Journals
2011 EN
YoungDo Nam · Mi-Ja Jung · Seong Woon Roh
+2 more
Human gut microbiota plays important roles in harvesting energy from the diet, stimulating the proliferation of the intestinal epithelium, developing the immune system, and regulating fat storage in the host. Characterization of gut microbiota, however, has been limited to western people and is not sufficiently extensive to fully describe microbial communities. In this study, we investigated the overall composition of the gut microbiota and its host specificity and temporal stability in 20 Koreans using 454-pyrosequencing with barcoded primers targeting the V1 to V3 region of the bacterial 16S rRNA gene. A total of 303,402 high quality reads covered each sample and 8,427 reads were analyzed on average. The results were compared with those of individuals from the USA, China and Japan. In general, microbial communities were dominated by five previously identified phyla: Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria. UPGMA cluster analysis showed that the species composition of gut microbiota was host-specific and stable over the duration of the test period, but the relative abundance of each member fluctuated. 43 core Korean gut microbiota were identified by comparison of sequences from each individual, of which 15 species level phylotypes were related to previously-reported butyrate-producing bacteria. UniFrac analysis revealed that human gut microbiota differed between countries: Korea, USA, Japan and China, but tended to vary less between individual Koreans, suggesting that gut microbial composition is related to internal and external characteristics of each country member such as host genetics and diet styles.
Public Library of Science
Journals
2011 EN
Nandan Deshpande · Nadeem O. Kaakoush · Hazel M. Mitchell
+4 more
Campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. Its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. Here, we sequence and analyze the genome of a C. concisus from a biopsy of a child with Crohn's disease (UNSWCD); the second such genome for this species. A 1.8 Mb genome was assembled with paired-end reads from a next-generation sequencer. This genome is smaller than the 2.1 Mb C. concisus reference BAA-1457. While 1593 genes were conserved across UNSWCD and BAA-1457, 138 genes from UNSWCD and 281 from BAA-1457 were unique when compared against the other. To further validate the genome assembly and annotation, comprehensive shotgun proteomics was performed. This confirmed 78% of open reading frames in UNSWCD and, importantly, provided evidence of expression for 217 proteins previously defined as ‘hypothetical’ in Campylobacter . Substantial functional differences were observed between the UNSWCD and the reference strain. Enrichment analysis revealed differences in membrane proteins, response to stimulus, molecular transport and electron carriers. Synteny maps for the 281 genes not present in UNSWCD identified seven functionally associated gene clusters. These included one associated with the CRISPR family and another which encoded multiple restriction endonucleases; these genes are all involved in resistance to phage attack. Many of the observed differences are consistent with UNSWCD having adapted to greater surface interaction with host cells, as opposed to BAA-1457 which may prefer a free-living environment.
Public Library of Science
Journals
2011 EN
Masaaki Minami · Mariko Ichikawa · Nanako Hata
+1 more
Background Streptococcus pyogenes ( S. pyogenes ) causes various serious diseases including necrotizing fasciitis and streptococcal toxic shock syndrome. One serious problem observed recently with S. pyogenes therapy is attenuation of the antibiotic effect, especially penicillin treatment failure and macrolide resistance. Hainosankyuto, a traditional Japanese medicine based on ancient Chinese medicine, has been used for treatment of infectious purulent diseases in Japan. In this study, we investigated the protective and therapeutic efficacy of Hainosankyuto against S. pyogenes -skin infection. Methodology/Principal Findings A broth microdilution method revealed that Hainosankyuto did not show a direct anti-bacterial effect against S. pyogenes . Force-feeding Hainosankyuto to infected mice for 4 consecutive days increased the survival rate and reduced the size of local skin lesions compared with mice fed PBS. Although we did not find the significant recovery of survival rate in Hainosankyuto administration only after S. pyogenes infection, the sizes of ulcer lesion were significant smaller after Hainosankyuto administration compared with mice fed PBS. No difference was observed in the anti-bacterial effect of Hainosankyuto between macrolide-susceptible and -resistant strains. Blood bactericidal assay showed that the survival rate of S. pyogenes using the blood from Hainosankyuto -treated mice was lower than that using the blood from untreated mice. We also found increased levels of IL-12, IFN-γ and a decreased level of TNF-α in the serum of S. pyogenes -infected mice treated with Hainosankyuto. Mouse peritoneal macrophage from Hainosankyuto-treated mice had significant phagocytic activity and increased mRNA levels of IL-12, IFN-γ and decreased mRNA level of TNF-α compared with control macrophage. Conclusions/Significance Hainosankyuto increased survival rate after S. pyogenes infection and up-regulated both blood bactericidal activity and macrophage phagocytic activity through modulation of inflammatory cytokines. Our data also suggest Hainosankyuto may be useful for the treatment of S. pyogenes infection more prophylactically than therapeutically.
Public Library of Science
Journals
2011 EN
Anna Chmiel · Julian Sienkiewicz · Mike Thelwall
+4 more
E-communities, social groups interacting online, have recently become anobject of interdisciplinary research. As with face-to-face meetings, Internetexchanges may not only include factual information but also emotionalinformation - how participants feel about the subject discussed or other groupmembers. Emotions are known to be important in affecting interaction partnersin offline communication in many ways. Could emotions in Internet exchangesaffect others and systematically influence quantitative and qualitative aspectsof the trajectory of e-communities? The development of automatic sentimentanalysis has made large scale emotion detection and analysis possible usingtext messages collected from the web. It is not clear if emotions ine-communities primarily derive from individual group members' personalities orif they result from intra-group interactions, and whether they influence groupactivities. We show the collective character of affective phenomena on a largescale as observed in 4 million posts downloaded from Blogs, Digg and BBCforums. To test whether the emotions of a community member may influence theemotions of others, posts were grouped into clusters of messages with similaremotional valences. The frequency of long clusters was much higher than itwould be if emotions occurred at random. Distributions for cluster lengths canbe explained by preferential processes because conditional probabilities forconsecutive messages grow as a power law with cluster length. For BBC forumthreads, average discussion lengths were higher for larger values of absoluteaverage emotional valence in the first ten comments and the average amount ofemotion in messages fell during discussions. Our results prove that collectiveemotional states can be created and modulated via Internet communication andthat emotional expressiveness is the fuel that sustains some e-communities.
Public Library of Science
Journals
2011 EN
Daniëlle van Manen · Olivier Delaneau · Neeltje A. Kootstra
+10 more
Background AIDS develops typically after 7–11 years of untreated HIV-1 infection, with extremes of very rapid disease progression (15 years). To reveal additional host genetic factors that may impact on the clinical course of HIV-1 infection, we designed a genome-wide association study (GWAS) in 404 participants of the Amsterdam Cohort Studies on HIV-1 infection and AIDS. Methods The association of SNP genotypes with the clinical course of HIV-1 infection was tested in Cox regression survival analyses using AIDS-diagnosis and AIDS-related death as endpoints. Results Multiple, not previously identified SNPs, were identified to be strongly associated with disease progression after HIV-1 infection, albeit not genome-wide significant. However, three independent SNPs in the top ten associations between SNP genotypes and time between seroconversion and AIDS-diagnosis, and one from the top ten associations between SNP genotypes and time between seroconversion and AIDS-related death, had P-values smaller than 0.05 in the French Genomics of Resistance to Immunodeficiency Virus cohort on disease progression. Conclusions Our study emphasizes that the use of different phenotypes in GWAS may be useful to unravel the full spectrum of host genetic factors that may be associated with the clinical course of HIV-1 infection.
Public Library of Science
Journals
2011 EN
Stephan Kitchovitch · Píetro Lió
During an infectious disease outbreak people will often change their behaviour to reduce their risk of infection. Furthermore, in a given population, the level of perceived risk of infection will vary greatly amongst individuals. The difference in perception could be due to a variety of factors including varying levels of information regarding the pathogen, quality of local healthcare, availability of preventative measures, etc. In this work we argue that we can split a social network, representing a population, into interacting communities with varying levels of awareness of the disease. We construct a theoretical population and study which such communities suffer most of the burden of the disease and how their awareness affects the spread of infection. We aim to gain a better understanding of the effects that community-structured networks and variations in awareness, or risk perception, have on the disease dynamics and to promote more community-resolved modelling in epidemiology.
Public Library of Science
Journals
2011 EN
Christina M. Carr · Sarah L. Mincks · Tanya M. Brown
+2 more
Background Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested. Methodology/Principal Findings Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI) gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada's three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%). Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas. Conclusions/Significance Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia fauna played a minor role in Arctic recolonization following deglaciation. This study highlights the value of DNA barcoding for providing rapid insights into species distributions and biogeographic patterns in understudied groups.
Public Library of Science
Journals
2011 EN
Freija Hauquier · Jeroen Ingels · Julian Gutt
+2 more
Background Recent climate-induced ice-shelf disintegration in the Larsen A (1995) and B (2002) areas along the Eastern Antarctic Peninsula formed a unique opportunity to assess sub-ice-shelf benthic community structure and led to the discovery of unexplored habitats, including a low-activity methane seep beneath the former Larsen B ice shelf. Since both limited particle sedimentation under previously permanent ice coverage and reduced cold-seep activity are likely to influence benthic meiofauna communities, we characterised the nematode assemblage of this low-activity cold seep and compared it with other, now seasonally ice-free, Larsen A and B stations and other Antarctic shelf areas (Weddell Sea and Drake Passage), as well as cold-seep ecosystems world-wide. Principal Findings The nematode community at the Larsen B seep site differed significantly from other Antarctic sites in terms of dominant genera, diversity and abundance. Densities in the seep samples were high (>2000 individuals per 10 cm 2 ) and showed below-surface maxima at a sediment depth of 2–3 cm in three out of four replicates. All samples were dominated by one species of the family Monhysteridae, which was identified as a Halomonhystera species that comprised between 80 and 86% of the total community. The combination of high densities, deeper density maxima and dominance of one species is shared by many cold-seep ecosystems world-wide and suggested a possible dependence upon a chemosynthetic food source. Yet stable 13 C isotopic signals (ranging between −21.97±0.86‰ and −24.85±1.89‰) were indicative of a phytoplankton-derived food source. Conclusion The recent ice-shelf collapse and enhanced food input from surface phytoplankton blooms were responsible for the shift from oligotrophic pre-collapse conditions to a phytodetritus-based community with high densities and low diversity. The parthenogenetic reproduction of the highly dominant Halomonhystera species is rather unusual for marine nematodes and may be responsible for the successful colonisation by this single species.
Public Library of Science
Journals
2011 EN
Nathan A. Haislip · Matthew J. Gray · Jason T. Hoverman
+1 more
Ranaviruses have caused die-offs of amphibians across the globe. In North America, these pathogens cause more amphibian mortality events than any other pathogen. Field observations suggest that ranavirus epizootics in amphibian communities are common during metamorphosis, presumably due to changes in immune function. However, few controlled studies have compared the relative susceptibility of amphibians to ranaviruses across life stages. Our objectives were to measure differences in mortality and infection prevalence following exposure to ranavirus at four developmental stages and determine whether the differences were consistent among seven anuran species. Based on previous studies, we hypothesized that susceptibility to ranavirus would be greatest at metamorphosis. Our results did not support this hypothesis, as four of the species were most susceptible to ranavirus during the larval or hatchling stages. The embryo stage had the lowest susceptibility among species probably due to the protective membranous layers of the egg. Our results indicate that generalizations should be made cautiously about patterns of susceptibility to ranaviruses among amphibian developmental stages and species. Further, if early developmental stages of amphibians are susceptible to ranaviruses, the impact of ranavirus epizootic events may be greater than realized due to the greater difficulty of detecting morbid hatchlings and larvae compared to metamorphs.
Public Library of Science
Journals
2011 EN
María Laura Gutiérrez · Luís MuñozBellvis · M. Abad
+4 more
The specific genes and genetic pathways associated with pancreatic ductal adenocarcinoma are still largely unknown partially due to the low resolution of the techniques applied so far to their study. Here we used high-density 500 K single nucleotide polymorphism (SNP)-arrays to define those chromosomal regions which most commonly harbour copy number (CN) alterations and loss of heterozygozity (LOH) in a series of 20 PDAC tumors and we correlated the corresponding genetic profiles with the most relevant clinical and histopathological features of the disease. Overall our results showed that primary PDAC frequently display (>70%) extensive gains of chromosomes 1q, 7q, 8q and 20q, together with losses of chromosomes 1p, 9p, 12q, 17p and 18q, such chromosomal regions harboring multiple cancer- and PDAC-associated genes. Interestingly, these alterations clustered into two distinct genetic profiles characterized by gains of the 2q14.2, 3q22.1, 5q32, 10q26.13, 10q26.3, 11q13.1, 11q13.3, 11q13.4, 16q24.1, 16q24.3, 22q13.1, 22q13.31 and 22q13.32 chromosomal regions (group 1; n = 9) versus gains at 1q21.1 and losses of the 1p36.11, 6q25.2, 9p22.1, 9p24.3, 17p13.3 and Xp22.33 chromosomal regions (group 2; n = 11). From the clinical and histopathological point of view, group 1 cases were associated with smaller and well/moderately-differentiated grade I/II PDAC tumors, whereas and group 2 PDAC displayed a larger size and they mainly consisted of poorly-differentiated grade III carcinomas. These findings confirm the cytogenetic complexity and heterogenity of PDAC and provide evidence for the association between tumor cytogenetics and its histopathological features. In addition, we also show that the altered regions identified harbor multiple cancer associate genes that deserve further investigation to determine their relevance in the pathogenesis of PDAC.
Public Library of Science