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

Comments:
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.
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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

Comments:
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.
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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

Comments:
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.
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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

Comments:
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.
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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.