Download or read book Models and Methods in Cell Signaling and Gene Expression written by Tammy M. Bray and published by . This book was released on 2000 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Modeling of Signaling Networks written by Lan K. Nguyen and published by Springer Nature. This book was released on 2023-04-19 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the computational modeling of cell signaling networks and the application of these models and model-based analysis to systems and personalized medicine. Chapters guide readers through various modeling approaches for signaling networks, new methods and techniques that facilitate model development and analysis, and new applications of signaling network modeling towards systems and personalized treatment of cancer. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Modeling of Signaling Networks aims to benefit a wide spectrum of readers including researchers from the biological as well as computational systems biology communities.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Modeling of Gene Regulatory Networks written by Hamid Bolouri and published by Imperial College Press. This book was released on 2008 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.
Download or read book Mechanobiology written by Ronen Zaidel-Bar and published by Springer Nature. This book was released on 2023-01-01 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book collects methodologies exploring mechanobiology, the involvement of mechanical forces in cell fate specification and in controlling single and collective cell behaviors such as directed migration, morphogenesis, wound healing, and the immune response. The volume features methods to quantify the mechanical properties of cells and adhesion proteins, to expose cells to external mechanical forces, to quantitatively characterize mechano-responses at various scales, to measure forces applied by cells on the extracellular matrix, as well as chapters on force measurement inside cells, probing cell signaling and gene expression in response to force, and biophysical modeling of cell shape and protein dynamics. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary material and reagents, step-by-step and readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mechanobiology: Methods and Protocols aims to provide meaningful tools for cell and developmental biologists approaching the study of cell and tissue dynamics from a mechanobiological perspective, molecular biologists interested in the effects of force on proteins, as well as for cancer biologists and biophysicists.
Download or read book Computational Methods in Cell Biology written by and published by Academic Press. This book was released on 2012-05-31 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational methods are playing an ever increasing role in cell biology. This volume of Methods in Cell Biology focuses on Computational Methods in Cell Biology and consists of two parts: (1) data extraction and analysis to distill models and mechanisms, and (2) developing and simulating models to make predictions and testable hypotheses. - Focuses on computational methods in cell biology - Split into 2 parts--data extraction and analysis to distill models and mechanisms, and developing and simulating models to make predictions and testable hypotheses - Emphasizes the intimate and necessary connection with interpreting experimental data and proposing the next hypothesis and experiment
Download or read book Systems Analysis of Mechano Sensitive Signaling Networks Regulating Gene Expression in Cardiomyocytes and Adventitial Fibroblasts written by Shulin Cao and published by . This book was released on 2021 with total page 207 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cells such as myocytes and adventitial fibroblasts are responsive to mechanical cues in their local environment. In response to mechanical loads, a variety of mechano-transduction mechanisms and signaling pathways are activated to regulate their response to the altered conditions. In order to define mechano-signaling networks and their role in cellular function and remodeling, we have adapted and refined previously published systems models of myocyte hypertrophy. Using uncertainty quantification, we first found that the model accuracy was robust to parameter changes over a wide range with model outputs being least sensitive to time constants and most affected by uncertainty in reaction weights. We also found epistemic uncertainty in the reaction logic of the model could greatly affect model accuracy while uncertainty in the validation data had a modest effect on model accuracy. As a step forward toward understanding myocyte response to external loading, including direction-dependent pathways, we extended this previous network model to include the transcriptional regulatory networks controlling gene expression as well as protein translation, and introduce a mass-action method to model quantitative gene expression. By incorporating RNA-sequencing data, this new approach displayed high accuracy with 69% agreement overall and 72% agreement for predicted differentially expressed genes in response to longitudinal stretch. We further found that the difference between transverse and longitudinal stretch responses in cardiomyocytes could be related to the sensitivity of directional mechanotransduction, with the sensitivity of longitudinal stretch being greater than transverse. Upon analyzing genes regulated by multiple TFs, we found that expression of these genes didn't monotonically change with the number of TFs, which indicates TF regulation effects may saturate faster when multiple TFs coregulate gene expression. Moreover, we identified AT1 and ET1 receptors as main regulators of the stretch induced responses through receptor inhibition simulations and subsequent experiments. A similar approach was used to study mechanical signaling and remodeling responses in PAAFs. In the current work, we have modified an existing systems model of cardiac fibroblast signaling to PAAFs and the cellular regulation of profibrotic signaling by combining both in-vitro and in-silico models of cell signaling in response to altered mechanical conditions. A UQ analysis on this model highlighted parameters to be optimized and network modules to be elucidated with more experiments. The signaling model in PAAFs and the subsequent experiments identified that both stretch and increased substrate stiffness regulated profibrotic genes, while no interaction effect was found between stretch and stiffness for several key genes studied. In addition, the activation of fibronectin expression by stretch in PAAFs may be angiotensin-independent when the cells are adhered on stiff but not soft substrates. While these signaling network models can help distinguish regulators and their sensitivity to different mechanical stimuli, it is not known how these regulators participate in gene regulation of in-vivo hypertrophy. In the future, these signaling network models can be used to identify key regulators of hypertrophy-related heart failure and tissue fibrosis and provide support for drug discovery.
Download or read book Study of Signaling and Regulatory Networks by Computational Methods written by Panwen Wang and published by . This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Study of Signaling and Regulatory Networks by Computational Methods" by Panwen, Wang, 王攀文, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: In order to communicate with extracellular and intracellular environments, cells have to be able to receive signals and via signaling pathways pass them to nucleus, where the genome responds through cascades of gene regulatory networks (GRNs). Many signal receptors on the cell membranes consist of extracellular part that can bind particular molecules, and intracellular part that accomplishes a conformation change or open binding sites for other proteins after the extracellular binding. Consequently, some proteins/enzymes are activated or recruited, and the signaling transduction then onsets via protein-protein interactions (PPIs). Once the signal reaches nucleus and related transcription factors (TFs) are activated, they will in turn regulate the gene transcription and change the gene expression. However, systematic identification of signaling network components and construction of GRNs are not easy to be achieved by pure experiments, which are costly and time-consuming. In this dissertation, we construct a workflow to study the signaling and regulatory networks by applying computational methods on public PPI and omics data. We first explore the phenotypic profiles of genes using a cross-species phenotype network and compile the them into a gene-phenotype association database; then a webserver is proposed using omics data to construct GRNs; next the phenotypic profiles, together with domain-domain interactions, phylogenetic profiles and expression profiles, are used as features to refine the PPI network using random forest classifier. The random walk with restart algorithm is applied to the refined PPI network to identify the signaling network components. The GRNs centered by the predicted TFs are finally constructed and with related omics data or putative binding information. With this workflow, we have successfully identified important TFs, including Pou5f1, Sox2 and Nanog, involved in the cell reprogramming mediated by vitamin C. For interaction partners and co-regulatory targets of core pluripotency factors, large parts of the results (154 out of 229 interactions) have been confirmed by literature. This workflow can also be applied to decode the signaling and regulatory networks via which the genome responds to the environmental stimuli (i.e. drug treatment). The results will not only help biologists and clinicians to better understand biological processes and diseases systematically, but also lead to further studies, such as drug repurposing. DOI: 10.5353/th_b5689282 Subjects: Gene regulatory networks - Computer simulation Cellular signal transduction - Computer simulation Cellular signal transduction - Mathematical models Gene regulatory networks - Mathematical models
Download or read book A Practical Guide to the Study of Calcium in Living Cells written by and published by Academic Press. This book was released on 1994-04-25 with total page 393 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Practical Guide to the Study of Calcium in Living Cells describes popular techniques along with helpful do's and don't's and computer programs. The volume enables investigators to evaluate confocal images, use the latest dyes, and design Calcium buffers appropriate to their research needs. This book is designed for laboratory use by graduate students, technicians, and researchers in many disciplines, ranging from molecular to cellular levels of investigation. - Describes techniques for detection of [Ca2+]I: Ca2+ - sensitive microelectrodes - Fluorescent dyes - Luminescent proteins - Includes techniques for perturbing intracellular Ca2+ - Covers detailed methodology plus problems and pitfalls of each technique - Contains a practical guide to preparing Ca2+ buffers with an easy-to-use computer program - Color plates illustrate techniques such as - Confocal ratio-imaging - Use of aequorin
Download or read book Gene Mapping Discovery and Expression written by Minou Bina and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Completion of the sequence of the human genome represents an unpar- leled achievement in the history of biology. The project has produced nearly complete, highly accurate, and comprehensive sequences of genomes of s- eral organisms including human, mouse, drosophila, and yeast. Furthermore, the development of high-throughput technologies has led to an explosion of projects to sequence the genomes of additional organisms including rat, chimp, dog, bee, chicken, and the list is expanding. The nearly completed draft of genomic sequences from numerous species has opened a new era of research in biology and in biomedical sciences. In keeping with the interdisciplinary nature of the new scientific era, the chapters in Gene Mapping, Discovery, and Expression: Methods and Protocols recapitulate the necessity of integration of experimental and computational tools for solving - portant research problems. The general underlying theme of this volume is DNA sequence-based technologies. At one level, the book highlights the importance of databases, genome-browsers, and web-based tools for data access and ana- sis. More specifically, sequencing projects routinely deposit their data in p- licly available databases including GenBank, at the National Center of Biotechnology (NCBI) in the United States; EMBL, maintained by the European Bioinformatics Institute; and DDBJ, the DNA Data Bank of Japan. Currently, several browsers offer facile access to numerous genomic DNA sequences for gene mapping and data retrieval.
Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.
Download or read book Dietary Modulation of Cell Signaling Pathways written by Zigang Dong and published by CRC Press. This book was released on 2008-09-26 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: A consequence of rapid progress in the science of nutrigenomics and nutrigenetics is the substantial accumulation of data covering nutrienal modulation of gene expression at the cellular and subcellular levels. Current research is increasingly focused on the role of nutrition and diet in modifying oxidative damage in the progression of disease. Die
Download or read book Signal Processing in Biological Cells written by Maya Rida Said and published by . This book was released on 2005 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis introduces systematic engineering principles to model, at different levels of abstraction the information processing in biological cells in order to understand the algorithms implemented by the signaling pathways that perform the processing. An example of how to emulate one of these algorithms in other signal processing contexts is also presented. At a high modeling level, the focus is on the network topology rather than the dynamical properties of the components of the signaling network. In this regime, we examine and analyze the distribution and properties of the network graph. Specifically, we present a global network investigation of the genotype/phenotype data-set recently developed for the yeast Saccharomyces cerevisiae from exposure to DNA damaging agents, enabling explicit study of how protein-protein interaction network characteristics may be associated with phenotypic functional effects. The properties of several functional yeast networks are also compared and a simple method to combine gene expression data with network information is proposed to better predict pathophysiological behavior. At a low level of modeling, the thesis introduces a new framework for modeling cellular signal processing based on interacting Markov chains. This framework provides a unified way to simultaneously capture the stochasticity of signaling networks in individual cells while computing a deterministic solution which provides average behavior. The use of this framework is demonstrated on two classical signaling networks: the mitogen activated protein kinase cascade and the bacterial chemotaxis pathway. The prospects of using cell biology as a metaphor for signal processing are also considered in a preliminary way by presenting a surface mapping algorithm based on bacterial chemotaxis.
Download or read book Networks in Cell Biology written by Mark Buchanan and published by Cambridge University Press. This book was released on 2010-05-13 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: Key introductory text for graduate students and researchers in physics, biology and biochemistry.
Download or read book Functional Genomics written by Michael J. Brownstein and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: This collection of robust, readily reproducible methods for microarray-based studies includes expert guidance in the optimal data analysis and informatics. On the methods side are proven techniques for monitoring subcellular RNA localization en masse, for mapping chromosomes at the resolution of a single gene, and for surveying the steady-state genome-wide distribution of DNA binding proteins in vivo. For those workers dealing with massive data sets, the book discusses the methodological aspects of data analysis and informatics in the design of microarray experiments, the choice of test statistic, and the assessment of observational significance, data reduction, and clustering.
Download or read book Regulation of T cell Signaling Networks written by Arvind Shankar Prabhakar and published by . This book was released on 2013 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: For a better understanding of how biology carries information within cells, it is not sufficient to look at individual protein or gene interactions, but to understand these networks of interactions as a whole. The goal of this thesis is to understand various aspects of how cells in general and T-cells in particular function, using models built from basic principles in chemical engineering, statistical physics and network theory, together with experiments performed by our collaborators. The ultimate objectives are to gain an insight into the mechanisms of certain key biological processes, understand the cause of certain diseases and to generate new ideas for methods of treating these diseases. First, we look at an example of a specific network built from previously published experiments and data collected by our collaborators, which governs the mechanism of activation of the T-cell receptor (TCR) by its kinase Lck and a negative regulator of Lck called Csk. We show that the mechanism by which the cell regulates TCR levels, together with the manner in which Lck activates the TCR produces interesting behavior, such as a "perfectly adaptive" system and a high-pass filter. Second, we look at heterogeneity in cancer cells at the level of protein signaling networks. Many common cancers are not treatable at the "source" or initial mutation, so one has to target downstream effector molecules. However, different cell lines bearing the same initial cancerous mutation exhibit varying signaling patterns due to differing secondary mutations which makes this difficult. The objective of this project is to try to characterize this heterogeneity and be able to identify molecules in the cell which would be the most effective drug targets. A general model for signaling in networks has been developed, analogous to models of neural networks, with mutations modeled as changes in the topology of this network. Keeping in mind that cancer cells are trying to maximize their growth, we are looking for patterns in secondary mutation during the directed evolution of these networks. A method for looking at free energy landscapes in topology space has also been developed. We find that lowest degree nodes along the shortest paths from the driver mutation to effector nodes tend to be the most conserved, and the frequency of multiple optima depends on the number of feedback loops. Finally, we look at the problem of constant activation thresholds for activation of various types of T-Cells. Despite having different TCRs, T-Cells of a certain type have a fixed activation threshold in terms of a peptide-MHC interaction strength (and a corresponding time, earlier than which they do not activate). We built a reaction-diffusion model for the network involved in the search process by which a pMHC-TCR finds a coreceptor-Lck, which enables us to understand how the threshold for activation is determined by the parameters of a particular cell type. We also developed an analytical solution for a simplified Markov Chain form of the model, which predicts how the activation rate scales with the parameters of interest in the system. We find that this rate is proportional to the fraction of coreceptors with Lck, increases (slowly) with diffusion and is independent of the number of coreceptors on the surface of the cell.
Download or read book Biology for AP Courses written by Julianne Zedalis and published by . This book was released on 2017-10-16 with total page 1923 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology for AP® courses covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology for AP® Courses was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum and includes rich features that engage students in scientific practice and AP® test preparation; it also highlights careers and research opportunities in biological sciences.
