Project description:62 individual Brassica napus plants of the same accession grown in the same field were expression-profiled in autumn 2016 and phenotyped extensively until harvest in spring 2017. Machine learning models were used to link gene expression to the phenotypes of individual plants, with the purpose of assessing how much phenotype information in encoded in ‘noisy’ gene expression variation among individual plants of the same background grown under the same uncontrolled field conditions. Rosette leaf 8 blades of 62 individual Brassica napus plants of the same winter-type accession (BnASSYST-120, Darmor) grown in the same field (50°58'24.9\\"N 3°46'49.1\\"E, Merelbeke, Belgium) were RNA-seq profiled. No treatments or stresses were applied, all plants were profiled individually under uncontrolled field conditions. Sown at 2016-09-08, rosette leaf 8 sampled for RNA-seq at 2016-11-28, plants harvested at 2017-06-13.
Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to investigate spring microbial functional genes in mesocosm-simulated shallow lake ecosystems having been undergoing nutrient enrichment and warming for nine years.
Project description:Vertical and seasonal preferences of freshwater bacterioplankton tribes in a deep mesotrophic lake with fully oxygenated hypolimnion (Lake Biwa, Japan)
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:Transcranial direct current stimulation (tDCS) has been applied in experimental and clinical settings for more than twenty years and may facilitate rehabilitation after stroke as suggested by clinical data (Hummel et al. 2005, Sparing et al. 2009). Intriguingly, tDCS evokes various cellular effects exceeding its primary neurophysiological actions: We previously described subacute effects of tDCS on immune- and stem cells in the rat brain (Rueger et al. 2012, Keuters et al. 2015, Pikhovych et al. 2016, Braun et al. 2016). However, the effects of tDCS on immune-mediating genes have not yet been investigated. To investigate the more immediate effects of tDCS regulating those cellular responses, we treated rats with a single session of either anodal or cathodal tDCS, and analyzed the gene expression by microarray; sham-stimulated rats served as control. We confirmed the effects of gene upregulation by immunohistochemistry at the protein level. We here report for the first time that acute anodal transcranial direct current stimulation enhanced the expression of several genes coding for MHC-I, affecting inflammation and synaptic plasticity (Neumann et al. 1995, Shatz et al. 2009). Moreover, cathodal tDCS increased expression of the gene encoding for the immunoregulatory protein Osteopontin. Osteopontin has beneficial effects on neural stem cells and microglia after brain damage such as stroke (Rabenstein et al. 2015, Rabenstein et al. 2016, Ladwig et al. 2017, Rogall et al. 2017). Overall, our data indicate that a specific modulation of neuroinflammatory processes by non-invasive brain stimulation constitutes a promising therapeutic option with immediate translational relevance.
