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.