Download or read book Field Guidelines for Genetic Experimental Designs in High Throughput Sequencing written by Ana M. Aransay and published by Springer. This book was released on 2016-06-02 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.
Download or read book Computational Methods for High throughput Pooled Genetic Experiments written by Matthew Douglas Edwards and published by . This book was released on 2011 with total page 65 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in high-throughput DNA sequencing have created new avenues of attack for classical genetics problems. This thesis develops and applies principled methods for analyzing DNA sequencing data from multiple pools of individual genomes. Theoretical expectations under several genetic models are used to inform specific experimental designs and guide the allocation of experimental resources. A computational framework is developed for analyzing and accurately extracting informative data from DNA sequencing reads obtained from pools of individuals. A series of statistical tests are proposed in order to detect nonrandom associations in pooled data, including a novel approach based on hidden Markov models that optimally shares data across genomic locations. The methods are applied to new and existing datasets and improve on the resolution of published methods, frequently obtaining single-gene accuracy.
Download or read book New High Throughput Technologies for DNA Sequencing and Genomics written by Keith R. Mitchelson and published by Elsevier. This book was released on 2011-09-22 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging. New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century.Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book.* 'Hot Topic' with DNA sequencing continuing as a major research activity in many areas of life science and medicine.* Bringing together new developments in DNA sequencing technology* Reviewing issues relevant to the new applications used
Download or read book Expanding the Applications of High throughput DNA Sequencing written by Jeffrey Alan Hussmann and published by . This book was released on 2015 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA sequencing is the process of determining the identities of the nucleotides that make up a molecule of DNA. The rapid pace of advancements in sequencing technologies in recent years have made it possible to simultaneously determine the sequences of hundreds of millions of short DNA fragments. The ability to perform sequencing with such high throughput has revolutionized the study of biological systems, but the types of questions that can be answered through sequencing-based experiments can be limited by the presence of different kinds of noise and biases in these experiments. One class of applications of high-throughput sequencing involves identifying genetic variation, such as finding rare mutations in the genomes of cancerous cells. In these applications, the sensitivity with which rare genetic variants can be detected is limited by the relatively high rate with which current DNA sequencing technologies incorrectly identify nucleotides. In the first half of this thesis, we present a method for dramatically reducing the rate at which these incorrect identifications occur. Our method, called circle sequencing, creates redundant copies of the sequence of each input molecule of DNA. This is accomplished by circularizing each DNA fragment and performing rolling circle amplification on these circles with a strand-displacing polymerase. The resulting products consist of several physically linked copies of the original sequence in each fragment. When these products are sequenced, this informational redundancy protects against random errors introduced during sequencing, allowing for highly accurate recovery of the original sequence of each input molecule. By eliminating the vast majority of incorrectly identified nucleotides from the resulting data, our method enables the sensitive detection of rare variants and opens up exciting new questions involving such variants to direct measurement by sequencing. An entirely different application of high-throughput sequencing is to selectively capture and sequence stretches of DNA or RNA that are participating in a process of interest within a cell. The accuracy of quantitative inferences made by this type of experiment can be severely impacted, however, by biases introduced during the experimental manipulations used to isolate biologically relevant fragments of DNA from cells. Ribosome profiling is an experimental technique that consists of sequencing short stretches of messenger RNAs that are protected from nuclease digestion by the presence of a bound ribosome. The resulting data represents millions of snapshots of the locations of actively translating ribosomes. In theory, these snapshots can be used to determine how long ribosomes take to translate each type of codon by quantifying how often ribosomes are observed positioned over that codon. In practice, different studies in yeast attempting to do this have reached contradictory and counterintuitive conclusions. In the second half of this thesis, we perform a large-scale comparative analysis of data from many different ribosome profiling experiments in order to resolve these contradictions. We identify a previously unappreciated source of systematic bias in a subset of these experiments. This bias prevents these experiments from accurately measuring ribosomes in proportion to how long they spend at each position in vivo. Understanding this bias provides insight into the true signatures of translation dynamics in yeast and offers important guidance for the future design and interpretation of sequencing-based approaches to measuring these dynamics.
Download or read book Botanical Gardens and Their Role in Plant Conservation written by T. Pullaiah and published by CRC Press. This book was released on 2023-09-29 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Approaching the contributions of a world-wide sector of scientific institutions to addressing the extinction crisis, Botanical Gardens and Their Role in Plant Conservation brings together a diversity of perspectives. There are more than 3,600 botanical gardens worldwide, where trees, shrubs, herbs, and other plants are studied and managed in collections. They are foremost among efforts to conserve the diversity of living plant species and ensure that crucial biodiversity is available for the future of humanity. This book is a showcase for plant conservation, restoration, biodiversity, and related scientific and educational work of botanical gardens around the world, featuring both thematic overview chapters and numerous case studies that illustrate the critical role these institutions play in fighting extinction and ensuring plant diversity is available for sustainable use. FEATURES A wide range of case studies derived from practical experience in a diversity of institutional, national, and biogeographical settings, Reviews of topics such as networking amongst institutions, the importance of global policy agreements such as the Convention on Biological Diversity and the Global Strategy for Plant Conservation, Profiles of botanical gardens contributions at the national level to conservation priorities, Real-world examples of programs in plant conservation for both critically endangered wild plant diversity and unique horticultural or cultural germplasm. Botanical Gardens and Their Role in Plant Conservation includes contributions from institutions from Africa, Asia, Australia, Europe, and the Americas, and institutions of all sizes and histories, from long-established national gardens to new gardens offering their perspectives on developing their roles in this vital undertaking.
Download or read book Biotechnological Tools in Fisheries and Aquatic Health Management written by Bijay Kumar Behera and published by Springer Nature. This book was released on 2023-11-22 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edited book is focused on SDG 14: life below water. This book covers all aspects of fish biotechnology and health management. A detailed description is provided of CRISPR Cas9 technology application in the development of superior variety of fish with better growth, disease resistance, etc., accompanied by numerous helpful photographs and schematic diagrams. In addition, recent developments in nanotechnology and its application in fisheries production enhancement have been discussed. Further, topics includes, probiotics, immunostimulants, fish genetic markers, bioremediation, metagenomics, transgenerational immune priming, application of cell culture in fisheries and nano-biosensor application on fish disease diagnosis, pollution monitoring, etc. are provided in details. . The book is helpful for researchers, teachers, students, farmers, and entrepreneurs in utilizing the knowledge on recent advancements in different aspects of fish genetics and biotechnology for future research and aquaculture production enhancement.
Download or read book Toxicoepigenetics written by Shaun D. McCullough and published by Academic Press. This book was released on 2018-11-02 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: Toxicoepigenetics: Core Principles and Applications examines the core aspects of epigenetics, including chromatin biology, DNA methylation, and non-coding RNA, as well as fundamental techniques and considerations for studying each of these mechanisms of epigenetic regulation. Although its integration into the field of toxicology is in its infancy, epigenetics have taken center stage in the study of diseases such as cancer, diabetes, and neurodegeneration. Increasing the presence of epigenetics in toxicological research allows for a more in-depth understanding of important aspects of toxicology such as the role of the environment and lifestyle influencing the individual susceptibility to these effects and the trans-generational transmission of these health effects and susceptibilities. Methods chapters are included to help improve efficacy and efficiency of protocols in both the laboratory and the classroom. Toxicoepigenetics: Core Principles and Applications is an essential book for researchers and academics using epigenetics in toxicology research and study. - Introduces the fundamental principles and practices for understanding the role of the epigenome in toxicology - Presents the foundation of epigenetics for toxicologists with a broad range of backgrounds - Discusses the incorporation of epigenetics and epigenomics into current toxicological studies and interpretation of epigenetic data in toxicological applications
Download or read book Microbial Metatranscriptomics Belowground written by Manoj Nath and published by Springer Nature. This book was released on 2021-06-02 with total page 677 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book emphasizes role of functional microbes in soil to improve fertility and plant health in agro-ecosystem. In this compendium main emphasis is on occurrence and distribution of microbial communities, In situ active microbial quorum in rhizosphere, metratranscriptomics for microflora- and fauna, and fnctional diversity in rhizosphere. The book also highlights the importance of PGPRs in rhizosphere, root endotrophic microbes, functional niche under biotic stress, functional niche under abiotic stress, functional root derived signals, as well as functional microbe derived signals. Approaches deployed in metatranscriptomics, and molecular Tools used in rhizosphere are also discussed in detail. The book presents content is useful for students, academicians, researchers working on soil rhizosphere and as a policy document on sustenance of agriculture.
Download or read book Next Generation Sequencing Technologies and Challenges in Sequence Assembly written by Sara El-Metwally and published by Springer Science & Business. This book was released on 2014-04-19 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt: The introduction of Next Generation Sequencing (NGS) technologies resulted in a major transformation in the way scientists extract genetic information from biological systems, revealing limitless insight about the genome, transcriptome and epigenome of any species. However, with NGS, came its own challenges that require continuous development in the sequencing technologies and bioinformatics analysis of the resultant raw data and assembly of the full length genome and transcriptome. Such developments lead to outstanding improvements of the performance and coverage of sequencing and improved quality for the assembled sequences, nevertheless, challenges such as sequencing errors, expensive processing and memory usage for assembly and sequencer specific errors remains major challenges in the field. This book aims to provide brief overviews the NGS field with special focus on the challenges facing the NGS field, including information on different experimental platforms, assembly algorithms and software tools, assembly error correction approaches and the correlated challenges.
Download or read book Industrial Microbiology and Biotechnology written by Pradeep Verma and published by Springer Nature. This book was released on 2023-07-08 with total page 751 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second volume of the Book-Industrial Microbiology and Biotechnology covers various emerging concepts in microbial technology which have been developed to harness the potential of the microbes. The book examines the microbes-based products that have widespread applications in various domains i.e., agriculture, biorefinery, bioremediation, pharmaceutical, and medical sectors. It focusses on recent advances and emerging topics such as CRISPR technology, advanced topics of genomics, including functional genomics, metagenomics, metabolomics, and structural and system biology approaches for enhanced production of industrially relevant products. It further gives an insight into the advancement of genetic engineering with special emphasis on value-added products via microalgal systems and their techno-economics analysis and life cycle assessment. The book towards the end presents recent advancements in the use of microbes for the production of industrial relevant enzymes, amino acids, vitamins, and nutraceuticals, on vaccine development and their biomedical applications. The book is an essential source for researchers working in allied fields of microbiology, biotechnology, and bioengineering.
Download or read book The Development and Utilization of Novel Antibiotic Alternatives written by Wang Jiajun and published by Frontiers Media SA. This book was released on 2022-10-07 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Methods in Yeast Genetics written by David C. Amberg and published by CSHL Press. This book was released on 2005 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Methods in Yeast Genetics" is a course that has been offered annually at Cold Spring Harbor for the last 30 years. This provides a set of teaching experiments along with the protocols and recipes for the standard techniques and reagents used in the study of yeast biology.
Download or read book Wastewater Treatment written by Maulin P. Shah and published by Elsevier. This book was released on 2021-01-30 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: Wastewater Treatment: Cutting-Edge Molecular Tools, Techniques and Applied Aspects reports new findings in existing molecular biology strategies, including their limitations, challenges and potential application to remove environmental pollutants through advancements made in cutting edge tools. In addition, the book introduces new trends and advances in environmental bioremediation with thorough discussions on recent developments in this field. - Describes the application of different omics tools in wastewater treatment plants (WWTPs) - Describes the role of microorganisms in WWTPs - Points out the reuse of treated wastewater through emerging technologies - Includes the recovery of resources from wastewater - Emphasizes the need for the use of cutting-edge molecular tools
Download or read book Hazardous Pollutants in Biological Treatment Systems written by Ferhan Çeçen and published by IWA Publishing. This book was released on 2017-11-15 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hazardous pollutants are a growing concern in treatment engineering. In the past, biological treatment was mainly used for the removal of bulk organic matter and the nutrients nitrogen and phosphorous. However, relatively recently the issue of hazardous pollutants, which are present at very low concentrations in wastewaters and waters but are very harmful to both ecosystems and humans, is becoming increasingly important. Today, treatment of hazardous pollutants in the water environment becomes a challenge as the water quality standards become stricter. Hazardous Pollutants in Biological Treatment Systems focuses entirely on hazardous pollutants in biological treatment and gives an elaborate insight into their fate and effects during biological treatment of wastewater and water. Currently, in commercial and industrial products and processes, thousands of chemicals are used that reach water. Many of those chemicals are carcinogens, mutagens, endocrine disruptors and toxicants. Therefore, water containing hazardous pollutants should be treated before discharged to the environment or consumed by humans. This book first addresses the characteristics, occurrence and origin of hazardous organic and inorganic pollutants. Then, it concentrates on the fate and effects of these pollutants in biological wastewater and drinking water treatment units. It also provides details about analysis of hazardous pollutants, experimental methodologies, computational tools used to assist experiments, evaluation of experimental data and examination of microbial ecology by molecular microbiology and genetic tools. Hazardous Pollutants in Biological Treatment Systems is an essential resource to the researcher or the practitioner who is already involved with hazardous pollutants and biological processes or intending to do so. The text will also be useful for professionals working in the field of water and wastewater treatment.
Download or read book High Throughput Next Generation Sequencing written by Young Min Kwon and published by Humana Press. This book was released on 2011-03-22 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to their novel concepts and extraordinary high-throughput sequencing capacity, the “next generation sequencing” methods allow scientists to grasp system-wide landscapes of the complex molecular events taking place in various biological systems, including microorganisms and microbial communities. These methods are now being recognized as essential tools for a more comprehensive and deeper understanding of the mechanisms underlying many biological processes. In High-Throughput Next Generation Sequencing: Methods and Applications, experts in the field explore the most recent advances in the applications of next generation sequencing technologies with an emphasis on microorganisms and their communities; however, the methods described in this book will also offer general applications relevant to the study of any living organisms. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, High-Throughput Next Generation Sequencing: Methods and Applications is an excellent collection of chapters to aid all scientists who wish to apply these innovative research tools to enhance their own pursuits in microbiology and also biology in general.
Download or read book Data Mining Techniques for the Life Sciences written by Oliviero Carugo and published by . This book was released on with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: Annotation This volume details several important databases and data mining tools. "Data Mining Techniques for the Life Sciences, Second Edition "guides readers through archives of macromolecular three-dimensional structures, databases of protein-protein interactions, thermodynamics information on protein and mutant stability, Kbdock protein domain structure database, PDB_REDO databank, erroneous sequences, substitution matrices, tools to align RNA sequences, interesting procedures for kinase family/subfamily classifications, new tools to predict protein crystallizability, metabolomics data, drug-target interaction predictions, and a recipe for protein-sequence-based function prediction and its implementation in the latest version of the ANNOTATOR software suite. 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, " Data Mining Techniques for the Life Sciences, Second Edition"" "aims to ensure successful results in the further study of this vital field."
Download or read book Sample Size Calculations in Clinical Research written by Shein-Chung Chow and published by CRC Press. This book was released on 2017-08-15 with total page 825 pages. Available in PDF, EPUB and Kindle. Book excerpt: Praise for the Second Edition: "... this is a useful, comprehensive compendium of almost every possible sample size formula. The strong organization and carefully defined formulae will aid any researcher designing a study." -Biometrics "This impressive book contains formulae for computing sample size in a wide range of settings. One-sample studies and two-sample comparisons for quantitative, binary, and time-to-event outcomes are covered comprehensively, with separate sample size formulae for testing equality, non-inferiority, and equivalence. Many less familiar topics are also covered ..." – Journal of the Royal Statistical Society Sample Size Calculations in Clinical Research, Third Edition presents statistical procedures for performing sample size calculations during various phases of clinical research and development. A comprehensive and unified presentation of statistical concepts and practical applications, this book includes a well-balanced summary of current and emerging clinical issues, regulatory requirements, and recently developed statistical methodologies for sample size calculation. Features: Compares the relative merits and disadvantages of statistical methods for sample size calculations Explains how the formulae and procedures for sample size calculations can be used in a variety of clinical research and development stages Presents real-world examples from several therapeutic areas, including cardiovascular medicine, the central nervous system, anti-infective medicine, oncology, and women’s health Provides sample size calculations for dose response studies, microarray studies, and Bayesian approaches This new edition is updated throughout, includes many new sections, and five new chapters on emerging topics: two stage seamless adaptive designs, cluster randomized trial design, zero-inflated Poisson distribution, clinical trials with extremely low incidence rates, and clinical trial simulation.
