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Evolutionary Dynamics And Pattern Generation In The Sequence And Secondary Structure Of Rna
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Book Synopsis Evolutionary dynamics and pattern generation in the sequence and secondary structure of RNA by : Martijn Adriaan Huynen
Download or read book Evolutionary dynamics and pattern generation in the sequence and secondary structure of RNA written by Martijn Adriaan Huynen and published by . This book was released on 1993 with total page 105 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Regulation by RNA-binding Proteins by : Maria Sarah Alexis
Download or read book Regulation by RNA-binding Proteins written by Maria Sarah Alexis and published by . This book was released on 2019 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-binding proteins (RBPs) regulate all aspects of RNA metabolism, such as splicing, localization, translation, and degradation. RNA processing is a critical component of gene expression regulation, and adaptive changes in RNA processing underlie many phenotypic differences between species. RBPs regulate RNA processing by recognizing RNA sequence elements (motifs) within RNAs. Studying the determinants of these RBP:RNA interactions is therefore key to understanding how RBPs select their targets, and how RNA processing evolves over time. This thesis presents three chapters revolving around these questions. First, I present a large-scale analysis of the evolution of gene expression across tissues, species, and studies. This study differs from previous studies in its usage of inter-sample distances to model gene expression divergence, a method that allowed us to reconcile disparate findings in the field. Second, I present a comprehensive study of the affinity landscapes of 78 human RBPs using RNA Bind-N-Seq (RBNS), an unbiased assay that determines the sequence, structure, and context preferences of RBPs. Integrated analysis of all 78 motifs reveals an unexpectedly low diversity of RNA motifs, implying frequent convergence of binding specificity towards a relatively small set of RNA motifs, many with low compositional complexity. Offsetting this trend, RBPs show extensive preferences for contextual features distinct from short linear motifs, including spaced "bipartite" motifs, biased flanking nucleotide composition, and bias away from or toward RNA structure. These results emphasize the importance of contextual features in RNA recognition, which likely enable targeting of distinct subsets of transcripts by different RBPs that recognize the same linear motif. Lastly, I compile a catalog of all known RBP specificities and examine their conservation patterns, in vivo binding patterns, and evolutionary trajectories across species. This work demonstrates that RNA regulation can be well conserved despite rapid evolution of RBP binding sites, and highlights mechanisms that may contribute to this robustness. This phenomenon is well-characterized for transcriptional regulation at promoters, but has not well been described for RNA regulation. Taken together, these studies advance our understanding of RBP target selection and how it evolves over time, thereby furthering our understanding of the basic mechanisms that govern gene regulation.
Download or read book Mitochondrial Genome Evolution written by and published by Academic Press. This book was released on 2012-11-27 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume features reviews on Mitochondrial genome evolution. Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology This thematic volume features reviews on mitochondrial genome evolution
Download or read book Genetics Abstracts written by and published by . This book was released on 2001 with total page 530 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods by : Jan Gorodkin
Download or read book RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods written by Jan Gorodkin and published by Humana. This book was released on 2014-03-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Evolutionary Dynamics on Random Structures by :
Download or read book Evolutionary Dynamics on Random Structures written by and published by . This book was released on 1997 with total page 17 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this paper the authors consider the evolutionary dynamics of populations of sequences, under a process of selection at the phenotypic level of structures. They use a simple graph-theoretic representation of structures which captures well the properties of the mapping between RNA sequences and their molecular structure. Each sequence is assigned to a structure by means of a sequence-to-structure mapping. The authors make the basic assumption that every fitness landscape can be factorized through the structures. The set of all sequences that map into a particular random structure can then be modeled as a random graph in sequence space, the so-called neutral network. They analyze in detail how an evolving population searches for new structures, in particular how they switch from one neutral network to another. They verify that transitions occur directly between neutral networks, and study the effects of different population sizes and the influence of the relatedness of the structures on these transitions. In fitness landscapes where several structures exhibit high fitness, the authors then study evolutionary paths on the structural level taken by the population during its search. They present a new way of expressing structural similarities which are shown to have relevant implications for the time evolution of the population.
Book Synopsis A Computational Approach for Identifying Evolutionarily Conserved Secondary Structure in RNA Molecules by : Veronica Juan
Download or read book A Computational Approach for Identifying Evolutionarily Conserved Secondary Structure in RNA Molecules written by Veronica Juan and published by . This book was released on 2000 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Evolutionary Dynamics and Optimization by : Christian V. Forst
Download or read book Evolutionary Dynamics and Optimization written by Christian V. Forst and published by . This book was released on 1995 with total page 20 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Dependence Among Sites in Protein and RNA Evolution by :
Download or read book Dependence Among Sites in Protein and RNA Evolution written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Widely used models of molecular evolution assume independent change among sequence sites. This assumption facilitates computation but it is biologically unrealistic. RNA secondary structure and protein tertiary structure both change more slowly over time than do the encoding DNA sequences. The constraints upon sequence evolution that serve to maintain structure induce dependent change among molecular sequence positions. The object of this thesis is to characterize the impact of structure on sequence evolution. The dependence among sites in protein evolution is first studied. Two simple and not very parametric hypothesis tests are introduced to study the spatial clustering of amino acid replacements within protein tertiary structure. Results of applying these tests to 273 protein families support the expectation that spatial clustering of amino acid replacements within tertiary structure is a ubiquitous phenomenon. More importantly, patterns of amino acid replacements do not seem to be solely attributable to spatial clustering of sequence positions that are independently evolving and have high rates of change. Instead, application of the newly introduced simple hypothesis tests yields evidence for dependent change among spatially clustered protein positions. This portion of the thesis work thereby casts doubt upon widely used methods for phylogeny inference. The second focus of this thesis is the impact of RNA secondary structure on RNA evolution. A model of RNA evolution incorporating RNA secondary structure is developed. The model introduces dependence among sites in RNA evolution via the effects of sequence changes on the approximate free energy of the resulting RNA secondary structure. This approximate free energy information can be thought as surrogate of fitness that serves as a link between genotype and phenotype in the model. Analysis of eukaryotic 5S ribosomal RNA sequences with this model shows the importance of RNA secondary structure on evolution. This an.
Book Synopsis RNA 3D Structure Analysis and Prediction by : Neocles Leontis
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
Download or read book RNA Folding written by Christina Waldsich and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on in vitro and intracellular RNA structure formation, RNA Folding: Methods and Protocols provides a comprehensive collection of experimental protocols which are suitable to dissect RNA folding pathways and to characterize the structure of RNA folding intermediates at nucleotide or even atomic resolution. The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. 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. Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule.
Book Synopsis Mutation by : Matthew Cranston Cowperthwaite
Download or read book Mutation written by Matthew Cranston Cowperthwaite and published by . This book was released on 2008 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mutation is a fundamental process in evolution because affects the amount of genetic variation in evolving populations. Molecular-structure models offer significant advantages over traditional population-genetics models for studying mutation, mainly because such models incorporate simple, tractable genotype-to-phenotype maps. Here, I use RNA secondary structure models to study four basic properties of mutation. The first section of this thesis studies the statistical properties of beneficial mutations. According to population genetics theory, the fitness effects of new beneficial mutations will be exponentially distributed. I show that in RNA there is sufficient correlation between a genotype and its point mutant neighbors to produce non-exponential distributions of fitness effects of beneficial mutations. These results suggest that more sophisticated statistical models may be necessary to adequately describe the distribution of fitness effects of new beneficial mutations. The second section of this thesis addresses the dynamics of deleterious mutations in evolving populations. There is a vast body of theoretical work addressing deleterious mutations that almost universally assumes that the fitness effects of deleterious mutations are static. I use an RNA simulation model to show that, at moderately high mutation rates, initially deleterious mutations may ultimately confer beneficial effects to the individuals harboring them. This result suggests that deleterious mutations may play a more important role in evolution than previously thought. The third section of this thesis studies the global patterns of mutations connecting phenotypes in fitness landscapes. I developed a network model to describe global characteristics of the relationship between sequence and structure in RNA fitness landscapes. I show that phenotype abundance varies in a predictable manner and critically influences evolutionary dynamics. A study of naturally occurring functional RNA molecules using a new structural statistic suggests that these molecules are biased towards abundant phenotypes. These results are consistent with an "ascent of the abundant" hypothesis, in which evolution yields abundant phenotypes even when they are not the most fit. The final section of this thesis addresses the evolution of mutation rates infinite asexual populations. I developed an RNA-based simulation model in which each individual's mutation rate is controlled by a neutral modifier locus. Using this model, I show that smaller populations maintain higher mutation rates than larger populations. I also show that genome length and shape of the fitness function do not significantly determine the evolved mutation rate. Lastly, I show that intermediate rates of environmental change favor evolution of the largest mutation rates.
Book Synopsis Theoretical and Computational Methods in Genome Research by : Sándor Suhai
Download or read book Theoretical and Computational Methods in Genome Research written by Sándor Suhai and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: The application ofcomputational methods to solve scientific and practical problems in genome research created a new interdisciplinary area that transcends boundaries tradi tionally separating genetics, biology, mathematics, physics, and computer science. Com puters have, of course, been intensively used in the field of life sciences for many years, even before genome research started, to store and analyze DNA or protein sequences; to explore and model the three-dimensional structure, the dynamics, and the function of biopolymers; to compute genetic linkage or evolutionary processes; and more. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function ofgenomes ofhigher organisms, has generated, how ever, not only a huge and exponentially increasing body of data but also a new class of scientific questions. The nature and complexity of these questions will also require, be yond establishing a new kind ofalliance between experimental and theoretical disciplines, the development of new generations both in computer software and hardware technolo gies. New theoretical procedures, combined with powerful computational facilities, will substantially extend the horizon of problems that genome research can attack with suc cess. Many of us still feel that computational models rationalizing experimental findings in genome research fulfill their promises more slowly than desired. There is also an uncer tainty concerning the real position of a "theoretical genome research" in the network of established disciplines integrating their efforts in this field.
Book Synopsis RNA Mapping by : M. Lucrecia Alvarez
Download or read book RNA Mapping written by M. Lucrecia Alvarez and published by Humana Press. This book was released on 2014-07-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In RNA Mapping- Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used to study RNA. These include protocols for the consequence of the emerging interest in the characterization of cellular RNAs urged by their potential use as diagnostic biomarkers or therapeutic targets. In particular, the biological relevance of microRNAs in human physiology and disease development is highlighted in the 16 chapters focused on methods for their physical and functional mapping. 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, RNA Mapping- Methods and Protocols provides instruction and inspiration for scientists who are facing the challenges of the discovery and/or functional characterization of RNA molecules for a wide variety of applications ranging from novel biomedical diagnostics to therapeutics and biomaterials.
Download or read book Index Medicus written by and published by . This book was released on 2004 with total page 2098 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.
Book Synopsis The Causes of Molecular Evolution by : John H. Gillespie
Download or read book The Causes of Molecular Evolution written by John H. Gillespie and published by Oxford University Press. This book was released on 1994-05-26 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work provides a unified theory that addresses the important problem of the origin and maintenance of genetic variation in natural populations. With modern molecular techniques, variation is found in all species, sometimes at astonishingly high levels. Yet, despite these observations, the forces that maintain variation within and between species have been difficult subjects of study. Because they act very weakly and operate over vast time scales, scientists must rely on indirect inferences and speculative mathematical models. However, despite these obstacles, many advances have been made. The author's research in molecular genetics, evolution, and bio-mathematics has enabled him to draw on this work, and present a coherent and valuable view of the field. The book is divided into three parts. The first consists of three chapters on protein evolution, DNA evolution, and molecular mechanisms. This section reviews the experimental observations on genetic variation. The second part gives a unified treatment of the mathematical theory of selection in a fluctuating environment. The final two chapters combine the earlier assessments in a treatment of the scientific status of two competing theories for the maintenance of genetic variation. Steeped in the enormous advances population genetics has made over the past 25 years, this book has proven highly popular among human geneticists, biologists, evolutionary theorists, and bio-mathematicians.
Book Synopsis Viral Fitness and Evolution by : Esteban Domingo
Download or read book Viral Fitness and Evolution written by Esteban Domingo and published by Springer Nature. This book was released on 2023-01-02 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book unifies general concepts of plant and animal virus evolution and covers a broad range of topics related to theoretical and experimental aspects of virus population dynamics and viral fitness. Timely topics such as viral mechanisms to cope with antiviral agents, the adaptability of the virus to new hosts, emergence of new viral phenotypes, and the connections between short- and long-term virus evolution are included. By comparing plant and animal viruses, universal mechanisms responsible for fitness variations, viral emergence and disease mechanisms are explored. Although emphasis is put on specific plant and human viral pathogens, relevant similarities and differences to other viruses are highlighted. Additionally, readers will learn more about the adaptability of coronaviruses, including the recently emerged SARS-CoV-2, the causative agent of the COVID-19 pandemic. The book is aimed at students and scientists interested in basic and applied aspects of plant and animal virus population dynamics and evolution.
