Similar Datasets
Project description:The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart. The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis. Three paired samples were analyzed: Uninjured, 7dpi and 21dpi newt hearts. Three arrays were hybridized comparing two-paired samples each time.
2013-09-24 | E-GEOD-44547 | biostudies-arrayexpress
Project description:The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart. The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis.
2013-09-24 | GSE44547 | GEO
Project description:MicroRNA sequencing using Ion Torrent Proton platform of the undamaged heart of the red spotted newt Notophthalmus viridescens. MicroRNAS were identified using MIRPIPE
2021-05-24 | GSE69537 | GEO
Project description:To obtain a quick glimpse into possible function of five novel Notopthalmus viridescens (newt) genes (and given certain restrains with transgenic newts, such as time) we express these genes using transgenic Drosophila melanogaster. We generated the transgenic flies containing newt candidate genes, and prepared samples for RNA sequencing to evaluate the overall role of candidate genes in tissue development and layout map for future studies.
2021-11-03 | GSE134348 | GEO
Project description:Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. Next, we used clodronate liposomes to deplete macrophages, which inhibited lens regeneration in both newt species. Macrophage depletion induced the formation of scar-like tissue, an increased and sustained inflammatory response, an early decrease in iris pigment epithelial cell (iPEC) proliferation and a late increase in apoptosis. Some of these phenotypes persisted for at least 100 days and could be rescued by exogenous FGF2. Re-injury alleviated the effects of macrophage depletion and re-started the regeneration process. Together, our findings highlight the importance of macrophages in facilitating a pro-regenerative environment in the newt eye, helping to resolve fibrosis, modulating the overall inflammatory landscape and maintaining the proper balance of early proliferation and late apoptosis.
2024-05-22 | GSE236907 | GEO
Project description:Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. Next, we used clodronate liposomes to deplete macrophages, which inhibited lens regeneration in both newt species. Macrophage depletion induced the formation of scar-like tissue, an increased and sustained inflammatory response, an early decrease in iris pigment epithelial cell (iPEC) proliferation and a late increase in apoptosis. Some of these phenotypes persisted for at least 100 days and could be rescued by exogenous FGF2. Re-injury alleviated the effects of macrophage depletion and re-started the regeneration process. Together, our findings highlight the importance of macrophages in facilitating a pro-regenerative environment in the newt eye, helping to resolve fibrosis, modulating the overall inflammatory landscape and maintaining the proper balance of early proliferation and late apoptosis.
2024-05-22 | GSE236906 | GEO
Project description:Pancreatic cancer is the 3rd most prevalent cause of cancer related deaths in United states alone, with over 55000 patients being diagnosed in 2019 alone and nearly as many succumbing to it. Late detection, lack of effective therapy and poor understanding of pancreatic cancer systemically contributes to its poor survival statistics. Obesity and high caloric intake linked co-morbidities like type 2 diabetes (T2D) have been attributed as being risk factors for a number of cancers including pancreatic cancer. Studies on gut microbiome has shown that lifestyle factors as well as diet has a huge effect on the microbial flora of the gut. Further, modulation of gut microbiome has been seen to contribute to effects of intensive insulin therapy in mice on high fat diet. In another study, abnormal gut microbiota was reported to contribute to development of diabetes in Db/Db mice. Recent studies indicate that microbiome and microbial dysbiosis plays a role in not only the onset of disease but also in its outcome. In colorectal cancer, Fusobacterium has been reported to promote therapy resistance. Certain intra-tumoral bacteria have also been shown to elicit chemo-resistance by metabolizing anti-cancerous agents. In pancreatic cancer, studies on altered gut microbiome have been relatively recent. Microbial dysbiosis has been observed to be associated with pancreatic tumor progression. Modulation of microbiome has been shown to affect response to anti-PD1 therapy in this disease as well. However, most of the studies in pancreatic cancer and microbiome have remained focused om immune modulation. In the current study, we observed that in a T2D mouse model, the microbiome changed significantly as the hyperglycemia developed in these animals. Our results further showed that, tumors implanted in the T2D mice responded poorly to Gemcitabine/Paclitaxel (Gem/Pac) standard of care compared to those in the control group. A metabolomic reconstruction of the WGS of the gut microbiota further revealed that an enrichment of bacterial population involved in drug metabolism in the T2D group.
2020-11-30 | E-MTAB-8739 | biostudies-arrayexpress
Project description:Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate aging associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 old (age>18 years) and 4 young (age 3-6 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in PBMC by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the old animals exhibited higher inflammatory biomarkers in plasma and lower CD4 T cells with altered distribution of naïve and memory T cell maturation subsets. The gut microbiome in old animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of old animals compared to the young. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile.
2022-02-01 | E-MTAB-10160 | biostudies-arrayexpress
Project description:We have developed a standardized and reproducible heart resection/regeneration model system in the red-spotted newt. In order to ascertain the involvement of microRNAs in this amazing process, we made and sequenced cDNA libraries for microRNAs in order to provide sequence data that we could use in further quantitative and qualitative studies.
2013-09-24 | GSE46527 | GEO