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]
Wednesday, July 2, 2008
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.
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
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.
[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
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.
[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
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.
[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
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.
[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.
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.
[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
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.
[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
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.
[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
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.
[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.
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