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Quantifying Dynamics Of Microbial Evolution For Nascent Beneficial Mutations In Barcode Lineage Tracking Experiment
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Book Synopsis Quantifying Dynamics of Microbial Evolution for Nascent Beneficial Mutations in Barcode Lineage Tracking Experiment by : Huan-Yu Kuo
Download or read book Quantifying Dynamics of Microbial Evolution for Nascent Beneficial Mutations in Barcode Lineage Tracking Experiment written by Huan-Yu Kuo and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantifying the evolutionary dynamics of beneficial mutations in microbial populations relies on a massive sampling of nascent mutations, which has recently become possible by innovative barcode techniques. Despite barcode lineage tracking (BLT) experiments offer a straightforward means of capturing mutation frequency trajectories, accurately quantifying their dynamics remains a challenge. This dissertation addresses the critical issue of precisely and accurately estimating the fitness effects, mutation rates, and the distribution of fitness effects (DFE) associated with beneficial mutations identified in BLT experiments. First, I investigate the limitations of existing methods used to infer fitness effects and identify potential reasons for failure. To address this issue, I develop a novel Bayesian filtering method for fitness inference, which significantly enhances the accuracy of estimation compared to current approaches. Secondly, to estimate the rate of beneficial mutations within specific classes, I develop a stochastic model of mutant population dynamics. By applying this model, I infer the rate of beneficial mutations in the BLT experiment, providing valuable insights into mutation dynamics. Lastly, I highlight an inherent bias in our observations of beneficial mutations through adaptive evolution relative to the true underlying DFE. To address this disparity, I propose a method for inferring the mutation rate spectrum by back-calculating the observed DFE. The work presented in this dissertation establishes a statistically solid foundation for the analysis of the BLT experiment.
Book Synopsis Adaptive Diversification by : Michael Doebeli
Download or read book Adaptive Diversification written by Michael Doebeli and published by Princeton University Press. This book was released on 2011-08-01 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the mechanisms driving biological diversity remains a central problem in ecology and evolutionary biology. Traditional explanations assume that differences in selection pressures lead to different adaptations in geographically separated locations. This book takes a different approach and explores adaptive diversification--diversification rooted in ecological interactions and frequency-dependent selection. In any ecosystem, birth and death rates of individuals are affected by interactions with other individuals. What is an advantageous phenotype therefore depends on the phenotype of other individuals, and it may often be best to be ecologically different from the majority phenotype. Such rare-type advantage is a hallmark of frequency-dependent selection and opens the scope for processes of diversification that require ecological contact rather than geographical isolation. Michael Doebeli investigates adaptive diversification using the mathematical framework of adaptive dynamics. Evolutionary branching is a paradigmatic feature of adaptive dynamics that serves as a basic metaphor for adaptive diversification, and Doebeli explores the scope of evolutionary branching in many different ecological scenarios, including models of coevolution, cooperation, and cultural evolution. He also uses alternative modeling approaches. Stochastic, individual-based models are particularly useful for studying adaptive speciation in sexual populations, and partial differential equation models confirm the pervasiveness of adaptive diversification. Showing that frequency-dependent interactions are an important driver of biological diversity, Adaptive Diversification provides a comprehensive theoretical treatment of adaptive diversification.
Book Synopsis Introduction to Single Cell Omics by : Xinghua Pan
Download or read book Introduction to Single Cell Omics written by Xinghua Pan and published by Frontiers Media SA. This book was released on 2019-09-19 with total page 129 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-cell omics is a progressing frontier that stems from the sequencing of the human genome and the development of omics technologies, particularly genomics, transcriptomics, epigenomics and proteomics, but the sensitivity is now improved to single-cell level. The new generation of methodologies, especially the next generation sequencing (NGS) technology, plays a leading role in genomics related fields; however, the conventional techniques of omics require number of cells to be large, usually on the order of millions of cells, which is hardly accessible in some cases. More importantly, harnessing the power of omics technologies and applying those at the single-cell level are crucial since every cell is specific and unique, and almost every cell population in every systems, derived in either vivo or in vitro, is heterogeneous. Deciphering the heterogeneity of the cell population hence becomes critical for recognizing the mechanism and significance of the system. However, without an extensive examination of individual cells, a massive analysis of cell population would only give an average output of the cells, but neglect the differences among cells. Single-cell omics seeks to study a number of individual cells in parallel for their different dimensions of molecular profile on genome-wide scale, providing unprecedented resolution for the interpretation of both the structure and function of an organ, tissue or other system, as well as the interaction (and communication) and dynamics of single cells or subpopulations of cells and their lineages. Importantly single-cell omics enables the identification of a minor subpopulation of cells that may play a critical role in biological process over a dominant subpolulation such as a cancer and a developing organ. It provides an ultra-sensitive tool for us to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. Besides, it also empowers the clinical investigation of patients when facing a very low quantity of cell available for analysis, such as noninvasive cancer screening with circulating tumor cells (CTC), noninvasive prenatal diagnostics (NIPD) and preimplantation genetic test (PGT) for in vitro fertilization. Single-cell omics greatly promotes the understanding of life at a more fundamental level, bring vast applications in medicine. Accordingly, single-cell omics is also called as single-cell analysis or single-cell biology. Within only a couple of years, single-cell omics, especially transcriptomic sequencing (scRNA-seq), whole genome and exome sequencing (scWGS, scWES), has become robust and broadly accessible. Besides the existing technologies, recently, multiplexing barcode design and combinatorial indexing technology, in combination with microfluidic platform exampled by Drop-seq, or even being independent of microfluidic platform but using a regular PCR-plate, enable us a greater capacity of single cell analysis, switching from one single cell to thousands of single cells in a single test. The unique molecular identifiers (UMIs) allow the amplification bias among the original molecules to be corrected faithfully, resulting in a reliable quantitative measurement of omics in single cells. Of late, a variety of single-cell epigenomics analyses are becoming sophisticated, particularly single cell chromatin accessibility (scATAC-seq) and CpG methylation profiling (scBS-seq, scRRBS-seq). High resolution single molecular Fluorescence in situ hybridization (smFISH) and its revolutionary versions (ex. seqFISH, MERFISH, and so on), in addition to the spatial transcriptome sequencing, make the native relationship of the individual cells of a tissue to be in 3D or 4D format visually and quantitatively clarified. On the other hand, CRISPR/cas9 editing-based In vivo lineage tracing methods enable dynamic profile of a whole developmental process to be accurately displayed. Multi-omics analysis facilitates the study of multi-dimensional regulation and relationship of different elements of the central dogma in a single cell, as well as permitting a clear dissection of the complicated omics heterogeneity of a system. Last but not the least, the technology, biological noise, sequence dropout, and batch effect bring a huge challenge to the bioinformatics of single cell omics. While significant progress in the data analysis has been made since then, revolutionary theory and algorithm logics for single cell omics are expected. Indeed, single-cell analysis exert considerable impacts on the fields of biological studies, particularly cancers, neuron and neural system, stem cells, embryo development and immune system; other than that, it also tremendously motivates pharmaceutic RD, clinical diagnosis and monitoring, as well as precision medicine. This book hereby summarizes the recent developments and general considerations of single-cell analysis, with a detailed presentation on selected technologies and applications. Starting with the experimental design on single-cell omics, the book then emphasizes the consideration on heterogeneity of cancer and other systems. It also gives an introduction of the basic methods and key facts for bioinformatics analysis. Secondary, this book provides a summary of two types of popular technologies, the fundamental tools on single-cell isolation, and the developments of single cell multi-omics, followed by descriptions of FISH technologies, though other popular technologies are not covered here due to the fact that they are intensively described here and there recently. Finally, the book illustrates an elastomer-based integrated fluidic circuit that allows a connection between single cell functional studies combining stimulation, response, imaging and measurement, and corresponding single cell sequencing. This is a model system for single cell functional genomics. In addition, it reports a pipeline for single-cell proteomics with an analysis of the early development of Xenopus embryo, a single-cell qRT-PCR application that defined the subpopulations related to cell cycling, and a new method for synergistic assembly of single cell genome with sequencing of amplification product by phi29 DNA polymerase. Due to the tremendous progresses of single-cell omics in recent years, the topics covered here are incomplete, but each individual topic is excellently addressed, significantly interesting and beneficial to scientists working in or affiliated with this field.
Book Synopsis Modern Clinical Molecular Techniques by : Peter Hu
Download or read book Modern Clinical Molecular Techniques written by Peter Hu and published by Springer Science & Business Media. This book was released on 2012-05-11 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: This timely book covers the need to know clinical practices for all those involved in molecular laboratory science. The field of molecular medicine is evolving at an astounding speed. Propelled by the new insights and technologies, advances are being made at an unprecedented rate. With dual measure given to today’s breakthroughs, this book is a collection of the most current practices relevant to the clinical molecular laboratorian. It begins with an introductory section on techniques and procedure. It then presents four separate sections on infectious disease, oncology, pre/post-natal, and identity testing, with specific chapters clearly outlining clinical protocols used in daily practice. Modern Clinical Molecular Techniques cuts to the heart of what is essential for the practicing molecular laboratory scientist. It is an outstanding resource for those operating within or looking to set up a clinical molecular laboratory.
Book Synopsis Escherichia Coli and Salmonella by : Frederick C. Neidhardt
Download or read book Escherichia Coli and Salmonella written by Frederick C. Neidhardt and published by . This book was released on 1996 with total page 2822 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the long–awaited second edition of an invaluable classic! Escherichia coli occupies a central role in contemporary molecular biology. It is the unicellular organism about which most is known – all molecular and cellular biologists will want a copy of this book. In 154 chapters, 250 expert authors and editors present the state of the art. Completely rewritten and restructured, the second edition offers a whole new approach to the subject.
Book Synopsis Omics Technologies and Bio-engineering by : Debmalya Barh
Download or read book Omics Technologies and Bio-engineering written by Debmalya Barh and published by Academic Press. This book was released on 2017-12-01 with total page 645 pages. Available in PDF, EPUB and Kindle. Book excerpt: Omics Technologies and Bio-Engineering: Towards Improving Quality of Life, Volume 1 is a unique reference that brings together multiple perspectives on omics research, providing in-depth analysis and insights from an international team of authors. The book delivers pivotal information that will inform and improve medical and biological research by helping readers gain more direct access to analytic data, an increased understanding on data evaluation, and a comprehensive picture on how to use omics data in molecular biology, biotechnology and human health care. - Covers various aspects of biotechnology and bio-engineering using omics technologies - Focuses on the latest developments in the field, including biofuel technologies - Provides key insights into omics approaches in personalized and precision medicine - Provides a complete picture on how one can utilize omics data in molecular biology, biotechnology and human health care
Book Synopsis Bioinformatics for Cancer Immunotherapy by : Sebastian Boegel
Download or read book Bioinformatics for Cancer Immunotherapy written by Sebastian Boegel and published by Humana. This book was released on 2021-03-17 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on a variety of in silico protocols of the latest bioinformatics tools and computational pipelines developed for neo-antigen identification and immune cell analysis from high-throughput sequencing data for cancer immunotherapy. The chapters in this book cover topics that discuss the two emerging concepts in recognition of tumor cells using endogenous T cells: cancer vaccines against neo-antigens presented on HLA class I and II alleles, and checkpoint inhibitors. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Bioinformatics for Cancer Immunotherapy: Methods and Protocols is a valuable research tool for any scientist and researcher interested in learning more about this exciting and developing field.
Book Synopsis Microbial Genomics in Sustainable Agroecosystems by : Vijay Tripathi
Download or read book Microbial Genomics in Sustainable Agroecosystems written by Vijay Tripathi and published by Springer Nature. This book was released on 2019-11-23 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: Today, microbiology is a rapidly growing discipline in the life sciences, and the technologies are evolving on a virtually daily basis. Next-generation sequencing technologies have revolutionized microbial analysis, and can help us understand the biology and genomic diversity of various bacterial species with significant impacts on agro-ecosystems. In addition, advances in molecular biology and microbiology techniques hold the potential to improve the productivity and sustainability of agriculture and forestry. This new volume addresses the role of microbial genomics in understanding the living systems that exist in the soil and their interactions with plants, an aspect that is also important for crop improvement. The topics covered focus on a deeper and clearer understanding of how microbes cause diseases, the genome-based development of novel antibacterial agents and vaccines, and the role of microbial genomics in crop improvement and agroforestry. Given its scope, the book offers a valuable resource for researchers and students of agriculture and infectious biology.
Download or read book Night Drives written by Samantha Camargo and published by . This book was released on 2020-07-11 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: Night Drives is a collection of poetry and writing that makes you feel like you're on a night drive.. the kind with the windows down, music up, and the night sky above you. The kind that slowly opens you up, allowing you to feel all of the emotions you've been holding in for so long and somehow helps you feel alive again. The kind that helps you appreciate the night sky again.
Book Synopsis Begomoviruses: Occurrence and Management in Asia and Africa by : Sangeeta Saxena
Download or read book Begomoviruses: Occurrence and Management in Asia and Africa written by Sangeeta Saxena and published by Springer. This book was released on 2017-10-14 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Begomoviruses are one of the most interesting plant viruses to study for basic and applied research as they cause huge economic losses to agriculture industries and farmers all over the world. They belong to family Geminiviridae and are emergent plant viral pathogens which cause diseases in various crops in the tropical and subtropical regions. They are transmitted by the whitefly (B. tabaci) and have either one (monopartite DNA-A) or two (bipartite DNA-A and DNA-B) genomic components. DNA-A and DNA-B are of ~2600 - 2800 nucleotides each. A number of serious diseases of cultivated crops of the Fabaceae, Malvaceae, Solanaceae and Cucurbitaceae families are caused by Begomoviruses which are considered as threat to their cultivation in many countries. Accurate diagnosis is important for successful diseases management, since plants infected by Begomovirus do not recover, suffer serious yield losses and act as further sources of inoculum, which is then picked up and spread by their vector whitefly (B. tabaci). Reports of occurrence of new viruses and re-emergence of several known viruses in new niches have become regular event. In such a dynamic system, growth of several crop species relies on an accurate diagnosis, management and better understanding of the biology of the casual virus. This is crucial to evolve appropriate control practices and to prevent the virus infection. Researchers have achieved considerable progress in characterization, detection and management of virus on different crop species in the last decade. This book covers latest information in diagnosis of begomoviruses in the present scenario and explores the new vistas in the field of genomics and proteomics. Chapters in Section 1 illustrates the occurrence, genome organisation, transmission and diagnostics of begomoviruses. It also details the diseases caused by begomoviruses on different crops, detection techniques and management strategies in support of research findings by presentation of data, graphics, figures and tables. Section 2 is a chapterwise collection of occurrence, diversity and status of begomoviruses in Asian Africa counties where the diseases are most prevalent. This book will provide wide opportunity to the readers to have complete information and status of begomovirus in Asia and Africa. This will be useful resource for researchers and extension workers involved in the begomvirus disease diagnosis and molecular biology. Expert detection, accurate diagnosis and timely management play a significant role in keeping plants free from pathogens. In this book expert researchers share their research knowledge and literature which are vital towards the diagnosis of begomoviruses, addressing traditional plant pathology techniques as well as advanced molecular diagnostic approach. The book deals with the economically important crops including fruits, vegetables along with challenges in crop protection against diseases caused by begomovirus. This will be resourceful and handy for researcher, practitioners and also students.
Book Synopsis Eco-evolutionary Dynamics by : Andrew P. Hendry
Download or read book Eco-evolutionary Dynamics written by Andrew P. Hendry and published by Princeton University Press. This book was released on 2020-06-09 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, scientists have realized that evolution can occur on timescales much shorter than the 'long lapse of ages' emphasized by Darwin - in fact, evolutionary change is occurring all around us all the time. This work provides an authoritative and accessible introduction to eco-evolutionary dynamics, a cutting-edge new field that seeks to unify evolution and ecology into a common conceptual framework focusing on rapid and dynamic environmental and evolutionary change.
Download or read book Hantaviruses written by C. Schmaljohn and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hantaviruses are found world-wide and are associated with two severe disease syndromes, hemorrhagic fever and hantavirus pulmonary syndrome. The recent studies in this volume provide a basis for understanding the high human pathogenicity of theses viruses and their continued maintenance and transmission within rodent populations.
Book Synopsis Proteomics for Biological Discovery by : Timothy D. Veenstra
Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.
Book Synopsis Evolutionary Bioinformatics by : Donald R. Forsdyke
Download or read book Evolutionary Bioinformatics written by Donald R. Forsdyke and published by Springer Science & Business Media. This book was released on 2010-11-11 with total page 511 pages. Available in PDF, EPUB and Kindle. Book excerpt: Books on bioinformatics which began appearing in the mid 80s primarily served gene-hunters, and biologists who wished to construct family trees showing tidy lines of descent. Given the great pharmaceutical industry interest in genes, this trend has continued in most subsequent texts. These deal extensively with the exciting topic of gene discovery and searching databases, but hardly consider genomes as information channels through which multiple forms and levels of information, including genic information, have passed through the generations.
Book Synopsis Hi-C Data Analysis by : Silvio Bicciato
Download or read book Hi-C Data Analysis written by Silvio Bicciato and published by Humana. This book was released on 2022-09-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.
Book Synopsis Molecular Neuroanatomy by : Fred W. Leeuwen
Download or read book Molecular Neuroanatomy written by Fred W. Leeuwen and published by Elsevier Publishing Company. This book was released on 1988 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: For a thorough study of the dynamics of particular brain compounds it is now possible to use and combine various molecular neuroanatomical methods (e.g. in situ hybridization, receptor localisation and immunocytochemistry) in a quantitative way on whole brain sections maintaining morphological details. Molecular Neuroanatomy deals with the many practical aspects and recent developments in these areas. The theoretical background of many techniques is presented, as well as clear, step-by-step instructions on the preparation and application of all the methods and techniques described in this book. It will be invaluable to all those working in the field of neuroscience. Available in both hardback and paperback, with colour illustrations.
Download or read book RNA Editing written by Ernesto Picardi and published by Humana. This book was released on 2021-08-13 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides an overview about main RNA editing mechanisms, focusing on their functions in physiological as well as pathological conditions. Chapters guide readers through state- of-the art methodologies to investigate RNA editing through wet and dry approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Editing: Methods and Protocols aims to ensure successful results in the further study of this vital field.
