Project description:Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia. Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps.
Project description:The aim of the study was to investigate differences in the gene expression profiles of selected tissues in two most popular goat’s breeds in Poland: Polish White Improved (PWI) and Polish Fawn Improved (PFI). Three different types of tissue samples were selected: somatic cells isolated from goats’ milk (MSC), milk fat globules (MFG) and peripheral nuclear blood cells (PBNC) Since there were no earlier genetic studies focused on genetic differences between these two goat breeds we decided to evaluate hypothetical genomic differences assuming that such a differences should be the consequence of genetic differences. We created the hypothesis that if genomic differences exist they should be revealed in hierarchical clustering of transcriptomic profiles of selected tissues. Should the genomic differences exist the clusters obtained are grouping goat breeds and not goat’s tissues. The results of hierarchical clustering however show something completely different. The clusters are grouping goat tissues (milk fat globules, milk somatic cells, peripheral blood nuclear cells) without any relation with goat breed. So the analytical tool does not recognize the goat breed as a driver of transcriptomic difference. Moreover, we were not able to find significantly regulated genes between two breeds
Project description:The steroid hormone brassinosteroids (BRs) play considerable roles in plant development and defence. Harnessing the extensive knowledge on Arabidopsis BR signalling network for improving productivity in crop species requires first to identify the conserved network components and their function in the target species. To investigate the function of SlBIM1a, the tomato closest homolog of AtBIM1, which is highly expressed in the developing fruit, we generated transgenic tomatoes, which overexpress or down-regulate SlBIM1a gene. Main alterations were observed in SlBIM1a overexpressing lines, which displayed a severe plant and fruit dwarfism. To unravel the molecular basis of phenotypical modifications in SlBIM1a overexpressing fruits, a microarray (Agilent) analysis was performed on Pro35S:SlBIM1aOX and WT fruits harvested at 15 DPA.
Project description:Demand for recombinant proteins is rapidly growing, driven by their use as 16 biotherapeutics, vaccine components, industrial enzymes, and food ingredients. The growing market requires novel strategies for increasing specific productivity (qp) of cellular hosts. Systems-level frameworks have been used to improve productivity, but have had difficulty relating complex cellular pathways with protein expression. Here, we demonstrate a method for mapping relationships between gene expression signatures and complex phenotypes related to recombinant protein productivity. Our approach induces systematic perturbations in cultures of K. Phaffii using varied co-feeds of carbon sources. The different carbon sources significantly impacted cell growth, specific productivity, and transcriptional states. With these data, we identified scale-independent metagenes that explained significant transcriptomic variance and strongly associated with complex cellular phenotypes, including qp and response to methanol induction for both IgG1 and VHH. We used these results to identify and knockout 31 novel gene targets whose expression inversely correlated with productivity. Ten of these genes improved productivity of IgG1 by up to 3x, and 17 genes increased productivity of VHH by up to 1.7x without impacting cell growth. This study identified ten groups of carbon co-feeds which induce similar transcriptomic states. We systematically perturbated cultures of K. phaffii using these co-feeds and identified phenotype-associated metagenes. Using the productivity-correlated metagene, we identified 10-17 genes which improved recombinant protein productivity when knocked out. This framework for relating gene signatures to complex cellular phenotypes could provide useful metrics for assessing 37 production processes and identifying new targets for cellular engineering.
Project description:Demand for recombinant proteins is rapidly growing, driven by their use as 16 biotherapeutics, vaccine components, industrial enzymes, and food ingredients. The growing market requires novel strategies for increasing specific productivity (qp) of cellular hosts. Systems-level frameworks have been used to improve productivity, but have had difficulty relating complex cellular pathways with protein expression. Here, we demonstrate a method for mapping relationships between gene expression signatures and complex phenotypes related to recombinant protein productivity. Our approach induces systematic perturbations in cultures of K. Phaffii using varied co-feeds of carbon sources. The different carbon sources significantly impacted cell growth, specific productivity, and transcriptional states. With these data, we identified scale-independent metagenes that explained significant transcriptomic variance and strongly associated with complex cellular phenotypes, including qp and response to methanol induction for both IgG1 and VHH. We used these results to identify and knockout 31 novel gene targets whose expression inversely correlated with productivity. Ten of these genes improved productivity of IgG1 by up to 3x, and 17 genes increased productivity of VHH by up to 1.7x without impacting cell growth. This study identified ten groups of carbon co-feeds which induce similar transcriptomic states. We systematically perturbated cultures of K. phaffii using these co-feeds and identified phenotype-associated metagenes. Using the productivity-correlated metagene, we identified 10-17 genes which improved recombinant protein productivity when knocked out. This framework for relating gene signatures to complex cellular phenotypes could provide useful metrics for assessing 37 production processes and identifying new targets for cellular engineering.
2026-03-11 | GSE302181 | GEO
Project description:Harnessing Rhizosphere Microbiota through Root-Root Interaction to Optimize Productivity in Maize-Soybean Intercropping
Project description:<p>Cryopreservation of Chengde polled goat semen plays a critical role in conserving genetic resources, enhancing the utilization efficiency of superior breeding rams, and advancing artificial insemination techniques. However, spermatozoa are vulnerable to oxidative stress during the freezing process, which can significantly compromise sperm motility. This study demonstrated that supplementation of the semen cryoprotectant with 0.6% sericin significantly improved post-thaw sperm viability to 65.25% in Chengde hornless goats, while concurrently reducing both the sperm abnormality rate and intracellular ROS levels. Integrated TMT proteomics and LC/MS metabolomics identified 256 differentially expressed proteins and 109 differential metabolites between sericin supplementation and frozen control groups. Functional analysis revealed significant enrichment of differential metabolites, such as glutamine, in the alanine, aspartate, and glutamate metabolism pathway, concomitant with marked upregulation of antioxidant proteins including LRP8, GSTM3, and SIRT2. Thus, sericin enhances cryotolerance primarily by improving sperm viability, reducing oxidative damage, and sustaining energy metabolism. These findings establish the molecular foundation for optimizing goat semen cryopreservation and advancing artificial insemination technology.</p>