Bacteriophages (viruses that infect bacteria) are fascinating organisms that have played and continue to play a key role in bacterial genetics and molecular biology. Phage can confer key phenotypes on their host for example, converting a non-pathogenic strain into a pathogen and they play a key role in regulating bacterial populations in all sorts of environments. The phage-bacterium relationship varies enormously, from the simple predator-prey model to a complex, almost symbiotic relationship that promotes the survival and evolutionary success of both. While infection of bacteria used in the fermentation industry can be very problematic and result in financial losses, in other scenarios, phage infection of bacteria can be exploited for industrial and/or medical applications. Interest in phage and phage gene products as potential therapeutic agents is increasing rapidly and is likely to have a profound impact on the pharmaceutical industry and biotechnology in general over the comi

Genetic investigations and manipulations of bacteria and bacteriophage have made vital contributions to our basic understanding of living cells and to the development of molecular biology and biotechnology. This volume is a survey of the genetics of bacteria and their viruses, and it provides students with a comprehensive introduction to this rapidly changing subject. The book is written for upper level undergraduates and beginning graduate students, particularly those who have had an introductory genetics course.

The fifth edition has been extensively revised to reflect recent advances in the field. The book now has a reader-friendly look, with end-of-chapter questions, "Thinking Ahead" and "Applications" boxes to challenge students comprehension and insights. A complete glossary of commonly used terms has been revised and expanded.

This updated volume reflects new and evolved techniques to study detection, profiling, and manipulation of microRNAs (miRNAs) in plants and animals. After overviews of how best to detect, identify, and validate microRNAs, the book continues by exploring state-of-the-art protocols for microRNA detection, approaches to profile the expression level of microRNAs, spatial expression analysis, describe in silico analysis of microRNAs and their targets, as well as protocols for functional analysis of microRNAs and their targets by CRISPR/Cas. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, MicroRNA Detection and Target Identification: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

With the completion of sequencing projects and the advancement of a- lytical tools for protein identification, proteomics-the study of the expressed part of the genome-has become a major region of the burgeoning field of functional genomics. High-resolution 2-D gels can reveal virtually all p- teins present in a cell or tissue at any given time, including posttranslationally modified proteins. Changes in the expression and structure of most cellular proteins caused by differentiation or external stimuli can be displayed and eventually identified using 2-D protein gels. 2-D Proteome Analysis Protocols covers all aspects of the use of 2-D protein electrophoresis for the analysis of biological problems. The contri- tors include many of the leaders in the fields of biochemistry and analytical chemistry who were instrumental in the development of high-resolution 2-D gels, immobilized pH gradients, computer analysis, and mass spectromet- based protein identification methodologies. This book is intended as a benchtop manual and guide both for novices to 2-D gels and for those aficionados who wish to try the newer techniques. Any group using protein biochemistry-especially in the fields of molecular biology, biochemistry, microbiology, and cell biology-should find this book eminently useful. 2-D Proteome Analysis Protocols takes the researcher through the c- plete process of working with 2-D protein gels from making the protein - tract to finally identifying the proteins of interest. It includes protocols for generating 2-D protein extracts from most of the standard model organisms, including bacteria, yeast, nematode, Drosophila, plants, mouse, and human.

Genomics, Transcriptomics, Proteomics and Metabolomics of Crop Plants presents current operational methods applied to model crop plants. Including subcellular organelles, DNA fingerprinting and barcoding, sRNA, gene expression, rhizosphere engineering, marker assisted and 5G breeding, plant-microorganism interactions, stress signaling and responses, the book highlights important factors that are often overlooked and explores the latest research. The book also explores cutting-edge approaches for immediate application in new research such as OMICS, genome-wide transcriptome profiling, bioinformatics and database, DNA fingerprinting and barcoding, sRNA, gene expression, genome editing, diagnostics, rhizosphere engineering, marker assisted and 5G breeding, crop plant-microorganism interactions, stress signaling and responses. Additionally, the book describes opportunities to manipulate crop plants genetic and metabolic systems, while also exploring the related bioethical and biosafety issues. These topics are chosen and covered in detail to fill the gap in this understanding of crop molecular biology.

Wheat (Triticum L.), an annual herbaceous plant in Poacae (Gramineae) family, settles in the Triticeae (Hordeae) subfamily. The grasses (Poaceae Barnhart) are the fifth largest (monocotyledonous flowering) plant family and of great importance for human civilization and life. Cereal crops such as maize, wheat, rice, barley, and millet are the domesticated ones in the family. It is still the most vital economical plant family in modern times, providing food, forage, building materials (bamboo, thatch), and fuel (ethanol). Wheat has many accessions in national and international gene banks. The estimated number of wheats by FAO in 2010 is 856,000, and, followed by rice (774,000), and barley (467,000). However, the recent consumer's (misdirected) focus on gluten content and nutritional value urges scientists to reexamine their knowledge about wheat (i.e., origin, evolution, and general and special quality characteristics), as well as their wild relatives and landraces for newer possible genetic resources. Cultured or non-cultured ancestral wheats: einkorn, emmer, wild emmer, spelt, macha, and vavilovii are still limitedly grown on the higher areas in Turkey, Italy, Germany, Morocco, Israel, and Balkan countries. They are exploited mostly for their desired agronomic, and specific quality. In some cultures, wheat species are believed to be therapeutic, with bioactive compounds that reduce and inhibit stubborn illnesses such as diabetes, cancer, Alzheimer, and cardiovascular diseases. In this book, we summarize the importance of ancestral wheat species, and provide a prospect for their future with special considerations in terms of species conservation and improvement.

This book provides detailed information on the etiology, pathogenesis, diagnosis, prognosis, and treatment strategies for breast cancer. The first section of the book presents epidemiology, risk factors, histopathological, immunohistochemistry, and molecular subtypes of breast cancer based on the receptor status. It also discusses the association of breast cancer with other hormone-sensitive cancers. The second section of the book covers cover BRCA1 and BRCA2-associated breast carcinogenesis, early-stage progression of breast cancer, and noninvasive biomarkers for the early detection of breast cancer. It also discusses the role of epigenetic modifications and non-coding RNAs in breast cancer metastasis and explores these as the biomarkers and therapeutic targets for breast cancer therapy. Further, it discusses the role of fibrinolytic mechanisms and circulating tumor cells in breast cancer diagnosis, prognosis, and treatment. The book also provides an update on oral poly(ADP-ribose) polymerase (PARP) inhibitors to treat breast cancer. Finally, it offers potential new options for personalized therapies for breast cancer patients, including optimizing drug dosage and identifying genetic changes associated with cancer symptom occurrence and severity.

This book will expound the latest information on the current state of persimmon genomics and transcriptomics, with a particular focus on the latest findings and analysis in relation to the most important agronomic traits. The genus Diospyros contains about 400 species distributed all continents of the globe. Most of Diospyros species are distributed in the tropical and subtropical regions, while cultivated persimmon or simply kaki (Diospyros kaki) originates in East Asia and has been grown in China, Japan and Korea for many years. World production of persimmon has been increasing continuously since 1990s, with China being the most producer. Outside Asia, kaki production has been rapidly increasing in Spain in recent years. Because kaki is mostly hexaploid (2n = 6x =90) and its genome size is quite large with the flow cytometric analysis estimation of about 900 Mb, genetic and molecular studies in persimmon are quite complicated. Diploid close relatives of kaki, D. lotus and D. oleifera have been recently used as model species of kaki. Utilizing these species, molecular basis of several economically molecular basis of important traits such as sexuality and astringency has been studied, giving important information for kaki breeding.

Epigenetic Regulation of Cancer in Response to Chemotherapy, Volume 158 of the Advances in Cancer Research series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of authors.

This book encapsulates and occupies recent advances and state-of-the-art applications of nature-inspired computing (NIC) techniques in the field of bioinformatics and computational biology, which would aid medical sciences in various clinical applications. This edited volume covers fundamental applications, scope, and future perspectives of NIC techniques in bioinformatics including genomic profiling, gene expression data classification, DNA computation, systems and network biology, solving personalized therapy complications, antimicrobial resistance in bacterial pathogens, and computer-aided drug design, discovery, and therapeutics. It also covers the role of NIC techniques in various diseases and disorders, including cancer detection and diagnosis, breast cancer, lung disorder detection, disease biomarkers, and potential therapeutics identifications.

Species are not functionally independent. From a long-term perspective, only ecosystem with a fully integrated nutrient cycle is alive. The lack of trophic autonomy should be considered one of the key factors that ensure and maintain biodiversity. The variability of abiotic conditions, both in space and in time, also creates a huge diversity of niches and subniches for genotypes and species. In addition, life maintains its essential variables (biomass and productivity) as stable as possible due to the diversity of structures (genes, macromolecules, metabolic pathways, genotypes, species, etc.): the structures that reach optima are multiplied and thus activated, while the functioning of those which lost their optima is suppressed. The facts and concepts presented in this monograph thus support the conclusions that (a) genotype and species diversity is supported by trophic specialisation (b) biodiversity helps to stabilise the functions (essential variables) of individuals, populations, and ecological communities (c) in evolution, the emergence of biodiversity is determined by heritable variation and the advantage of specialised (more effective) structures over non-specialised ones (d) biodiversity is characterised by its ability to increase itself and to organise itself into relatively consistent structures, which we call production pyramids and nutrient cycles. This book therefore provides an answer to the question "why the diversity of life is of such and such a nature".

This detailed volume collects updates on the technical advances in hematopoietic stem cell research and incorporates new techniques focused on the molecular/genetic, cellular, and whole organism levels. Exploring methods that apply stress to hematopoiesis, the book also contains chapters focused on better understanding the role of hematopoietic niches and their cellular components, as well as in vivo models that test and quantitate stem cell function and are key to further development of therapeutic applications. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Hematopoietic Stem Cells: Methods and Protocols serves as a valued addition to laboratories focused on understanding hematopoietic stem cell biology and the therapeutic advances that can be derived from it.

RNA viruses provide unique insights into the patterns and processes of evolutionary change in real time. The study of viral evolution is especially topical given the growing awareness that emerging and re-emerging diseases (most of which are caused by RNA viruses) represent a major threat to public health. However, while the study of viral evolution has developed rapidly in the last 30 years, relatively little attention has been directed toward linking work on the mechanisms of viral evolution within cells or individual hosts, to the epidemiological outcomes of these processes. This novel book fills this gap by considering the patterns and processes of viral evolution across their entire range of spatial and temporal scales. The Evolution and Emergence of RNA Viruses provides a comprehensive overview of RNA virus evolution, with a particular focus on genomic and phylogenetic approaches. This is the first book to link mechanisms of viral evolution with disease dynamics, using high-profile examples in emergence and evolution such as influenza, HIV, dengue fever, and rabies. It also reveals the underlying evolutionary processes by which emerging viruses cross species boundaries and spread in new hosts.

This work is the first compilation of comprehensive deliberations on botany, cytogenetics and sex determination, genetic resources and diversity, classical breeding, molecular markers and genome sequence resources, and application of omics technology including transcriptomics, proteomics, and metabolomics resources in the multipurpose medicinal plant seabuckthorn. The book also presents a detailed narrative on antioxidative, radioprotective nutraceutical, and medicinal applications of seabuckthorn products. A detailed treatment has been included on analytical techniques and processing technologies. Altogether, the book contains about 300 pages over 17 chapters contributed by globally reputed experts on the relevant field in this important plant species. This book will be useful to the research students, teachers, and scientists in the academia and private sector engaged in horticulture, genetics, breeding, molecular biology, biotechnology, and breeding. The book will also be a useful source for workers involved in the development of plant-based medicines, nutraceuticals, therapeutics, and cosmeceuticals and extension workers involved in the development of rural farmers and small-scale industries.

This book explores recent progress in RNA secondary, tertiary structure prediction, and its application from an expansive point of view. Because of advancements in experimental protocols and devices, the integration of new types of data as well as new analysis techniques is necessary, and this volume discusses additional topics that are closely related to RNA structure prediction, such as the detection of structure-disrupting mutations, high-throughput structure analysis, and 3D structure design. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice that leads to quality research results. Authoritative and practical, RNA Structure Prediction serves as a valuable guide for both experimental and computational RNA researchers.

This volume explores base editors (BEs), an invaluable CRISPR-based genome editing tool with a wide variety of versatile applications. Beginning with an overview of BEs, their diverse variants, and computational tools, the book continues with experimental applications of BEs for disease modeling in mammalian cells and generating mutagenic mice, therapeutic base editing strategies, which covers delivery methods of BE-encoded DNA plasmids, mRNAs, or ribonucleoproteins through viruses or non-viral lipid nanoparticles, and lastly, the use of BEs in plants and bacteria. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Base Editors: Methods and Protocols serves as an ideal guide for researchers looking to use base editors to continue their studies in an array of fields.

This book establishes the theoretical foundations of a general methodology for multiple hypothesis testing and discusses its software implementation in R and SAS. The methods are applied to a range of testing problems in biomedical and genomic research, including the identification of differentially expressed and co-expressed genes in high-throughput gene expression experiments, such as microarray experiments; tests of association between gene expression measures and biological annotation metadata (e.g., Gene Ontology); sequence analysis; and the genetic mapping of complex traits using single nucleotide polymorphisms. The book is aimed at both statisticians interested in multiple testing theory and applied scientists encountering high-dimensional testing problems in their subject matter area.

Stem Cell Transcriptional Networks: Methods and Protocols collects techniques used to increase our understanding of the underlying transcriptional programs of stem cells that promote self-renewal and differentiation. The volume opens with a section on next-generation sequencing library preparation and data analysis. Continuing with a collection of protocols on visual analysis and interpretation of large-scale interaction networks, this detailed compilation features transcriptional networks in embryonic and adult stem cells, embryo culture and derivation of stem cells, as well as transcriptional programs that promote self-renewal, reprogramming, and transdifferentiation. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Stem Cell Transcriptional Networks: Methods and Protocols aims to provide a key resource for biologists seeking to interrogate these vital networks.

Cellular-molecular approach to evolution has led to radical changes in our understanding of biologic principles ranging from the Cell, to the Life Cycle, Development, Homeostasis, Senescence/Aging, Heterochrony, Pleiotropy, Phenotype, and perhaps the purpose of life itself. Much of this new way of thinking about biology and medicine emanates from experimental evidence for epigenetic inheritance. This leads one to question whether our unicellular state is the actual primary level of selection. One particular system that is now recognized as being under the auspices of epigenetic inheritance is the endocrine system, which is conventionally thought to regulate physiologic homeostasis. However, because the sex hormones play such a major role in behaviors related to the acquisition of epigenetic data, and the processing of such epigenetic data by the gonads during meiosis, their role in the evolution of the organism become tractable. The composite of the activities of the individual over the course of its lifetime can now be understood causally, resulting from the orchestration of its physiology by hormones, prenatally, postnatally and during the aging process, across the entire life span of the organism. Specific behaviors over the course of the life cycle during childhood, adolescence, puberty, adulthood and aging can now be understood mechanistically rather than merely as milestones in the various stages of life. With the above considerations in mind, this book presents the cellular-evolutionary perspective towards the relationship of the organism with its surroundings, human and non-human alike renders biology and medicine a continuum instead of fragmented, un-related anecdotes.

Over the past decade, neuroproteomics has shed light on the molecular features of schizophrenia by depicting biological processes involved with its establishment, maintenance and treatment. These studies have also pointed to potential biomarkers applicable to diagnosis and medication monitoring. Edited by a leader in the field of neuroproteomics with contributions from subject experts, this new volume will address recent findings and compile evidence from difference perspectives-such as human samples, animal models, pluripotent stem cell-derived in vitro pre-clinical models-and provide findings to inform the development of innovative future treatment strategies. This volume will be useful for a broad audience of researchers and professionals, including biologists, neurologists, psychiatrists, analytical chemists, and pharmacists, among others.

This book covers the important diseases and pests of potato which are of global significance. The pests and diseases in potato lead to huge economic losses by reducing the yield and quality of the produce. This book describes major pests and diseases in detail with particular emphasis on the latest developments with respect to their biology, ecology, and management. It highlights the importance of virus infection for seed potato production and diagnostic symptoms, along with management guidelines. The book brings forth tips for judicious use of pesticides for sustainable potato production and management of pesticide resistance. Use of novel approaches such as RNA interference, genome editing, and other genomic resources for drug designing in diseases and pest management is also emphasized in the book. This book is of interest to teachers, researchers, extension workers, potato growers, and policy makers. Also, the book serves as additional reading material for undergraduate and graduate students of agriculture and plant pathology. National and international agricultural scientists and policy makers will also find this to be a useful read.

This detailed volume explores a variety of cutting-edge techniques used to interrogate spatial genome organization. Beginning with a section covering the vital chromosome conformation capture (3C) technique, this collection continues with chapters on targeted Hi-C approaches, sequencing-based approaches to assess nuclear environment, as well as single-cell technologies to better characterize the heterogeneity and dynamics of nuclear architectures and approaches to visualize them by microscopy. Finally, in order to be able to ask functional questions about the role of spatial chromatin organization in genomic control, the last section provides methods for acute manipulations of chromatin architecture. Written for the highly successful Methods in Molecular Biology series, 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 practical, Spatial Genome Organization: Methods and Protocols is an ideal resource for researchers searching for the best techniques to address their own specific research questions.

This second edition provides an overview of recent developments and approaches used by researchers to investigate the properties and functions of mammary epithelial and stem cells, which will contribute to understand the heterogeneity of the mammary gland and of breast cancer. Chapters detail processes used to characterize stem cells, single cell RNA sequencing, computational methods, sophisticated imaging techniques, and a variety of model systems, among others. 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, Mammary Stem Cells: Methods and Protocols, Second Edition aims to make available protocols used to navigate the intricate behavior of mammary stem cells and to gain further knowledge to take us closer to the design of innovative strategies to prevent and treat breast cancer.

The Chlamydomonas Sourcebook: Introduction to Chlamydomonas and Its Laboratory Use, Volume One, Third Edition has been fully revised and updated to include a wealth of new resources for the Chlamydomonas community (new mutant libraries, new omics studies, and potentially more information about different Chlamydomonas species in the environment). In addition to updates on molecular techniques and analysis of the sequenced genome, the book presents the latest in research and best practices for applications in research, including methods for culture, preservation of cultures, preparation of media, and more.

This volume provides protocols on evidence for polyploidy and how it can be unveiled. Chapters guide readers through evolutionary experiments, measure effects of polyploidy, evidence for (remnants of) ancient WGDs, models of chromosome number evolution, population genomics approaches to study polyploidy, analysing genetic data from polyploid populations, Phylogenetic and phylogenomic methods, gene expression, gene regulation, unicellular alga (Chlamydomonas), and a fast-growing duckweed (Spirodela). 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 reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Polyploidy: Method and Protocols aims to be of interest to experimental and computational (evolutionary) biologists, molecular biologists, and biotechnologists.