The availability of genomic blueprints for hundreds of species has led to a transformation in biology, encouraging the proliferation of adaptive arguments for the evolution of genomic features. This text explains why the details matter and presents a framework for how the architectural diversity of eukaryotic genomes and genes came to arise.
The traditional view of genomes suggests that they are static entities changing slowly in sequence and structure through time (e.g. evolving over geological time-scales). This outdated view has been challenged as our understanding of the dynamic nature of genomes has increased. Changes in DNA content (i.e. polyploidy) are common to specific life-cycle stages in a variety of eukaryotes, as are changes in genome content itself. These dramatic genomic changes include chromosomal deletions (i.e. paternal chromosome deletion in insects; Goday and Esteban 2001; Ross, et al. 2010), developmentally regulated genome rearrangements (e.g. the V(D)J system in adaptive immunity in mammals; Schatz and Swanson 2011) and the specialization of a distinct somatic genome through epigenetically regulate DNA elimination during development (found in protists and some animals; Coyne, et al. 2012; Prescott 1994; Wang and Davis 2014; Wyngaard, et al. 2011). What likely allows genomes to be highly flexible is the separation of germline (i.e. 'heritable') and somatic (i.e. 'functional') material, even in the context of a single nucleus. Germline-soma distinctions have been best described (and most easily seen) in lineages of multicellular eukaryotes (e.g. plants, animals and fungi) due to obvious sexual structures. Germline genomes of these taxa are restricted to specialized cells (e.g. gametes; for example, pollen grains, eggs and spores) and remain undifferentiated (and often transcriptionally inactive), whereas the somatic cells (e.g. skin, leaves, hyphae) provide the basis for ensuring organismal survival to reproductive life-stages. Sequestered germline and somatic genomes are not restricted to these well-known multi-cellular lineages but are also well-described among ciliates (the focus of this dissertation) and some foraminifera. However, in these protists, germline and somatic genomes are not isolated into distinct cells and tissues but rather are isolated into distinct nuclei that share a common cytoplasm. Ciliates are a diverse and ancient clade of eukaryotes (~1-1.2 GYA old) and their study has led to the discovery of broad uniting eukaryotic features such as telomeres (Blackburn and Gall 1978) and self-splicing RNAs (Kruger, et al. 1982). As in the "macrobial" eukaryotes, the somatic genome (macronucleus; MAC) is transcriptionally active, transcribing all the genes necessary to maintain the cell, while the germline genome (micronucleus; MIC) remains transcriptionally inactive during the asexual portions of the life cycle. While the germline chromosomes in ciliates are physically similar to other 'traditional' eukaryotic chromosomes (e.g. being multi-Mbp with centromeres), the physical structure of the somatic chromosomes is highly variable. For example, in the model ciliate Tetrahymena thermophila, the somatic genome is composed of 225 unique chromosomes (most of them being ~200-400Kbp), with each at approximately 45 copies, whereas Oxytricha trifallax's somatic genome is composed of ~16,000 gene-sized chromosomes (~2-3Kbp) with each chromosome at its own independent copy number (average copy number ~2,000). Despite dramatic differences in somatic genome architecture in ciliates, the development of a new somatic genome involves. For all ciliates studied to date, this metamorphosis from 'traditional' germline chromosomal architecture to the incredibly variable somatic genome architecture includes large-scale genome rearrangements and DNA elimination. This transformation involves the epigenetically-guided retention of somatically destined DNA from the background germline genome. While genomic rearrangements in most other eukaryotes are often fatal and are symptoms of well-known diseases (e.g. some cancers), this traditionally 'catastrophic' event is a fundamental part of ciliate life-cycles. Although studies of ciliate germline genomes have largely been restricted to only a few genera, there appear to be broad similarities in gene organization that may be phylogenetically conserved. Ciliate germline genome architecture has been categorized as either non-scrambled or scrambled, where non-scrambled architectures are often defined as possessing macronuclear destined sequences (MDSs; soma) that are separated by germline-limited DNA and remain in consecutive order (e.g. 1-2-3-4; Figure 3.1A and Figure 4.4A). Scrambled germline architectures are highly variable, but are broadly defined as MDSs being maintained in non-consecutive order (e.g. 1-3-4-2) and/or on opposing strands of DNA (Figure 3.1 B-D and Figure 4.4B). The germline genomes of Chilodonella uncinata (the main focus of this dissertation) possess a combination of scrambled and non-scrambled architectures. Before my thesis work, only those ciliates with gene-sized chromosomes have been demonstrated to have scrambled germline loci. Interestingly, previous work has implicated somatic genome architecture impacting the observable accelerated rates of protein evolution in ciliates, where the proteins of those ciliates possessing 'gene-sized' chromosomes experience the greatest evolutionary rates. These observations highlight the need for further work exploring the evolutionary impacts of different germline genome architectures, as the germline structure itself has direct impact on the development of the somatic genome. While this dissertation aims to elucidate some aspects of the evolution of germline-soma distinctions and the impact of genome and nuclear architecture (Chapters 2-4), there remain several fundamental questions that we can start addressing. For instance, in this work we observe that the most expanded gene families in Chilodonella uncinata are composed of genes that are disproportionately found at scrambled germline loci (Chapter 3). A major step future step will be to explore the functional implications of this increased paralog diversity through forward and reverse genetics techniques. Similarly, it will be incredibly valuable to better understand the nuclear architecture of the differing genomic contents of the three distinct nuclei present during ciliate development (i.e. the degrading parental MAC, the 'new' MIC, and the developing MAC). There may be observable compartmentalization that is exploitable or critical to the accurate rearrangement of the germline genome into a functional somatic genome. Finally, with the increasingly apparent utility of single-cell 'omics techniques (which we use in Chapters 3 and 4), there is opportunity to probe into taxonomic groups where physical germline-soma separations exist, which will provide a far more expansive understanding of the evolutionary and functional impacts of harboring multiple distinct genomes inside of a single cell/organism.
Nuclear Architecture and Dynamics provides a definitive resource for (bio)physicists and molecular and cellular biologists whose research involves an understanding of the organization of the genome and the mechanisms of its proper reading, maintenance, and replication by the cell. This book brings together the biochemical and physical characteristics of genome organization, providing a relevant framework in which to interpret the control of gene expression and cell differentiation. It includes work from a group of international experts, including biologists, physicists, mathematicians, and bioinformaticians who have come together for a comprehensive presentation of the current developments in the nuclear dynamics and architecture field. The book provides the uninitiated with an entry point to a highly dynamic, but complex issue, and the expert with an opportunity to have a fresh look at the viewpoints advocated by researchers from different disciplines. Highlights the link between the (bio)chemistry and the (bio)physics of chromatin Deciphers the complex interplay between numerous biochemical factors at task in the nucleus and the physical state of chromatin Provides a collective view of the field by a large, diverse group of authors with both physics and biology backgrounds
TSRchitect is capable of handling both tag and sequence-based TSS information and efficiently computes TSRs from global TSS datasets on a desktop computer. We find support for TSRchitect's annotations in human from a CAGE experiment from the ENCODE (Encyclopedia of DNA Elements) project. Finally, we use TSRchitect to identify TSRs from the transcriptomes of diverse eukaryotes. We investigated the conservation of TSRs among orthologous genes. We frequently identify multiple TSRs for a given gene, suggesting that alternative promoter usage is widespread. Overall, using TSS profiling data derived from separate tissues within mouse and human, we find that the positions of TSRs are relatively stable across tissues surveyed; however, a small fraction of genes exhibit tissue-specific differences in TSR use. As transcriptome profiling information continues to be generated at an rapid pace, computational approaches are increasingly important. It is anticipated that the method and approach we describe within this dissertation will contribute to an improved of gene regulation and promoter architecture in eukaryotes.
The Control of Fat and Lean Deposition is a collection of papers dealing with the methods of influencing fat and lean deposition in whole animals, such as the use of the immune response, the use of exogenously applied materials, transgenesis, or the diet itself. The papers also consider the results of fat manipulation and lean deposition on meat quality to achieve suitabilty for human consumption. Some papers review the hormonal regulation of muscle protein synthesis, degradation, and cell growth, noting that muscle protein turnover involves the regulation of cellular growth and metabolism of the whole body. Another paper investigates the surge in lipid accumulation during fattening, as well as the correlation between changes in flux or enzyme activities in growing animals to changes in lipid accretion. One paper examines the responsiveness of prenatal development of key tissues, such as skeletal tissue and adipose, to nongenetic influences. The paper also analyzes how such responsiveness influence the rate and composition of postnatal growth. Another paper discusses the observation that reducing fat content especially on the muscle tissue itself can adversely affect the eating quality and tenderness of meat. The collection is suitable for veterinarians, livestock growers, and researchers engaged in food processing and preservation.
Bioinformatics, the use of computers to address biological questions, has become an essential tool in biological research. It is one of the critical keys needed to unlock the information encoded in the flood of data generated by genome, protein structure, transcriptome and proteome research. Bioinformatics: Genes, Proteins & Computers covers both the more traditional approaches to bioinformatics, including gene and protein sequence analysis and structure prediction, and more recent technologies such as datamining of transcriptomic and proteomic data to provide insights on cellular mechanisms and the causes of disease.
This timely volume brings together expert reviews of the recentsignificant advances in our knowledge and understanding of theorganisation of the higher plant nucleus, and in particular in therelationship between nuclear organisation and the regulation ofgene expression. Rapid progress has been made in a number of keyareas over the last five years, including description andcharacterization of proteins of the nuclear envelope and nuclearpore complex, novel insights into nucleoskeletal structures, aswell as developments related to chromatin organization, functionand gene expression. These advances open the way for new researchinto areas such as stress tolerance, plant-pathogen interactionsand ultimately crop improvement and food security. Continuedresearch into plant nuclear structure, genome architecture and generegulation also enriches our understanding of the origin andevolution of the nucleus and its envelope. Edited by world-class researchers in plant cell biology, andcomprising contributions from internationally-renowned academics,this latest volume in the prestigious Annual Plant Reviews seriesbrings together a wealth of knowledge in the burgeoning field ofplant nuclear structure and genetics. Annual Plant Reviews, Volume 46: Plant Nuclear Structure,Genome Architecture and Gene Regulation is a vitalresource for advanced students, researchers and professionals inplant science and related disciplines. Libraries in all researchestablishments where plant science, biochemistry, molecularbiology, genetics and genomics and agricultural science are taughtand studied will find this excellent volume an essential additionto their shelf.
This advanced textbook is tailored for an introductory course in Systems Biology and is well-suited for biologists as well as engineers and computer scientists. It comes with student-friendly reading lists and a companion website featuring a short exam prep version of the book and educational modeling programs. The text is written in an easily accessible style and includes numerous worked examples and study questions in each chapter. For this edition, a section on medical systems biology has been included.
In this comprehensive and stimulating text and reference, the authors have succeeded in combining experimental data with current hypotheses and theories to explain the complex physiological functions of plants. For every student, teacher and researcher in the plant sciences it offers a solid basis for an in-depth understanding of the entire subject area, underpinning up-to-date research in plant physiology. The authors vividly explain current research by references to experiments, they cite original literature in figures and tables, and, at the end of each chapter, list recent references that are relevant for a deeper analysis of the topic. In addition, an abundance of detailed and informative illustrations complement the text.
This eBook presents all 10 articles published under the Frontiers Research Topic "Evolutionary Feedbacks Between Population Biology and Genome Architecture", edited by Scott V. Edwards and Tariq Ezaz. With the rise of rapid genome sequencing across the Tree of Life, challenges arise in understanding the major evolutionary forces influencing the structure of microbial and eukaryotic genomes, in particular the prevalence of natural selection versus genetic drift in shaping those genomes. Additional complexities in understanding genome architecture arise with the increasing incidence of interspecific hybridization as a force for shaping genotypes and phenotypes. A key paradigm shift facilitating a more nuanced interpretation of genomes came with the rise of the nearly neutral theory in the 1970s, followed by a greater appreciation for the contribution of nonadaptive forces such as genetic drift to genome structure in the 1990s and 2000s. The articles published in this eBook grapple with these issues and provide an update as to the ways in which modern population genetics and genome informatics deepen our understanding of the subtle interplay between these myriad forces. From intraspecific to macroevolutionary studies, population biology and population genetics are now major tools for understanding the broad landscape of how genomes evolve across the Tree of Life. This volume is a celebration across diverse taxa of the contributions of population genetics thinking to genome studies. We hope it spurs additional research and clarity in the ongoing search for rules governing the evolution of genomes.
With one volume each year, this series keeps scientists and advanced students informed of the latest developments and results in all areas of the plant sciences. The present volume includes reviews on genetics, cell biology, physiology, comparative morphology, systematics, ecology, and vegetation science.
Plant Biotechnology provides an introduction to the fundamental life processes and reviews topics relevant to plant biotechnology. This book discusses the manipulation of biological systems to solve practical problems in industry or agriculture. Organized into four parts encompassing 18 chapters, this book begins with an overview of the fundamental techniques essential to plant biotechnology. This text then describes the various aspects of the regulation of gene expression in plants and reviews the molecular architecture of plant genes. Other chapters consider chloroplast genome from various organisms and present the practical examples of the significance and uses of biotechnology in crop improvement. This book discusses as well the methods for inducing plant gene expression in heterologous prokaryotic and eukaryotic systems. The final chapter deals with the potential for using gene transfer technology for crop improvement. This book is a valuable resource for plant physiologists, biochemists, plant scientists, genetic engineers, and evolutionary biologists.
The annual Evolutionary Biology Meetings in Marseille aim to bring together leading scientists, promoting an exchange of state-of-the-art knowledge and the formation of inter-group collaborations. This book presents the most representative contributions to the 13th meeting, which was held in September 2009. It comprises 21 chapters, which are organized into the following three categories: • Evolutionary Biology Concepts • Genome/Molecular Evolution • Morphological Evolution/Speciation This book offers an up-to-date overview of evolutionary biology concepts and their use in the biology of the 21st century.
Understanding of the origin of species and their adaptability to new environments is one of the main questions in biology. This is fueled by the ongoing debate on species concepts and facilitated by the availability of an unprecedented large number of genomic resources. Genomes are organized into chromosomes, where significant variations in number and morphology are observed among species due to large-scale structural variants such as inversions, translocations, fusions, and fissions. This genomic reshuffling provides, in the long term, new chromosomal forms on which natural selection can act upon, contributing to the origin of biodiversity. This book contains mainly articles, reviews, and an opinion piece that explore numerous aspects of genome plasticity among taxa that will help in understanding the dynamics of genome composition, the evolutionary relationships between species and, in the long run, speciation.
A protein requires its own three-dimensional structure for its biological activity. If a chemical agent is added, the biological activity is lost, and the three dimensional structure is destroyed to become a random coil state. But when the chemical agent is removed, the biological activity is recovered, implying that the random coil state turns back into the original complex structure spontaneously. This is an astonishing event. The Physical Foundation of Protein Architecture is intended to solve this mystery from the physicochemical basis by elucidating the mechanism of various processes in protein folding. The main features of protein folding are shown to be described by the island model with long range hydrophobic interaction which is capable of finding the specific residue, and the lampshade criterion for disulfide bonding. Various proteins with known structure are refolded, with the purpose of uncovering the mechanism of protein folding. In addition, ab initio method for predicting protein structure from its amino acid sequence is proposed. Contents:Generalities:Helix-Coil Transition in PolypeptideSome Aspects of Protein FoldingMechanism of Protein Folding:Island Modelα-Helical ProteinsLysozyme and PhospholipaseBovine Pancreatic Trypsin InhibitorFlavodoxin and ThioredoxinFerredoxinFolding of a Protein of Unknown Structure:Ab Initio Method of Prediction of Protein StructureSearch for the Conformation of Minimum EnergyTopics Related to Protein Structures:Phase TransitionModuleMolecular ChaperonesMembrane ProteinsStructure Prediction Based on Protein Data Readership: Advanced graduate students and researchers in the biosciences. Keywords:Mechanism of Protein Folding;Folding Pathway of Protein;Helix-Coil Transition;Anfinsen's Dogma;Levinthal Paradox;Molten Globule;Hydrophobic Interaction;Island Model;Disulfide Bonding;Ab Initio Method of Prediction