This volume aims to provide a new perspective on the broader usage of Hidden Markov Models (HMMs) in biology. Hidden Markov Models: Methods and Protocols guides readers through chapters on biological systems; ranging from single biomolecule, cellular level, and to organism level and the use of HMMs in unravelling the complex mechanisms that govern these complex systems. 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, Hidden Markov Models: Methods and Protocols aims to demonstrate the impact of HMM in biology and inspire new research.

This project follows on the success of the book "25 years of p53", published by Springer in 2006. Since this publication, there have been considerable advances on the potential application of p53 into the clinics. The goal of this book is to capture these developments and to appeal to a clinical and medical audience beyond the one which was the primary target of "25 years of p53".

Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements, responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation.
The control of biological processes, such as cellular growth and differentiation, is dependent on how the genetic material within a cell is expressed. The cellular physiology of mRNA-including mRNA processing, transport, localization, and turnover-is central to the process of gene expression.
Covers the nonsense-mediated mRNA decay (NMD) or mRNA surveillance pathway.
Expert researchers introduce the most advanced technologies and techniques to identify mRNA processing, transport, localization and turnover which are central to the process of gene expression.
Offers step-by-step lab instructions including necessary equipment and reagents

The importance of protein folding has been recognized for many years. It is the underlying etiology in a large number of human diseases and it appears to be a novel method for cellular regulation of the expression of newly translated proteins. These volumes (Parts A & B) address this important topic. As a volume in Progress in Nucleic Acid Research and Molecular Biology, this book provides the latest information on the expanding research being conducted on protein folding.
*Follow the new editor-in-chief, P. Michael Conn, as he introduces this first thematic volume in the series an in-depth aid to researchers who are looking for the best techniques and tools for understanding the complexities of protein folding
*Understand the advantages of protein folding over other therapeutic approaches and see how protein folding plays a critical role in the development of diseases such as Alzheimer s and diabetes
*Decipher the rules of protein folding through compelling and timely reviews combined with chapters written by international authors in engineering, biochemistry, physics and computer science"

Single molecule techniques, including single molecule fluorescence, optical tweezers, and scanning probe microscopy, allow for the manipulation and measurement of single biological molecules within a live cell or in culture. These approaches, amongst the most exciting tools available in biology today, offer powerful new ways to elucidate biological function, both in terms of revealing mechanisms of action on a molecular level as well as tracking the behaviour of molecules in living cells. This book provides the first complete and authoritative treatment of this rapidly emerging field, explicitly from a biological perspective.

The contents are organized by biological system or molecule. Each chapter discusses insights that have been revealed about their mechanism, structure or function by single molecule techniques. Among the topics covered are enzymes, motor proteins, membrane channels, DNA, ribozymes, cytoskeletal proteins, and other key molecules of current interest. An introduction by the editor provides a concise review of key principles and an historical overview. The last section discusses applications in molecular diagnostics and drug discovery.

* Organized by biological system or molecule.

* Each chapter discusses insights into mechanism of action, structure, and function

* Covers enzymes, motor proteins, membrane channels, DNA, ribozymes, etc.

* Includes an introduction to key principles and an historical overview.

* Discusses applications in molecular diagnostics and drug discovery.

* Provides an expert's perspective on future developments.

Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume.
*Follow the new editor-in-chief, P. Michael Conn, as he introduces this second thematic volume in the series an in-depth aid to researchers who are looking for the best techniques and tools for understanding the complexities of protein folding
*Understand the advantages of protein folding over other therapeutic approaches and see how protein folding plays a critical role in the development of diseases such as Alzheimer s and diabetes
*Decipher the rules of protein folding through compelling and timely reviews combined with chapters written by international authors in engineering, biochemistry, physics and computer science"

Driven in part by the development of genomics, proteomics, and bioinformatics as new disciplines, there has been a tremendous resurgence of interest in physical methods to investigate macromolecular structure and function in the context of living cells. This volume in "Methods in Cell Biology" is devoted to biophysical techniques "in vivo" and their applications to cellular biology. The volume covers methods-oriented chapters on fundamental as well as cutting-edge techniques in molecular and cellular biophysics. This book is directed toward the broad audience of cell biologists, biophysicists, pharmacologists, and molecular biologists who employ classical and modern biophysical technologies or wish to expand their expertise to include such approaches. It will also interest the biomedical and biotechnology communities for biophysical characterization of drug formulations prior to FDA approval.
* Describes techniques in the context of important biological problems
* Delineates critical steps and potential pitfalls for each method

Volume 3 reviews virtually everything that is known about cell motility and behavior in Chlamydomonas. World experts in each area focus on mitosis and cytokinesis; flagellar assembly and motility; intraflagellar transport; dynein; the structure and function of centrioles/basal bodies and their associated structures; ciliary signaling; mating and gamete fusion; photobehaviors; and Chlamydomonas as a model for understanding human diseases of the cilium. The volume is richly illustrated and is supplemented by a website containing both classic and previously unpublished videos of cell motility in Chlamydomonas. A unique and especially valuable feature is the inclusion of tables listing the known proteins (with NCBI accession numbers) for each structure discussed, and the known mutations that affect each structure and process. Because Chlamydomonas has been the premier model for investigating the function and behavior of cilia and flagella, the chapters summarize the current state of knowledge in these areas as it applies to all ciliated organisms. Thus, this volume will be an essential source for all students and researchers interested in cell motility.
* Essential reference to a model species for the study of mechanisms of motility in free living cells
* Includes methods for Chlamydomonas motility research.
* Companion Website with videos illustrates the marvels of the Chlamydomonas flagella in action

Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences, including genetics, biochemistry, and cell biology. "Progress in Nucleic Acid Research and Molecular Biology" is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume.
* This series provides a forum for discussion of new discoveries, approaches, and ideas
* Contributions from leading scholars and industry experts
* Reference guide for researchers involved in molecular biology and related fields

"International Review of Cell & Molecular Biology" presents current advances and comprehensive reviews in cell biology-both plant and animal. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation and cell transformation and growth.
* Authored by some of the foremost scientists in the field
* Provides up-to-date information and directions for future research
* Valuable reference material for advanced undergraduates, graduate students and professional scientists

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.

DESCRIPTION:
International Review of Cell & Molecular Biology presents current advances and comprehensive reviews in cell biology both plant and animal. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. Authored by some of the foremost scientists in the field, each volume provides up-to-date information and directions for future research
Key Features
* Authored by some of the foremost scientists in the field
* Provides up-to-date information and directions for future research
* Valuable reference material for advanced undergraduates, graduate students and professional scientists

The 2002 Nobel Prize in Physiology or Medicine was awarded to Sydney Brenner (United Kingdom), H. Robert Horvitz (US) and John E. Sulston (UK) "for their discoveries concerning genetic regulation of organ development and programmed cell death." Cell death is a fundamental aspect of embryonic development, normal cellular turnover and maintenance of homeostasis (maintaining a stable, constant environment) on the one hand, and aging and disease on the other. This volume addresses the significant advances with the techniques that are being used to analyze cell death.
* This volume provides the necessary, trusted methods to carry out this research on the latest techniques. Once researchers understand the molecular mechanisms of the apoptotic pathways, they can begin to develop new therapies.
* Presents key methods on studying tumors and how these cancer cells evade cell death.
* Eliminates searching through many different sources to avoid pitfalls so the same mistakes are not made over and over.

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.

DESCRIPTION:
International Review of Cell & Molecular Biology presents current advances and comprehensive reviews in cell biology-both plant and animal. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. Authored by some of the foremost scientists in the field, each volume provides up-to-date information and directions for future research.
Key Features
* Authored by some of the foremost scientists in the field
* Provides up-to-date information and directions for future research
* Valuable reference material for advanced undergraduates, graduate students and professional scientists

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.

International Review of Cell & Molecular Biology presents current advances and comprehensive reviews in cell biology - both plant and animal. Authored by some of the foremost scientists in the field, each volume provides up-to-date information and directions for future research. Articles in this volume include Transgenic Mouse Models in Angiogenesis and Lymphangiogenesis,
Morphogenesis in Giant-celled Algae,
Plasmodium in the Post-Genomic Era: New Insight into the Molecular Cell Biology of Malaria Parasites, Role of Nuclear Lamins in Nuclear Organization, Cellular Signalling and Inherited Diseases, New Insights into the Mechanisms of Macroautophagy in Mammalian Cells.
*Covers the latest on transgenic mouse models in angiogenesis and lymphangiogenesis.
*Includes information on morphogenesis in giant-celled algae.
*Provides new insights into the mechanisms of macroautophagy in mammalian cells.

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.

This volume in the Advances in Protein Chemistry series features cutting-edge articles on topics in protein chemistry. This volume includes chapters on the structural basis of effector regulation and signal termination in heterotrimeric G N n nproteins; How do receptors activate G proteins; Some mechanistic insights into GPCR activation from detergent solubilized ternary complexes on beads; Activation of G protein coupled receptors; Kinetic analysis of g-protein-coupled receptor signaling using fluorescence resonance energy transfer in living cells; Regulation of Rho Guanine Nucleotide Exchange Factors (RhoGEFs) by G proteins.