Project description:Dysregulation of sleep has widespread health consequences and represents an enormous health burden. Short-sleeping individuals are predisposed to the effects of neurodegeneration, suggesting a critical role for sleep in the maintenance of neuronal health. While the effects of sleep on cellular function are not completely understood, growing evidence has identified an association between sleep loss and DNA damage, raising the possibility that sleep facilitates efficient DNA repair. The Mexican tetra fish, Astyanax mexicanus provides a model to investigate the evolutionary basis for changes in sleep and the consequences of sleep loss. Multiple cave-adapted populations of these fish have evolved to sleep for substantially less time compared to surface populations of the same species without identifiable impacts on healthspan or longevity. To investigate whether the evolved sleep loss is associated with DNA damage and aging, we compared the transcriptional response to aging between surface and cave morphs of A. mexicanus
Project description:Caves are populated with a diverse fauna of highly adapted species that tend to exhibit a consistent suite of both regressive and constructive trait modifications. Because molecular studies of cave adaptation have largely concentrated on vertebrate models, our ability to recognize universalities in the genetic trajectories underlying cave adaptation remains limited. We have initiated efforts to elucidate the molecular evolution of the flightless small carrion beetle Ptomaphagus hirtus (Ptomaphagus hirtus), which represents one of the highly endemic signature inhabitants of the Mammoth Cave system of Kentucky. Ptomaphagus hirtus has been considered blind despite the presence of lateral eye rudiments. However, analysis of the Ptomaphagus hirtus adult head transcriptome by deep RNA sequencing reveals the conservation and expression of all essential insect phototransduction genes including a single long wavelength-sensitive opsin. Consistent with the preservation of visual ability, Ptomaphagus hirtus expresses all core members of the clock gene network and exhibits a similar degree of negative phototaxis as does a closely related flight-active species in light-dark choice assays. The structural reduction of the peripheral Ptomaphagus hirtus visual system is reflected by the lack of five eye pigmentation specific genes in the head transcriptome. Taken together our data suggest that wavelength contingent and probably also spatial vision have been lost in Ptomaphagus hirtus, while irradiance vision and contingent behavioral modules have remained preserved. We predict that the adaptive state of Ptomaphagus hirtus is representative for a large number of microphthalmic species adapted to the twilight zone of caves and other subterranean habitats Poly(A)+ transcripts were isolated from a pooled sample of 25 adult Ptomaphagus hirtus heads, reverse transcribed and sequenced on the Illumina GAII
Project description:Recent improvements in the analysis ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and past genetic diversity of our species. Here we present a “multi-omics” study, integrating genomic and proteomic analyses of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified “Villabruna cluster”. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analyses of dental calculus using genomics and proteomics showed a similar oral microbiome composition as Neandertals, but distinct from later foragers and farmers, revealing also a diet based on mammals, fish and plants. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.
Project description:Exceedingly abundant p300 histone acetylase binding was reported upstream Furin in mouse Th1 cells. We aimed to investigate the role of this genomic area in RNA expression by deleting it from EL-4 mouse thymoma cells and comparing the RNA expression profiles in steady-state and after PMA/ionomycin stimulation.
Project description:Spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances being found between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for the phylogenetic reconstruction of ancient fauna previously thought to be unreachable using ancient DNA.
Project description:Transcriptional profiling of an El Tor biotype crp mutant The virulent V. cholerae El Tor Ogawa strain C7258 (Peru isolate 1991) and an isogenic deletion mutant (WL7258) lacking DNA sequences encoding the cAMP receptor protein were grown in LB medium to optical density at 600 nm of 1.5. The cultures were chilled in ice, cells quickly collected by centrifugation and total RNA imediately extracted. RNAwas extracted and purified using the Trizol plus RNA purification system (Invitrogen) followed RNEasy miniElute cleanup (Qiagen). RNA samples were conserved at - 80 C and used within a week. Keywords: Genetic modification
Project description:RNA microarrays technology was used to compare hESC-derived cell populations to undifferentiated hESC and to human EL cell populations. Microarrays confirmed the hematoendothelial, endothelial and hematopoietic identity of hPSC-derived CD144+-EBs, BCs and ECs, respectively, and the similarities between hESC-derived cell populations and human EL equivalent populations.