Gene expression in the olfactory epithelia of parasitic and reproductive adult sea lampreys
ABSTRACT: To determine gene expression differences in the olfactory epithelium of sea lamprey between sequential yet behaviorally distinct adult life history stages 2 samples: parasitic adults removed from fish in northern Lake Huron and Lake Michigan in February and March, and reproductive adults collected from Lake Huron and Lake Michigan tributaries in June
Project description:To determine gene expression differences in the olfactory epithelium of sea lamprey between sequential yet behaviorally distinct adult life history stages Overall design: 2 samples: parasitic adults removed from fish in northern Lake Huron and Lake Michigan in February and March, and reproductive adults collected from Lake Huron and Lake Michigan tributaries in June
Project description:Early environmental experiences and life histories profoundly influence adult phenotypes via as yet poorly understood mechanisms. We previously showed that wild-type adult C. elegans that transiently passed through the stress-induced dauer larval stage (post-dauers) exhibit different gene expression patterns, genome-wide chromatin structure, and life history traits when compared to adults that bypassed the dauer stage (controls). Here we show that endogenous small inhibitory RNAs (endo-siRNAs) and siRNA pathways may mediate developmental history-dependent phenotypic diversity. Deep sequencing of small RNA libraries show changes in endo-siRNA levels in post-dauer as compared to control animals, and meta analyses indicate that specific endo-siRNA pathways are targets of developmental history-dependent reprogramming. We demonstrate that mutations in specific endo-siRNA pathways affect the expected gene expression and chromatin state changes in post-dauer animals, and also disrupt their increased brood size phenotype. We find that the chromatin state and endo-siRNA distribution in dauers is also distinct and suggest that this remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Together, our results imply a critical mechanistic role for endo-siRNA pathways in mediating early experience-dependent phenotypic divergence in adults, and suggest that regulation of these pathways contribute to increased fitness via non-genetic mechanisms. We deep-sequenced small RNA libraries from 2 biological replicates each of control and postdauer adults, and one biological each of larval L3 and dauer stages.
Project description:In this study, we compared the transcriptome map of maize and sorghum using PacBio single-molecule long-read sequencing from multiple matched tissues in each species. Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the transcriptional profiles of both protein-coding and non-coding transcripts in matched tissues using large-scale single-molecule sequencing from 130 RSII cells and 5 Sequel cells, as well as deep short-read RNA sequencing. The use of multiple size-fractionated libraries (<1 kb, 12 kb, 23 kb, 35 kb, and >5 kb) enhanced our capture of non-redundant transcripts in these tissues.
Project description:Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation and/or allocation. To identify candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments. One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus. The other was the complex natural seston from a large lake. In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting. For both ecotypes, we used replicate clones drawn from a number of separate populations. We compared gene expression in whole Daphnia pulex that had been raised in the lab for 10 days, and then exposed to alternate resource environments for 24 hours. One resource environment was a 24 hour continuation of the lab resource, a satiating level of Ankistrodesmus falcatus. The alternate environment was the natural seston present in the epilimnion of Lake Murray, South Carolina. Two ecotypes were analyzed, one adapted to large lakes, and one adapted to temporary ponds. For each ecotype, eight replicate clones were used. Clones of the lake ecotype were isolated from eight independent lakes, clones of the pond ecotype were isolated from six different ponds. The total number of arrays is 16 (8 replicate clones x 2 ecotypes) x 2 resource environments). Total RNA was extracted from eight whole organisms pooled together. Pools were then converted to cDNA and labelled with a single round of amplification. For array hybridizations, samples from the two resource environments were paired for each clone, and dyes were swapped across clones.
Project description:We sampled lake-type and riverine sockeye in the pristine natural habitats of Aniakchak National Monument and Preserve, Alaska USA. Samples were taken on the same day and close proximite in time. We sampled 17 riverine individuals from Albert Johnson Creek and 13 individuals from Surprise Lake. cDNA from a single individual on the Cy5 was compared with a reference of aRNA on the Cy3.
Project description:miRNAs can regulate target gene expression by mRNA cleavage. Rice degradome sequencing was employed to validate mRNA targets of rice miRNAs. Two rice samples, 3-week-old seedling and young panicles were included in the study.
Project description:To date, miRNA expression studies on cerebral ischemia in both human and animal models have focused mainly on acute phase of ischemic stroke. In this study, we present the roles played by microRNAs in the spontaneous recovery phases in cerebral ischemia using rodent stroke models. In this study presented here, Middle Cerebral Artery Occlusion stroke model was established by using embolus and the brain samples of stroke model were harvested at 0hrs, 3hrs, 6hrs, 12hrs, 24hrs, 48hrs, 72hrs, 120hrs and 168hrs. RNAs were extracted from these samples and microRNA array and mRNA array were performed.
Project description:Tobacco mature pollen has extremely desiccated cytoplasm, and is metabolically quiescent. Upon re-hydration it becomes metabolically active and that results in later emergence of rapidly growing pollen tube. These changes in cytoplasm hydration and metabolic activity are accompanied by protein phosphorylation. In this study, we subjected mature pollen, 5-min-activated pollen, and 30-min-activated pollen to TCA/acetone protein extraction, trypsin digestion and phosphopeptide enrichment by titanium dioxide. The enriched fraction was subjected to nLC-MS/MS. We identified 471 phosphopeptides that carried 432 phosphorylation sites, position of which was exactly matched by mass spectrometry. These 471 phosphopeptides were assigned to 301 phosphoproteins, since some proteins carried more phosphorylation sites. Of the 13 functional groups, the majority of proteins were put into these categories: transcription, protein synthesis, protein destination and storage, and signal transduction. Many proteins were of unknown function, reflecting the fact that male gametophyte contains many specific proteins that have not been fully functionally annotated. The quantitative data highlighted the dynamics of protein phosphorylation during pollen activation; the identified phosphopeptides were divided into seven groups based on the regulatory trends. The major group comprised mature pollen-specific phosphopeptides that were dephosphorylated during pollen activation. Several phosphopeptides representing the same phosphoprotein had different regulation, which pinpointed the complexity of protein phosphorylation and its clear functional context. Collectively, we showed the first phosphoproteomics data on activated pollen where the position of phosphorylation sites was clearly demonstrated and regulatory kinetics was resolved.