Project description:This project characterizes the metabolic consequences of the daily physiological rhythms and diel vertical migration for the model subtropical copepod, Pleuromamma xiphias. P. xiphias were collected near the Bermuda Atlantic Time Series in plankton tows at different times of day, representing different parts of their daily vertical migration. Single copepods were isolated from the tows and flash-frozen for proteomics analysis.
Project description:The diel vertically migrating copepod, Pleuromamma xiphias, migrates approximately 600 m daily, up and down in the water column. At the surface, the copepods feed on plankton at night, and then descend to the depths during the day, likely to escape visual predators. Both the migratory behavior and the physiological pathways that are up- and down-regulated throughout the migration are likely under at least partial circadian clock control. This experiment compares the protein abundances of select physiological processes from copepods collected in situ with copepods incubated in the dark to remove the influence of exogenous stimuli on physiology.
Project description:One of the greatest cyclical patterns in the pelagic ecosystem is the daily vertical migration of various zooplankton and fish to depth, a process referred to as diel vertical migration (DVM). DVM is considered to be energetically costly as tiny plankton migrate hundreds of meters in a 24 hour period. To study the metabolic demands of DVM, the copepod Pleuromamma xiphias was collected during upwards and downwards migration off of Bermuda. Data-dependent acquisition on the Q-Exactive detected >1600 proteins, 180 of which were differentially abundant between the two sampling periods.
Project description:The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.