Questions and Answers (117) View all
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Answer added in Molecular Biological Techniques29 Checking RNA integrity through TAE gel?Actually the Turbo DNA-free kit from Ambion comes with DNAse inactivation reagent. This works well in our hands. Also, phenol/chloroform extraction me... [more]
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Answer added in Molecular Biological Techniques29 Checking RNA integrity through TAE gel?Thanks very much for your detailed response. I gather that continuous presence of formaldehyde is no longer necessary once the RNA has been denatured ... [more]
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Answer added in Molecular Biological Techniques29 Checking RNA integrity through TAE gel?Tzu: Just a clarification. From the original post, I do not see any mention of DNAse treatment of the samples. Am I missing a part of the original pos... [more]
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Answer added in Molecular Biological Techniques29 Checking RNA integrity through TAE gel?Use TURBO DNA-free kit (Applied Biosystems) to minimize gDNA contamination. It works very well. You can check the RNA quality using formaldehyde agaro... [more]
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Answer added in Expression Microarrays22 Affymetrix GeneChip Human Genome U133 Plus 2.0 Array - which probe sets to be considered?I agree with the comments made by Daniel Cohen and others. I would concentrate on finding if there is a considerable variation in gene expression betw... [more]
Publications (62) View all
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Article: Transcriptome Analysis of Epigenetically Modulated Genome Indicates Signature Genes in Manifestation of Type 1 Diabetes and Its Prevention in NOD Mice.
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ABSTRACT: Classic genetic studies implicated several genes including immune response genes in the risk of developing type 1 diabetes in humans. However, recent evidence including discordant diabetes incidence among monozygotic twins suggested a role for epigenetics in disease manifestation. NOD mice spontaneously develop type 1 diabetes like humans and serve as an excellent model system to study the mechanisms of type 1 diabetes as well as the efficacy of maneuvers to manipulate the disease. Using this preclinical model, we have recently demonstrated that pharmacological inhibition of histone deacetylases can lead to histone hyperacetylation, selective up-regulation of interferon-γ and its transactivator Tbx21/Tbet, and amelioration of autoimmune diabetes. In the current study, we show that chromatin remodeling can render splenocytes incapable of transferring diabetes into immunodeficient NOD.scid mice. To elucidate the underlying mechanisms of drug-mediated protection against type 1 diabetes, we performed global gene expression profiling of splenocytes using high throughput microarray technology. This unbiased transcriptome analysis unraveled the exaggerated expression of a novel set of closely related inflammatory genes in splenocytes of acutely diabetic mice and their repression in mice cured of diabetes by chromatin remodeling. Analysis of gene expression by qRT-PCR using RNA derived from spleens and pancreata of cured mice validated the suppression of most of these genes, indicating an inverse correlation between the high levels of these inflammatory genes and protection against diabetes in NOD mice. In addition, higher-level expression of genes involved in insulin sensitivity, erythropoiesis, hemangioblast generation, and cellular redox control was evident in spleens of cured mice, indicating their possible contribution to protection against type 1 diabetes. Taken together, these results are consistent with the involvement of epistatic mechanisms in the manifestation of autoimmune diabetes and further indicate the utility of chromatin remodeling in curing this complex autoimmune disorder.PLoS ONE 01/2013; 8(1):e55074. · 4.09 Impact Factor -
Dataset: Defective T cell apoptosis in type 1 diabetes patients
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Article: Epigenetic mechanisms of metabolic memory in diabetes.
Circulation Research 04/2012; 110(8):1039-41. · 9.49 Impact Factor -
Article: Patients with Type 1 Diabetes Display Selective Defect in Antigen Receptor Mediated T Cell Apoptosis Corresponding Author & Address
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ABSTRACT: Open Journal of Biology and Biochemistry, 2012, 1-2 © Jayaraman et al.; licensee Ross Science Publishers ROSS Open Access articles will be distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided that the original work will always be cited properly. ABSTRACT Type 1 diabetes is an autoimmune disease in which insulin-producing beta cells are destroyed by auto-reactive T lymphocytes. Studies in mice indicate that incomplete deletion of self-reactive T-cells and compromised peripheral tolerance mechanisms can contribute to the manifestation of autoimmune diabetes. In patients with type 1 diabetes, defects in T regulatory cell numbers and function have been previously reported. In this study, we have ascertained the integrity of activation-induced cell death, a mechanism of peripheral T cell tolerance, in long-standing type 1 diabetes patients. Activation of peripheral blood derived T cells from non-diabetic individuals with a T cell mitogen and interleukin-2 rendered them susceptible to subsequent T-cell receptor/CD3-mediated apoptosis, as indicated by the dissipation of the mitochondrial membrane potential and activation of intracellular caspases. In contrast, similarly activated T lymphocytes from type 1 diabetes patients failed to undergo apoptosis when challenged with a bacterial superantigen or anti-CD3 antibody. Supplementation of T cell cultures with interleukin-4 or interleukin-18 failed to restore self-tolerance. However, both the expression of the Fas receptor and its ability to transduce apoptotic signal were comparable in T cells of type 1 diabetes patients and controls. Additionally, no marked difference in the T cell subsets was observed between controls and diabetes patients under all activation conditions analyzed. These data suggest that the abnormality in T-cell receptor-mediated apoptosis is cell autonomous in long-standing type 1 diabetes patients, which in addition to other defective peripheral tolerance mechanisms, likely to contribute to the manifestation of autoimmune diabetes.Open Journal of Biology and Biochemistry. 01/2012; -
Article: Epigenetics of autoimmune diabetes.
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ABSTRACT: Classical genetic studies established a link between Type 1 diabetes, a common childhood autoimmune disease and genes that encode MHC antigens and several immune-related determinants. The mechanisms by which these genes contribute to the initiation and perpetuation of Type 1 diabetes remain enigmatic. Emerging data indicate a role for epigenetic mechanisms involving hyperacetylation of histones in the differential gene expression and amelioration of autoimmune diabetes in a mouse model. In this article the implications of these and other epigenetic mechanisms including ncRNA-mediated gene regulation in the abrogation of autoimmune diabetes are discussed. Concerted efforts to decipher the epigenetics of Type 1 diabetes may provide novel perspectives on autoimmune diabetogenesis.Epigenomics 10/2011; 3(5):639-48.
