Project description:Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments identified with chromosome conformation capture, with our imaging we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of an entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method – integrative modeling of genomic regions (IMGR) – to increase the genomic resolution of our traces to 10 kb. Grant: 1DP2OD008540: Exploring how the genome folds through proximity ligation and sequencing Grant: 4DP2OD008540: Exploring how the genome folds through proximity ligation and sequencing Grant: U01HL130010: Beyond Pairwise DNA Contacts: Exploring Higher-order Genome Structure Using Proximity Ligation NIH/4D Nucleome Consortium Grant: UM1HG009375: Genome-wide mapping of loops using in situ Hi-C
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
Project description:Responsible aquaculture growth requires practices adjusted to higher knowledge based industrial standards that can secure good fish welfare, health, and low environmental impacts, alongside with the production of safe and nutritious consumer products and the economic sustainability of the business. The fish feed ingredient pallet is ever changing, from marine to plant based, and recently evolving to incorporate increasing amounts of low trophic, side stream and circular economy based raw materials, each one contributing with variable amounts and qualities of macro- and micronutrients. Meeting the micronutrient requirement of farmed fish for healthy and efficient growth under normal and challenging conditions is of paramount importance. Trace minerals are essential for critical life processes, including respiration, protein and lipid metabolism, immune responses, and cell REDOX balance. The study results bring new knowledge on Atlantic salmon physiology, growth, welfare status and utilization efficiency of trace minerals of different origin and dietary inclusion levels revealing differential effects on fillet yield, fillet technical and nutritional quality, bone strength, skin morphology, organ mineralization, midgut transcriptome, trace mineral apparent digestibility and retention efficiency, and growth.