Focused manuscript on the potential use/role of miRNAs in bioprocessing, specifically the production of complex proteins in mammalian cells. With that in mind I propose a draft list of topics/chapters along the following lines: Intro on CHO/bioprocessing/engineering challenges to set scene, Genomic organization, biogenesis and mode of action, Identifying miRNA targets: Computational prediction, transcriptomics, proteomices, UTR analysis, etc., miRNA expression in Chinese Hamster Ovary cells, miRNAs as engineering targets: pathway manipulation to impact bioprocess phenotypes, miRNAs as biomarkers, Detection methods: Northern, PCR, hybridization arrays, Next Gen Seq, Manipulation of expression in cultured cells: Transient/stable disregulation, Knockout.

This thesis outlines the development of the very first technology for high-throughput analysis of paired heavy and light-chain antibody sequences, opening an entirely new window for antibody discovery and the investigation of adaptive immune responses to vaccines and diseases. Previous methods for high-throughput immune repertoire sequencing have been unable to provide information on the identity of immune receptor pairs encoded by individual B or T lymphocytes. The author directly addresses these limitations by designing two new technologies for sequencing multiple mRNA transcripts from up to 10 million isolated, single cells. The techniques developed in this work have enabled comprehensive interrogation of human B-cell repertoires and have been applied for rapid discovery of new human antibodies, to gain new insights into the development of human antibody repertoires, and for analysis of human immune responses to vaccination and disease.

Genome Mapping and Molecular Breeding in Plants presents the current status of the elucidation and improvement of plant genomes of economic interest. The focus is on genetic and physical mapping, positioning, cloning, monitoring of desirable genes by molecular breeding and the most recent advances in genomics. The series comprises seven volumes: Cereals and Millets; Oilseeds; Pulses, Sugar and Tuber Crops; Fruits and Nuts; Vegetables; Technical Crops; and Forest Trees.

Technical Crops includes plants of great agricultural importance. One chapter is devoted to cotton, the most important fiber crop on which significant progress in molecular genetic research has been made. Reviews on oil palm, coffee, tea, cocoa and rubber describe traditional breeding and preliminary molecular results. Chapters on forage crops, ornamentals, and medicinal and aromatic plants each cover a large number of crops and may serve as road maps for further molecular research.

Over the past decade, our laboratory and others have been concerned with molecular archaeological studies aimed at revealing the origins and evolutionary histories of permeases (1). These studies have revealed that several different families, defined on the basis of sequence similarities, arose independently of each other, at different times in evolutionary history, following different routes. When complete microbial genomes first became available for analysis, we adapted p- existing software and designed new programs that allowed us quickly to identify probable transmembrane proteins, estimate their topologies and determine the likelihood that they function in transport (2). This work allowed us to expand previously-recognized families and to identify dozens of new families. All of this work then led us to attempt to design a rational but comprehensive classification system that would be applicable to the complete complement of transport systems found in all living organisms (3). The classification system that we have devised is based primarily on mode of transport and energy coupling mechanism, secondarily on molecular phylogeny, and lastly on the substrate specificities of the individual permeases (4).

Since the publication of the first edition, lentivirus vector-based technologies, through in vitro and in vivo gene transfer in eukaryotic animal cells, continue to offer the most promising opportunities for curing genetic disorders, as well as cancer and infectious diseases. Lentivirus Gene Engineering Protocols, Second Edition reflects the spectacular progress made in the field with a set of cutting-edge methods contributed by highly respected scientists. Beginning with a thorough overview of the most recent lentivirus developments, the book continues with detailed protocols including sections on the advances in lentiviral vector technology, new lentiviral vector applications, involving transgenic human embryonic stem cells and fetal gene therapy among other topics, as well as the invaluable breakthroughs in LV-mediated expression of microRNAs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes sections, highlighting tips on troubleshooting and avoiding known pitfalls.

Authoritative and timely, Lentivirus Gene Engineering Protocols, Second Edition covers the most relevant issues and techniques of LV-based gene engineering, thus representing a complete theoretical and practical guide for scientists still unfamiliar with LV technologies and those who simply wish to know more about this vital area of study.

Under the expert guidance of Bernd H.A. Rehm, the authors of this book provide a survey of the most striking and successful approaches for the production of biogenic nanodevices considering not only living organisms as manufacturer but also in vitro processes that utilise the self-assembly of isolated biomolecules.

This book reviews the latest advances in multiple fields of plant biotechnology and the opportunities that plant genetics, genomics and molecular biology have offered for agriculture improvement. Advanced technologies can dramatically enhance our capacity in understanding the molecular basis of traits and utilizing the available resources for accelerated development of high yielding, nutritious, input-use efficient and climate-smart crop varieties. In this book, readers will discover the significant advances in plant genetics, structural and functional genomics, trait and gene discovery, transcriptomics, proteomics, metabolomics, epigenomics, nanotechnology and analytical & decision support tools in breeding. This book appeals to researchers, academics and other stakeholders of global agriculture.

Bacterial genomics is a mature research interdisciplinary field, which is approached by ecologists, geneticists, bacteriologists, molecular biologists and evolutionary biologists working in medical, industrial and basic science. Thanks to the large diffusion of bacterial genome analysis, Bacterial Pangenomics: Methods and Protocols is able to provide the most recent methodologies about the study of bacterial pangenomes by covering the three major areas: the experimental methods for approaching bacterial pangenomics, the bio informatic pipelines for analysis and annotation of sequence data and finally the methods for inferring functional and evolutionary features from the pangenome. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Bacterial Pangenomics: Methods and Protocols will serve as a field guide for both qualified bacterial genomics investigators who want to update their technical knowledge, for less experienced researchers who want to start working with bacterial genomics and pangenomics, as well as serving as a manual and supplemental textbook for graduate students of genomics and bioinformatics.

Genome Mapping and Molecular Breeding in Plants presents the current status of the elucidation and improvement of plant genomes of economic interest. The focus is on genetic and physical mapping, positioning, cloning, monitoring of desirable genes by molecular breeding and the most recent advances in genomics. The series comprises seven volumes: Cereals and Millets; Oilseeds; Pulses, Sugar and Tuber Crops; Fruits and Nuts; Vegetables; Technical Crops; and Forest Trees.

Cereals and Millets form the leading group of field crops, providing staple food for most of the earth s population. This volume, with contributions by 27 eminent scientists, includes chapters on rice, wheat, maize, barley, oats, rye, sorghum, pearl millet, foxtail millet and finger millet. The emphasis is on advanced research on the major crops, including the model plants maize and rice, as well as on future road maps of genomic research for the less-often considered but equally deserving cereals and millets. "

Genome Mapping and Molecular Breeding in Plants presents the current status of the elucidation and improvement of plant genomes of economic interest. The focus is on genetic and physical mapping, positioning, cloning, monitoring of desirable genes by molecular breeding and the most recent advances in genomics. The series comprises seven volumes: Cereals and Millets; Oilseeds; Pulses, Sugar and Tuber Crops; Fruits and Nuts; Vegetables; Technical Crops; and Forest Trees.

Fruits and nuts form the largest group among crop plants. Several constraints such as long life cycle, heterozygosity and large plant size caused comparatively slow research progress in the past. The chapters on 20 fruit and nut crops authored by 56 renowned scientists from 12 countries include for the first time comprehensive reviews on mango, banana, olive, pineapple, pistachio, persimmon and papaya. Other crops covered are apple, grape, cherry, plum, peach, pear, apricot, strawberry, raspberry, blueberry, almond, citrus and avocado.

Changing environmental conditions substantially affect genetic variation and its dynamics in forest ecosystems and various systems of plantations. In response to these challenges, the present book focuses on the response to stress in terms of case studies which address physiological and genetic characters as well as various metric traits. Furthermore a choice of studies is presented which refers to diversity and geographic variation of various species and site conditions, respectively. In addition, genetic resources are characterised and a variety of studies is compiled which address reproduction and migration as well as management aspects. Finally, a set of studies is presented which focus on forest tree breeding with respect to uncertain climatic futures.

These contributions, written by the foremost international researchers and practitioners of Genetic Programming (GP), explore the synergy between theoretical and empirical results on real-world problems, producing a comprehensive view of the state of the art in GP. Topics in this volume include: exploiting subprograms in genetic programming, schema frequencies in GP, Accessible AI, GP for Big Data, lexicase selection, symbolic regression techniques, co-evolution of GP and LCS, and applying ecological principles to GP. It also covers several chapters on best practices and lessons learned from hands-on experience. Readers will discover large-scale, real-world applications of GP to a variety of problem domains via in-depth presentations of the latest and most significant results.

Maximizing the potential of RNA interference in functional genomics - as well as in the development of therapeutics - continues to be at the forefront of biomedical research. Unlike journal articles, Gene Silencing by RNA Interference: Technology and Application combines essential background to the RNAi field with practical techniques designed by renowned researchers to provide the most diverse and in-depth examination of the subject yet. This book describes methods and protocols for gene silencing and RNA interference. Each chapter provides necessary background to the subject and then gives detailed methods in easy-to-follow steps, along with troubleshooting hints and tips. Following a general and historical introduction, chapters two through eight focus on technical details of the various methods of siRNA design, chemical and enzymatic production, plasmid- and virus-mediated intracellular expression, and other RNAi tools. Chapter nine discusses the exogenous delivery of siRNAs into cells, and the final chapters of the book detail the application of RNAi to dissect gene function in a number of biological systems, including cell-free systems, cultured cells, and whole organisms. From the design and production of RNAi tools to their applications, Gene Silencing by RNA Interference: Technology and Application is the first to present the entire spectrum of activity, design, production, and delivery of RNAi reagents, providing a welcome guide for both academic and commercial use.

Parasitic, bacterial and viral agents continue to challenge the welfare of humans, livestock, wild life and plants worldwide. The public health impact and financial consequences of these diseases are particularly hard on the already overburdened economies of developing countries especially in the tropics. Many of these disease agents utilize insect hosts (vectors) to achieve their transmission to mammals. In the past, these diseases were largely controlled by insecticide-based vector reduction strategies. Now, many of these diseases have reemerged in the tropics, recolonizing their previous range, and expanding into new territories previously not considered to be endemic. Habitat change, irrigation practices, atmospheric and climate change, insecticide and drug resistance as well as increases in global tourism, human traffic and commercial activities, have driven the reemergence and spread of vector borne diseases. While these diseases can be controlled through interventions aimed at both their vertebrate and invertebrate hosts, no effective vaccines exist, and only limited therapeutic prospects are available for their control in mammalian hosts. Molecular technologies such as transgenesis, which is the subject of this book, stand to increase the toolbox and benefit disease management strategies.

Why has genetically modified food become a focal point in international conflicts over agriculture, trade and the environment? What are the chances for achieving effective global governance of new technologies such as genetic engineering? This book brings together state-of-the-art analyses of the international politics of biotechnology regulation. It presents explanations for the transatlantic biotech dispute, explores the growing North-South differences over how to ensure biosafety, and discusses the implications of the GM food battle for international trade and environmental law.

Genome sequence studies have become more and more important for plant breeding. Brassicas and Legumes: From Genome Structure to Breeding comprises 16 chapters and presents both an overview and the latest results of this rapidly expanding field. Topics covered include: genome analysis of a flowering plant, Arabidopsis thaliana; the sequence of the Arabidopsis genome as a tool for comparative structural genomics in Brassicaceae; application of molecular markers in Brassica coenospecies; the molecular genetic basis of flowering time variation in Brassica species; quantitative trait loci for clubroot resistance in Brassica oleracea; structural differences of S locus between Brassica oleracea and Brassica rapa; Brassica and legume chromosomes; sequence analysis of the Lotus japonicus genome; introduction of an early flowering accession ‘Miyakojima’ MG-20 to molecular genetics in Lotus japonicus; genetic linkage map of the model legume Lotus japonicus; construction of a high quality genome library of Lotus japonicus; genome analysis of Mesorhizobium loti: a symbiotic partner to Lotus japonicus; molecular linkage map of the model legume Medicago truncatula; genetic mapping of seed and nodule protein markers in diploid alfalfa (Medicago sativa); mapping the chickpea (Cicer arietinum) genome: localization of fungal resistance genes in interspecific crosses.  

With contributions from nearly 130 internationally renowned experts in the field, this reference details advances in transgenic plant construction and explores the social, political, and legal aspects of genetic plant manipulation. It provides analyzes of the history, genetics, physiology, and cultivation of over 30 species of transgenic seeds, fruits, and vegetables. Stressing the impact of genetic engineering strategies on the nutritional and functional benefit of foods as well as on consumer health and the global market economy, the book covers methods of gene marking, transferring, and tagging public perceptions to the selective breeding, hybridization, and recombinant DNA manipulation of food.

Early anthropological evidence for plant use as medicine is 60,000 years old as reported from the Neanderthal grave in Iraq. The importance of plants as medicine is further supported by archeological evidence from Asia and the Middle East. Today, around 1.4 billion people in South Asia alone have no access to modern health care, and rely instead on traditional medicine to alleviate various symptoms. On a global basis, approximately 50 to 80 thousand plant species are used either natively or as pharmaceutical derivatives for life-threatening conditions that include diabetes, hypertension and cancers. As the demand for plant-based medicine rises, there is an unmet need to investigate the quality, safety and efficacy of these herbals by the "scientific methods". Current research on drug discovery from medicinal plants involves a multifaceted approach combining botanical, phytochemical, analytical, and molecular techniques. For instance, high throughput robotic screens have been developed by industry; it is now possible to carry out 50,000 tests per day in the search for compounds which act on a key enzyme or a subset of receptors. This and other bioassays thus offer hope that one may eventually identify compounds for treating a variety of diseases or conditions. However, drug development from natural products is not without its problems. Frequent challenges encountered include the procurement of raw materials, the selection and implementation of appropriate high-throughput bioassays, and the scaling-up of preparative procedures. Research scientists should therefore arm themselves with the right tools and knowledge in order to harness the vast potentials of plant-based therapeutics. The main objective of Plant and Human Health is to serve as a comprehensive guide for this endeavor. Volume 1 highlights how humans from specific areas or cultures use indigenous plants. Despite technological developments, herbal drugs still occupy a preferential place in a majority of the population in the third world and have slowly taken roots as alternative medicine in the West. The integration of modern science with traditional uses of herbal drugs is important for our understanding of this ethnobotanical relationship. Volume 2 deals with the phytochemical and molecular characterization of herbal medicine. Specifically, it will focus on the secondary metabolic compounds which afford protection against diseases. Lastly, Volume 3 focuses on the physiological mechanisms by which the active ingredients of medicinal plants serve to improve human health. Together this three-volume collection intends to bridge the gap for herbalists, traditional and modern medical practitioners, and students and researchers in botany and horticulture.

Brings together in a single volume many cellular systems, allowing for better comparison of research results and helping to establish global strategies and standards. This unique reference/text presents the basic theory and practical applications of metabolic engineering (ME)-offering systematic analysis of complex metabolic pathways and ways of employing recombinant DNA techniques to alter cell behavior, metabolic patterns, and product formation. Covering ME as a distinct subfield of genetic engineering, Metabolic Engineering demonstrates new means of enabling cells to produce valuable proteins, polypeptides, and primary and secondary metabolites. Proposes a new paradigm for the directed modification of cellular metabolism and properties Written by more than 35 leading international experts in this field, Metabolic Engineering discusses metabolic engineering in plant and mammalian cells, bacteria, and yeasts illuminates the potential of the "cell factory" model for production of chemicals and therapeutics showcases methods of toxic waste management examines techniques for developing new antiviral and antibacterial molecules and effective gene and somatic-cell therapies investigates engineering strategies for increased production of bulk or specialty chemicals, including alcohols, organic and amino acids, aromatic compounds, antibiotics, novel polyketide metabolites, biopolymers, and plant secondary metabolites addresses uses of metabolic flux analysis, metabolic control analysis, and online metabolic flux analysis illustrates navigation of metabolic pathways in mammalian cell systems and new approaches to the degradation of xenobiotics assesses metabolic engineering applications in agriculture, pharmaceuticals, and environmental systems and more Containing over 1000 references, tables, equations, and drawings, Metabolic Engineering serves as an indispensable reference for bioprocess technologists, metabolic and chemical engineers, bi

Plant protoplasts have proved to be an excellent tool for in vitro manipu- lations, somatic hybridization, DNA uptake and genetic transformation, and for the induction of somaclonal variation. These studies reflect the far- reaching impact of protoplast alterations for agriculture and forest bio- technology. Taking these aspects into consideration, the series of books on Plant Protoplasts and Genetic Engineering provides a survey of the litera- ture, focusing on recent information and the state of the art in protoplast Plant Protoplasts manipulation and genetic transformation. This book, and Genetic Engineering VI, like the previous five volumes published in 1989,1993, and 1994, is unique in its approach. It comprises 27 chapters dealing with the regeneration of plants from protoplasts, and genetic transformation in various species of Arachis, Bupleurum, Capsella, Dendrobium, Dianthus, Diospyros, Fagopyrum, Festuca, Gentiana, Glycyrrhiza, Gossypium, Hemerocallis, Levisticum, Lonicera, Musa, Physallis, Platanus, Prunus, Saposhnikovia, Solanum, Spinacia, Trititrigia, Tulipa, and Vaccinium; including fruits such as apricot, banana, cranberry, pepino, peach, and plum. This book may be of special interest to advanced students, teachers, and research scientists in the field of plant tissue culture, molecular biology, genetic engineering, plant breeding, and general bio- technology. New Delhi, August 1995 Professor Y. P. S. BAJA] Series Editor Contents Section I Regeneration of Plants from Protoplasts 1. 1 Regeneration of Plants from Protop1asts of Arachis Species (Peanut) Z. LI, R. L. JARRET, and J. W. DEMSKI (With 2 Figures) 1 Introduction ...3 2 Isolation of Pro top lasts ...4 3 Culture of Protoplasts ...

Genomics, the mapping of the entire genetic complement of an organism, is the new frontier in biology. This handbook on the statistical issues of genomics covers current methods and the tried-and-true classical approaches.

Several years ago, when the discovery of catalytic RNA was recognized in a public manner,many people asked if new ?elds of therapy would soon be available. Although some tentative positive answers were given,nobody would say with certainty that RNA of various kinds was a truly promising means of altering gene expression. In fact,over the past decade,both our knowledge of RNAs with different functions and the utility of RNA in the inhibition or enhancement of gene expression have occurred with great drama. We proceeded in terms of possible therapeutic tools from RNase P and group I introns through "hammerhead" RNA enzymes, antisense technology, and more recently, to RNAi and its derivatives. A useful practical method of RNA delivery in animals will complete the picture. The diversity of RNA and the varied role of it inside cells and in therapy should be a tremendous challenge for young molecular biologists. This volume will make their task easier. Sidney Altman Sterling Professor of Molecular,Cellular & Devel- mental Biology,Nobel Laureate Department of Molecular,Cellular and Developm- tal Biology Yale University V NGTPR 4/23/05 1:00 PM Page VI VI Foreword Delivery of nucleic acids to cells in an animal remains a challenging problem. It is the major obstacle to success of therapeutic approaches using genes and oli- nucleotides,including siRNAs. Solutions found so far by chemists are satisfactory only for transfection of cells in culture.

Darwin's Pangenesis and its Rediscovery Part B explores Darwin's Pangenesis, an expanded cell theory and unified theory of heredity and variation from over 150 years ago that strengthened his theory of evolution and explained many phenomena of life. Now, new discoveries on circulating DNA, mobile RNAs, prions and extracellular vesicles are providing striking evidence for the chemical existence of Darwin's imaginary gemmules. In addition, new evidence for the inheritance of acquired characters, graft hybridization, and many other phenomena that Pangenesis supposedly explains are progressing, and are hence explored in this comprehensive volume. Specific chapters in this new volume include Darwin and Mendel: The Historical Connection, Darwin's Pangenesis and Graft Hybridization, Darwin's Pangenesis and Medical Genetics, Darwin's Pangenesis and Certain Anomalous Phenomena, and Natural Selection and Pangenesis: The Darwinian Synthesis.

Over 20 years have elapsed since publication of the seminal two volume series entitled Q Fever: The Biology of Coxiella burnetii (edited by J. C. Williams and H. A. Thompson) and Q fever: The Disease (edited by T. J. Marrie) that described the current state of Coxiella burnetii research. The ensuing years have brought the post-genomic era and accompanying technologies that have catalyzed major advances in the field, including milestones discoveries of genetic transformation and host cell-free growth of this former obligate intracellular bacterium. Understanding how the bacterium resists the degradative functions of vacuole, and the host cell functions coopted for successful parasitism, are central to understanding Q fever pathogenesis. Recent achievements in glycomics and proteomics are guiding development of enhanced detection schemes for the bacterium in addition to shedding light on the host immune response to the pathogen. The book covers the current state-of-the-art knowledge in the selected fields of C. burnetii/Q fever research. Coxiella has matured from a niche organism, investigated by a handful of laboratories worldwide, to a model system to study macrophage parasitism, developmental biology, host-pathogen interactions, and immune evasion/modulation.