In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics.

Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. This book provides an overview of the statistical theory and methods used in studies of molecular evolution. It includes an introductory section suitable for readers that are new to the field, a section discussing practical methods for data analysis, and more specialized sections discussing specific models and addressing statistical issues relating to estimation and model choice. The chapters are written by the leaders of field and they will take the reader from basic introductory material to the state-of-the-art statistical methods.

This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. The chapters of the book assume no advanced mathematical skills beyond basic calculus, although familiarity with basic probability theory will help the reader. Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory.

Rasmus Nielsen received his Ph.D. form the University of California at Berkeley in 1998 and after a postdoc at Harvard University, he assumed a faculty position in Statistical Genomics at Cornell University. He is currently an Ole Romer Fellow at the University of Copenhagen and holds a Sloan Research Fellowship. His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book.

From the reviews:

..".Overall this is a very useful book in an area of increasing importance." Journal of the Royal Statistical Society

"I find Statistical Methods in Molecular Evolution very interesting and useful. It delves into problems that were considered very difficult just several years ago...the book is likely to stimulate the interest of statisticians that are unaware of this exciting field of applications. It is my hope that it will also help the 'wet lab' molecular evolutionist to better understand mathematical and statistical methods." Marek Kimmel for the Journal of the American Statistical Association, September 2006

"Who should read this book? We suggest that anyone who deals with molecular data (who does not?) and anyone who asks evolutionary questions (who should not?) ought to consult the relevant chapters in this book." Dan Graur and Dror Berel for Biometrics, September 2006

"Coalescence theory facilitates the merger of population genetics theory with phylogenetic approaches, but still, there are mostly two camps: phylogeneticists and population geneticists. Only a few people are moving freely between them. Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. Although Nielsen did not contribute a chapter to his book, his work permeates all its chapters. This book gives an overview of his interests and current achievements in molecular evolution. In short, this book should be on your bookshelf." Peter Beerli for Evolution, 60(2), 2006"

General inspection of a role performed in the cell by RNAs allows us to distinguish three major groups of transcripts: I. protein-coding mRNAs, II. non-coding housekeeping and III. regulatory RNAs.

The housekeeping RNAs include RNA classes that are generally, constitutively expressed and whose presence is required for normal function and viability of the cells. On the other hand, a group of regulatory RNAs includes RNA species that are expressed at certain stages of organism development or cell differentiation or as a response to external stimuli and can affect expression of other genes on the levels of transcription or translation.

Non-coding RNA transcripts form a heterogeneous class of RNAs that can not be characterized by a single specific function. Initially, the term non-coding RNA (ncRNA) was used primarily to describe polyadenylated and a capped eukaryotic RNAs transcribed by RNA polymerase II, but lacking long open reading frames. Now, this definition can be extended to cover all RNA transcripts that do not show protein-coding capacity and is sometimes used to describe any RNA that does not encode protein, including introns.

This book is an in-depth look at the function of Non-Coding RNAs and their relationship to Molecular Biology and Molecular Biology.

Bioinformatics of Genome Regulation and Structure covers:

-regulatory genomic sequences: databases, knowledge bases, computer analysis, modeling, and recognition;
-large-scale genome analysis and functional annotation;
-gene structure detection and prediction;
-comparative and evolutionary genomics;
-computer analysis of genome polymorphism and evolution; computer analysis and modeling of transcription, splicing, and translation; structural computational biology: structure-function organization of genomic DNA, RNA, and proteins;
-gene networks, signal transduction pathways, and genetically controlled metabolic pathways: principles of organization, operation, and evolution;
-data warehousing, knowledge discovery and data mining; and,
-analysis of basic patterns of genome operation, organization, and evolution. The data presented may be used while solving a wide range of problems, both basic and applied, in various directions of molecular biology, molecular genetics, biotechnology, pharmacogenetics, pharmacology, and adjacent fields of medicine, veterinary, and agrobiology.

This book examines the increasing significance of DNA profiling for crime investigation in modern society. It focuses on developments in the UK as the world-leader in the development and application of forensic DNA technology, and in the construction of DNA databases as an essential element in the successful use of DNA for forensic purposes. The book uses data collected from funded research into police uses of the UK National DNA Database (NDNAD) to describe the relationship between scientific knowledge and police investigations. It refers to some of the major UK criminal cases in which DNA evidence has been presented and contested. Chapters in the book explain the scientific developments which have enabled DNA profiling to be applied to criminal investigation, the ways in which the state has directed this, and how genetic technology has risen to such preeminence; how DNA evidence moved from its use in individual prosecutions to a major role in intelligence led policing, and saw the de

The determination of protein function has been a major goal of molecular biology since the founding of the discipline. However, as we learn more about gene function, we discover that the context within which a gene is expressed controls the specific function of that gene. It has become critical to establish the background in which gene function is determined and to perform experiments in multiple applicable backgrounds.In "Gene Function Analysis, Second Edition," a number of computational and experimental techniques are presented for identifying not only the function of an individual gene, but also the partners that work with that gene. The theme of data integration runs strongly through the computational techniques, with many focusing on gathering data from different sources and different biomolecular types. Experimental techniques have evolved to determine function in specific tissues and at specific times during development. 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, "Gene Function Analysis, Second Edition" seeks to serve both professionals and novices with a growing understanding of the complexity of gene function."

Why do modern agricultural techniques, which are environmentally damaging, continue to be used? This book seeks the answer to that question, by looking at the evolution of agricultural research in its cultural context. The theoretical framework is supported by historical case studies concerning hybrid maize in the United States, and the Green Revolution in Mexico. A chapter is also devoted to biotechnology, and its implications for the disturbing trend towards genetic uniformity.

Protocols for Nucleic Acid Analysis by Non-radioactive Probes, Second Edition provides a firm background on the basic preparative protocols required for the analysis of nucleic acids by nonradioactive methods. Presenting the methodologies using amazing new applications, this volume offers guide chapters on nucleic acid extractions, preparation of nucleic acid blots, and labeling of nucleic acids with nonradioactive haptens. New fluorescent techniques such as Real Time PCR and microarrays are also included, allowing users to get a nonradioactive protocol implemented in the laboratory with minimum adaptation required and fastest time to results.
The protocols follow the successful Methods in Molecular Biology series format, each offering step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

Genetic investigations and manipulations of bacteria and bacteriophage have made vital contributions to our basic understanding of living cells and to the development of molecular biology and biotechnology. This volume is a survey of the genetics of bacteria and their viruses, and it provides students with a comprehensive introduction to this rapidly changing subject. The book is written for upper level undergraduates and beginning graduate students, particularly those who have had an introductory genetics course.

The fifth edition has been extensively revised to reflect recent advances in the field. The book now has a reader-friendly look, with end-of-chapter questions, "Thinking Ahead" and "Applications" boxes to challenge students comprehension and insights. A complete glossary of commonly used terms has been revised and expanded.

This detailed volume provides a comprehensive resource covering the existing and state-of-the-art tools in the field of profiling chromatin accessibility and its dynamics. Beginning with a section on bulk-cell methods for profiling chromatin accessibility and nucleosome positioning that rely on enzymatic cleavage of accessible DNA and produce information about relative accessibility, the book continues with methods that use single-molecule and enzymatic approaches to solving the problem of mapping absolute occupancy/accessibility, emerging tools for mapping DNA accessibility and nucleosome positioning in single cells, imaging-based methods for visualizing accessible chromatin in its nuclear context, as well as computational methods for the processing and analysis of chromatin accessibility datasets. 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 and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Chromatin Accessibility: Methods and Protocols serves as an extensive and useful reference for researchers studying different facets of chromatin accessibility in a wide variety of biological contexts. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.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, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing or extending technologies and techniques in their laboratories.

The identification of normal and breast cancer stem cells has offered a new vision of this heterogeneous disease and new hopes for its prognosis and treatment. This volume provides an overview of recent developments in mammary stem cell research and discusses the many varieties of approaches used by researchers to investigate the properties and functions of mammary stem cells. The beginning chapters provide readers with an introduction to mammary stem cells, and the processes used to characterize stem cells and isolate them via fluorescent activated cell sorting. The next few chapters discuss DNA and mRNA sequencing, proteomic techniques to help profile cells, lentiviral cell transduction for gene expression, and in vivo lineage tracing. The final few chapters are dedicated to following stem cells from their initial niche to the new microenvironment at their metastasis site, and to studying these cells using physical and mathematical approaches. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Authoritative and cutting-edge, Mammary Stem Cells: Methods and Protocols aims to help members of the scientific community explore the behavior of stem cells and how to work with them in order to guide the design of new and complimentary strategies to be applied in the clinic with the ultimate end goal of fighting breast cancer.

This book highlights the latest findings and techniques related to nutrition and feed efficiency in animal agriculture. It addresses the key challenges facing the nutrition industry to achieve high animal productivity with minimal environmental impact. The concept of smart nutrition involves the use of smart technologies in the feeding and management of livestock. The first chapters focus on advances in biological fields such as molecular agriculture and genotype selection, as well as technologies that enhance or enable the collection of relevant information. The next section highlights applications of smart nutrition in a variety of livestock systems, ranging from intensive indoor housing of broilers and pigs to extensive outdoor housing of cattle and sheep, and marine fish farms. Finally, because of the worldwide attention to this issue, the authors address the environmental consequences. This work, which takes a serious look at how nutrition can be used to improve sustainability in animal agriculture, is a key literature for readers in animal and veterinary sciences, the food industry, sustainability research, and agricultural engineering.

In the past few years, antisense methodology has moved from in vitro studies to in vivo studies and first human trials. While the basic concept of antisense technology is simple, the methodological problems associated with its use are numerous and complex. Antisense- based methods have proven to be a field of research where careful attention to experimental protocols and appropriate controls is necessary. The Manual of Antisense Methodology emphasizes the application of antisense oligonucleotides, and is a guide for the identification of antisense and non-antisense effects in different experimental settings. The work is organized into three sections: antisense application in vitro, antisense application in vivo (animal models) and finally, clinical antisense studies. Where at all possible, the methods are described in sufficient detail to allow reproduction of a given experiment. The Manual of Antisense Methodology will be of interest to researchers in immunology, cancer research, pharmacology and internal medicine; and physicians conducting clinical studies in these fields.

A better "casting" could not be conceived. The authors of this book are gold smiths on the subject. I have followed their work since their "entry" into cyto genetics and I have a high esteem for them. I consider it an honour to be asked to write the preface of their opus. Paul Popescu, Directeur de Recherche at INRA, has also played a promi nent part in the development of animal cytogenetics, especially in domestic animals. He is able to tell you the cost of a translocation in a pig breeding farm or a cow population: a fortune! P. Popescu has played a great part in gene mapping of these species using "in situ DNA hybridisation". His contributions are recognised world-wide. His laboratory receives many visitors every year and it serves as a reference for domestic animal cytogenetics. Helene Hayes, Charge de Recherche at INRA, has collaborated with P. POPESCU in the elaboration of the "at hand" techniques and in many other discoveries which are listed in her bibliography. She showed the fascinating correspondence between bovine and human chromosomes and the com pared gene maps of domestic bovidae.

The genome sequences of several pseudomonads have become available in recent years and researchers are beginning to use the data to make new discoveries about this bacterium. This concise volume reviews the most current and topical aspects of Pseudomonas molecular biology and genomics and is aimed at a readership of research scientists, graduate students and other specialists. Renowned international authors have contributed chapters on diverse topics including taxonomy, genome diversity, oligonucleotide usage, polysaccharides, pathogenesis, virulence, biofilms, antibiotic resistance and iron uptake. In addition an entire chapter is devoted to the genetic tools being developed to take full advantage of the wealth of information generated by the genome sequencing efforts. This book is essential reading for anyone involved in Pseudomonas research.

Stem cells have the ability to differentiate into all types of cells within the body, thus have great therapeutic potential for regenerative medicine to treat complicated disorders, like Parkinson s disease and spinal cord injury. There will also be many applications in drug development. However, several roadblocks, such as safety issues and low efficiency of pluripotent stem cell (PSC) line derivation need to be resolved before their clinical application. This thesis focuses on these two areas, so as to find methods to overcome the limitation. It covers deriving embryonic stem cells (ESCs) from several different species and reports an efficient system to generate induced pluripotent stem cells (iPSCs), and the first iPSC mice in the world. The results in this thesis confirm that somatic cells can be fully reprogrammed with the four Yamanaka factors. In addition, we have found that the Dlk1-Dio3 region can be a potential molecular marker to distinguish the fully reprogrammed iPSCs from partially reprogrammed ones. All of these results will help improve the safety of PSCs in the clinical applications and increase the current low induction efficiency of their production."

Chromosomes Today Volume 12 records the plenary proceedings of the 12th triennial International Chromosone Conference, presenting an overview of the current concerns in the developing studies of animal, plant and human cytogenetics. As well as giving an accurate historical record of the achievements in chromosome studies, this important series points the way forword, emphasizing the areas in which new developments will take place. Volume 12 explores the complete integration of molecular biology and cytogenetics, evaluating the concensus of the world's cytogeneticists concerning the nature and activities of the chromosome.It reinforces our view of the chromosome as the genetic organelle whose structure, behaviour and modification underlie our modern concept ofeukaryote genetics.

This volume is divided in four sections; covering genome wide approaches, techniques for characterize of paRNA structural features are described, selecting pa-RNA, and paRNA therapeutic potential. Chapters describe how siRNAsdirected against paRNAs can be applied in vivo to modulate transcription of important genes controlled by paRNAs. 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, Promoter Associated RNA: Methods and Protocols aims to demonstrate paRNAs as new class of regulatory molecules, to further investigate and value as tools for fine transcriptional tuning.

This text is based on a set of not es produced for courses given for gradu- ate students in mathematics, computer science and biochemistry during the academic year 1998-1999 at the University of Turku in Turku and at the Royal Institute of Technology (KTH) in Stockholm. The course in Turku was organized by Professor Mats Gyllenberg's groupl and was also included 2 within the postgraduate program ComBi , a Graduate School in Compu- tational Biology, Bioinformatics, and Biometry, directed by Professor Esko Ukkonen at the University of Helsinki. The purpose of the courses was to give a thorough and systematic intro duc ti on to probabilistic modelling in bioinformatics for advanced undergraduate and graduate students who had a fairly limited background in prob ability theory, but were otherwise well trained in mathematics and were already familiar with at least some of the techniques of algorithmic sequence analysis. Portions of the material have also been lectured at shorter graduate courses and seminars both in Finland and in Sweden. The initial set of notes circulated also for a time outside those two countries via the World Wide Web. The intermediate course in probability theory and techniques of discrete mathematics held by the author at the University College of Sodertorn (Hud- dinge, Sweden) during the academic year 1997-1998 has also influenced the presentation. The opportunity to give this course is hereby gratefully ac- knowledged.

This volume covers a wide range of various fields of research, with the common thread being Next Generation Sequencing (NGS) related methods and applications, as well as analysis and interpretation of the data obtained. Chapters guide readers through the highly dynamic processes of translational and transcriptional profiling of a cell, method to detect copy number alterations (CNAs), targeted sequencing applications, method called "Hi-Plex" to characterize known polymorphic loci, single-cell of DNA or RNA, identify and characterize rare circulating CD4 T cells, and computational pipeline for RNAseq analysis. 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, Next Generation Sequencing: Methods and Protocols aims to be useful and informative for further study into this vital field.

Although numerous studies have been made of the Western educated political elite of colonial Nigeria in particular, and of Africa in general, very few have approached the study from a perspective that analyzes the impacts of indigenous institutions on the lives, values, and ideas of these individuals. This book is about the diachronic impact of indigenous and Western agencies in the upbringing, socialization, and careers of the colonial Igbo political elite of southeastern Nigeria. The thesis argues that the new elite manifests the continuity of traditions and culture and therefore their leadership values and the impact they brought on African society cannot be fully understood without looking closely at their lived experiences in those indigenous institutions where African life coheres. The key has been to explore this question at the level of biography, set in the context of a carefully reconstructed social history of the particular local communities surrounding the elite figures. It starts from an understanding of their family and village life, and moves forward striving to balance the familiar account of these individuals in public life, with an account of the ongoing influences from family, kinship, age grades, marriage and gender roles, secret societies, the church, local leaders and others. The result is not only a model of a new approach to African elite history, but also an argument about how to understand these emergent leaders and their peers as individuals who shared with their fellow Africans a dynamic and complex set of values that evolved over the six decades of colonialism.

Y.A. Berlin, I.V. Kurnikow, D. Beratan, M.A. Ratner, A.L. Burin: DNA Electron Transfer Processes: Some Theoretical Notions; N. Rosch, A.A. Voityuk: Quantum Chemical Calculation of Donor-Acceptor Coupling for Charge Transfer in DNA; E. Conwell: Polarons and Transport in DNA; Z. Cai, M.D.