AIM: To studythe role of intestinal flora in inflammatory bowel disease (IBD).METHODS: The spatial organization of intestinal flora was investigated in normal mice and in two models of murine colitis using fluorescenc...AIM: To studythe role of intestinal flora in inflammatory bowel disease (IBD).METHODS: The spatial organization of intestinal flora was investigated in normal mice and in two models of murine colitis using fluorescence in situ hybridization.RESULTS: The murine small intestine was nearly bacteriafree. The normal colonic flora was organized in three distinct compartments (crypt, interlaced, and fecal), each with different bacterial compositions. Crypt bacteria were present in the cecum and proximal colon. The fecal compartment was composed of homogeneously mixed bacterial groups that directly contacted the colonic wall in the cecum but were separated from the proximal colonic wall by a dense interlaced layer. Beginning in the middle colon, a mucus gap of growing thickness physically separated all intestinal bacteria from contact with the epithelium. Colonic inflammation was accompanied with a depletion of bacteria within the fecal compartment, a reduced surface area in which feces had direct contact with the colonic wall, increased thickness and spread of the mucus gap, and massive increases of bacterial concentrations in the crypt and interlaced compartments. Adhesive and infiltrative bacteria were observed in inflamed colon only, with dominant Bacteroides species.CONCLUSION: The proximal and distal colons are functionally different organs with respect to the intestinal flora, representing a bioreactor and a Segregation device.The highly organized structure of the colonic flora, its specific arrangement in different colonic segments, and its specialized response to inflammatory stimuli indicate that the intestinal flora is an innate part of host immunity that is under complex control.展开更多
The Changbai Mountains, located in northeastern China, show clear vertical zonation of vegetation types. Six different habitats,namely Pinus koraiensis mixed broad-leaved forest, Pinus koraiensis-Picea forest, spruce-...The Changbai Mountains, located in northeastern China, show clear vertical zonation of vegetation types. Six different habitats,namely Pinus koraiensis mixed broad-leaved forest, Pinus koraiensis-Picea forest, spruce-fir forest, Betula ermanii forest, alpine meadow and alpine semi-desert, at elevations ranging from 780 to 2 480 m, covering almost all ecosystems on the north slope of the Changbai Mountains, were investigated to determine: i) whether or not the community composition of soil mesofauna varied significantly at different elevations; ii) if different soil mesofauna groups would respond differently to elevation and iii) which factors influenced the spatial distribution of soil mesofauna along elevation. Soil mesofauna were collected from each habitat in spring(May),summer(July) and autumn(September) of 2009. The soil mesofauna communities were comprised of at least 44 groups and were dominated by Acari and Collembola, followed by Coleoptera, Diptera larvae and Enchytraeidae. The composition, diversity and abundance of soil mesofauna varied among the six habitats. Meanwhile, significant seasonal variations were observed in the composition,abundance and diversity of the soil mesofauna in each habitat. The taxonomic richness and Shannon index were affected by elevation and soil properties, while the abundance was only significantly affected by soil properties. With regard to taxa, the habitats and seasons had significant effects on almost all the abundances of the major taxonomic groups. The abundance of more taxonomic groups was significantly influenced by the soil properties, while those of Geophilomorpha, Araneae and other taxa were affected by elevation.It is concluded that the composition and spatial distribution of the soil mesofauna varied along the elevation gradient on the north slope of the Changbai Mountains, which might be largely related to the variations of the plant community, soil properties and climate change resulting from the elevation gradient.展开更多
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial...Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region （e.g., geographical distance, average sea surface temperature, average salinity）. We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water （experienced by most marine taxa at some point in their life cycle）, require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for land- scape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.展开更多
基金Supported by Broad Medical Research Program of the Eli and Edy the L. Broad foundation
文摘AIM: To studythe role of intestinal flora in inflammatory bowel disease (IBD).METHODS: The spatial organization of intestinal flora was investigated in normal mice and in two models of murine colitis using fluorescence in situ hybridization.RESULTS: The murine small intestine was nearly bacteriafree. The normal colonic flora was organized in three distinct compartments (crypt, interlaced, and fecal), each with different bacterial compositions. Crypt bacteria were present in the cecum and proximal colon. The fecal compartment was composed of homogeneously mixed bacterial groups that directly contacted the colonic wall in the cecum but were separated from the proximal colonic wall by a dense interlaced layer. Beginning in the middle colon, a mucus gap of growing thickness physically separated all intestinal bacteria from contact with the epithelium. Colonic inflammation was accompanied with a depletion of bacteria within the fecal compartment, a reduced surface area in which feces had direct contact with the colonic wall, increased thickness and spread of the mucus gap, and massive increases of bacterial concentrations in the crypt and interlaced compartments. Adhesive and infiltrative bacteria were observed in inflamed colon only, with dominant Bacteroides species.CONCLUSION: The proximal and distal colons are functionally different organs with respect to the intestinal flora, representing a bioreactor and a Segregation device.The highly organized structure of the colonic flora, its specific arrangement in different colonic segments, and its specialized response to inflammatory stimuli indicate that the intestinal flora is an innate part of host immunity that is under complex control.
基金supported by the National Natural Science Foundation of China (Nos. 41471211 and 41171207)
文摘The Changbai Mountains, located in northeastern China, show clear vertical zonation of vegetation types. Six different habitats,namely Pinus koraiensis mixed broad-leaved forest, Pinus koraiensis-Picea forest, spruce-fir forest, Betula ermanii forest, alpine meadow and alpine semi-desert, at elevations ranging from 780 to 2 480 m, covering almost all ecosystems on the north slope of the Changbai Mountains, were investigated to determine: i) whether or not the community composition of soil mesofauna varied significantly at different elevations; ii) if different soil mesofauna groups would respond differently to elevation and iii) which factors influenced the spatial distribution of soil mesofauna along elevation. Soil mesofauna were collected from each habitat in spring(May),summer(July) and autumn(September) of 2009. The soil mesofauna communities were comprised of at least 44 groups and were dominated by Acari and Collembola, followed by Coleoptera, Diptera larvae and Enchytraeidae. The composition, diversity and abundance of soil mesofauna varied among the six habitats. Meanwhile, significant seasonal variations were observed in the composition,abundance and diversity of the soil mesofauna in each habitat. The taxonomic richness and Shannon index were affected by elevation and soil properties, while the abundance was only significantly affected by soil properties. With regard to taxa, the habitats and seasons had significant effects on almost all the abundances of the major taxonomic groups. The abundance of more taxonomic groups was significantly influenced by the soil properties, while those of Geophilomorpha, Araneae and other taxa were affected by elevation.It is concluded that the composition and spatial distribution of the soil mesofauna varied along the elevation gradient on the north slope of the Changbai Mountains, which might be largely related to the variations of the plant community, soil properties and climate change resulting from the elevation gradient.
文摘Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region （e.g., geographical distance, average sea surface temperature, average salinity）. We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water （experienced by most marine taxa at some point in their life cycle）, require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for land- scape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.
