Homing Endonucleases: Methods and Protocols aims at providing molecular biologists with a comprehensive resource to identify and characterize homing endonucleases from genomic sequence, to deduce the biological basis of binding and cleavage specificity, as well as to provide protocols to redesign endonuclease target specificity for genome-editing applications. Engineering of designer homing endonucleases has set the stage for genome editing of complex eukaryotic genomes with a broad range of potential applications including targeted gene knockouts in model organisms and gene therapy in humans, making this book a valuable resource for future research. 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 practical, Homing Endonucleases: Methods and Protocols serves as a key reference for all labs studying site-specific DNA endonucleases.

This book surveys recent advances related to the application of single molecule techniques in various fields of science. The topics, each described by leading experts in the field, range from single molecule experiments in quantum optics and solid-state physics to analogous investigations in physical chemistry and biophysics. A unifying theme of all chapters is the power of single molecule techniques to unravel fluctuations and heterogeneities usually hidden in the ensemble average of complex systems. The concept for the book originated from a gathering of some of the world's leading scientists at the Nobel Conference in Sweden.

This detailed volume presents a comprehensive technical overview of DNA nanotechnology with an emphasis on 3D DNA nanostructure design and applications. Coverage spans from basic design principles for DNA and RNA nanostructures to their cutting-edge applications in a variety of fields, with the book divided into basic DNA and RNA nanostructure design strategies as well as applications utilizing DNA nanostructures, including but not limited to nanomedicine, bioimaging, biosensing, nanoplasmonics, nanoelectronics, nanofabrication, crystallography, biophysics, and analytical chemistry. 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. Comprehensive and authoritative, 3D DNA Nanostructure: Methods and Protocols provides the most up-to-date tutorial style overviews and technical style protocols to benefit researchers in a wide variety of areas.

Gene function annotation has been a central question in molecular biology. The importance of computational function prediction is increasing because more and more large scale biological data, including genome sequences, protein structures, protein-protein interaction data, microarray expression data, and mass spectrometry data, are awaiting biological interpretation. Traditionally when a genome is sequenced, function annotation of genes is done by homology search methods, such as BLAST or FASTA. However, since these methods are developed before the genomics era, conventional use of them is not necessarily most suitable for analyzing a large scale data. Therefore we observe emerging development of computational gene function prediction methods, which are targeted to analyze large scale data, and also those which use such omics data as additional source of function prediction. In this book, we overview this emerging exciting field. The authors have been selected from 1) those who develop novel purely computational methods 2) those who develop function prediction methods which use omics data 3) those who maintain and update data base of function annotation of particular model organisms (E. coli), which are frequently referred

The discovery that most of the chronic infections in humans, including the oral, lung, vaginal and foreign body-associated infections, are biofilm-based, has prompted the need to design new and properly focused preventive and therapeutic strategies for these diseases. Microbial Biofilms: Methods and Protocols provides a detailed description of the currently available methods and protocols to investigate bacterial and fungal biofilms, exhaustively illustrated and critically annotated in 25 chapters written by authors well known for their experience in the respective fields. The book has joined together microbiologists and specialists in infectious diseases, hygiene and public health involved in exploring different aspects of microbial biofilms as well as in designing new methods and/or developing innovative laboratory protocols. 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, Microbial Biofilms: Methods and Protocols presents readers with the most established and validated experimental procedures to investigate microbial biofilms.

Historically the field of endocrine research has always been at the forefront of scientific endeavors. The investigators of these important breakthroughs in research have been rewarded by numerous Nobel awards. In the field of diabetes alone, Nobel prizes have been awarded to researchers who discovered insulin, characterized the protein and invented radioimmunoassays using insulin as a paradigm. Not surprisingly, biomedical researchers have always been attracted by the endocrine system and other similar systems of intercellular communication.
Over the past two decades, endocrine research has developed rapidly and adapted modern molecular and cellular biology techniques for its specific use. These changes have allowed researchers in the field to maintain their edge. Thus, endocrine disease-related genes have been characterized and mutations in these genes have helped explain common and
less common endocrine disorders. Our understanding of the regulation of gene expression has been greatly enhanced by molecular techniques.
In an attempt to bring investigators up to date with the recent advances in this exploding field we have decided to publish a series entitled Advances in Molecular and Cellular Endocrinology. Internationally famous investigators have agreed to participate and their contributions are appreciated.
Volume 1 has focused on aspects of the hypothalamic-pituitary axis including GnRH and GH gene regulation, molecular aspects of insulin, insulin-like growth factors and glucagon. In addition, reviews on the recently cloned calcium receptor and steroid receptor interactions with DNA are presented.

Micropropagation is a reliable technology applied commercially worldwide for large-scale plant multiplication, germplasm conservation, pathogen elimination, genetic manipulations and supply of selected plants. In Protocols for Micropropagation of Selected Economically-Important Horticultural Plants, well recognised researchers in the field compile step-wise protocols for rapid plant multiplication of economically-important horticultural species. The book contains 35 chapters, divided into four major sections. The first three sections (Section A, B and C) contain 29 micropropagation protocols of selected fruit and nut species, indoor and outdoor ornamental plants, cut flowers, and vegetables. In addition to the detailed protocols of in vitro shoot initiation, proliferation, root induction and acclimatization, chapters also include detailed information on medium preparation, explant selection and preparation. The six chapters of Section D cover specific reviews on pivotal topics, such as in vitro rejuvenation, synthetic seed technology, thermotherapy and meristem culture in banana, genetic transformation of pineapple, flower color somaclonal variation in torenia, and cryotherapy of horticultural crops. Moreover, as a part of the highly successful Methods in Molecular Biology series, chapters include introductions to the respective topic, lists of necessary materials, notes, and illustrative photos. Comprehensive and well-written, Protocols for Micropropagation of Selected Economically-Important Horticultural Plants offers a useful resource for horticulturists, researchers, commercial companies, plant propagators, biotechnologists and students interested in micropropagation.

The lipid-rich and otherwise challenging nature of many key tissues complicates many aspects of current research, and applications of the unique nature of lipoproteins and their biological effects has engendered unique and vital methodologies. In Lipoproteins and Cardiovascular Disease: Methods and Protocols, experts in the field present a compendium of advanced and classical molecular biology methods targeted towards lipoprotein, atherosclerosis, and vascular biology research, bringing together in a single volume an updated set of protocols and strategies for methods now driving the most recent advances, along with classical methods that are still widely used. Among the many topics covered in this cutting-edge work, the book delves into crucial techniques such as quantitative real-time PCR, microarrays, RT-PCR laser capture microdissection, and tissue-specific gene overexpression, knockout, and knockdown methodologies, including AAV as a liver-directed gene delivery vehicle. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and valuable notes which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and easy to use, Lipoproteins and Cardiovascular Disease: Methods and Protocols serves both novices and experts alike as a complete guide for any researcher with an interest in lipoproteins and their significant biological effects.

What Arieh Warshel and fellow 2013 Nobel laureates Michael Levitt and Martin Karplus achieved - beginning in the late 1960s and early 1970s when computers were still very primitive - was the creation of methods and programs that describe the action of biological molecules by 'multiscale models'. In this book, Warshel describes this fascinating, half-century journey to the apex of science.From Kibbutz Fishponds to The Nobel Prize is as much an autobiography as an advocacy for the emerging field of computational science. We follow Warshel through pivotal moments of his life, from his formative years in war-torn Israel in an idealistic kibbutz that did not encourage academic education; to his time in the army and his move to the Technion where he started in his obsession of understanding the catalytic power of enzymes; to his eventual scientific career which took him to the Weizmann Institute, Harvard University, Medical Research Council, and finally University of Southern California. We read about his unique contributions to the elucidation of the molecular basis of biological functions, which are combined with instructive stories about his persistence in advancing ideas that contradict the current dogma, and the nature of his scientific struggle for recognition, both personal and for the field to which he devoted his life. This is, in so many ways, more than just a memoir: it is a profoundly inspirational tale of one man's odyssey from a kibbutz that did not allow him to go to a university to the pinnacle of the scientific world, highlighting that the correct mixture of persistence, talent and luck can lead to a Nobel Prize.

The quantity of information available about membrane proteins is now too large for any one person to be familiar with anything but a very small part of the primary literature. A series of volumes concentrating on molecular aspects of biological membranes therefore seems timely. The hope is that, when complete, these volumes will provide a convenient introduction to the study of a wide range of membrane functions.
Application of the techniques of molecular biology has provided the sequences of a very large number of membrane proteins, and has led to the discovery of superfamilies of membrane proteins of related structure. The classic example of the superfamily is the seven helix receptor superfamily, all related in structure to bacteriorhodpsin, and named after the seven trans-membrane a-helices identified in bacteriorhodpsin. This volume explores the structures and functions of this super family.

Focusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. 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. Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.

While extremely large datasets describing gene sequences, mRNA transcripts, protein abundance, and metabolite concentrations are increasingly commonplace, these represent only starting 'parts lists' that are usually insufficient to unlock mechanistic insights on their own right. Fortunately, as "Network Biology: Methods and Applications" examines, concepts emerging from the study of biological entities such as networks (e.g. functional interactions linking genes, proteins, metabolites, etc.) suggest that order rather than chaos prevails, with such principles as modular and hierarchical organization, reactive information-driven causal-response behaviours, systems robustness, co-evolution, and self-organization guiding the way. This volume presents detailed, practical descriptions of the experimental and computational approaches currently prevalent in network biology as written by practiced experts in the field. Written in the highly successful "Methods in Molecular Biology " series format, relevant chapters contain introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.

Comprehensive and accessible, "Network Biology: Methods and Applications" provides an ensemble of procedures that will be of great value to a broad assortment of readers, ranging from graduate students to seasoned professionals looking to polish their skill sets."

With the ever-increasing volume of information in clinical medicine, researchers and health professionals need computer-based storage, processing and dissemination. In this book, leading experts in the field provide a series of articles focusing on software applications used to translate information into outcomes of clinical relevance. This book is the perfect guide for researchers and clinical scientists working in this emerging "omics" era.

Nonmammalian model organisms have become a cornerstone of systems biology research. Like the Rosetta Stone, which enabled modern scholars to decode ancient Egyptian hieroglyphics, model organisms enable biologists to decipher the genetic code underlying the complex physiological processes common to all life. C. elegans provides a particularly striking example of the experimental utility of model organisms. Genetic, molecular and systems biological characterization of this organism is greatly facilitated by its short life cycle and high rate reproduction, and by the ease with which it can be cultured in the laboratory. C. elegans also has a fully sequenced and well-annotated genome, which is assembled in readily accessible public databases along with virtually all other biological data on this organism.
C. elegans: Methods and Applications aims to enhance the readily available methodologies for the study of C. elegans by providing overviews and concise, step-by-step descriptions of the most state-of-the-art methods currently being utilized in the field. Some of the methods presented include forward and reverse genetic analysis, data mining and comparative genomics strategies, electron and fluorescence microscopy methods, automated imaging methods for worm behavioral analysis, functional genomics strategies, and cutting-edge methods for physiological analyses. This comprehensive collection of methods, written by experts in the field, endeavors to serve as a roadmap for researchers, illustrating the type or research that is possible with C. elegans, and illuminating its potential as a vehicle for future discovery.

This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret's research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.

This book introduces time-stretch quantitative phase imaging (TS-QPI), a high-throughput label-free imaging flow cytometer developed for big data acquisition and analysis in phenotypic screening. TS-QPI is able to capture quantitative optical phase and intensity images simultaneously, enabling high-content cell analysis, cancer diagnostics, personalized genomics, and drug development. The authors also demonstrate a complete machine learning pipeline that performs optical phase measurement, image processing, feature extraction, and classification, enabling high-throughput quantitative imaging that achieves record high accuracy in label -free cellular phenotypic screening and opens up a new path to data-driven diagnosis.

This volume details protocols for genetic, molecular, cytological, and bioinformatic methods for determining haplotypes. Haplotyping: Methods and Protocols guides readers through methods that directly type haploid cells, difficult-to-resolve gene families, high-resolution, short range haplotyping for targeted loci, and long-range haplotyping for whole chromosomes or genomes. 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 practical Haplotyping: Methods and Protocols, aims to provide researchers with an overview of experimental methods for haplotyping.

This volume will address an important emergent area within the field of immunomics: the discovery of antigens and adjuvants within the context of reverse vaccinology. Conventional approaches to vaccine design and development requires pathogens to be cultivated in the laboratory and the immunogenic molecules within them to be identifiable. Conventional vaccinology is no longer universally successful, particularly for recalcitrant pathogens. By using genomic information we can study vaccine development in silico: 'reverse vaccinology', can identify candidate subunits vaccines by identifying antigenic proteins and by using equally rational approaches to identify novel immune response-enhancing adjuvants.

This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood without dealing with interfacial behaviour. There is an urge to grasp how biologically relevant behaviour is shaped by the structuring of biomolecular interfaces and how interfacial tension affects the molecular events that take place in the cell. This book squarely addresses these needs from a physicist perspective. The book may serve as a monograph for practitioners and, alternatively, as an advanced textbook. Fruitful reading requires a background in physical chemistry and some basics in biophysics. The selected problems at the end of the chapters and the progression in conceptual difficulty make it a suitable textbook for a graduate level course or an elective course for seniors majoring in chemistry, physics, biomedical engineering or related disciplines.

This book provides a theoretical background of branching processes and discusses their biological applications. Branching processes are a well-developed and powerful set of tools in the field of applied probability. The range of applications considered includes molecular biology, cellular biology, human evolution and medicine. The branching processes discussed include Galton-Watson, Markov, Bellman-Harris, Multitype, and General Processes. As an aid to understanding specific examples, two introductory chapters, and two glossaries are included that provide background material in mathematics and in biology. The book will be of interest to scientists who work in quantitative modeling of biological systems, particularly probabilists, mathematical biologists, biostatisticians, cell biologists, molecular biologists, and bioinformaticians. The authors are a mathematician and cell biologist who have collaborated for more than a decade in the field of branching processes in biology for this new edition. This second expanded edition adds new material published during the last decade, with nearly 200 new references. More material has been added on infinitely-dimensional multitype processes, including the infinitely-dimensional linear-fractional case. Hypergeometric function treatment of the special case of the Griffiths-Pakes infinite allele branching process has also been added. There are additional applications of recent molecular processes and connections with systems biology are explored, and a new chapter on genealogies of branching processes and their applications. Reviews of First Edition: "This is a significant book on applications of branching processes in biology, and it is highly recommended for those readers who are interested in the application and development of stochastic models, particularly those with interests in cellular and molecular biology." (Siam Review, Vol. 45 (2), 2003) "This book will be very interesting and useful for mathematicians, statisticians and biologists as well, and especially for researchers developing mathematical methods in biology, medicine and other natural sciences." (Short Book Reviews of the ISI, Vol. 23 (2), 2003)

As functional genomics has become one of the major focuses in molecular biology, the need for more sophisticated tools to assist in the identification of the functionality of undefined genes and the correlation of DNA variants with a particular phenotype has increased greatly. In Silico Tools for Gene Discovery collects many common and useful in silico tools available today. The volume begins by investigating locus mapping information on linkage analysis, association mapping, integrative analysis, and exome analysis as well as tools for DNA marker selection, in silico PCR, and statistical analysis. It continues with a section on gene discovery from a defined locus, including gene prioritization, knowledge tracking, and data mining, and concludes with several useful in silico tools presented for the functional characterization of genes, which include DNA sequencing analysis, variant characterization, as well as RNA and protein analysis. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, step-by-step, readily reproducible protocols, and vital notes on troubleshooting and avoiding known pitfalls. Resourceful and easy to follow, In Silico Tools for Gene Discovery seeks to facilitate scientists with further key research on locus mapping, to accelerate gene identification, and to help ascertain the functionality of DNA variation.

Lactobacillus is a genus of Gram-positive facultative anaerobic or microaerophilic bacteria. In humans, they are symbiotic and are found in the gut flora. Lactobacillus species are used for the production of yogurt, cheese, sauerkraut, pickles, beer, wine, cider, kimchi, chocolate, and other fermented foods, as well as animal feeds such as silage. In recent years, much interest has been shown in the use of lactobacilli as probiotic organisms and their potential for disease prevention in humans and animals. This major new work focuses on recent research on the molecular biology and genomics of Lactobacillus. Written by an international team of scientists, the volume is an essential reference for all dairy technologists, microbiologists, and biotechnologists in the academic and industrial sectors. Topics covered include phylogenetics, taxonomy, comparative genomics, functional genomics, the intestinal microflora, surface proteins, stress responses, interaction with the immune system, probiotics, anti-cancer potential, and much more. This is essential reading for all scientists involved with lactic acid bacteria or probiotic research and is recommended for all microbiology laboratories.

This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.

Biological nitrogen fixation (BNF) - the conversion of molecular nitrogen into ammonia - is one of the most important reactions in ecology and agriculture. It is performed exclusively by microbes (prokaryotes) that live in symbiosis with plants. This book summarizes the latest research on this reaction, the participating microbes and the genetics of how their relevant genes could be transferred into the plants. In the light of a more sustainable and less ecologically damaging agriculture, this is becoming an increasingly pressing issue.

In DNA Electrophoresis: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study DNA using electrophoresis as the major approach. A powerful tool that allows separating DNA molecules according to their size and shape, this volume includes methods and techniques such as 2-dimentional gel electrophoresis as the major approach. These include methods and techniques such as 2-dimentional gel electrophoresis, DNA electrophoresis under conditions in which DNA molecules are completely or partially denatured during the runs, Pulse Field Gel Electrophoresis, electrophoresis coupled to fluorescence in situ hybridization, as well as protein-DNA interactions studied using electrophoreses. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, DNA Electrophoresis: Methods and Protocols aids scientists in continuing to study DNA dynamics both in live cells and in test tubes.