This volume focuses on the use of system genetic methods and the use of murine models to study the role of gene variants and environmental factors on human health and disease-what is now often called personalized or precision health care. The protocols in this book will help readers analyze genetic causes of heritable variation across a wide range of systems and traits using rodent models. The chapters in this book are separated into three sections that cover: 1) resources for systems genetics; 2) tools for analysis and integration in systems genetics; and 3) systems genetics use cases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and tools, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and thorough, Systems Genetics: Methods and Protocols is a valuable resource for anyone who is interested in this diverse field.

As a college student, Werner Maas took a course in genetics in 1941 and wondered why so little was said about the biochemical action of genes in controlling the specific function of an organism. Just at that time, biochemists and geneticists began to investigate jointly the basis of gene action, especially in microorganisms. Thus, Maas was able to witness firsthand the spectacular developments that led in the next twenty-five years to a clear picture of the action of genes. The history of these remarkable discoveries is the core of this book. After 1965, building on insights gained from the work with microorganisms, studies of gene action turned to animals and plants and concentrated on processes not present in microorganisms, such as embryonic development, the role of genes in diseases, and the function of the nervous system. Because of the rapidity of technical advances made in handling genes, it has been possible to learn much about these complex processes. The last part of the book deals with these developments, which are ongoing parts of the history of gene action.

Electroporation gene therapy, or gene electrotransfer, has evolved greatly over the last few decades as a result of the remarkable progress in genetic sequencing, gene array analysis, gene cloning, gene expression detection, DNA manufacture and discovery and synthesis of siRNA. Electroporation Protocols: Preclinical and Clinical Gene Medicine, Second Edition provides in-depth knowledge on the delivery of naked DNA and small-interfering RNA (siRNA) to the targeted cells, tissues, and animals for prevention and treatment of disease. It builds on the success of the first edition and on the progress made in siRNA delivery and DNA vaccines for large animals as well as discovery of electroporation applications for the fragile tissues and for internal organs. 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, Electroporation Protocols: Preclinical and Clinical Gene Medicine, Second Edition aims to provide not only comprehensive coverage of the basic theory and practical application of electroporation siRNA therapy, gene therapy, and vaccine, but also elaborates on the most current views from the experts in this field, serving as an invaluable resource for investigators both in and outside of this field.

Animal Endo-SiRNAs: Methods and Protocols presents a variety of approaches to investigate endo-siRNAs. These include protocols applicable to study short RNAs expressed at a low level and model systems that are particularly suitable to investigate specific aspects of endo-siRNAs, their synthesis, their genomics or regulatory role. 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, Animal Endo-SiRNAs: Methods and Protocols contains practical tips that are absent in standard lab manuals.

Detection and analysis of DNA damage is of critical importance in a variety of biological disciplines studying apoptosis, cell cycle and cell di- sion, carcinogenesis, tumor growth, embryogenesis and aging, neu- degenerative and heart diseases, anticancer drug development, environmental and radiobiological research, and others. Individual cells within the same tissue or in cell culture may vary in the extent of their DNA damage and, consequently, can display different re- tions to it. These differences between individual cells in the same cell popu- tion are detected using in situ approaches. In situ is a Latin term meaning "on site" or "in place." It is used to denote the processes occurring or detected in their place of origin. In mole- lar and cell biology this usually refers to undisrupted mounted cells or tissue sections. In that meaning "in situ" is used as part of the terms "in situ PCR," "in situ transcription," "in situ hybridization," "in situ end labeling," and "in situ ligation." Sometimes the "in situ" term is applied at the subcellular level to cells disrupted in the process of analysis, for example, in the detection of specific sequences in chromosomes using fluorescent in situ hybridization (FISH). Historically, the term was used primarily in methods dealing with nucleic acids.

Systems Metabolic Engineering is changing the way microbial cell factories are designed and optimized for industrial production.
Integrating systems biology and biotechnology with new concepts from synthetic biology enables the global analysis and engineering of microorganisms and bioprocesses at super efficiency and versatility otherwise not accessible. Without doubt, systems metabolic engineering is a major driver towards bio-based production of chemicals, materials and fuels from renewables and thus one of the core technologies of global green growth. In this book, Christoph Wittmann and Sang-Yup Lee have assembled the world leaders on systems metabolic engineering and cover the full story from genomes and networks via discovery and design to industrial implementation practises.
This book is a comprehensive resource for students and researchers from academia and industry interested in systems metabolic engineering. It provides us with the fundaments to targeted engineering of microbial cells for sustainable bio-production and stimulates those who are interested to enter this exiting research field.

This volume presents detailed laboratory protocols for in vitro synthesis of mRNA with favorable properties, its introduction into cells by a variety of techniques, and the measurement of physiological and clinical consequences such as protein replacement and cancer immunotherapy. Synthetic techniques are described for structural features in mRNA that provide investigational tools such as fluorescence emission, click chemistry, photo-chemical crosslinking, and that produce mRNA with increased stability in the cell, increased translational efficiency, and reduced activation of the innate immune response. Protocols are described for clinical applications such as large-scale transfection of dendritic cells, production of GMP-grade mRNA, redirecting T cell specificity, and use of molecular adjuvants for RNA vaccines. 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Synthetic mRNA: Production, Introduction into Cells, and Physiological Consequences is a valuable and cutting-edge resource for both laboratory investigators and clinicians interested in this powerful and rapidly evolving technology.

Recent studies have indicated that epigenetic processes may play a major role in both cellular and organismal aging. These epigenetic processes include not only DNA methylation and histone modifications, but also extend to many other epigenetic mediators such as the polycomb group proteins, chromosomal position effects, and noncoding RNA. The topics of this book range from fundamental changes in DNA methylation in aging to the most recent research on intervention into epigenetic modifications to modulate the aging process. The major topics of epigenetics and aging covered in this book are: 1) DNA methylation and histone modifications in aging; 2) Other epigenetic processes and aging; 3) Impact of epigenetics on aging; 4) Epigenetics of age-related diseases; 5) Epigenetic interventions and aging: and 6) Future directions in epigenetic aging research.

The most studied of epigenetic processes, DNA methylation, has been associated with cellular aging and aging of organisms for many years. It is now apparent that both global and gene-specific alterations occur not only in DNA methylation during aging, but also in several histone alterations. Many epigenetic alterations can have an impact on aging processes such as stem cell aging, control of telomerase, modifications of telomeres, and epigenetic drift can impact the aging process as evident in the recent studies of aging monozygotic twins.

Numerous age-related diseases are affected by epigenetic mechanisms. For example, recent studies have shown that DNA methylation is altered in Alzheimer s disease and autoimmunity. Other prevalent diseases that have been associated with age-related epigenetic changes include cancer and diabetes. Paternal age and epigenetic changes appear to have an effect on schizophrenia and epigenetic silencing has been associated with several of the progeroid syndromes of premature aging. Moreover, the impact of dietary or drug intervention into epigenetic processes as they affect normal aging or age-related diseases is becoming increasingly feasible.

This book covers the statistical models and methods that are used to understand human genetics, following the historical and recent developments of human genetics. Starting with Mendel's first experiments to genome-wide association studies, the book describes how genetic information can be incorporated into statistical models to discover disease genes. All commonly used approaches in statistical genetics (e.g. aggregation analysis, segregation, linkage analysis, etc), are used, but the focus of the book is modern approaches to association analysis. Numerous examples illustrate key points throughout the text, both of Mendelian and complex genetic disorders. The intended audience is statisticians, biostatisticians, epidemiologists and quantitatively- oriented geneticists and health scientists wanting to learn about statistical methods for genetic analysis, whether to better analyze genetic data, or to pursue research in methodology. A background in intermediate level statistical methods is required. The authors include few mathematical derivations, and the exercises provide problems for students with a broad range of skill levels. No background in genetics is assumed.

Mitosis: Methods and Protocols provides state-of-the-art overviews on the most important approaches currently used in mitosis research spanning from the analysis of single molecules in isolation to their utilization within the complex environment of the cell. The volume is divided into four parts, each focused on methods pertaining to distinct aspects of mitosis research. Part I presents approaches for visualizing and analyzing the dynamic behaviors of the spindle apparatus, the microtubule based machine that drives chromosome segregation. Part II focuses more generally on methods for studying and manipulating the microtubule cytoskeleton in cells and complex cell free extracts. Part III provides state of the art biophysical and high resolution microscopy approaches for assessing complex interactions between microtubules and microtubule-associated proteins in isolation as well as microtubule structure in cells. Part IV provides methods for studying the effects of cell shape on cell division and methods for quantifying aneuploidy (aberrant chromosome number) which frequently results from mitotic defects and has been linked to human maladies ranging from birth defects to cancer. 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, Mitosis: Methods and Protocols seeks to provide diverse methods and new techniques to address new or old questions related to the mechanisms of mitosis.

This volume includes comprehensive descriptions of miRNA biogenesis and their role in the development and progression of various human diseases. The first few chapters of MicroRNA Profiling: Methods and Protocols discuss the effects of over-expressing and repressing of a target miRNA and their effects on cell viability and proliferation. The next few chapters explore the protocols for total RNA isolation from cells and cell-derived product including formalin fixed paraffin embedded tissue and plant tissue. The last few chapters discuss isolation and characterization of exosomes from medium conditioned by cell lines, serum, and plasma specimens. This book also includes discussions of several software tools, such as miRandola, PicTar, DIANA, and miRWalk. 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. Comprehensive and cutting-edge, MicroRNA Profiling: Methods and Protocols is a valuable resource for anyone interested in the field of Micro RNAs.

Epigenetic modifications underlie all aspects of human physiology, including stem cell renewal, formation of cell types and tissues. They also underlie environmental impacts on human health, including aging and diseases like cancer. Consequently, cracking the epigenetic "code" is considered a key challenge in biomedical research. Chromatin structure and function are modified by protein complexes, causing genes to be turned "on" or "off" and controlling other aspects of DNA function. Yet while there has been explosive growth in the epigenetics field, human chromatin-modifying machines have only recently started to be characterized. To meet this challenge, our book explores complementary experimental tracks, pursued by expert international research groups, aimed at the physical and functional characterization of the diverse repertoire of chromatin protein machines - namely, the "readers, writers and erasers" of epigenomic marks. These studies include the identification of RNA molecules and drugs that interact selectively with components of the chromatin machinery. What makes this book distinctive is its emphasis on the systematic exploration of chromatin protein complexes in the context of human development and disease networks.

This volume provides insight into recent developments on experimental and clinical strategies for cancer gene therapy. Gene Therapy of Solid Cancers: Methods and Protocols guides readers through protocols on gene therapeutic strategies in combination with helpful technical notes. 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. Concise and easy-to-use, Gene Therapy of Solid Cancers: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Timing, racing, combating, struggling and targeting are some actions through which cellular fate could be reflected and evaluated. Interaction between cell territory and environment occur during pre-embryonic, fetal development, and post-natal periods. What the researchers observe as the outcome of telomeres behavior is only the peak of an ice mountain within a stormy ocean. Cellular life depends on programmed behavior of telomeres, capable to surprise the cells. Telomeres provide an introduction to the history of our cells which govern the quality of life and status of health. Telomeres as the cooperative territory are capable of stabilizing the chromosomal territory. The status of telomeres reflects the key information, announcing the real age of individuals, and may be a valuable marker for prognosis and predicting cancer. Telomere territory is characterized with a multi-disciplinary manner. Therefore, this book is aimed to offer a wide range of chapters, hoping to be useful for diverse audiences, including hematologists-oncologists, radiotherapists, surgeons, cancer researchers, and all the sectors who affect the macro- and micro- environmental domains. Finally, telomeres are sensitive, cooperative, and trustable targets. It is worth to state that 'telomeres are messengers of NATURE', let's to know them as they are.

There is a saying "he is a person who can charm the birds from the trees." This might well be applied to Kurt Benirschke. Indeed, it describes both his warm personality and his intimate interaction with nature. He might be considered a modern adept of the Greek and Roman Stoic school of philosophy, which taught an understanding of man as integrated into nature in its totality. The right way to live is according to nature, with nature as part of it. This at the same time means humanity, and Kurt Benirschke impresses us not only as an outstanding scientist, but also as a humanist who has had a lifelong love affair with nature. The foundation of Springer-Verlag New York in 1964 offered a great opportunity for getting together with eminent authors in the United States. Kurt Benirschke was one of them, and his book Pathology of the Placenta was highly acclaimed all over the world. My attention was first called to him by my dear friend Dr. Ernst Uhlinger, then a pathologist in Zurich. With a sharp and critical eye, he followed the international literature on pathology and discovered "the genius of Kurt Benirschke." Our first encounters led to a relationship of trust which in turn grew into friendship. I soon learned to esteem the special qualities of the man and the scientist; in fact they cannot be separated.

W. French Anderson, M.D. The publication of this book comes at an opportune time for the young field of human gene therapy. After a decade of long struggle at the laboratory bench and many long hours under the harsh lights of the federal review process, gene therapy has emerged as a legitimate scientific discipline. It is now time to move away from the period of questioning whether gene therapy will be a useful part of the physician armamentarium to begin to actively teach the concepts and practices that make gene therapy a reality. This book is a comprehensive collection of chapters that describe the basic biology and potential application of viruses as gene transfer reagents. It is not a coincidence that a modified virus was the reagent used in the first human gene therapy trials. Viruses have evolved with the human species (and most likely with all forms of life) to be the masters of gene transfer.

Neuropsychiatric disorders such as schizophrenia, mood disorders, Alzheimer's disease, epilepsy, alcoholism, substance abuse and others are some of the most debilitating illnesses worldwide characterized by the complexity of causes, and lacking the laboratory tests that may promote diagnostic and prognostic procedures. Recent advances in neuroscience, genomic, genetic, proteomic and metabolomic knowledge and technologies have opened the way to searching biomarkers and endophenotypes, which may offer powerful and exciting opportunities to understand the etiology and the underlying pathophysiological mechanisms of neuropsychiatric disorders. The challenge now is to translate these advances into meaningful diagnostic and therapeutic advances.

This book offers a broad synthesis of the current knowledge about diverse topics of the biomarker and endophenotype strategies in neuropsychiatry. The book is organized into four interconnected volumes: Neuropsychological Endophenotypes and Biomarkers (with overview of methodological issues of the biomarker and endophenotype approaches in neuropsychiatry and some technological advances), Neuroanatomical and Neuroimaging Endophenotypes and Biomarkers, Metabolic and Peripheral Biomarkers and Molecular Genetic and Genomic Markers . The contributors are internationally and nationally recognized researchers and experts from 16 countries.

This four-volume handbook is intended for a broad spectrum of readers including neuroscientists, psychiatrists, neurologists, endocrinologists, pharmacologists, clinical psychologists, general practitioners, geriatricians, health care providers in the field of neurology and mental health interested in trends that have crystallized in the last decade, and trends that can be expected to further evolve in the coming years. It is hoped that this book will also be a useful resource for the teaching of psychiatry, neurology, psychology and mental health. "

Myc controls multiple cellular functions, including cell proliferation, growth, differentiation and death, both directly and indirectly, through its modulation of downstream transcriptional programs. In The Myc Gene: Methods and Protocols, experts in the field summarize the standard and novel techniques that allow the studying of Myc mechanism of action in normal and cancer cells, in vitro and in vivo, in one succinct manual. 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.

ss-barrel outer membrane channel proteins (OMP) are useful as robust and flexible models or components in nanotechnology. Over the last decade biotechnological techniques allowed to expand the natural characteristics of OMPs by modifying their geometry and properties. The present book is oriented towards a broad group of readers including graduate students and advanced researchers. It gives a general introduction to the field of OMP based nano-component development as well as the state of the art of the involved research. On the example of the E. coli FhuA the transformation of an OMP into a tailored nano-channel will be outlined. An exhaustive description of the scientific strategy, including protein selection, analytical methods and "in-silico" tools to support the planning of protein modifications for a targeted application, consideration on the production of a custom made OMP, and an overview on technological applications including membrane/polymersome technology, will be provided.

This stimulating volume addresses vital questions about gene/environment interactions as they affect cell health from the prenatal period through later life. Beginning with a tour of epigenetic processes in the human body, the book assembles current theoretical and empirical developments across the discipline, among them transgenerational epigenetic inheritance, the effects of maternal nutrition on epigenetic change, and possible links between epigenetics and childhood obesity. Public health and policy aspects of the field are discussed in depth, with the understanding that much can be done to improve our epigenetic health as a species. And in this vein, contributors consider future possibilities, such as the reprogramming of genes to reverse cancer and other diseases. Included in the coverage: The role of environmental epigenetics in perinatal and neonatal development The epigenetic biomarker H2AX: from bench science to clinical trials What's the risk? Dental amalgam, mercury exposure, and human health risks throughout the lifespan Post-traumatic stress disorder: neurological, genetic, and epigenetic bases Children's exposure to alcohol, tobacco, and drugs: long-term outcomes Ethical implications of epigenetics Epigenetics, the Environment, and Children's Health Across Lifespans brings real-world knowledge and applications of this increasingly important field to public health practitioners, maternal and child health researchers, and environmental health experts.

The current demand for the development of techniques for controlled genetic manipulations is driven by the anatomical and physiological complexity of the brain and by the need for experimental models that can address this complexity through selective manipulation of defined components of the system: specific neuronal populations or selected synapses. In Controlled Genetic Manipulations, expert researchers present detailed chapters to supply basic technical information about controlled genetic manipulations and to provide examples of creative implementation of this methodology when addressing a unique biological problem. Some chapters of the book describe the most recent developments in the basic methodology, which includes use of Cre-recombinase, methods for delivery of genetic material into the brain and the use of optogenetics, whereas other chapters focus on applying these techniques to addressing particular biological questions like structural and functional mapping of neuronal circuits, analysis of specific synaptic connections, modeling or gene therapy of neurological disorders. As part of the Neuromethods series, chapters include key implementation advice that is crucial for getting optimal results. Authoritative and practical, Controlled Genetic Manipulations serves as a valuable guide to a variety of techniques, provided by many of the pioneers of the approaches.

This book brings together and updates the latest information on the diversity of yeasts, their molecular features and their applications in the welfare of mankind. Yeasts are eukaryotic microfungi widely found in natural environments, including those with extreme conditions such as low temperatures, low oxygen levels and low water availability. To date, approximately 2,000 of the estimated 30,000 to 45,000 species of yeast on Earth, belonging to around 200 genera have been described. Although there are a few that are opportunistic human and animal pathogens, the vast majority of yeasts are beneficial, playing an important role in the food chain and in the carbon, nitrogen and sulphur cycles. In addition, yeasts such as Saccharomyces cerevisiae, Hansenula polymorpha and Pichia pastoris are used in expressing foreign genes to produce proteins of pharmaceutical interest. A landmark in biotechnology was reached in 1996 with the completion of sequencing of the entire S. cerevisiae genome, and it has now become a central player in the development of an entirely new approach to biological research and synthetic biology. The sequencing of genomes of several yeasts including Schizosaccharomyces pombe, Candida albicans and Cryptococcus neofromans has also recently been completed.

The field of toxicogenomics is moving rapidly, so it is impossible at the timeofthiswritingtocompileaclassicmethodstextbook.Instead,wechose to identify experts in all aspects of this field and challenged them to write reviews, opinion pieces, and case studies. This book covers the main areas important to the study and use of toxicogenomics. Chapter 1 speaks to the convergenceofclassicapproachesalongsidetoxicogenomics.Chapter2deals withtheusefulnessoftoxicogenomicstoidentifythemechanismoftoxicity. Chapter3callsattentiontotheissuesthataffectthequalityoftoxicogenomics experiments, as well as the implications of using microarrays as diagnostic devices. The need for appropriate statistical approaches to genomic data is discussed in Chapter 4, and Chapters 5 and 6 describe the use of genomic datatobuildtoxicogenomicmodelsandprovideinsightsfromtheapproaches oftwocompanies.Theimportanttopicofstoringthedatageneratedinsuch experiments and the correct annotation that must accompany such data is considered in Chapter 7. The discussion in Chapter 8 speaks to the use of toxicogenomicstoidentifyspeciessimilaritiesanddifferences.Chapters9and 10dealwiththeuseofgenomicstoidentifybiomarkerswithinthepreclinical andclinicalarenas. Biomarkerswillonlybeusefulifthecommunityatlarge acceptsthemasmeaningful.Consortiaareimportanttodrivethisfunction,and Chapter11discussescurrenteffortsinthisarea.Lastbutnotleast,Chapter12 presentsaperspectiveontheregulatoryimplicationsoftoxicogenomicdataand someofthehurdlesthatcanbeseeninitsimplicationinGLPstudies.Although thisbooktendstofocusonpharmaceuticals,theissuesfacingtoxicologyare sharedbythechemicalmanufacturers,thetobaccoindustry,andtheirregulators. We want to thank our contributors for their generous time and energy in providingtheirinsights.Sadly,wemustnotetheunexpectedpassingofone ofourauthors,Dr.JosephHackettoftheFDA.Joe'scontributionservesasa testimonytohisaccomplishmentsinthisfield,andhisinsightwillbemissed intheyearstocome.