Project description:This study describes a genome-wide CRISPR-Cas9 knockout (GeCKO) screen performed in two porcine cell lines, PK15 and IPEC-J2. A custom-designed porcine GeCKO (pGeCKO) library targeting protein-coding genes, lncRNAs, and miRNAs was used. Genomic DNA was harvested from GeCKO cell populations at four timepoints between 3-26 days post-transduction in each cell line. Amplicon sequencing libraries were generated from guide RNA regions using custom primers with Illumina adapter sequences, and sequenced on the NovaSeq 6000 platform (PE150). This dataset enables quantification of guide RNA abundance over time and identification of essential genes in pig cells, supporting research in comparative genomics, functional genomics, and translational animal models.
Project description:Interventions: CRC group:Nil;Healthy control group:Nil
Primary outcome(s): Identification of clostridium species
Study Design: Factorial
Project description:Interventions: Tumor tissue group and tumor-adjacent tissue group:Nil
Primary outcome(s): Identification of clostridium species
Study Design: Factorial
Project description:Various species of teleost fish, amphibians, and neonatal mammals can regenerate their hearts following injury. Certain processes, including extracellular matrix remodelling, a switch from oxidative to glycolytic metabolism and sarcomere disorganization are believed to be critical to heart regeneration. However, whether all regenerating species follow the same pathway to regeneration is not known. Here, we use mass-spectrometry based proteomics to characterize the cellular processes that occur in the heart of a reptile, the leopard gecko (Eublepharis macularius) following injury. The hearts were damaged using a cryoprobe and wound sites were sampled at 3-, 14-, 30- and 100-days post injury (dpi). The proteomes of these were compared to those from sham operated geckos. Overall, 1116 proteins were identified in the wound sites and 579 were differentially expressed across at least two time points. This includes an increase in agrin at 14-dpi, a protein thought to be required for cardiomyocyte proliferation and heart regeneration. Interaction network analysis indicates that there is enrichment of Gene Ontology (GO) terms related to transcription and translation by 14-dpi, but a concurrent decrease in GO terms related to oxidative and glycolytic metabolism, and sarcomere organization. Importantly, GO terms related to the structure and function of mitochondria as well as sarcomere organization were enriched at 100-dpi compared to 3-dpi, and 14-dpi. There were no GO terms identified as differing between sham and 100 dpi hearts, suggesting full regeneration. This work indicates that the gecko heart can regenerate and that this involves reorganization of cellular pathways associated with mitosis, energy production and contractile function.
Project description:Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of small RNAs that change their pattern of expression in apple buds during dormancy.