Wednesday, December 24, 2008

New PLoS ONE articles evaluated at F1000 Biology

It appears that the year 2008 is closing on a good note - in the last 6 days three important articles from PLoS ONE were evaluated by the F1000 Biology faculty. These articles were graded as significantly novel reports (see below).

Rapid SNP discovery and genetic mapping using sequenced RAD markers. Baird NA, Etter PD, …, Cresko WA, Johnson EA PLoS ONE 2008 3(10):e3376

Evaluated by: Tony Long on December 23, 2008

F1000 Factor: 6.0 (Must Read)

If I were you: perceptual illusion of body swapping. Petkova VI, Ehrsson HH PLoS ONE 2008 3(12):e3832

Evaluated by: Aina Puce on December 19, 2008

F1000 Factor: 6.0 (Must Read)

The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways. Fukada T, Civic N, …, Superti-Furga A, Hirano T PLoS ONE 2008 3(11):e3642

Evaluated by Bruce Pitt on December 18, 2008

F1000 Factor: 9.0 (Exceptional)

All PLoS ONE content is freely available on the web and readers could themselves rate and evaluate the articles. However, those evaluated on F1000 are certainly the crème de la crème kind of material; at any given time about 4% of the PLoS ONE articles are evaluated at the F1000.

Saturday, December 20, 2008

PLoS ONE second birthday blogging competition: winners in waiting

A blogging competition to mark second birthday of the revolutionary Open Access publishing project by name PLoS ONE, was organized on December 18. Bora Zivkovic has posted on his blog the final list of eligible posts that discuss some of the most interesting articles published in recent times in PLoS ONE. I have read all the posts and they are really very nice. I think the jury will have a tough time deciding the winner. Here are the winners in waiting:

Barn Owl of Guadalupe Storm-Petrel: DNA Repair During Spermatogenesis: Gimme a Break! about the article: Deletion of Genes Implicated in Protecting the Integrity of Male Germ Cells Has Differential Effects on the Incidence of DNA Breaks and Germ Cell Loss

Ed Yong of Not Exactly Rocket Science: Predatory slime mould freezes prey in large groups about the article: Exploitation of Other Social Amoebae by Dictyostelium caveatum

Scicurious of Neurotopia (version 2.0): Why Did the Dolphin Carry a Sponge? about the article: Why Do Dolphins Carry Sponges?

Scicurious of Neurotopia (version 2.0): Einstein was smart, but Could He Play the Violin? about the article: Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning

Allyson of Systems Biology & Bioinformatics (Semantically Speaking) on One way for RDF to help a bioinformatician build a database: S3DB (also cross-posted on The mind wobbles: One way for RDF to help a bioinformatician build a database: S3DB) about the article: A Semantic Web Management Model for Integrative Biomedical Informatics

Simon Cockell of Fuzzier Logic: Contextual Specificity in Peptide-Mediated Protein Interactions about the article: Contextual Specificity in Peptide-Mediated Protein Interactions

Mike Haubrich of Tangled Up in Blue Guy : Small-Bodied Humans on Palau - A Disagreement about the articles: Small-Bodied Humans from Palau, Micronesia and Small Scattered Fragments Do Not a Dwarf Make: Biological and Archaeological Data Indicate that Prehistoric Inhabitants of Palau Were Normal Sized

Martin of The Lay Scientist : Catching Snowflakes: The Media and Public Perceptions of Disease about the article: Medicine in the Popular Press: The Influence of the Media on Perceptions of Disease

Nir London of Macromolecular Modeling Blog: Model for the Peptide-Free Conformation of Class II MHC Proteins about the article: Model for the Peptide-Free Conformation of Class II MHC Proteins

Greg Laden of Greg Laden's blog: How to make an elephant turn invisible about the articles: Risk and Ethical Concerns of Hunting Male Elephant: Behavioural and Physiological Assays of the Remaining Elephants, Roadless Wilderness Area Determines Forest Elephant Movements in the Congo Basin, Elephant (Loxodonta africana) Home Ranges in Sabi Sand Reserve and Kruger National Park: A Five-Year Satellite Tracking Study and Population and Individual Elephant Response to a Catastrophic Fire in Pilanesberg National Park.

The Neurocritic of The Neurocritic blog: Can You Reread My Mind? about the article: Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings

Moneduloides of Moneduloides blog: A trypanosome and a tsetse walk into a bar... about the article: Factors Affecting Trypanosome Maturation in Tsetse Flies

El-Ho of Pas d'il y'on que nous: The Etiology of Fear about the article: Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations

Ian of Further thoughts: Evolution and conservation in Mexican dry forests about the article: Sources and Sinks of Diversification and Conservation Priorities for the Mexican Tropical Dry Forest

Alun Salt of Archaeoastronomy: If you put a snail shell to your ear can you hear the sound of your thoughts? about the article: Climate Change, Genetics or Human Choice: Why Were the Shells of Mankind's Earliest Ornament Larger in the Pleistocene Than in the Holocene?

Michael Tobis of Only In It For The Gold: The Singularity about the article: Ecosystem Overfishing in the Ocean

PodBlack Cat of PodBlack blog: Pet Ownership - Maybe Not For Better Health, Perhaps Sense Of Humour? about the article: To Have or Not To Have a Pet for Better Health?

Juan Nunez-Iglesias of I Love Symposia!: Randomise your samples! about the article: Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

Munger of Cognitive Daily is one of the judges: Make sure you get some sleep -- or at least some caffeine -- before that test about the article: Sleep Loss Produces False Memories

Friday, December 12, 2008

A PLoS ONE article that is hot favourite of F1000 Editors

Last month I evaluated on F1000 an article from PLoS ONE that addressed infection as a driving force for the extinction of rats native of Christmas Island. The importance of this timely study was also discussed on BLoG ONE. Apparently, it appears that the F1000 evaluation of this article has been taken on quite a good note. It just appeared in the latest issue of the F1000 update wherein the Editors of F1000 reinforce the opinion that the PLoS ONE paper indeed provides important evidence that infectious diseases are a potential cause of future extinctions of endangered mammalian species. The original article is freely available for anyone to read, rate and comment.

Good-bye CDFD

Finally, today I said good-bye to CDFD, the institute where I worked for more than 10 years. It has been a wonderful experience being there and having enjoyed each and every moment of a busy scientific career. The University of Hyderabad, my new employer, extended a warm welcome also to my advocacy of Science 2.0, PLoS ONE and Open Access in general. Change is for the betterment - lets see how true.

Tuesday, November 18, 2008

The first case of mammalian extinction due to an exotic disease – an alarm bell for conservation efforts?

An interesting article that we accepted last month for PLoS ONE describes a very fine DNA detective work to put forth the hypothesis of mammalian extinction due to an introduced infectious disease. The research published on November 6 suggests that a century ago the black rat species, which led to the emergence of the bubonic plague in Medieval Europe and considered one of the worst invasive species on the planet, sheltered a parasitic disease that eliminated two immunologically naive rat species native to the Christmas Island in the Indian Ocean.

Alex Greenwood from the Old Dominion University in Norfolk, Virginia, and colleagues brilliantly attempted to solve the mystery of the mammalian extinctions. They collected samples from 21 historical rat specimens from Christmas Island stored at natural history museums across the United Kingdom. These researchers analyzed preserved remains of black rats, the extinct species, and the crosses of the two. The century old specimens were then analyzed for genetic signatures of crossbreeding as well as for the presence of Trypanosoma lewisi, the close relative of the sleeping sickness pathogen, T. evansii.

The interesting part of the story is that the authors argue they did not find any evidence of hybridization between black rats and Christmas Island rats. They emphasize that mere invasion does not necessarily lead to extinction and, that on Christmas Island, the Christmas Island shrew survived until 1985 even in the presence of black rats, arguing against general competitive exclusion or predation. Therefore, it appears that their data are more consistent with disease as a reason for extinction rather than competition.

The authors speculate that the extinction of Christmas Island rats (Rattus macleari) was due to a trypanosome pathogen present in fleas carried by black rats introduced to the island (Rattus rattus). The study presents acceptable evidence for the presence of trypanosome infection in the Christmas Island rats after black rats have been introduced to the island, but not before.

However, if we consider some of the arguments, the scenario becomes little implausible - Trypanosome diseases do not normally have short and acute progression and T. lewisi (which the authors tested for) is not reported to be acutely pathogenic in rats. The other question could be - what is the reason to believe that the Christmas Island rats would reveal a different pathology compared with the black rats which were putatively carrying the disease? Nevertheless, it is possible that R. macleari would have been immunologically naïve to black rat pathogens which acted more deadly in a naïve host compared to its natural host or to a host adapted to it. But the next argument could be - why the Christmas Island rats were not killed by some other pathogen (for example a rodent virus) introduced by the black rats? Also, it is possible that the authors missed a possible interspecific ecological competition that might have served as an important extinction force. But no one knows ways to test that!

Leaving this debate to the scientific community (and the PLoS ONE readership at large) to choose among different explanations, I thought the paper was indeed worthy of publication because some of the emerging and re-emerging infectious diseases could possibly serve as a strong force to future extinctions, especially of the wildlife that are increasingly threatened and we thus have a warning bell in the form of this important study.

Friday, October 31, 2008

The Cancer Week - Nagoya: Paradigm shift in Japanese Science Communication

Traditionally, a majority of the Japanese researchers and clinicians have been shying off the mainstream communication skills in science and technology. However, this seems fast becoming history. The Japanese Cancer Association (JCA) meeting, a grand annual event in cancer science and medicine, started this year with a new trend – compulsory communication in English!

The cancer week witnessing the annual congregations of the JCA and the Japan Society for Clinical Oncology began on October 27 this year in Nagoya. The twin meeting was attended by 5000 attendees comprising of cancer specialists, doctors, basic researchers and students. Reportedly, for the first time in the last 66 years’ history of the Japanese cancer meetings, it was made compulsory for the presenters to write their abstracts in English only and 12 dedicated International sessions (with English only presentations) were organized. Also, the aspects of World Cancer Declaration were presented for the want of advocacy and solidarity of the Japanese cancer community to the cause of global cancer prevention.

This new beginning has also made possible for International academics and doctors to participate and communicate through the platform of JCA. It was especially a great opportunity for me to have shaped, participated and chaired one of their international sessions. This was also a nice platform for Open Access advocacy and I was excited to note the growing interest of Japanese biosciences community towards OA journals in general and PLoS ONE in particular.

The next JCA meeting is planned in Tokyo in 2009. Let us hope it will be equally successful and rewarding.

Tuesday, October 28, 2008

PLoS ONE - what is going unnoticed?

I feel so proud each time PLoS ONE is attached to some high profile science personalities. Françoise Barré-Sinoussi is one such icon - Nobel Laureate and a PLoS ONE author. This was announced and highlighted soon after she won the Nobel Prize, earlier this month. The other great thing that happened during the same time-period (and went largely unnoticed!) was the F1000 evaluation (of a PLoS ONE article) by none other than Rino Rappuoli !

Here is his evaluation:

Extensive adaptive changes occur in the transcriptome of Streptococcus agalactiae (group B streptococcus) in response to incubation with human blood. Mereghetti L, Sitkiewicz I, Green NM, Musser JM. PLoS ONE 2008 3(9):e3143

'In this work, the group of James Musser applied a microarray approach in order to understand how Streptococcus agalactiae (GBS) adapts its transcriptional profile to growth in human blood during invasive disease. The authors observe the up-regulation of GBS virulence genes involved in host-bacteria interaction, such as factors involved in the interaction with the complement system and the coagulation/fibrinolysin system. Ex-vivo blood cultures were used to mimic sepsis and overcome the limitations of animal models (i.e. bias due to species-specific differences, appropriate volumes of blood and adaptation throughout time during animal blood exposure). The findings validate the use of ex-vivo human blood cultures as a surrogate of the invasive infection. Approaches like this one, pioneered by the group of James Musser, will be instrumental to understanding the mechanisms by which bacterial pathogens evade the host immune system leading to survival and proliferation in the human body'.

Complete evaluation of this article including ratings etc. is available via F1000 Biology. A total of 130 articles from PLoS ONE have been evaluated at F1000.

Friday, August 22, 2008

TB and Mycobacteria community publishes in PLoS ONE

Tuberculosis (TB) continues to cause increasing deaths globally and last year alone about 1.7 million lives were lost (The World Health Organization, 2006). The human immunodeficiency virus (HIV) epidemic has worsened the situation as the incidence rates dramatically jumped in recent times ( Most countries that are crippled by the menace of TB have negligible flow of international funding for research and new fruits of post genomic discovery are yet to percolate to these zones. Library budgets are seriously dwindling and the researchers, clinicians and higher degree students have no access to TB research that has been traditionally published in ‘closed access’ journals. I recall my days (1997) at the National Dairy Research Institute, Karnal (India), where, I had to run on almost weekly basis to the National Medical Library in Delhi (100 Kilometers) or to the library of the Post Graduate Institute of Medical Research (PGI) at Chandigarh (~100 Kilometers) to refer to some of the 'print only' journals for my dissertation work on TB. The situation has not improved much even today. Thankfully, Open Access publishing has arrived as the new ray of hope for many who hold dear to their hearts the cause of poverty alleviation through epidemic control. PLoS ONE has been seriously partnering this cause since its inception in 2006 and has since then published about 73 landmark articles addressing the broad areas of TB control, mycobacterial biology and medicine. We at PLoS ONE are overwhelmed with this response of the TB and mycobacteria community and thank the authors who opted for the journal to showcase their research and to widen access to those who desperately need it - the developing world. In particular, it is quite pleasing for me to put on record the patronage extended by the mycobacterial research community from India by publishing highest number of papers on the topic from a high burden country.

Thursday, July 31, 2008

Exciting and noteworthy in PLoS ONE: My picks

There are 62 brand new articles published at PLoS ONE this week which certainly reflects quite diverse food for thought. You can always join in discussion on interesting articles by creating an account on the journal site and posting your comments for others to read. Also, you may like to rate the articles. Ratings are the quickest and easiest way for users to indicate their support for the authors and to highlight which articles are of potential impact for the readers and the community. I suggest why not to begin with these exciting ones?

Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms:

A scanning electron microscope survey was initiated to determine if the previously reported findings of "dinosaurian soft tissues" could be identified in situ within the bones. The results obtained allowed a reinterpretation of the formation and preservation of several types of these "tissues" and their content. Mineralized and non-mineralized coatings were found extensively in the porous trabecular bone of a variety of dinosaur and mammal species across time. They represent bacterial biofilms common throughout nature. Biofilms form endocasts and once dissolved out of the bone, mimic real blood vessels and osteocytes. Bridged trails observed in biofilms indicate that a previously viscous film was populated with swimming bacteria. Carbon dating of the film points to its relatively modern origin. A comparison of infrared spectra of modern biofilms with modern collagen and fossil bone coatings suggests that modern biofilms share a closer molecular make-up than modern collagen to the coatings from fossil bones. Blood cell size iron-oxygen spheres found in the vessels were identified as an oxidized form of formerly pyritic framboids. Our observations appeal to a more conservative explanation for the structures found preserved in fossil bone.

Remodeling of the Streptococcus agalactiae Transcriptome in Response to Growth Temperature

To act as a commensal bacterium and a pathogen in humans and animals, Streptococcus agalactiae (group B streptococcus, GBS) must be able to monitor and adapt to different environmental conditions. Temperature variation is a one of the most commonly encountered variables. To understand the extent to which GBS modify gene expression in response to temperatures encountered in the various hosts, we conducted a whole genome transcriptome analysis of organisms grown at 30°C and 40°C. We identified extensive transcriptome remodeling at various stages of growth, especially in the stationary phase (significant transcript changes occurred for 25% of the genes). A large proportion of genes involved in metabolism was up-regulated at 30°C in stationary phase. Conversely, genes up-regulated at 40°C relative to 30°C include those encoding virulence factors such as hemolysins and extracellular secreted proteins with LPXTG motifs. Over-expression of hemolysins was linked to larger zones of hemolysis and enhanced hemolytic activity at 40°C. A key theme identified by our study was that genes involved in purine metabolism and iron acquisition were significantly up-regulated at 40°C. Growth of GBS in vitro at different temperatures resulted in extensive remodeling of the transcriptome, including genes encoding proven and putative virulence genes. The data provide extensive new leads for molecular pathogenesis research.

Streptococcus iniae M-Like Protein Contributes to Virulence in Fish and Is a Target for Live Attenuated Vaccine Development

Streptococcus iniae is a significant pathogen in finfish aquaculture, though knowledge of virulence determinants is lacking. Through pyrosequencing of the S. iniae genome we have identified two gene homologues to classical surface-anchored streptococcal virulence factors: M-like protein (simA) and C5a peptidase (scpI). S. iniae possesses a Mga-like locus containing simA and a divergently transcribed putative mga-like regulatory gene, mgx. In contrast to the Mga locus of group A Streptococcus (GAS, S. pyogenes), scpI is located distally in the chromosome. Comparative sequence analysis of the Mgx locus revealed only one significant variant, a strain with an insertion frameshift mutation in simA and a deletion mutation in a region downstream of mgx, generating an ORF which may encode a second putative mga-like gene, mgx2. Allelic exchange mutagenesis of simA and scpI was employed to investigate the potential role of these genes in S. iniae virulence. Our hybrid striped bass (HSB) and zebrafish models of infection revealed that M-like protein contributes significantly to S. iniae pathogenesis whereas C5a peptidase-like protein does not. Further, in vitro cell-based analyses indicate that SiMA, like other M family proteins, contributes to cellular adherence and invasion and provides resistance to phagocytic killing. Attenuation in our virulence models was also observed in the S. iniae isolate possessing a natural simA mutation. Vaccination of HSB with the ΔsimA mutant provided 100% protection against subsequent challenge with a lethal dose of wild-type (WT) S. iniae after 1,400 degree days, and shows promise as a target for live attenuated vaccine development. Analysis of M-like protein and C5a peptidase through allelic replacement revealed that M-like protein plays a significant role in S. iniae virulence, and the Mga-like locus, which may regulate expression of this gene, has an unusual arrangement. The M-like protein mutant created in this research holds promise as live-attenuated vaccine.

Effect of Attenuation of Treg during BCG Immunization on Anti-Mycobacterial Th1 Responses and Protection against Mycobacterium tuberculosis

The functional equilibrium between natural regulatory T cells (Treg) and effector T cells can affect the issue of numerous infections. In unvaccinated mice, the influence of Treg in the control of primary infection with mycobacteria remains controversial. Here, we evaluated the role of Treg during prophylactic vaccination with Mycobacterium bovis BCG (Bacillus Calmette-Guérin) on the induction of T cell responses and on the protective effect against subsequent M. tuberculosis challenge in mice. We demonstrated that, subsequent to BCG injection, Treg were recruited to the draining lymph nodes and negatively control anti-mycobacterial CD4+ — but not CD8+ — T-cell responses. Treatment of BCG-immunized mice with an anti-CD25 mAb (PC61) induced an increase IFN-γ response against both subdominant and immunodominant regions of the protective immunogen TB10.4. In Treg-attenuated, BCG-immunized mice, which were then infected with M. tuberculosis, the lung mycobacterial load was significantly, albeit moderately, reduced compared to the control mice. Our results provide the first demonstration that attenuation of Treg subset concomitant to BCG vaccination has a positive, yet limited, impact on the protective capacity of this vaccine against infection with M. tuberculosis. Thus, for rational design of improved BCG, it should be considered that, although the action of Treg does not represent the major cause of the limited efficiency of BCG, the impact of this cell population on the subsequent control of M. tuberculosis growth is significant and measurable.

Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.

Thursday, July 17, 2008

100th PLoS ONE article evaluated at Faculty of 1000 Biology

As a part of its thematic focus for the month of July, PLoS ONE announced a call for papers addressing gene expression studies. It appears that the gene expression community has already embraced PLoS ONE in a great style - here appears the authoritative and insightful review [by Charles Auffray] of one of the gene expression articles published by PLoS ONE: ‘High throughput gene expression measurement with real time PCR in a microfluidic dynamic array’. Interestingly, Auffray’s is the 100th evaluation of PLoSONE articles at the Faculty of 1000 Biology.

Below is the simplified version of Charles Auffray’s evaluation of the article. Full evaluation can be read at F1000Biology website.

‘The novel microfluidic device described in this paper transforms real-time quantitative PCR into a much higher throughput technology for gene expression measurement. The authors have used a dynamic array of microfluidic channels, valves and nanoliter reaction chambers to perform simultaneously 2304 real-time qPCR assays, monitoring expression of 45 human genes in 18 tissues with very high sensitivity (down to <10 RNA molecules). The results presented compare very well with those obtained with conventional microliter RT-PCR, outperforming DNA microarrays. Miniaturization and parallelization result in faster delivery of results with much less reagents and handling. This technological advance should prove useful for validation of expression profile signatures obtained with microarrays, and their extensive use for diagnosis and prognosis. In order to compete directly with microarrays for transcriptome analysis, the number of genes that can be assayed in parallel would have to be increased by at least two orders of magnitude’.

Of its 2600 articles in PubMED, one hundred (4%) articles have been already evaluated and commented upon by F1000 Members. For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations constitute important quality indexes for individual articles apart from hundreds of articles already reviewed through PLoS ONE’s unique rating and discussion tools and journal clubs which are fully compliant to the cutting edge concepts of Science 2.0. Such 'article level metrics' are especially relevant when the significance of a popular bibliometric index, the 'impact factor' is increasingly being questioned.

Conflict of interest: I volunteer as Section Editor of PLoS ONE and as a Faculty Member at F1000 Biology and F1000 Medicine.

Thursday, July 10, 2008

Birds are singing again!

PLoS ONE had a thematic focus last month on avian research. Several high profile papers related to birds were highlighted and discussed also through an avian journal club. This week again 2 more bird articles have been published; both the articles are being quite enthusiastically discussed in popular media as well as on science channels. While the first article deals with how superfast muscle movements are harnessed by birds to produce their tunes, the other one describes bird’s behavior and personality exhibition during singing and that only high-quality individuals can afford to display attractive songs, and they will necessarily be risk takers:

Superfast Vocal Muscles Control Song Production in Songbirds

Birdsong is a widely used model for vocal learning and human speech, which exhibits high temporal and acoustic diversity. Rapid acoustic modulations are thought to arise from the vocal organ, the syrinx, by passive interactions between the two independent sound generators or intrinsic nonlinear dynamics of sound generating structures. Additionally, direct neuromuscular control could produce such rapid and precisely timed acoustic features if syringeal muscles exhibit rare superfast muscle contractile kinetics. However, no direct evidence exists that avian vocal muscles can produce modulations at such high rates. Here, we show that 1) syringeal muscles are active in phase with sound modulations during song over 200 Hz, 2) direct stimulation of the muscles in situ produces sound modulations at the frequency observed during singing, and that 3) syringeal muscles produce mechanical work at the required frequencies and up to 250 Hz in vitro. The twitch kinematics of these so-called superfast muscles are the fastest measured in any vertebrate muscle. Superfast vocal muscles enable birds to directly control the generation of many observed rapid acoustic changes and to actuate the millisecond precision of neural activity into precise temporal vocal control. Furthermore, birds now join the list of vertebrate classes in which superfast muscle kinetics evolved independently for acoustic communication.

Birds Reveal their Personality when Singing

Individual differences in social behaviour may have consequences for mate choice and sexual signalling, because partners should develop preferences for personalities that maximize reproductive output. Here we propose that behavioural traits involved in sexual advertisement may serve as good indicators of personality, which is fundamental for sexual selection to operate on temperament. Bird song has a prominent and well-established role in sexual selection, and it displays considerable variation among individuals with a potentially strong personality component. Therefore, we predicted that features of song would correlate with estimates of personality. In a field study of free-living male collared flycatchers, Ficedula albicollis, we characterised personality based on the exploration of an altered breeding environment, and based on the risk taken when a potential predator was approaching during a simulated territorial interaction. We found that explorative and risk-taker individuals consistently sang at lower song posts than shy individuals in the presence of a human observer. Moreover, males from lower posts established pair-bonds relatively faster than males from higher posts. Our results may demonstrate that risk taking during singing correlates with risk taking during aggression and with exploration, thus personality may be manifested in different contexts involving sexual advertisement. These findings are in accordance with the hypothesis that the male's balance between investment in reproduction and risk taking is reflected in sexual displays, and it may be important information for choosy females that seek partners with personality traits enhancing breeding success.

Tuesday, July 8, 2008

Thematic Journal Clubs at PLoS ONE

I liked the idea at PLoS ONE to have a thematic focus each month to assess how well the journal is doing in that particular area. This is gauged most often with the help of statistics obtained from Google Analytics on page views related to each article in that category and the most accessed article is highlighted on the main page of the journal. At this stage PLoS ONE receives from the authors of the article their comments on the editorial processes and their feelings on seeing the article fetching community attention/response. Also, the article receives at this occasion additional comments from experts and young scientists in the academia through PLoS ONE's unique discussion and response forum with ratings and annotations. This can effectively catalyze community engagement through PLoS ONE Journal Clubs (JCs). Such JCs involve groups of scientists, post docs and graduate students who volunteer to discuss PLoS ONE articles and post their discussions as a series of questions, comments, annotations, and ratings eventually triggering discussions within a broader scientific community.

Sunday, July 6, 2008

The ‘threatening’ success of PLoS; now heard aloud!

I was so happy to have published in May this year an invited perspectives article in a Nature Reviews journal. I considered Nature a prestigious place to publish and that they are highly organized and professional. However, sadly, this belief stand shaken after reading a slanted story in the recent issue of Nature, apparently attacking PLoS (that Nature sees as competitor!). I am kinda surprised; sometime back a similar slang on PLoS was passed by another group, although it was not heard aloud. Well that means PLoS is fast becoming a threatening success! Thanks to the cause that it bolsters and the public support that it enjoys globally.

As the matter currently dominantes blogosphere (see links below), I think I am not alone with my shaken belief; this should be sorrowfully the case of many who proudly published in journals of both Nature and PLoS. I wonder, if Nature risks alienating many of its well-wishers with such a stand it has taken against PLoS and Open Access.

I found the overall tone and spirit of the news article quite disturbing and distasteful. Especially, their painting of PLoS ONE journal as a ‘dumping ground’ and mention of its peer review process as ‘light’ is not at all correct and ignores facts. I see it as an unsuccessful attempt to dump all the ground-breaking work that PLoS ONE has been publishing since its launch in 2006 (see these posts for exmple; here, here and here). As I said in my response to the story, it is a simple fact that the ~300 scientists who publish in PLoS ONE every month and the 500 Editors who devote their time on rounds of peer reviewing are certainly not the fools out there.

The story referred PLoS as resorting to ‘bulk and cheap publishing’; what a slang! Apparently, however, the "bulk, cheap and lower quality papers" published by PLoS are not going unnoticed by Nature. Three of the ‘Research Highlights’ articles in the same issue report on articles published in PLoS journals (two from PLoS ONE! and one from PLoS Genetics). And I quote Scott Ramsey: ‘If it (the research that PLoS published) is not interesting enough to publish in Nature, at least it provides enough free copy to help round out an issue’!

Finally, I do not want to add more on my own perspective here as it is no different than what many others have already rolled out. There has been tremendous outrage to Nature’s self serving article (apparently all going in favor of PLoS!) in the blogosphere, as well as in the comments thread of the article itself. A summary of the relevant posts on the article can be found at:

Links to other related posts are here:

Conflict of interest statement: I volunteer as Section Editor for PLoS ONE.

Wednesday, July 2, 2008

New in PLoS ONE: Genetic structure of Adi tribes of North-East India

PLoS ONE today published a crop of 60 brand new articles, several of them are hitting the headlines. An interesting article from India by TS Vasulu and colleagues is also being talked about a lot since this morning (see below). The paper discusses 'Microsatellite based analysis of the genetic status of Adi tribes of Northeast India'.

Population biologists and anthropologists have been traditionally interested in aspects of human history and population migration in India -a homeland of a large number of genetic lineages of tribals and mainstream populations which speak 1600 different languages and dialects.

The article by Vasulu presents important genetic data from a number of closely related Tibeto-Burman speaking tribes from north-east India. The authors correctly present this region of India of utmost importance with respect to ancient human migration processes. In addition, the novel results obtained from these populations are compared with similar data from a range of other populations obtained from the literature.

Based on 15 autosomal microsatellite (STR) markers, the authors studied the genetic affinity, differentiation and sub-structuring among six Adi subgroups, as well as their genetic affinity with other neighbouring, Tibeto-Burman-speaking, tribes of India and with the linguistically divergent east and south-east Asian populations, with whom they share common ethno-historical and cultural attributes. The researchers investigated to what extent the six Adi subgroups are genetically divergent or affiliated. A comparison with the 16 Tibeto-Burman-speaking tribes of the neighbouring region in northern and north-eastern parts of the country as revealed by the cluster analyses indicates geographically proximate populations forming a close cluster. This is to be expected if these populations have indeed diverged from a common source after their settlement in different regions of the country in the recent past. In a comparison of the 50 populations (including populations from east and south-east Asia) for genetic diversity based on the autosomal loci, the resultant clustering tree showed some of the Tibeto-Burman tribes clustering with the populations from Tibet and China and whereas other Tibeto-Burman tribes of India cluster with linguistically different Southeast Asian populations. These results support the possibility that Tibeto-Burman populations were derived from more than one common source. Overall, the Adi and other Tibeto-Burman speaking populations of India are regionally well differentiated and exhibit genetic affinity with the neighboring populations of East/Southeast Asia, based on their shared ethno-history. However, a clearer picture may well emerge from the analysis of increased number of informative genetic markers and from the uniparental markers like mitochondrial DNA and Y chromosome.

You can read the news coverage about this study here and you may post your own reactions and comments directly on the article of Vasulu and colleagues by creating an account on the PLoS ONE website.

[Source: Press release of T S Vasulu, Indian Statistical Institute, Kolkata, India]

Sunday, June 29, 2008

My picks from PLoS ONE: Malaria and tularemia – diagnostic markers and vaccine candidates

PLoS ONE published 54 new articles last week. I had a chance to thoroughly read two of them also because they were edited by me and that they have some real potential towards the development of diagnostics and vaccines for infection control.

The paper - Novel Peptide Marker Corresponding to Salivary Protein gSG6 Potentially Identifies Exposure to Anopheles Bites from Anne Poinsingnon’s group is highly relevant in the context of devising vector control strategies in malaria endemic regions. This study combined a bio-informatics approach with standard immunoepidemiological assays to identify an Anopheles specific salivary peptide that could be developed as a marker of exposure to Anopheles bites. Such an epidemiological tool would have direct application in identifying high risk areas for malaria transmission and areas where vector control strategies should be implemented. I really think that this work is of interest not only for those who work in malaria control and in the evaluation of vector control strategies but also in the field of the immune response to arthopod salivary components. If this approach proved to be succesful, it could be applied to the control of other vector-borne diseases.

Another study - A Francisella tularensis Schu S4 Purine Auxotroph Is Highly Attenuated in Mice but Offers Limited Protection against Homologous Intranasal Challenge from the group of Thomas Zahrt was another interesting article to recommend. It describes the use of type A and LVS-derived purine auxotroph mutants of Francisella as potential candidates for live attenuated vaccines against tularemia. The intranasal challenge approach taken by the investigators is new and is more representative of a real exposure than other studies, and was judged a major strength of the study. However, there are certain shortcomings of this study that would invite future research efforts by this and other groups working in the field of tularemia prophylaxis - the type A-derived mutant offered a little bit of protection of challenged animals in terms of lethality but the vaccinated animals still exhibited bacterial survival in the lungs, and many of them succumbed to infection. Nonetheless, the results clearly inform us that the development of next generation live attenuated vaccine for Francisella should be based on the use of less aggressive B type strains rather than the more reactogenic type A.

Thursday, June 26, 2008

Recent PLoS ONE Evaluations at the Faculty of 1000 Biology

This week, 4 new articles from PLoS ONE have been tagged at the F1000 Biology. The articles have been judged as conveying significantly novel observations:

1) The molecular diversity of freshwater picoeukaryotes reveals high occurrence of putative parasitoids in the plankton. Lefèvre E, Roussel B, Amblard C, Sime-Ngando T. PLoS ONE 2008 3(6):e2324

Selected by: Carlos Pedrós-Alió, Instituto de Ciencies del Mar, Spain [ECOLOGY]
Evaluated 24 Jun 2008

Tags: Confirmation, Hypothesis
F1000 Factor: 3.0

This paper proposes that parasitism plays a larger role than previously thought in aquatic microbial food webs. This has implications for both the natural history of microorganisms and for carbon flow. Molecular surveys of microbial diversity of aquatic systems regularly provide many sequences related to organisms that are known to be parasites. This paper presents another example of this from a freshwater lake. About 65% of the sequences obtained belonged to Alveolates, Stramenopiles and Fungi. Many of the known organisms in these groups are either parasites or saprotrophs and their abundance suggests they must have a significant role in carbon flow. It is true that molecular surveys overestimate organisms with a large copy number of the 18S rRNA gene and that similarity of sequence does not necessarily imply the same function. However, the proposal of a "parasite loop" within the microbial food web is a welcome stimulus to try to quantify this process in ecosystems.
[Why not rate this article yourself?]

2) The yeast Tor signaling pathway is involved in G2/M transition via polo-kinase. Nakashima A, Maruki Y, Imamura Y, Kondo C, Kawamata T, Kawanishi I, Takata H, Matsuura A, Lee KS, Kikkawa U, Ohsumi Y, Yonezawa K, Kamada Y. PLoS ONE 2008 3(5):e2223

Selected by: Joe Heitman with Cecelia Shertz and Maria E. Cardenas, Duke University Medical Center, United States of America [MICROBIOLOGY]
Evaluated 23 Jun 2008

Tags: Hypothesis, New Finding, Novel Drug Target
F1000 Factor: 3.0

The ubiquitous Tor nutrient sensor cascade was discovered to evoke G2/M cell cycle transition via the polo-like kinase Cdc5 in Saccharomyces cerevisiae. It was known that inhibition of Tor with rapamycin causes a G1 cell cycle arrest, whereas these new findings by Nakashima et al. demonstrate that disruption of the Tor complex 1 (TORC1) provokes a G2/M delay. This effect is attributable to TORC1-protein phosphatase 2A mediated Cdc5 nuclear import, which has multiple mitotic roles including Swe1 phosphorylation which controls G2/M transition, cytokinesis, and CLB2 expression. This study reveals Tor is active throughout the cell cycle via key cell cycle regulators. This scenario differs from that found in Schizosaccharomyces pombe, where rapamycin stimulates mitotic entry {1}. Future studies should address if TORC1 governs the G2/M transition in multi-cellular eukaryotes such as humans. Reference: {1} Petersen et al. Nat Cell Biol 2007, 9:1263-1272.
[Why not rate this article yourself?]

3) Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi. Corradi N, Akiyoshi DE, Morrison HG, Feng X, Weiss LM, Tzipori S, Keeling PJ. PLoS ONE 2007 2(12):e1277

Selected by: Joe Heitman with Soo Chan Lee, Duke University Medical Center, United States of America [MICROBIOLOGY]
Evaluated 20 Jun 2008

Tags: Hypothesis, New Finding
F1000 Factor: 3.0

Genomic inspection for three microsporidians, obligate intracellular eukaryotic pathogens, reveals a high degree of synteny conserved in their otherwise reduced, compact, rapidly evolving genomes. Comparative genomic analysis between the completed Encephalitozoon cuniculi genome (2.9 Mb) with corresponding representative segments (~429 kb) from the genomes of Antonospora locustae and Enterocytozoon bieneusi reveals a high degree of gene conservation across all three, despite considerable evolutionary distance, but with less frequent changes in higher scale genomic architecture. The microsporidia were once thought to be ancestral eukaryotes devoid of a mitochondria, but with the discovery that they harbor a mitochondrial relic (the mitosome), it is now appreciated that they are highly evolved eukaryotes that emerged either from within the fungi or as a sister group to fungi. Their genomes have been compacted, not only by rampant gene loss, but also by the loss of repetitive sequences and transposons, a purging of nearly all introns, by a shortening of each protein by an average of 15%, and by virtue of having very short intergenic regions. While their gene sequences have been evolving at an accelerated pace, their higher order genome architecture has become constrained, likely as a consequence of the shortened intergenic regions, which limits the translocations that can occur without disrupting neighboring gene structure or expression. As a consequence, syntenic genomic relationships, rather than phylogenetic sequence relationships, represent a novel window on their evolutionary trajectory.
[Why not rate this article yourself?]

4) Ex vivo generation of human alloantigen-specific regulatory T cells from CD4(pos)CD25(high) T cells for immunotherapy. Peters JH, Hilbrands LB, Koenen HJ, Joosten I PLoS ONE 2008, 3(5):e2233

Selected by: Mohamed Sayegh with Jessamyn Bagley, Brigham and Women’s Hospital and Children’s Hospital Boston, United States of America [IMMUNOLOGY]
Evaluated 19 Jun 2008

Tags: Tech Advance
F1000 Factor: 3.0

The authors describe an efficient protocol for the generation of antigen-specific human regulatory T cells (Treg). This may advance the goal of using Treg to generate specific tolerance to antigens, such as those present on organ allografts.
[Why not rate this article yourself?]

Faculty of 1000 Biology is a new revolutionary literature evaluation service which helps researchers identify most significant and impacting publications in their field. Evaluations at the F1000 are considered as authoritative insights on individual articles. Being on F1000 I always enjoyed to analyze how post publication evaluations of articles might throw up a new bibliometric tool to gauge the worth of individual articles. While keeping a tab on this , I can say that the Faculty of 1000 Members are increasingly inclined to evaluate high quality Open Access articles from journals such as PLoS ONE. Thanks to the fact that these articles are reader (and media) friendly and picked easily by the F1000 Faculty. It is evident from the fact that nearly 100 articles from PLoS ONE have been evaluated there between January 2007 and June 2008. This boolean search may be helpful to track PLoS ONE evaluations at the F1000 Biology as compared to evaluations from journals such as Nature.

Thursday, June 19, 2008

The surfeit of chimp articles at PLoS ONE

Please don’t laugh if I say the word ‘chimp’ is getting more and more auspicious and luckier for

Yesterday, two cool articles published in PLoS ONE turned out to be quite hot in the media and blogosphere this morning. The loud story discussed everywhere (such as Female chimps keep quiet while mating at Times Online; Chimp’s Sex Calls May Reflect Calculation at New York Times; Squeaky chimp sex, or not at Science News; Why chimps scream during sex - it's a bit complicated San Francisco Chronicle, and so on) highlighted why female chimps keep quite during the sexual engagement. You may like to comment on the paper and rate it right here.

Another important study on how young chimps die due to social networking, spread over 20 years of observations, analyzed links between behavioral patterns, social networking, mortality cycles and synchronization of breeding in a chimpanzee colony in Ivory Coast. Nature carried a breaking news article on its website (here) highlighting significance and impact of this study and included comments from the authors. While the story is at the moment actively being discussed at Nature, several other news channels started discussing the article – Play can be fatal for young chimps at The Cheers, Estonia; Infant play drives chimpanzee respiratory disease cycles at Eureka! Science News, Canada; Chimpanzees' Terrible Twos at Science Now; Play can be fatal for young chimps at; etc. Being an Academic Editor on this important paper it is indeed quite pleasing for me although I was reluctant initially to handle this nice article as an Editor because I am not a primatologist. However, upon close reading also in consultation with my fellow Editor, Sarah Brosnan, I found the study quite near to my interest in infectious diseases and during the process the manuscript sort of ‘resurrected’ the Veterinarian inside me! We found the authors very cooperative and prompt to the editorial queries and revised the manuscript in a highly professional style. Timeliness is really very important in science publishing and we, as always, ensured that the revisions are completed expeditiously so the story catches its full worth at just a right time point. This indeed involves a greater co-ordination and involvement on the part of editors, reviewers and the authors – a working principle at PLoS ONE.

Another chimp tale - Sarah previously studied the circumstances under which chimpanzees exchange a lower-value food item (like an apple slice) for one valued more highly (like a grape). The article was extensively covered by the media and was discussed in blogosphere. You can, as always, join in the discussion by posting your comments onto the online version of Brosnan’s paper. Another paper on Chimps’ diet by researchers at the Max Planck Institute for Evolutionary Anthropology was picked up by Newsweek and Wired, as well as The Daily Mirror and was discussed in several blogs.

Back in the month of September a remarkable article (Chimpanzees Share Forbidden Fruit), by Kimberley Hockings and colleagues, also from Max Plank, discussed that male chimpanzees steal desirable fruits, like papayas, to engage their female counterparts, who trade sexual favours in return for a share of the spoils. This was again a big media event.

All content published at PLoS ONE, from chimps to birds to corals to genomes and metagenomes is freely available online and articles can be commented upon, rated and discussed to enjoy the full power of Web 2.0 technology that the PLoS ONE is currently harnessing. There is certainly quite diverse food for thought here and you can always join in the discussion yourself by creating an account on the journal site and posting your comments for others to read. Also, you may like to rate the articles. Ratings are the quickest and easiest way for users to indicate which articles are of potential impact for the readers and the scientific community.

Friday, June 13, 2008

Soothing rains, soothing papers

My month long summer holidays just ended with the first rains after a very hot season (42 ℃) here in Hyderabad. Within the last 2 days the rejoice of Monsoon intensified also with the recent PLoS ONE evaluations at the F1000 Biology!! It appears that the Faculty Members of F1000 are now regularly picking up papers from PLoS series. Whereas this article Adaptation and mal-adaptation to ambient hypoxia; Andean, Ethiopian and Himalayan patterns. Xing G, Qualls C, .., Verma A, Appenzeller O, PLoS ONE 2008 3(6):e2342- [abstract on PubMed] [related articles] [free full text], by Xing and colleagues was rated as exceptional, the other two papers 1) Imaging cyclic AMP changes in pancreatic islets of transgenic reporter mice. Kim JW, Roberts CD, .., Roper SD, Chaudhari N, PLoS ONE 2008 3(5):e2127- [abstract on PubMed] [related articles] [free full text] and 2) East learns from West: Asiatic honeybees can understand dance language of European honeybees. Su S, Cai F, .., Tautz J, Chen S, PLoS ONE 2008 3(6):e2365- [abstract on PubMed] [related articles] [free full text] were tagged significant and with novel findings.

Roughly about 4-5% 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). For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations constitute important quality indexes for individual articles especially when a much controversial bibliometric index such as 'impact factor' is becoming increasingly redundant.

Another soothing observation was that the Viking DNA paper from Jørgen Dissing’s group, Evidence of Authentic DNA from Danish Viking Age Skeletons Untouched by Humans for 1,000 Years, which I handled recently was very well taken by the popular and science press. The paper was Slashdotted and subsequently received several thousand hits within the space of a couple of days as also reported in PLoS Blog by Rebecca Walton. Some of the coverage of this article is listed below:
Live Science – DNA Retrieved from 1000-year-old Vikings; Wired – Researchers Recover Thousand-Year-Old Viking DNA; People's Daily, China Impossible! Scientists retrieve ancient Viking DNA; Zee News (India) DNA from 1000 yr old skeletons!; Malaysia Sun Viking DNA retrieved from 1000-year-old skeletons; Newsweek – Bring Back the Vikings: Ancient DNA; Discover Magazine – Hide the Women and Children! Researchers Dig up Viking DNA Scientist Live, UK – Authentic Viking DNA; Huffington Post – Viking DNA Recovered From Ten 1,000-Year-Old Skeletons: Report; – Recovering 1,000 Year Old Viking mtDNA; Science a Gogo Viking DNA Retrieved etc.

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]