RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods


Book Description

The existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. 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. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.




Living Dinosaurs


Book Description

Living Dinosaurs offers a snapshot of our current understanding of the origin and evolution of birds. After slumbering for more than a century, avian palaeontology has been awakened by startling new discoveries on almost every continent. Controversies about whether dinosaurs had real feathers or whether birds were related to dinosaurs have been swept away and replaced by new and more difficult questions: How old is the avian lineage? How did birds learn to fly? Which birds survived the great extinction that ended the Mesozoic Era and how did the avian genome evolve? Answers to these questions may help us understand how the different kinds of living birds are related to one another and how they evolved into their current niches. More importantly, they may help us understand what we need to do to help them survive the dramatic impacts of human activity on the planet.




Statistical Population Genomics


Book Description

This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.




Bird Species


Book Description

The average person can name more bird species than they think, but do we really know what a bird “species” is? This open access book takes up several fascinating aspects of bird life to elucidate this basic concept in biology. From genetic and physiological basics to the phenomena of bird song and bird migration, it analyzes various interactions of birds – with their environment and other birds. Lastly, it shows imminent threats to birds in the Anthropocene, the era of global human impact. Although it seemed to be easy to define bird species, the advent of modern methods has challenged species definition and led to a multidisciplinary approach to classifying birds. One outstanding new toolbox comes with the more and more reasonably priced acquisition of whole-genome sequences that allow causative analyses of how bird species diversify. Speciation has reached a final stage when daughter species are reproductively isolated, but this stage is not easily detectable from the phenotype we observe. Culturally transmitted traits such as bird song seem to speed up speciation processes, while another behavioral trait, migration, helps birds to find food resources, and also coincides with higher chances of reaching new, inhabitable areas. In general, distribution is a major key to understanding speciation in birds. Examples of ecological speciation can be found in birds, and the constant interaction of birds with their biotic environment also contributes to evolutionary changes. In the Anthropocene, birds are confronted with rapid changes that are highly threatening for some species. Climate change forces birds to move their ranges, but may also disrupt well-established interactions between climate, vegetation, and food sources. This book brings together various disciplines involved in observing bird species come into existence, modify, and vanish. It is a rich resource for bird enthusiasts who want to understand various processes at the cutting edge of current research in more detail. At the same time it offers students the opportunity to see primarily unconnected, but booming big-data approaches such as genomics and biogeography meet in a topic of broad interest. Lastly, the book enables conservationists to better understand the uncertainties surrounding “species” as entities of protection.







Molecular and Genome Evolution


Book Description

This book describes the driving forces behind the evolutionary process at the molecular and genome levels, the effects of the various molecular mechanisms on the structure of genes, proteins, and genomes, the methodology and the analytical tools involved in dealing with molecular data from an evolutionary perspective, and the logic of evolutionary hypothesis testing. Evolutionary phenomena at the molecular level are detailed in a way that can be understood without much prerequisite knowledge of molecular biology, evolution, or mathematics. Numerous examples that support and clarify the theoretical arguments and methodological discussions are included.




Gene Sharing and Evolution


Book Description

In Gene Sharing and Evolution Piatigorsky explores the generality and implications of gene sharing throughout evolution and argues that most if not all proteins perform a variety of functions in the same and in different species, and that this is a fundamental necessity for evolution.




Avian Growth and Development


Book Description

This is the first re-appraisal in 50 years of concepts of development made in birds. This book is a case study in evolutionary diversification of life histories. Although birds have a rather uniform body plan and physiology, they exhibit marked variation in development type, parental care, and rate of growth. Altricial birds are fully dependent on their parents for warmth and nutrition and begin posthatching life in a more or less embryonic condition. At the other extreme, such superprecocial species as the megapodes are independent of all parental care from hatching, and the neonate, able to fly, resembles an adult bird. This book thus attempts to present an integrative perspective of organism biology, ecology, and evolution.




The Pangenome


Book Description

This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.




Avian Biochemistry and Molecular Biology


Book Description

The biology of birds is diverse and frequently differs significantly from that of other vertebrates. Many birds migrate or fly at high altitudes, while egg-laying and feather production places high demands on nutrient uptake and storage. This book is the only comprehensive and up-to-date survey of avian biochemistry and molecular biology available. It emphasises the similarities and differences between birds and other vertebrates, concentrating on new developments. The first section deals with protein, lipid and carbohydrate metabolism, its hormonal control and the adaptations that occur in birds. The second covers the avian genome, gene expression, and avian immunology. Growth and embryological development are also discussed. Avian Biochemistry and Molecular Biology will be of interest to all those working on birds, especially postgraduate students and researchers.