Frontiers in Computational and Systems Biology


Book Description

Biological and biomedical studies have entered a new era over the past two decades thanks to the wide use of mathematical models and computational approaches. A booming of computational biology, which sheerly was a theoretician’s fantasy twenty years ago, has become a reality. Obsession with computational biology and theoretical approaches is evidenced in articles hailing the arrival of what are va- ously called quantitative biology, bioinformatics, theoretical biology, and systems biology. New technologies and data resources in genetics, such as the International HapMap project, enable large-scale studies, such as genome-wide association st- ies, which could potentially identify most common genetic variants as well as rare variants of the human DNA that may alter individual’s susceptibility to disease and the response to medical treatment. Meanwhile the multi-electrode recording from behaving animals makes it feasible to control the animal mental activity, which could potentially lead to the development of useful brain–machine interfaces. - bracing the sheer volume of genetic, genomic, and other type of data, an essential approach is, ?rst of all, to avoid drowning the true signal in the data. It has been witnessed that theoretical approach to biology has emerged as a powerful and st- ulating research paradigm in biological studies, which in turn leads to a new - search paradigm in mathematics, physics, and computer science and moves forward with the interplays among experimental studies and outcomes, simulation studies, and theoretical investigations.




The Life Sciences


Book Description




Frontiers in Mathematical Biology


Book Description

From a mathematical point of view, physiologically structured population models are an underdeveloped branch of the theory of infinite dimensional dynamical systems. We have called attention to four aspects: (i) A choice has to be made about the kind of equations one extracts from the predominantly verbal arguments about the basic assumptions, and subsequently uses as a starting point for a rigorous mathematical analysis. Though differential equations are easy to formulate (different mechanisms don't interact in infinites imal time intervals and so end up as separate terms in the equations) they may be hard to interpret rigorously as infinitesimal generators. Integral equations constitute an attractive alternative. (ii) The ability of physiologically structured population models to increase our un derstanding of the relation between mechanisms at the i-level and phenomena at the p-level will depend strongly on the development of dynamical systems lab facilities which are applicable to this class of models. (iii) Physiologically structured population models are ideally suited for the for mulation of evolutionary questions. Apart from the special case of age (see Charlesworth 1980, Yodzis 1989, Caswell 1989, and the references given there) hardly any theory exists at the moment. This will, hopefully, change rapidly in the coming years. Again the development of appropriate software may turn out to be crucial.




Systems and Synthetic Biology


Book Description

This textbook has been conceptualized to provide a detailed description of the various aspects of Systems and Synthetic Biology, keeping the requirements of M.Sc. and Ph.D. students in mind. Also, it is hoped that this book will mentor young scientists who are willing to contribute to this area but do not know from where to begin. The book has been divided into two sections. The first section will deal with systems biology – in terms of the foundational understanding, highlighting issues in biological complexity, methods of analysis and various aspects of modelling. The second section deals with the engineering concepts, design strategies of the biological systems ranging from simple DNA/RNA fragments, switches and oscillators, molecular pathways to a complete synthetic cell will be described. Finally, the book will offer expert opinions in legal, safety, security and social issues to present a well-balanced information both for students and scientists.




Frontiers of Biological Energetics


Book Description

Frontiers of Biological Energetics, Volume II: Electrons to Tissues contains most of the papers presented at the International Symposium on "Frontiers of Biological Energetics: Electrons to Tissues," held at the University of Pennsylvania School of Medicine in Philadelphia, Pennsylvania on July 20-21, 1978. The symposium provided a forum for discussing the common problems of biological energetics from different perspectives and from various levels of cellular organization. Comprised of 84 chapters, this volume begins with a section on electrons and oxygen and covers topics ranging from the chemical constitutions and subunit function of cytochrome oxidase polypeptides to the structure and function of copper atoms in cytochrome oxidase. The next section deals with structural-functional approaches to membrane energetics and includes chapters that explore rhodopsin and bacteriorhodopsin in model membranes; the mechanism of free energy utilization for active transport of calcium ions; and the regulation of cytoplasmic calcium by liver mitochodria. The final section focuses on nondestructive measurements of tissue function, paying particular attention to phosphorus nuclear magnetic resonance of diseased muscle and extracellular oxygen gradients in shock, among other topics. This book should be of interest to scientists from a variety of disciplines, including medicine and biology.




New Frontiers and Applications of Synthetic Biology


Book Description

New Frontiers and Applications of Synthetic Biology presents a collection of chapters from eminent synthetic biologists across the globe who have established experience and expertise working with synthetic biology. This book offers several important areas of synthetic biology which allow us to read and understand easily. It covers the introduction of synthetic biology and design of promoter, new DNA synthesis and sequencing technology, genome assembly, minimal cells, small synthetic RNA, directed evolution, protein engineering, computational tools, de novo synthesis, phage engineering, a sensor for microorganisms, next-generation diagnostic tools, CRISPR-Cas systems, and more. This book is a good source for not only researchers in designing synthetic biology, but also for researchers, students, synthetic biologists, metabolic engineers, genome engineers, clinicians, industrialists, stakeholders and policymakers interested in harnessing the potential of synthetic biology in many areas. - Offers basic understanding and knowledge in several aspects of synthetic biology - Covers state-of-the-art tools and technologies of synthetic biology, including promoter design, DNA synthesis, DNA sequencing, genome design, directed evolution, protein engineering, computational tools, phage design, CRISPR-Cas systems, and more - Discusses the applications of synthetic biology for smart drugs, vaccines, therapeutics, drug discovery, self-assembled materials, cell free systems, microfluidics, and more




Tissue Regeneration: Where Nano-structure Meets Biology


Book Description

This unique volume presents the recent advances in tissue regeneration. The authors are all active researchers in their respective fields with extensive experiences. The focus of the book is on the use of stem cells and nano-structured biomaterials for tissue regeneration/tissue engineering. It includes the use of stem cells, naturally derived extracellular matrix (ECM), synthetic biomimetic nano-fibers, synthetic nano-structured ceramics and synthetic nano-structured polymer/ceramic composites that can help/promote tissue regeneration. Methods on how to produce these nano-structured biomaterials are also discussed in several chapters. Future challenges and perspectives in the field of regenerative medicine (tissue regeneration) are also discussed.




Transport Equations in Biology


Book Description

This book presents models written as partial differential equations and originating from various questions in population biology, such as physiologically structured equations, adaptive dynamics, and bacterial movement. Its purpose is to derive appropriate mathematical tools and qualitative properties of the solutions. The book further contains many original PDE problems originating in biosciences.




Frontiers in Physicochemical Biology


Book Description

Frontiers in Physicochemical Biology ...




Prokaryotic Gene Expression


Book Description

Prokaryotic gene expression is not only of theoretical interest but also of highly practical significance. It has implications for other biological problems, such as developmental biology and cancer, brings insights into genetic engineering and expression systems, and has consequences for important aspects of applied research. For example, the molecular basis of bacterial pathogenicity has implications for new antibiotics and in crop development. Prokaryotic Gene Expression is a major review of the subject, providing up-to-date coverage as well as numerous insights by the prestigious authors. Topics covered include operons; protein recognition of sequence specific DNA- and RNA-binding sites; promoters; sigma factors, and variant tRNA polymerases; repressors and activators; post-transcriptional control and attenuation; ribonuclease activity, mRNA stability, and translational repression; prokaryotic DNA topology, topoisomerases, and gene expression; regulatory networks, regulatory cascades and signal transduction; phosphotransfer reactions; switch systems, transcriptional and translational modulation, methylation, and recombination mechanisms; pathogenicity, toxin regulation and virulence determinants; sporulation and genetic regulation of antibiotic production; origins of regulatory molecules, selective pressures and evolution of prokaryotic regulatory mechanisms systems. Over 1100 references to the primary literature are cited. Prokaryotic Gene Expression is a comprehensive and authoritative review of current knowledge and research in the area. It is essential reading for postgraduates and researchers in the field. Advanced undergraduates in biochemistry, molecular biology, and microbiology will also find this book useful.