Am Soc Nephrol 2007 Jun 18 (6):1922-7 Section Global health Recommended by Neil Turner "The harsh realities of end stage renal disease (ESRD) in a country with limited provision are cle..." [F1000 Factor 3.0 - Recommended]

5) Host defense peptide LL-37, in synergy with inflammatory mediator IL-1beta, augments immune responses by multiple pathways. Yu J, Mookherjee N, ..., Rehaume L, Hancock RE J Immunol 2007 Dec 1 179 (11):7684-91 Section Allergy & clinical immunology Recommended by Helgi Valdimarsson with Sigrun Sigurdardóttir "This study indicates that the antimicrobial peptide cathelicidin ll-37 has a highly selective imm..." [F1000 Factor 3.0 - Recommended]

Tuesday, April 15, 2008

Welcome the 2000th article of PLoS ONE

Thanks to the Open Access movement, PLoS ONE (PONE) shall be publishing its 2000th article in a few hours from now. This is perhaps becoming a special moment for all those linked to the success of this wonderful publishing project. I think the credit goes to its managers, an overwhelmingly efficient editorial board, thousands of qualified referees who respond to a fast peer-review process and a seamless electronic workflow.

Having said that, I feel it’s getting almost a norm to listen about PONE’s strides and therefore, I can’t say how festive this occasion is going to be! …happening and burgeoning, going from strength to strength in such a short period of not even 2 years, PONE is often making (and breaking) records.

This reminds me of a shouting blog post when PONE published its 500th paper in just 25 weeks of its launch. Soon after, the 1000th article was accepted on September 20, 2007. Although the corresponding blog post was not that shouting, it mentioned the article acceptance was chosen to match another special occasion - birthday of Chris Surridge, first Managing Editor of PONE. What a special birth day gift!
… it will be interesting to know whose birthday coincides with 2000th PONE article!

Monday, April 14, 2008

Latest PLoS ONE evaluation at Faculty of 1000

On April 11, Frank de Gruijl from the Leiden University Medical Center/LUMC, Netherlands evaluated at the F1000Biology an article published in PLoSONE (The Vitamin D Receptor Is a Wnt Effector that Controls Hair Follicle Differentiation and Specifies Tumor Type in Adult Epidermis.Pálmer HG, Anjos-Afonso F, Carmeliet G, Takeda H, Watt FM. PLoS ONE 2008, 3(1):e1483). He rated this article with the F1000 factor of 6.00; this value denotes that the article is of major interest to community in the corresponding research area and that every researcher in the field must read it. Here are the evaluator's specific remarks:
"Both the WNT pathway and the vitamin D receptor (VDR) are known to be important to the development of hair follicles, but the latter can now also be considered a downstream transcription factor of WNT, next to its canonical transcription factor TCF/Lef. The branching point is beta-catenin, which can activate both transcription factors. Remarkably, some beta-catenin-responsive genes have VDR, but not TCF/Lef promoter sites. The ligand-activated VDR was shown to prevent follicular tumor formation by beta-catenin, most likely by restoring natural differentiation, and infiltrative human basal cell carcinomas were found to have low VDR expression next to a clear nuclear beta-catenin expression".

On an average about 5% of PLoSONE articles are evaluated on the Faculty of 1000 at a given time, which roughly means a fourth position in terms of number of evaluations, after Science (~17% of the published articles evaluated), Nature (~15% of the published articles evaluated) and PNAS(~15% of the published articles evaluated).

PS: F1000Biology is available to subscribers only. All major research institutions across the world already subscribe to the service. All contents at F1000 are usable through the creative commons attribution license unless otherwise stated.

Friday, April 11, 2008

PLoS ONE’s strides at the Faculty-of-1000-Biology

The emergence of Open Access Publishing has brought into practice the long envisioned model of post publication peer review. The success of such models is largely spearheaded by the new technologies based on Web 2.0. For example, the multidisciplinary journal, PLoS ONE, launched in late 2006 has been successfully strengthening the spirit and mission of Open Access while harnessing the power of web technology; at the same time its hosted on a powerful TOPAZ platform for community based review, evaluation and dialogue. It makes a terrific resource when an open access journal combines the power of rating and evaluation in real time.
Another revolution of our time is the authoritative, post-publication benchmarking and rating of most impacting articles through services such as the Faculty of 1000. Faculty of 1000 Biology is a web based, authoritative, next generation literature awareness tool. Run by the Medicine reports Limited (UK), it is a revolutionary online research service that comprehensively and systematically highlights and reviews path-breaking papers based on the recommendations of a faculty of well over 2300 selected leading researchers ("Faculty Members"). This service is run by scientists for scientists and provides ‘a rapidly updated consensus map of the important papers and trends across biology’. F1000Medicine is the sister concern of F1000Biology run by medical academics and clinicians and is rapidly gaining popularity among medical doctors and paramedics.
I consider myself fortunate to have published in Open Access journals in both PLoSONE and BMC and to be associated in editorial capacities with PLoS ONE, F1000Medicine, F1000Biology and the BMC led journals, Annals of Clinical Microbiol Antimicrobials, Infect Agents Cancer, Acta Vet Scand and Gut Pathogens (to be launched soon). I must say that I am thoroughly enjoying open access publishing and witnessing the success and impact of the revolutionary evaluating services.
Since a few weeks I have been associated with PLoS ONE in a more dedicated capacity of a Section Editor (Microbiology and Genomics) and therefore, got further opportunity to look into how this journal is going from strength to strength in such a short time of not even two years? Well that was evident from the number of articles published and their quality. However, I was keen in seeing this from the lenses of giants! I did some analyses involving tools at F1000Biology to know how inclined are the opinion leaders in biological sciences about PLoSONE articles given that the Faculty Members of F1000 have been traditionally ‘jumping’ to articles from a few top tier journals such as Nature or Cell. Good to say, the trend is reversing, although slow. Here is how - I was very much pleased to note PLoS ONE’s visible impact; 55 of the1241 articles (4.4%) published in PLoS ONE in 2007 have been evaluated and recommended by the experts at F1000Biology. What this means in terms of impact? As a comparison I modeled PLoS ONE statistics alongside one highly established journal, Nature (the only journal with which PLoS ONE can be compared due to its multidisciplinary nature). A total of 349 articles out of 2892 (12%) published by Nature in 2007 were evaluated at F1000Biology. Seemingly, the difference in terms of number of articles evaluated looks large. However, as I mentioned, if we consider the current visible bias of F1000 faculty towards Nature journals and the publishing criteria (at Nature) linked to space (huge rejection rates due to subjective criteria), PLoS ONE stands distinctly tall given the fact that it is just born. Performances of all other titles were nowhere near. Other 66 Open Access titles (all BMC series + Genome Biology put together) from Biomed Central (4740 articles in 2007) could yield only 47 evaluations at F1000Biology (0.9%) during 2007. Given that BMC titles are also freely available, it is intriguing to know what makes PLoSONE so successful at F1000? In my perception - it is the high quality of the articles plus the ease with which they can be judged on face - PLoSONE sandbox makes it extremely simple for the evaluators to quickly pick the articles based on notes, referee’s comments, ratings, reader responses and community feedback etc.
The future is even brighter – more and more F1000 members are inclined to using open access articles for their benchmarking. It makes life easy. I remember, I once had almost begged for a reprint from an author of a beautiful review article on genome duplications (many authors do not respond to reprint requests in a reasonable time frame). I wanted to have it evaluated at F1000Medicine and the closed access article was costing me USD 60.00 (in India, this equals to a monthly rent for a 2 bedroom house!!) – how shame!
Finally, I do not know how useful will be these initial statistics on F1000 ratings; but, I am sure this could mean a good indicator for the prospective authors at PLoSONE (especially in the absence of any bibliometric index such as Impact Factor) to foresee its reputation and peer-acceptance that the journal has earned in a short time.

Monday, April 7, 2008

Today's pick: Toxigenic Helicobacter pylori Infection and Gastric Cancer risk to Relatives

I read this article (Argent et al., Clinical Cancer Research 2008 14:2227 -2235) today and quickly gauged that its going to be a citation classic. I submitted an evaluation to F1000Medicine where it was rated as an exceptional article that can change clinical practice ( Since F1000 Medicine is a paid service, not many can see the evaluation. I therefore, take liberty to provide here a simplified version of the evaluation:

This beautiful article provides yet another evidence linking virulent Helicobacter pylori infection to gastric cancer development. The paper describes a novel finding of early childhood transmission of H. pylori among the non-cohabiting relatives of gastric cancer patients. Such patients share with their non-cohabiting relatives the strains that have variable virulence potentials finetuned through microevolution. This work has important clinical implications for the families of gastric cancer patients. Author's investigation of gastric cancer families shows that strains are usually shared. However, this should not mean that different individuals have H. pylori with the same virulence potentials. Toxigenic (vacA type s1/m1) H. pylori was shown to be associated with precancerous gastric hypochlorhydria. Adult family members with this type of H. pylori harbored the same strain as those colonizing their currently noncohabiting adult family members in 68% cases; this simply means acquisition during childhood from each other or a source of infection common to the entire family. The authors believe that the clinical practice should change such that young relatives of cancer patients should be compulsarily screened for H. pylori, and the safest option they suggest to treat all who are positive. Beside this, the paper comprises an excellent approach to study microevolution in a persistent organism as an important measure of virulence gain or loss on a short time scale during colonization. The frequency with which microevolution of virulence factors occurs within families has important bearings for bacterial persistence and thereby the development of atrophic gastritis which preceded transformation to precancerous lesions.

Changes Clinical Practice: It should be compulsory for young relatives of gastric cancer patients to be screened for Helicobacter pylori and all who are positive should be treated.

Sunday, April 6, 2008

TB treatment end point - do we have any sterilization marker?

TB is a highly contagious infection which usually spreads through droplet. Transmission dynamics of TB aerosols depend on crowding, weather conditions and the extent of exposure. People with prolonged, frequent, or intense contact such as those sharing a long haul flight with infected persons on-board are at highest risk of becoming infected, with an estimated infection rate of 22%. The chain of transmission can therefore, be broken by isolating patients with active disease and starting effective anti-tubercular therapy. After two weeks of such treatment, people with non-resistant active TB generally cease to be contagious. If this is so, then why an extended regimen for six months? Can this be shortened to prevent against liver cirrhosis and toxicity due to anti-TB drugs, rifampicin in particular? I think yes, it can be, but only after an indication that the patient has been ‘sterilized’ and has started to recover. Weight gain, BMI, feeling of wellness and improved appetite etc. could be some of the vague indicators. However, sadly, we do not have any personalized biomarker that determines the end point for this painful treatment course which should I think be very much variable for different individuals. Some of our research efforts are being pushed in this direction. So watch out, patiently!