The Experts below are selected from a list of 3804 Experts worldwide ranked by ideXlab platform
Kenji Yasuda - One of the best experts on this subject based on the ideXlab platform.
-
Novel Technology to Assay the Multicellular Network: On-Chip Cellomics Technology
Vascular Engineering, 2016Co-Authors: Kenji YasudaAbstract:A series of studies aimed at developing methods and technologies of analyzing Epigenetic Information in cells and in those networks, as well as that of genetic Information, was examined to expand our understanding of how living systems are determined. Technologies of analyzing Epigenetic Information was developed starting from the twin complementary viewpoints of cell regulation as an “algebraic” system (emphasis on temporal aspects) and as a “geometric” system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technologies and measurement technologies, which we call on-chip cellomics technology, we can select, control, and reconstruct the environments, interaction of single cells and cell networks from “algebraic” and “geometric” viewpoints. In this chapter, our developed technolgoeis and some results for spatial viewpoint of Epigenetic Information as a part of a series of cell-network-based “geometric” studies of celluler systems in our research groups are summarized and reported. The knowlege and technolgies acquired from these viewpoints may lead to the use of cells that fully control practical applications like cell-network-based drug screening and the regeneration of organs from cells.
-
On-chip cellomics: Single-cell-based constructive cell-network assay for quasi-in vivo screening of cardiotoxicity
2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2013Co-Authors: Kenji YasudaAbstract:We have developed methods and systems of analyzing Epigenetic Information in cells, as well as that of genetic Information, to expand our understanding of how living systems are determined. A system of analyzing Epigenetic Information was developed starting from the twin complementary viewpoints of cell regulation as an `algebraic' system (emphasis on temporal aspects) and as a `geometric' system (emphasis on spatial aspects). As an example of the `geometric' system, we have developed an quasi-in vivo hiPS cardiomyocyte network assay and confirmed that it can predict the risk of lethal arrythmia correctly in 22 compounds. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.
-
EMBC - On-chip cellomics: Single-cell-based constructive cell-network assay for quasi-in vivo screening of cardiotoxicity
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and, 2013Co-Authors: Kenji YasudaAbstract:We have developed methods and systems of analyzing Epigenetic Information in cells, as well as that of genetic Information, to expand our understanding of how living systems are determined. A system of analyzing Epigenetic Information was developed starting from the twin complementary viewpoints of cell regulation as an `algebraic' system (emphasis on temporal aspects) and as a `geometric' system (emphasis on spatial aspects). As an example of the `geometric' system, we have developed an quasi-in vivo hiPS cardiomyocyte network assay and confirmed that it can predict the risk of lethal arrythmia correctly in 22 compounds. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.
-
On-Chip Cellomics: Constructive Understanding of Multicellular Network Using On-Chip Cellomics Technology
Japanese Journal of Applied Physics, 2012Co-Authors: Kenji YasudaAbstract:We have developed methods and systems of analyzing Epigenetic Information in cells to expand our understanding of how living systems are determined. Because cells are minimum units reflecting Epigenetic Information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional deonucleotide (DNA) Information-processing events. The role of Epigenetic Information on cells, which complements their genetic Information, was inferred by comparing predictions from genetic Information with cell behaviour observed under conditions chosen to reveal adaptation processes and community effects. A system of analyzing Epigenetic Information, on-chip cellomics technology, has been developed starting from the twin complementary viewpoints of cell regulation as an "algebraic" system (emphasis on temporal aspects) and as a "geometric" system (emphasis on spatial aspects) exploiting microfabrication technology and a reconstructive approach of cellular systems not only for single cell-based subjects such as Escherichia coli and macrophages but also for cellular networks like the community effect of cardiomyocytes and plasticity in neuronal networks. One of the most important contributions of this study was to be able to reconstruct the concept of a cell regulatory network from the "local" (molecules expressed at certain times and places) to the "global" (the cell as a viable, functioning system). Knowledge of Epigenetic Information, which we can control and change during cell lives, complements the genetic variety, and these two types of Information are indispensable for living organisms. This new knowlege has the potential to be the basis of cell-based biological and medical fields such as those involving cell-based drug screening and the regeneration of organs from stem cells.
-
on chip cellomics assay enabling algebraic and geometric understanding of Epigenetic Information in cellular networks of living systems 1 temporal aspects of Epigenetic Information in bacteria
Sensors, 2012Co-Authors: Kenji YasudaAbstract:A series of studies aimed at developing methods and systems of analyzing Epigenetic Information in cells and in cell networks, as well as that of genetic Information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting Epigenetic Information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA Information-processing events. The role of Epigenetic Information on cells, which complements their genetic Information, was inferred by comparing predictions from genetic Information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing Epigenetic Information was developed starting from the twin complementary viewpoints of cell regulation as an “algebraic” system (emphasis on temporal aspects) and as a “geometric” system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from “algebraic” and “geometric” viewpoints. In this review, temporal viewpoint of Epigenetic Information, a part of the series of single-cell-based “algebraic” and “geometric” studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.
Shriprakash Sinha - One of the best experts on this subject based on the ideXlab platform.
-
integration of prior biological knowledge and Epigenetic Information enhances the prediction accuracy of the bayesian wnt pathway
Integrative Biology, 2014Co-Authors: Shriprakash SinhaAbstract:Computational modeling of the Wnt signaling pathway has gained prominence for its use as a diagnostic tool to develop therapeutic cancer target drugs and predict test samples as tumorous/normal. Diagnostic tools entail modeling of the biological phenomena behind the pathway while prediction requires inclusion of factors for discriminative classification. This manuscript develops simple static Bayesian network predictive models of varying complexity by encompassing prior partially available biological knowledge about intra/extracellular factors and incorporating Information regarding Epigenetic modification into a few genes that are known to have an inhibitory effect on the pathway. Incorporation of Epigenetic Information enhances the prediction accuracy of test samples in human colorectal cancer. In comparison to the Naive Bayes model where β-catenin transcription complex activation predictions are assumed to correspond to sample predictions, the new biologically inspired models shed light on differences in behavior of the transcription complex and the state of samples. Receiver operator curves and their respective area under the curve measurements obtained from predictions of the state of the test sample and the corresponding predictions of the state of activation of the β-catenin transcription complex of the pathway for the test sample indicate a significant difference between the transcription complex being on (off) and its association with the sample being tumorous (normal). The two-sample Kolmogorov–Smirnov test confirms the statistical deviation between the distributions of these predictions. Hitherto unknown relationship between factors like DKK2, DKK3-1 and SFRP-2/3/5 w.r.t. the β-catenin transcription complex has been inferred using these causal models.
-
prior biological knowledge and Epigenetic Information enhances prediction accuracy of bayesian wnt pathway
arXiv: Molecular Networks, 2013Co-Authors: Shriprakash Sinha, Marcel J T Reinders, Wim VerhaeghAbstract:Computational modeling of Wnt signaling pathway has gained prominence for its use as computer aided diagnostic tool to develop therapeutic cancer target drugs and predict of test samples as cancerous and non cancerous. This manuscript focuses on development of simple static bayesian network models of varying complexity that encompasses prior partially available biological knowledge about intra and extra cellular factors affecting the Wnt pathway and incorporates Epigenetic Information like methylation and histone modification of a few genes known to have inhibitory affect on Wnt pathway. It might be expected that such models not only increase cancer prediction accuracies and also form basis for understanding Wnt signaling activity in different states of tumorigenesis. Initial results in human colorectal cancer cases indicate that incorporation of Epigenetic Information increases prediction accuracy of test samples as being tumorous or normal. Receiver Operator Curves (ROC) and their respective area under the curve (AUC) measurements, obtained from predictions of state of test sample and corresponding predictions of the state of activation of transcription complex of the Wnt pathway for the test sample, indicate that there is significant difference between the Wnt pathway being on (off) and its association with the sample being tumorous (normal). Two sample Kolmogorov-Smirnov test confirm the statistical deviation between the distributions of these predictions. At a preliminary stage, use of these models may help in understanding the yet unknown effect of certain factors like DKK2, DKK3-1 and SFRP-2/3/5 on {\beta}-catenin transcription complex.
Zdenko Herceg - One of the best experts on this subject based on the ideXlab platform.
-
Epigenetic Information in chromatin and cancer
European Journal of Cancer, 2009Co-Authors: Zdenko HercegAbstract:Abstract It is now widely recognised that Epigenetic changes are implicated in human cancer. Epigenetic Information in chromatin (known as the ‘histone code’) has been proposed to extend and modulate the genetic (DNA) code in the regulation of key cellular processes. Histone modifications and histone modifying complexes have been traditionally associated with transcriptional regulation; however, recent studies indicated that the mechanisms involving the histone code play important roles in DNA replication, DNA damage detection and DNA repair. The histone code is believed to be ‘read’ by cellular machineries to regulate accessibility to, and functions of, chromatin DNA and the disruption of this code may lead to diseases, notably cancer.
-
Epigenetic Information in chromatin the code of entry for dna repair
Cell Cycle, 2006Co-Authors: Joanna I Loizou, Rabih Murr, Martin G Finkbeiner, Carla Sawan, Zhaoqi Wang, Zdenko HercegAbstract:Epigenetic changes are important etiological factors of human cancer. Epigenetic Information in chromatin (known as 'histone code') is a fascinating feature used by cells to extend and modulate the genetic (DNA) code. The histone code is thus proposed to be 'read' by cells to regulate accessibility to, and functions of, chromatin DNA. While the role of the Epigenetic code involving chromatin modifying/remodeling complexes in transcriptional regulation is well established, it is only recently that these mechanisms have been implicated in DNA damage detection and DNA repair. However, how the components of the DNA damage sensing and repair machinery gain access to broken DNA in compacted chromatin remains a mystery. Recent studies in this field provide important insights into DNA damage-specific and DNA repair-specific modifications to histones and encourage us that the Epigenetic code in chromatin during DNA repair will be understood in terms of precisely defined players and mechanisms.
Nathan M. Springer - One of the best experts on this subject based on the ideXlab platform.
-
Epigenetics and crop improvement
Trends in Genetics, 2013Co-Authors: Nathan M. SpringerAbstract:There is considerable excitement about the potential for Epigenetic Information to contribute to heritable variation in many species. Our understanding of the molecular mechanisms of Epigenetic inheritance is rapidly growing, and it is now possible to profile the epigenome at high resolution. Epigenetic Information plays a role in developmental gene regulation, response to the environment, and in natural variation of gene expression levels. Because of these central roles, there is the potential for Epigenetics to play a role in crop improvement strategies including the selection for favorable Epigenetic states, creation of novel epialleles, and regulation of transgene expression. In this review we consider the potential, and the limitations, of Epigenetic variation in crop improvement. © 2012 Elsevier Ltd.
-
Epigenetics and crop improvement
Trends in Genetics, 2012Co-Authors: Nathan M. SpringerAbstract:There is considerable excitement about the potential for Epigenetic Information to contribute to heritable variation in many species. Our understanding of the molecular mechanisms of Epigenetic inheritance is rapidly growing, and it is now possible to profile the epigenome at high resolution. Epigenetic Information plays a role in developmental gene regulation, response to the environment, and in natural variation of gene expression levels. Because of these central roles, there is the potential for Epigenetics to play a role in crop improvement strategies including the selection for favorable Epigenetic states, creation of novel epialleles, and regulation of transgene expression. In this review we consider the potential, and the limitations, of Epigenetic variation in crop improvement.
C Oneill - One of the best experts on this subject based on the ideXlab platform.
-
5 methylcytosine and 5 hydroxymethylcytosine each provide Epigenetic Information to the mouse zygote
PLOS ONE, 2013Co-Authors: Yan Li, C OneillAbstract:Covalent modification of cytosine nucleotides within the genome encode essential Epigenetic Information, with methylation (5meC) and hydroxymethylation (5hmC) having received most attention. It has been proposed that the formation of 5hmC is an intermediate in the active demethylation of 5meC. Some reports show that global loss of 5meC in the newly fertilised embryo is accompanied by increased 5hmC, but others have failed to confirm this finding. These analyses have relied on immuno-localization of these modifications. In this study we have established the conditions required for equilibrium binding of antibodies to 5meC and 5hmC in zygotes. Simultaneous detection of these antigens required denaturation of chromatin by acid treatment followed by antigen retrieval by tryptic digestion. Equilibrium binding then required incubation at 4°C for greater than 6 h. These are more demanding conditions than generally reported and resulted in the consistent detection of 5meC and 5hmC in both male and female pronuclei throughout zygotic maturation. No dynamic reciprocal change in the level of 5meC relative to 5hmC was observed. Both 5meC and 5hmC accumulated within the peri-nucleolar regions and this was more pronounced in the male pronucleus. Staining of 5meC was relatively more intense within the cortical and 5hmC in the central regions of pronuclei. The results are not consistent with a role for 5hmC in global demethylation in the zygote. The persistence of both modifications throughout zygotic maturation, and their differing patterns of localization and solvent exposure infer each modification provides its own Epigenetic Information to the early embryo.