Homo sapiens
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PROVIDER: PRJNA662928 | ENA |
REPOSITORIES: ENA
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Project description:Genomic data archive from the Network for Pancreatic Organ donors with Diabetes
| PRJNA821969 | ENA
Project description:Genomic data archive from the Network for Pancreatic Organ donors with Diabetes
| PRJNA821970 | ENA
Project description:These experiments were performed to identify differentially expressed genes in the pancreas of healthy humans, auto-antibody positive and type 1 diabetic patients. All samples were obtained from the network of pancreatic organ donors with diabetes (nPOD). ID numbers are specified. Patient information can be obtained at http://www.jdrfnpod.org/
2015-11-01 | GSE72492 | GEO
Project description:Type 1 Diabetes (T1D) is an autoimmune disease characterized by T cell-mediated destruction of insulin-producing pancreatic β-cells. The pathogenesis of T1D is not fully understood but involves development of autoantibodies (AAbs) followed by a progressive decline in first phase insulin response. Live imaging of T1D pancreatic slices has revealed β cell dysfunction irrespective of the acute presence or absence of CD3+ T cells. However, the mechanisms that drive this dysfunction in the prediabetic period remain unclear. In-situ longitudinal studies of human islet cell biology in the context of T1D are essentially impossible. Hence, we leveraged the availability of pancreas tissues from the Network for Pancreatic Organ donors with Diabetes (nPOD) program to phenotypically and transcriptionally characterize laser capture-microdissected islets across the natural history of T1D.
2024-12-31 | GSE284772 | GEO
Project description:Analysis of ex vivo isolated lymphatic endothelial cells from the dermis of patients to define type 2 diabetes-induced changes. Results preveal aberrant dermal lymphangiogenesis and provide insight into its role in the pathogenesis of persistent skin inflammation in type 2 diabetes. The ex vivo dLEC transcriptome reveals a dramatic influence of the T2D environment on multiple molecular and cellular processes, mirroring the phenotypic changes seen in T2D affected skin. The positively and negatively correlated dLEC transcripts directly cohere to prolonged inflammatory periods and reduced infectious resistance of patients´ skin. Further, lymphatic vessels might be involved in tissue remodeling processes during T2D induced skin alterations associated with impaired wound healing and altered dermal architecture. Hence, dermal lymphatic vessels might be directly associated with T2D disease promotion.
2012-06-02 | GSE38396 | GEO
Project description:Type 1 diabetes is an autoimmune disease caused by the destruction of the insulin producing beta cells. We characterized the gene expression profile of pancreatic tissue from four type 1 diabetes patients (Cases 1-4), who died at different stages of the disease (onset and longstanding) by microarray analysis. All samples from patients and controls were obtained after death, at the time of organ donation. Pancreatic blocks from the four diabetic patients and three organ donors (Controls 1-3) were obtained and snap frozen. At the same time, islets from Cases 1 and 4 were isolated from a piece of the pancreas tail by enzymatic digestion (using automated method and handpicking) and snap frozen. Islets from three different organ donors (Controls 4-6) were obtained similarly to those of the diabetic patients. Both pancreatic blocks and islets were stored in liquid nitrogen until the mRNA extraction. For pancreas gene expression profiles, we compared data from three blocks of each of the four type 1 diabetic pancreas with pancreases data from the Controls 1-3. For islets expression profile, we compared data from Cases 1 and 4 islets with islets data from the Controls 4-6. <br><br>
2009-12-01 | E-MEXP-1140 | biostudies-arrayexpress
Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
| S-EPMC2531291 | biostudies-literature
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO
Project description:As the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of miRNA genes in two archaic hominines, Homo sapiens neanderthalensis and Homo sapiens denisova, and elucidated the expression of their target mRNAs in bain.A comparative analysis of the genomes of primates, including species in the genus Homo, identified a group of miRNA genes having fixed substitutions with important implications for the evolution of Homo sapiens neanderthalensis and Homo sapiens denisova. The mRNAs targeted by miRNAs with mutations specific for Homo sapiens denisova exhibited enhanced expression during postnatal brain development in modern humans. By contrast, the expression of mRNAs targeted by miRNAs bearing variations specific for Homo sapiens neanderthalensis was shown to be enhanced in prenatal brain development.Our results highlight the importance of changes in miRNA gene sequences in the course of Homo sapiens denisova and Homo sapiens neanderthalensis evolution. The genetic alterations of miRNAs regulating the spatiotemporal expression of multiple genes in the prenatal and postnatal brain may contribute to the progressive evolution of brain function, which is consistent with the observations of fine technical and typological properties of tools and decorative items reported from archaeological Denisovan sites. The data also suggest that differential spatial-temporal regulation of gene products promoted by the subspecies-specific mutations in the miRNA genes might have occurred in the brains of Homo sapiens denisova and Homo sapiens neanderthalensis, potentially contributing to the cultural differences between these two archaic hominines.
| S-EPMC4686780 | biostudies-literature
Project description:PurposeWe investigated the evidence of recent positive selection in the human phototransduction system at single nucleotide polymorphism (SNP) and gene level.MethodsSNP genotyping data from the International HapMap Project for European, Eastern Asian, and African populations was used to discover differences in haplotype length and allele frequency between these populations. Numeric selection metrics were computed for each SNP and aggregated into gene-level metrics to measure evidence of recent positive selection. The level of recent positive selection in phototransduction genes was evaluated and compared to a set of genes shown previously to be under recent selection, and a set of highly conserved genes as positive and negative controls, respectively.ResultsSix of 20 phototransduction genes evaluated had gene-level selection metrics above the 90th percentile: RGS9, GNB1, RHO, PDE6G, GNAT1, and SLC24A1. The selection signal across these genes was found to be of similar magnitude to the positive control genes and much greater than the negative control genes.ConclusionsThere is evidence for selective pressure in the genes involved in retinal phototransduction, and traces of this selective pressure can be demonstrated using SNP-level and gene-level metrics of allelic variation. We hypothesize that the selective pressure on these genes was related to their role in low light vision and retinal adaptation to ambient light changes. Uncovering the underlying genetics of evolutionary adaptations in phototransduction not only allows greater understanding of vision and visual diseases, but also the development of patient-specific diagnostic and intervention strategies.
| S-EPMC3743458 | biostudies-literature