chromatin immunoprecipitation based analysis of gene regulatory networks operative in human embryonic stem cells
Roles of long non coding RNAs in human embryonic stem cell pluripotency and neural differentiation 1
... characterization of lncRNAs involved in differentiation has been carried out in human cells In this thesis, functional characterization of lncRNAs in human development is addressed using human embryonic stem ... differentiation of pluripotent stem cells into neuroepithelial stem cells and radial glia 15 Figure 1.5 Correlation of expression profiles of lncRNAs with protein-coding gene markers during embryoid ... dissociating into single cells following incubation with Accutase for minutes, collecting cells by centrifugation at 1000 rpm for minutes and replating at a ratio of 1:6 3.6.2 Differentiation of ReN-VM cells...
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Roles of long non coding RNAs in human embryonic stem cell pluripotency and neural differentiation 3
... lincRNAs, which in turn regulate global gene expression by binding to multiple chromatin regulatory proteins, thereby controlling the ES cell state In this study by Guttman et al (2011), loss -of- function ... roles of lncRNAs in the maintenance of hESC pluripotency, and their involvement in neuronal differentiation respectively 82 Chapter VI – Long Non-coding RNAs Regulate Human Embryonic Stem Cell ... 27) bivalent epigenetic marks, reminiscent of “poised” protein-coding genes in mESCs These bivalent domains usually mark developmental genes whose expressions were “poised”, or lineage-specifically...
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Roles of long non coding RNAs in human embryonic stem cell pluripotency and neural differentiation 4
... database indicates the presence of a REST binding site upstream of RMST REST (or NRSF) binding sites were observed upstream of RMST in three human cell lines, namely GM12878, a lymphoblastoid cell line, ... chromatin binding Quantitative PCR of the ChIP DNA revealed REST occupancy at the region upstream of RMST (pRMST), confirming that REST binds upstream of RMST in the human neural stem cell line (Figure ... determine if a similar tissuespecific expression was observed in humans To this end, the expression of RMST was profiled in a panel of human somatic tissues, as well as in the H1 hESC line (Figure...
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Roles of long non coding RNAs in human embryonic stem cell pluripotency and neural differentiation 5
... R., and Freed, W.J (2008) Assessment of stromal-derived inducing activity in the generation of dopaminergic neurons from human embryonic stem cells Stem Cells 26, 1517-1525 Walker, E., Chang, ... expression in human embryonic stem cells Stem Cells 27, 2114-2125 Chen, G., Yin, K., Shi, L., Fang, Y., Qi, Y., Li, P., Luo, J., He, B., Liu, M., and Shi, T (2011) Comparative analysis of human protein-coding ... established in the mouse model system, and very few human lncRNAs have been studied with such extent In this thesis, I focused on examining lncRNAs involved in the pluripotency maintenance of human embryonic...
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Role of sonic hedgehog signalling in human embryonic stem cells and its neural derivatives
... culture feeding 3.2.3 Human embryonic stem cells and induced pluripotent stem cells Human embryonic stem cell line HES-3 (46, XX) was from ES Cell International (Singapore, http://www.escellinternational.com) ... 2006) 2.7 Embryonic stem cells and induced pluripotent stem cells Embryonic stem cells (ESC) have two characteristics that distinguish them from other stem cells, in that they are capable of long-term ... understanding of the role of SHH in humans, that is based largely on the mouse model Figure 2.6 Human embryonic stem cells (hESC) derived from the blastocyst are able to differentiate into cells...
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Identification of oct4 and sox2 targets in mouse embryonic stem cells
... Genome-wide Mapping of Oct4-DNA Interactions in Mouse Embryonic Stem Cells 4.1 Introduction 74 4.2 Results 76 4.2.1 Optimisation of large-scale ChIP 76 4.2.2 Global mapping of Oct4 binding sites in mESCs ... shown to increase Sox2 dependent transcription of the Sox2 gene Cooperative binding of Oct4 and Sox2 results in embryonic expression of the F-box containing protein 15 (Fbx15) and mutation of either ... genome binding sites of Oct4 and Sox2 Thousands of novel Oct4 and Sox2 binding sites were identified, mapping to genes implicated in important cellular functions including maintenance of pluripotency...
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Báo cáo hóa học: " Research Article Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length" pot
... resulted in improved accuracy of Boolean network esimation Using the theoretically grounded stochastic complexity instead of ad hoc encodings genuinely reflects the intent of the MDL principle In addition, ... connectivity -based approach to constructing probabilistic gene regulatory networks, ” Bioinformatics, vol 20, no 17, pp 2918–2927, 2004 [10] W Zhao, E Serpedin, and E R Dougherty, “Inferring gene regulatory ... using log g bits to represent the number of predecessors (assuming a uniform prior on k) g g and log k bits to select one of the k possible sets of size k However, the indegrees of genetic networks...
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Báo cáo hóa học: " Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks" docx
... d’Alche-Buc, Gene networks inference using dynamic Bayesian networks, Bioinformatics 19, 138–148 (2003) 10 N Radde, L Kaderali, Bayesian Inference of Gene Regulatory Networks Using Gene Expression ... finding all polynomials that vanish on a set of points This is equivalent to computing the ideal of these points and computation of an ideal of points boils down to intersection of ideals of polynomials ... consideration of more-than-binary discrete models in the Boolean network community In the context of PBNs, generalizations of Boolean networks for ternary gene expression have been proposed in [28-31] In...
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Báo cáo hóa học: " Research Article Reverse Engineering of Gene Regulatory Networks: A Comparative Study" ppt
... Strimmer [7], the authors of the GeneNet a package including GGM, pointed out that their method is intended for analysis of small sample sizes It requires a large number of genes in the dataset to estimate ... January 1999 [6] K Basso, A A Margolin, G Stolovitzky, U Klein, R DallaFavera, and A Califano, “Reverse engineering of regulatory networks in human B cells, ” Nature Genetics, vol 37, no 4, pp 382–390, ... testing microarray data analysis tools An artificial data generator has to be independent of the reverse engineering algorithms to avoid a bias in the test results In addition, the underlying...
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Báo cáo hóa học: " Research Article Comparison of Gene Regulatory Networks via Steady-State Trajectories" pdf
... concentrations of mRNA and proteins induced by gene i, respectively, ci (t) is the fraction of DNA fragments committed to transcription of gene i, κi is the transcription rate of gene i, and τ ... constraints in the reference model The application of constraints modifies the original model, thereby obtaining a simpler one We focus on quantization of the gene expression levels (which are continuous-valued ... transcriptional regulatory system (tRS) We generate networks using this model and a fixed set θ of parameters We call these networks reference networks A reference network is identified by its set θ of parameters,...
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Báo cáo y học: "Construction of Gene Regulatory Networks using biclustering and Bayesian networks" docx
... points with respect to a large number of genes Reducing the data dimensions is one of the interesting problems in GRN modelling The most common and important design rule for modelling gene networks ... subnetworks; ISA: This network is generated by integrating ISA [31] subnetworks; OPSM: This network is generated by integrating OPSM [23] subnetworks; CC: This network is generated by integrating ... of different biclustering networks that have learned using linear regression method [41] A performance comparison of networks generated from learning corresponding biclustering algorithms using...
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báo cáo hóa học:" MicroRNA and gene expression patterns in the differentiation of human embryonic stem cells" doc
... expression in embryonic stem cells suggest they are involved in maintaining "stemness" Identifying mRNAs that are directly targeted by a specific miRNA is a major obstacle in understanding the miRNA ... upregulated genes (D) Adult cells upregulated genes hESC cells EB adult cells Figure supervised hierarchical clustering of genes supervised hierarchical clustering of genes Supervised clustering using ... names of human embryonic stem (hES) cells lines P denoted the number of passages of the cell lines H9-EB denoted embryoid body (EB) prepared from cell line H9 and the day indicates the time in culture...
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Báo cáo y học: "The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells" pot
... loss of chromatin components In this regard, compensatory chromatin modifications have been previously described, including an increase in H3K27me3 levels in Suv39h1/h2 deficient ES cells [25] Minor ... replication in ES cells is altered by mutation of chromatin modifiers Satellite Satellite replication in ES cells is altered by mutation of chromatin modifiers (a) Summary of replication timing of repeat ... fibroblasts remained after 20-25 minutes plating in non-gelatinized plates Pre-plating of feeder-dependent ES cells in this way may result in a slight delay in the apparent time of replication for genes...
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The derivation, propagation, storage and gene expression of human embryonic stem cells on human feeders
... involving blastocyst injections and ectopic grafting in adult hosts cannot be performed in the human Animal embryonic stem cells Embryonic stem cells were first derived from certain strains of ... classes of pluripotent stem cells in humans, other primates and mice These are embryonic stem cells, embryonic germ cells, embryonic carcinoma cells and recently the discovery of a fourth class of ... (neuronal stem cells) , skin (epidermal stem cells) , eye (retinal stem cells) and gut (intestinal crypt stem cells) (Spradling et al 2001) However, 15 not all organs and tissues may contain stem cells...
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Báo cáo y học: "Low temperature tolerance of human embryonic stem cells"
... use of pre-warmed and pre-equilibrated culture media [15, 16] Indeed, minimizing low temperature exposure of human embryos and oocytes is a critical factor in determining the success of clinical ... layer of mitomycin C-inactivated murine embryonic fibroblast feeder (MEF) cells [7, 8] These were harvested from CF1 inbred mouse strain purchased from Charles River Laboratories Inc (Wilmington, ... of ATP in the dynamics of the actin filaments of the cytoskeleton Biol Chem 2006;387(4):401-6 Lopez LA, Bertini F The in vivo effect of low body temperatures on the degree of polymerization of...
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Báo cáo khoa học: Ionizing radiation utilizes c-Jun N-terminal kinase for amplification of mitochondrial apoptotic cell death in human cervical cancer cells pptx
... nasopharyngeal carcinoma cells [13] Further studies have shown that phosphorylation of Bcl-2 on residues of in its loop domain, including Ser70 and Ser87, is critically involved in the apoptotic ... phosphorylation of Bcl-2 following a variety of stimuli These include paclitaxel-activated Raf-1 [15], paclitexel- or vincristine-induced protein kinase A [16], bryostatin-1induced mitochondrial localized ... development of molecular targets for cancer treatment Results To examine the kinetics of the apoptotic cell death induced by ionizing radiation in human cervical cancer cells, we treated HeLa cells...
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báo cáo hóa học:" Transplantation of vascular cells derived from human embryonic stem cells contributes to vascular regeneration after stroke in mice" docx
... human ES cells We induced differentiation of human ES cells in an in vitro two-dimensional culture on OP9 stromal cell line and examined the expression of VEGF-R2, VE-cadherin and TRA-1 during the ... purposes) Journal of Translational Medicine 2008, 6:54 cells, the number (cells/ mm2/mouse) of single stranded DNA (ss-DNA)+ cells in one field in the ischemic core from each mouse in the saline- or hES-ECs+MCs-injected ... angiogenesis in the ischemic area increased partially via the promotion of the expression of VEGF and bFGF in stroke areas [3], and in the present study, the increase of vascular density in saline-injected...
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Báo cáo y học: "Identification of a truncated form of methionine sulfoxide reductase a expressed in mouse embryonic stem cells" pps
... writing and final approval of the manuscript AK was involved in manuscript writing and data analysis SL was involved in the conception and design, administrative support, data analysis and interpretation, ... library in Genbank (Genbank ID: BG970953.1) with the same intron splicing pattern as the truncated form of MsrA cloned from embryonic stem cells, indicating this isoform might not be stem cell ... configuration of the subcellular localization of the truncated protein than a single view On the focal point of the scans (crosspoint of the horizontal green line and the vertical pink line), clearly...
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báo cáo khoa học: "Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease" potx
... methylcytosine cells, chromatin of pluripotent cells appears to have unique features, such as the increased mobility of many structural chromatin proteins, including histones and heterochromatin protein ... of chromatin profiling in annotating functional genomic elements in specific cell types Indeed, chromatin signatures that characterize different classes of regulatory elements, including promoters, ... Aberrant chromatin signature Figure Epigenomics as a tool to assess iPSC identity Chromatin signatures obtained by epigenomic profiling of a cohort of human embryonic stem cell (hESC) lines can...
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