High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.

Mass Spectroscopy Imaging (MSI) has emerged as an enabling technique to provide insight into the molecular entities within cells, tissues and whole-body samples and to understand inherent complexities within biological metabolomes. In "Mass ""Spectrometry"" Imaging of Small Molecules"" Methods and Protocols," experts in the MSI field present techniques for 2D and 3D visualization and quantification of a wide array of small molecular species present in biologically relevant samples. Chapters provide detailed operational instructions from sample preparation to method selection, from comparative quantification to structural identification and from data collection to visualization of small molecule mapping in complex samples. 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, "Mass ""Spectrometry"" Imaging of Small Molecules"" Methods and Protocols" aims to bring the rapidly maturing methods of metabolic imaging to life science researchers and to minimize technical intimidation in adapting new technological platforms in biological research.

The intersection of nanotechnology with biology has given rise to numerous ideas for new ways to use nanotechnology for biological applications. Nanomaterials possess unique size- and material-dependent properties which make them attractive for improving regular biomedical fields, such as drug delivery, imaging, therapy, and diagnostics. Divided into three convenient sections, Nanomaterial Interfaces in Biology: Methods and Protocols covers protocols describing synthesis, fabrication, and construction of bio-nanomaterial interfaces, characterization protocols of bio-nanomaterial interfaces, and applications which utilize the bio-nanomaterial interfaces. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible Nanomaterial Interfaces in Biology: Methods and Protocols will serve the new and emerging scientific community, enabling new capabilities and technologies that were not previously possible in medicine and biology.

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.

"Next generation" sequencing techniques allow for more detailed analysis of exons and introns in multiple genes at the same time. This will reveal many mutations that potentially lead to exon skipping. To functionally test these a lot can be achieved with a limited set of protocols, while for the intentional induction of exon skipping different tools and target genes are involved and the translational path from in vitro splicing to in vivo tests in animal models requiring a more extensive set of protocols. Exon Skipping: Methods and Protocols provides scientist with a comprehensive guide to many of the methods and techniques used for exon skipping, such as methods on how to discriminate "real polymorphisms" from mutations that affect splicing. Written in the highly successful Methods in Molecular Biology (TM) 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 Exon Skipping: Methods and Protocols seeks to aid scientists in the continuing study of exon skipping.

This volume arranged into three sections describes biochemical, in vitro, and in vivo protocols on Semaphorins. Chapters focus on approaches that would allow the novice to study Semaphorins and employ robust assays to characterize mechanisms of action. 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, Semaphorin Signaling: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This detailed volume presents protocols for advancing the utility of nanotechnology in cancer research toward improving our understanding of cancer biology, prevention, diagnosis, and therapy. There are continuous new discoveries in the field of nanotechnology, thus creating new imaging systems or therapies, and this book focuses on how to employ certain discoveries for studying cancer by presenting principles along with techniques to allow for the transformation of any new discoveries in the field into cancer-studying tools with the hope of bringing in the involvement of biomedical scientists who can enhance the speed of discoveries toward cancer diagnosis and therapy. 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 motivating, Cancer Nanotechnology: Methods and Protocols serves as an ideal resource for biomedical scientists interested in the potential of this field as well as for physical scientists and engineers interested in employing nanotechnology in cancer diagnosis and therapy.

While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.

1. The Role of Heat Shock Proteins in the Regulation of Steroid Receptor Function.- 2. Subcellular and Subnuclear Trafficking of Steroid Receptors.- 3. Structure and Function of the Steroid and Nuclear Receptor Ligand-Binding Domain.- 4. Structure and Function of the Steroid and Nuclear Receptor DNA Binding Domain.- 5. Modulation of Steroid/Nuclear Receptor Dimerization and DNA Binding by Ligands.- 6. Molecular Mechanisms of Nuclear-Receptor-Mediated Transcriptional Activation and Basal Repression.- 7. Transcriptional Cross-Talk by Steroid Hormone Receptors.- 8. Chromatin and Steroid-Receptor-Mediated Transcription.- 9. Regulation of Glucocorticoid and Estrogen Receptor Activity by Phosphorylation.- 10. Monomeric Nuclear Receptors.- 11. Orphan Nuclear Receptors and Their Ligands.

Today, cells are commonly analyzed en masse, with thousands of cells per sample, yielding results on the average response of the cells. However, cellular heterogeneity implies that in order to learn more about cellular behaviour, it is important to study how individual cells respond, one by one. In Single-Cell Analysis: Methods and Protocols, experts in the field provide an update on the field of single-cell analysis wherein the latest findings and applications are described in detail. The methods described in this book include a few examples of conventional methods and several examples of miniaturized methods. Written in the highly successful Methods in Molecular Biology (TM) 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 accessible, Single-Cell Analysis: Methods and Protocols encourages readers to explore new ways of studying cells that may help lead to exciting new discoveries.

This volume presents a compendium of the most recent and advanced methods applied to the rapidly expanding field of telomerase inhibition. The techniques described provide the researcher with a diverse and comprehensive set of tools for the study of telomerase inhibition. The volume is aimed at biochemists, molecular biologists, cancer researchers, and geneticists.

This monograph provides a mathematical foundation to the theory of quantum information and computation, with applications to various open systems including nano and bio systems. It includes introductory material on algorithm, functional analysis, probability theory, information theory, quantum mechanics and quantum field theory. Apart from standard material on quantum information like quantum algorithm and teleportation, the authors discuss findings on the theory of entropy in C*-dynamical systems, space-time dependence of quantum entangled states, entangling operators, adaptive dynamics, relativistic quantum information, and a new paradigm for quantum computation beyond the usual quantum Turing machine. Also, some important applications of information theory to genetics and life sciences, as well as recent experimental and theoretical discoveries in quantum photosynthesis are described.

Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it mostly focuses on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. Unlike other bioinformatics books which are mostly theoretical, this book provides practical examples for the readers on state-of-the-art open source tools to solve biological problems. Flow charts of experiments, graphical illustrations, and mock data are included for quick reference. Volume I is therefore an ideal companion for students and early stage professionals wishing to master this blooming field.

This volume on iron-sulfur proteins includes chapters that discuss how microbes, plants, and animals synthesize these complex prosthetic groups, and why it is important to understand the chemistry and biogenesis of iron sulfur proteins. In addition to their vital importance in mitochondrial respiration, numerous iron sulfur proteins are important in maintenance of DNA integrity. Multiple rare human diseases with different clinical presentations are caused by mutations of genes in the iron sulfur cluster biogenesis pathway. Understanding iron sulfur proteins is important for understanding a rapidly expanding group of metabolic pathways important in all kingdoms of life, and for understanding processes ranging from nitrogen fixation to human disease.

In 1996, we organized a workshop, inter alia, at the National Research Co- cil in Milan under the generous sponsorship of the European Science Foun- tion. On that occasion, a small group of investigators convened from many countries and presented early evidence of the possibility of assembling basic units of mammalian chromosomes into artificial constructs (or, indeed, red- ing the relevant components to more manageable dimensions and defined c- stitution). Progress in the following years has been slow but steady. Many scientists who took part in the workshop have since been engaged in active and prod- tive research. It goes to the credit of Humana Press to have realized the need for a book on artificial chromosomes that aims to provide better tools to all scientists committed to this field who are confronted with very difficult tech- cal problems. We have strived to cover in Mammalian Artificial Chromosomes: Methods and Protocols all relevant areas of artificial chromosome research, from basic genetics to daring attempts to build new tools for genetic therapy. We are of course grateful to the authors who have accepted the task of describing the technical steps and pitfalls that can be encountered in their research. Rarely has a very delicate methodology been presented with such meticulous care. We have been helped in this enterprise by the excellent librarian of the LITA Institute in Segrate, Italy, Ms. Claudia Piergigli, whom we thank warmly. Ms.

International Review of Cytology 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 address cell and molecular biology of spindle poles and NuMa; organelle-nuclei in higher plants; the centrosome in higher organisms; functions of myc; and electrophysiological approaches to the study of protein translocation in mitochondria.

International Review of Cytology 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 address transcription in haploid male germ cells, free radicals in cell biology, experimental studies on sexual reproduction in diatoms, vertebrate thymus and the neurotrophin system, and visualization of molecular activities inside living cells with fluorescent labels.

Innovative technologies are propelling microbiology into an exciting new era which will witness the harnessing and control of complex microbial communities in a huge variety of applications in the industrial, medical and environmental spheres. This book presents emerging molecular methods that allow the diversity of a microbial community to be surveyed and its functions to be investigated.

As a high throughput method for analyzing gene function, cell-based microarrays have proven to be of vital importance, allowing high throughput analysis of over expression and knock down of proteins. In Cell-Based Microarrays: Methods and Protocols, experts in the field provide an up to date synopsis of cell-based microarrays and meticulous coverage of all aspects of the array, including emerging technology. Beginning with a detailed overview of the whole subject area, the volume continues with protocols for over-expression arrays and downstream functional assays, infectious disease research, increasing transfection efficiencies, as well as the development of cell-based array technology by use of microfluidic image cytometry for the analysis of small diagnostic samples with few cells. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Cell-Based Microarrays: Methods and Protocols serves as a key resource for molecular biologists, geneticists, immunologists, and chemists, and supplies scientists with access to set up a technology that is truly high throughput for the functional analysis of proteins.

International Review of Cytology 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.

International Review of Cytology 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 address endocrine disruption in invertebrates, the biology of lysenin, testican-1, transgenic mice as in vivo models of lymphomagenesis, bacterial endocytobionts of ciliophora, and Basic helix-loop-helix proteins expressed during early embryonic organogenesis.

Cultured cells have combined accessibility and the ability to expand a homogeneous cell population from a relatively limited source, thus opening up a wealth of possibilities for researchers. In Mouse Cell Culture: Methods and Protocols, expert researchers provide a number of methods for the culture of a wide range of specific cells and tissues isolated from the key genetic model of the fetal or adult mouse. Including protocols for the explant of fetal tissues and stem cells that allow developmental processes to be followed ex vivo as well as protocols for the culture of isolated cell types that allow for the study of relatively homogeneous cell populations, this volume brings together a selection of the most current methods in order to make them available in one convenient source. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Practical and authoritative, Mouse Cell Culture: Methods and Protocols serves as an immediately applicable springboard for the development of new tissue culture methods in order to advance the study and treatment of human disorders.

This book caters to the needs of: (i) graduate students who mostly learn such techniques from senior post-docs in the laboratory; (ii) those who are not experts in NMR but wish to understand if a particular problem in animal, plant, medical and pharmaceutical sciences can be answered by NMR; and (iii) those who are experts in chemistry and biochemistry and wish to know how NMR can provide them information on structural or functional aspect of proteins, nucleic acids, cells and tissues, human and plant organs and other biological materials.This book builds a means of knowledge transfer between the beginners and the experts in NMR as applied to all aspects of life sciences.

This manual reflects practical approaches to handling bacteria in the labora- tory. It is designed to recall historical methods of bacterial genetics that have had recent developments and to present new techniques that allow full genome analysis. It has been written for microbiologists who need to group their protocols at the state of the art of a new millennium and also for scientists in other fields of life sciences who need to use bacteria for their research. Teachers, graduate students, and postdocs also will benefit from having these protocols to help them understand modern bacterial genetics. I learned so much from these contributions from my colleagues that I have no doubt about the daily usefulness of this book. April 2002 Michel Blot XII Abbreviations Acyl-HSL N-acyl homoserine lactone moi multiplicity of infection Amp or Ap ampicillin N amino C carboxy NMR nuclear magnetic resonance CIO-HSL N-decanoyl-L-homoserine lactone 3-0H-C14:1-HSL N-(3-hydroxy-7 -cis-tetra- C12-HSL N-dodecanoyl-L-homoserine lac- decanoyl)homo-serine lactone tone 3-0H-C4-HSL N-3-hydroxybutanoyl-L- C14-HSL N-tetradecanoyl-L-homoserine homoserine lactone lactone ONPG o-nitrophenyl ~-D-galactopyranoside C4-HSL N-butanoyl-L-homoserine lactone ORF open reading frame C6-HSL N-hexanoyl-L-homoserine lactone OTG I-S-octyl-~-D-thioglucoside C8-HSL N-octanoyl-L-homoserine lactone 3-oxo-CIO-HSL N-3-oxodecanoyl-L-homo- Cam or Cm chloramphenicol serine lactone CBD chitin binding domain 3-oxo-C12-HSL N-3-oxododecanoyl-L- CHEF contour clamped homogenous electric homoserine lactone field 3-oxo-C14-HSL N-3-oxotetradecanoyl-L- CI consistency index homoserine lactone CRIM conditional-replication, integration, 3-oxo-C4-HSL N-3-oxobutanoyl-L-homoser- and modular ine lactone dCTP deoxycytidine triphosphate 3-oxo-C6-HSL N-3 -oxohexanoyl-L-homoser- deg.

Although our understanding of the structure and activities of the cell nucleus and of the nanomachines which it contains is increasing rapidly, much remains to be learned. The application and continuing development of the new, powerful biochemical and biophysical methodologies described here are essential in this quest. In The Nucleus, researchers from more than forty leading international laboratories describe state-of-the-art methods for isolating nuclei and their components and for studying their structure and activities, including some pathology-associated features. Volume I: Nuclei and Subnuclear Structures presents an overview of features of the intranuclear environment, followed by the most recent procedures for isolating nuclei from a wide range of cell types including muscle cells, yeast, oocytes, cells with polytene nuclei, Arabidopsis, trypanosomes, and dinoflagellates. The latest methods are described for isolating and working with nucleoli, constitutive heterochromatin, pathology-associated inclusions, and chromatin and for examining glycosylation, sumoylation, and ADP-ribosylation of nuclear proteins. Written in the highly successful Methods in Molecular BiologyT series format, chapters contain lists of necessary materials and reagents, readily reproducible protocols, and tips for troubleshooting and avoiding known pitfalls. The Nucleus, Volume I: Nuclei and Subnuclear Structures is an essential reference for scientists who are working on our rapidly growing understanding of the cell nucleus and its activities. Written for: Nucleic acid chemists, cellular biologists, biochemists