Project description:The reason why prostate cancer is significantly more common in Western than Asian men is unknown. Using a genome-wide approach to compare the genomic changes in prostate cancer tissues, we determined that those from Chinese patients lack key somatic genomic changes commonly found in Western patients, including the 21q22.2-22.3 deletion which causes the TMPRSS2:ERG fusion gene, and 10q deletion which leads to PTEN inactivation. The results were confirmed and their consequence on ERG expression was identified by study of a large series of Chinese and UK samples using tissue-microarrays. Subsequently, we identified significant AR genotype differences between UK and Chinese prostate cancer patients. The identification of specific somatic genomic differences in cancers from distinct populations may provide an opportunity to identify cancer-causing or protective factors.
Project description:Honeybee brain has distHoneybee brain has distinct anatomical and functional regions, knowledge on molecular underpinnings of sub-organ to achieve the distinct neural function and the difference between the eastern and western honeybees are still missing. Here, the proteomes of three sub-organs of eastern and western honeybee brains were compared. Mushroom bodies (MBs) and optical lobes (OLs) may by employed similar proteome architectures to drive their domain-specific neural activity in both bee species. In MBs, protein metabolism and Ca2+ transmembrane transport are the key role players in driving the learning and memory by modulating the synaptic structure and signal transduction to consolidate memory trace. In OLs, ribonucleoside metabolism and energy production play major roles to underpin visual system by maintaining G-protein cycle and membrane electrical charge potential. However, in antennal lobes (ALs), it has evolved distinct proteome settings to prime the olfactory learning and memory in two bee species. In ALs of Apis cerana cerana (Acc), actin cytoskeleton organization is key for plasticity of glomeruli and intracellular transport to sustain the olfactory signaling. Whereas, in ALs of Apis mellifera ligustica (Aml), hydrogen and hydrogen ion transport are vital to support olfactory process by supplying energy and maintaining molecule transport. Noticeably, in ALs of Acc, the exclusively enriched functional groups acting as second messenger and neurontransmitter of signal transduction, and the enhanced protein metabolism to regulate the plasticity of synaptic structure for formation of memory, suggest that Acc may have evolved a better sense of smell than that of Aml. Our first proteome data is helpful as starting point for further analysis of neural activity in brain sub-area of honeybee and other insects.inct anatomical and functional regions, knowledge on molecular underpinnings of sub-organ to achieve the distinct neural function and the difference between the eastern and western honeybees are still missing. Here, the proteomes of three sub-organs of eastern and western honeybee brains were compared. Mushroom bodies (MBs) and optical lobes (OLs) may by employed similar proteome architectures to drive their domain-specific neural activity in both bee species. In MBs, protein metabolism and Ca2+ transmembrane transport are the key role players in driving the learning and memory by modulating the synaptic structure and signal transduction to consolidate memory trace. In OLs, ribonucleoside metabolism and energy production play major roles to underpin visual system by maintaining G-protein cycle and membrane electrical charge potential. However, in antennal lobes (ALs), it has evolved distinct proteome settings to prime the olfactory learning and memory in two bee species. In ALs of Apis cerana cerana (Acc), actin cytoskeleton organization is key for plasticity of glomeruli and intracellular transport to sustain the olfactory signaling. Whereas, in ALs of Apis mellifera ligustica (Aml), hydrogen and hydrogen ion transport are vital to support olfactory process by supplying energy and maintaining molecule transport. Noticeably, in ALs of Acc, the exclusively enriched functional groups acting as second messenger and neurontransmitter of signal transduction, and the enhanced protein metabolism to regulate the plasticity of synaptic structure for formation of memory, suggest that Acc may have evolved a better sense of smell than that of Aml. Our first proteome data is helpful as starting point for further analysis of neural activity in brain sub-area of honeybee and other insects.
Project description:Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum- MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between House Finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG, and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population.
Project description:Through the use of proteomic analysis of 32 dental calculus samples from anceint Mongolia, we show that ruminant dairying was present in Mongolia by at least 3000 B.C.E., over 1500 years prior to previously published work. Excitingly, the earliest site with dairy evidence has been identified as archaeologically Afanasievo, supporting the hypothesis that dairy practices and animals likely entered the Eastern steppe with migrating western steppe populations. Furthermore, at 1200 B.C.E. we detect the first direct evidence for horse milk consumption, demonstrating the Bronze Age origins of equine dairying on the eastern steppe which occurred concomitantly with early evidence for horse bridling and riding in the region. The incorporation of horse milk and riding into early Mongolian subsistence strategies led to dramatic economic and demographic shifts that enabled the formation of the well-known steppe empires.
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are sex-specific and environmental condition dependent.
Project description:Innate immunity is expected to play a primary role in conferring resistance to novel infectious diseases, but few studies have attempted to examine its role in the evolution of resistance to emerging pathogens in wild vertebrate populations. Here we used experimental infections and cDNA microarrays to examine whether changes in the innate and/or acquired immune responses likely accompanied the emergence of resistance in house finches (Carpodacus mexicanus) in the eastern United States subject to a recent outbreak of conjunctivitis-causing bacterium (Mycoplasma gallisepticum- MG). Three days following experimental infection with MG, we observed differences in the splenic transcriptional responses between House Finches from eastern U.S. populations, with a 12-year history of MG exposure, versus western U.S. populations, with no history of exposure to MG. In particular, western birds down-regulated gene expression, while eastern finches showed no expression change relative to controls. Studies involving poultry have shown that MG can manipulate host immunity, and our observations suggest that pathogen manipulation occurred only in finches from the western populations, outside the range of MG. Fourteen days after infection, eastern finches, but not western finches, up-regulated genes associated with acquired immunity (cell-mediated immunity) relative to controls. These observations suggest population differences in the temporal course of the response to infection with MG, and imply that innate immune processes were targets of selection in response to MG in the eastern U.S. population. Birds were randomly selected to be kept either as controls or infected via ocular inoculation with 20 μl of culture containing 1 x 104 to 1 x 106 color changing units/ml of an early 2007 Auburn MG isolate. All infected birds were inoculated with precisely the same volume of the same culture. Control birds were sham infected using sterile SP4 medium (Whitcomb 1983). Infected birds were euthanized three days (N=6 from Arizona and N=11 from Alabama) and 14 days (N=11 from Arizona and N=12 from Alabama) after treatment. Control birds were euthanized 14 days after sham-inoculation; Control (N=11 birds from Arizona and 9 from Alabama) and infected birds were maintained under identical conditions, but in separate rooms of an aviary. Infected birds were euthanized three days (N=6 from Arizona and N=11 from Alabama) and 14 days (N=11 from Arizona and N=12 from Alabama) after treatment. Control birds were euthanized 14 days after sham-inoculation. We used a common reference design (Yang & Speed 2002), in which we pooled 2 to 6 spleens from birds from the same population in the same treatment to generate enough mRNA for microarray hybridizations and hybridized two pools for each treatment from each population.
Project description:We confirmed the role of the Sahel belt as a main corridor for human migrations across the African continent. Strong admixture was observed in both Central and Eastern Sahelian populations, with North Africans and Near Eastern/Arabians respectively, but it was inexistent in Western Sahelian populations. Genome-wide local ancestry inference in admixed Sahelian populations revealed several candidate regions that were significantly enriched for non-autochthonous haplotypes, and many showed to be under positive selection.
Project description:The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod from different regions, western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through oligonucleotide microarray.
Project description:The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod subpopulation: western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through genome-wide oligonucleotide microarray.