Download or read book Uncovering the Circadian Output Pathways of Neurospora Crassa written by Michael William Vitalini and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The ubiquity of circadian systems has allowed their characterization in a broad range of model systems, which has greatly improved knowledge of how these systems are organized and the vast range of cellular and organismal processes under circadian control. Most of the advances, however, have come in describing the central oscillators of these systems, and, in some cases, the input pathways used to coordinate these oscillators to external time. Very little progress has been made in understanding the output pathways that allow circadian systems to regulate the breadth of processes shown to be clock-controlled. A genetic selection was designed to obtain mutations in genes involved in circadian regulated expression of the Neurospora crassa ccg-1 and ccg-2 genes. Some, but not all, of the strains obtained display altered regulation of more than one ccg as well as an 'Eas-like' appearance on solid media, and altered circadian period on race tubes. The data suggest a model in which output from the clock to these two genes is through a single, bifurcated pathway. The cloning of the gene mutated (rrg-1) in one of the strains from the above selection led to the first molecular description of a circadian output pathway in Neurospora, the HOG MAP kinase pathway. The HOG pathway has been previously described with regard to its role in the osmotic-stress response. The discovery of the involvement of rrg-1 in circadian regulation of ccg-1 and ccg-2 led to the discovery of regulation of the HOG pathway by the circadian clock. The data indicate that osmotic stress information and time-of-day information are transduced through the HOG pathway and implicate a role for the clock in preparing the organism for daily occurrences of hyperosmotic stress associated with sun exposure. The genetic selection, and the description of the HOG pathway with regard to circadian output, provide a basis for further characterization of circadian output in Neurospora. The ubiquity of MAP kinase pathways, such as the HOG pathway, and the observed similarities in the mechanisms of circadian clock function across multiple phyla, indicate that these findings may well be applicable to other model systems.

Download or read book Mapping Circadian Output Pathways in Neurospora Crassa written by Lindsay Danielle Bennett and published by . This book was released on 2014 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt: Circadian clocks are ubiquitous in eukaryotic organisms, providing the ability to anticipate regularly occurring stressful environmental changes. The molecular clock leads to a change in physiology of the organism such that it is prepared for predictable changes. While the external signals detected by the clock, as well as the molecular mechanism of clock components have been extensively characterized, less is known about how the clock manifests time of day information to the organism as a whole. Our lab has focused on identifying output pathways from the clock, using the model organism Neurospora crassa. We have previously demonstrated the circadian regulation of the conserved Mitogen Activated Protein Kinase (MAPK) OS-2 pathway, a homolog of the mammalian p38 pathway, and necessary for maintaining osmotic homeostasis in Neurospora. I present data indicating the circadian regulation of the 2 other MAPK pathways in Neurospora, the mammalian ERK1 and ERK2 like MAPKs, MAK-1 and MAK-2, and show that they are outputs of the clock. Furthermore, I identified around 500 genes that are mis-regulated when MAK-1 is deleted; greater than 25% of those genes are predicted to be clock-controlled. I demonstrated that the clock is signaling through the MAK-1 pathway to regulate 3 clock-controlled genes (ccgs) that encode proteins involved in several different biological processes including, stress response, cell wall formation, and mitochondrial phosphate transport. I established the circadian regulation of the transcript levels of 2 of the MAK-1 cascade components, mek-1 and mak-1. Additionally, I found that the accumulation of MEK-1 protein is clock-controlled, suggesting this is one mechanism by which the clock regulates the activity of MAK-1. Additional studies were carried out to elucidate the proteins that directly regulate the expression of mek-1 and mak-1; however, the mechanisms of direct clock control remain unclear and require further investigation. The finding that the circadian clock regulates all MAPK pathways in Neurospora, combined with the conservation of both the circadian clock and MAPK pathways in mammals provide compelling evidence that mammalian MAPK pathways are also regulated as clock output pathways to control circadian physiology. There is a strong link between aberrations in mammalian clocks, MAPKs, and disease, and therefore, an urgent need to further characterize the circadian regulation of the MAPK families, which will reveal new avenues for therapeutic treatments. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/151801

Download or read book Understanding Circadian Output Networks in Neurospora Crassa written by Rigzin N. Dekhang and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The Neurospora crassa circadian clock is based on a highly regulated molecular negative feedback loop, similar to molecular clocks in all eukaryotes. A core component of the N. crassa molecular clock is the White Collar complex (WCC), composed of the blue light photoreceptor WC-1 and its partner WC-2. The WCC serves as a master regulator that controls light signaling, and the precise timing of target gene expression. Up to 40% of the eukaryote genome is under the control of the clock at the level of transcript abundance, but the molecular links between the core oscillator and downstream target genes, as well as the mechanisms controlling the phase of rhythmic gene expression, are not understood. Using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq), about 400 binding sites for the WCC were identified throughout the N. crassa genome. We found that 24 transcription factors (TFs) were significantly enriched among the direct WCC target genes. As expected for genes that are controlled by the WCC, the first-tier TFs are both clock- and light-regulated. These data led to the hypothesis that the WCC functions to control rhythms in TFs, which in turn control rhythmicity and phase of downstream target genes and processes. To test this hypothesis, the first-tier TF ADV-1 (Arrested Development-1) was investigated in detail to characterize the downstream circadian genetic network. ADV-1 target genes were identified using ChIP- and RNA-seq, and as expected many ADV-1 downstream target genes were light-responsive and/or clock-controlled. An enrichment for ADV-1 target genes involved in cell fusion, a process that is critical for normal vegetative and sexual development in N. crassa, provided a rationale for the observed developmental defects in ADV-1 deletion cells, and suggested that cell fusion is clock-controlled. Importantly, this work revealed that the transduction of time-of-day information through ADV-1 to its downstream targets is more complex than anticipated. Specifically, I show that deletion of ADV-1 does not always lead to predicted changes in rhythmic gene expression and/or phase, suggesting that ADV-1 functions in combination with other first-tier TFs to control rhythmicity. In support of this idea, genome-wide binding profiles of all of the first-tier TFs uncovered complex feedback and feed forward regulation involving ADV-1. Thus, my data revealed that in order to fully understand how the clock signals phase information to downstream targets, we need to go beyond the candidate gene approach, and instead develop computational models from our TF ChIP-seq and rhythmic transcriptome data to model how time of day information is transduced in the molecular circadian output gene network. Predictions of the model can then be validated using ADV-1 deletion cells alone, or in combination with deletion of other first-tier TFs in the network, with the goal of deriving design principles that define conserved aspects of the circadian output network in all eukaryotes, and important in human health. To test this hypothesis, the first-tier TF ADV-1 (Arrested Development-1) was investigated in detail to characterize the downstream circadian genetic network. ADV-1 target genes were identified using ChIP- and RNA-seq, and as expected many ADV-1 downstream target genes were light-responsive and/or clock-controlled. An enrichment for ADV-1 target genes involved in cell fusion, a process that is critical for normal vegetative and sexual development in N. crassa, provided a rationale for the observed developmental defects in ADV-1 deletion cells, and suggested that cell fusion is clock- controlled. Importantly, this work revealed that the transduction of time-of-day information through ADV-1 to its downstream targets is more complex than anticipated. Specifically, I show that deletion of ADV-1 does not always lead to predicted changes in rhythmic gene expression and/or phase, suggesting that ADV-1 functions in combination with other first-tier TFs to control rhythmicity. In support of this idea, genome-wide binding profiles of all of the first-tier TFs uncovered complex feedback and feed forward regulation involving ADV-1. Thus, my data revealed that in order to fully understand how the clock signals phase information to downstream targets, we need to go beyond the candidate gene approach, and instead develop computational models from our TF ChIP-seq and rhythmic transcriptome data to model how time of day information is transduced in the molecular circadian output gene network. Predictions of the model can then be validated using ADV-1 deletion cells alone, or in combination with deletion of other first-tier TFs in the network, with the goal of deriving design principles that define conserved aspects of the circadian output network in all eukaryotes, and important in human health. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/155195

Download or read book Role of RCO 1 in the Control of Circadian Gene Expression and Metabolic Compensation of the Neurospora Crassa Circadian Clock written by Consuelo del Pilar Olivares Yáñez and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Circadian clocks are endogenous molecular timekeepers, which organize physiology of organisms with respect to the external world, conferring daily rhythms to a large number of biological processes within the cell. These clocks are present in various organisms, impinging close to 24 hours rhythms in the regulation of gene expression, physiology and behavior. A circadian system can be conceptualized as composed of three parts: input mechanisms, a central oscillator and output pathways. Although a detailed molecular description of the core oscillator is available in model eukaryotes, there is limited information on the mechanisms that allows it to regulate rhythmic processes. Such "output pathways" are the least characterized aspect of circadian systems. The filamentous fungus Neurospora crassa has served for decades as a model organism for the study of circadian biology. In an effort to improve current knowledge of output pathways identifying new components involved in this process, a genetic screen was conducted in this fungus, and we identified potential regulatory candidates, among which we characterized the coKrepressor RCOK1 and its role in regulating circadian biology. RCOK1 is the orthologue of the Saccharomyces cerevisiae transcriptional coK repressor Tup1. Contrary to reports that emerged while developing this thesis, we provide evidence that RCOK1 is not an essencial core-clock component in Neurospora. We evaluated the status of the central clock observing that expression of the negative element of the core oscillator, frequency (frq), remains rhythmic in the absence of RCOK1.

Download or read book The Genetics of Circadian Rhythms written by and published by Academic Press. This book was released on 2011-09-16 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: This latest volume in Advances in Genetics covers the genetics of Circadian rhythms. With an international group of authors this volume is the latest offering in this widely praised series.

Download or read book The Circadian Clock written by Urs Albrecht and published by Springer Science & Business Media. This book was released on 2010-01-23 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the invitation to edit this volume, I wanted to take the opportunity to assemble reviews on different aspects of circadian clocks and rhythms. Although most c- tributions in this volume focus on mammalian circadian clocks, the historical int- duction and comparative clocks section illustrate the importance of various other organisms in deciphering the mechanisms and principles of circadian biology. Circadian rhythms have been studied for centuries, but only recently, a mole- lar understanding of this process has emerged. This has taken research on circadian clocks from mystic phenomenology to a mechanistic level; chains of molecular events can describe phenomena with remarkable accuracy. Nevertheless, current models of the functioning of circadian clocks are still rudimentary. This is not due to the faultiness of discovered mechanisms, but due to the lack of undiscovered processes involved in contributing to circadian rhythmicity. We know for example, that the general circadian mechanism is not regulated equally in all tissues of m- mals. Hence, a lot still needs to be discovered to get a full understanding of cir- dian rhythms at the systems level. In this respect, technology has advanced at high speed in the last years and provided us with data illustrating the sheer complexity of regulation of physiological processes in organisms. To handle this information, computer aided integration of the results is of utmost importance in order to d- cover novel concepts that ultimately need to be tested experimentally.

Download or read book Genetics and Biotechnology written by J. Philipp Benz and published by Springer Nature. This book was released on 2020-10-28 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: This fully revised third edition includes up-to-date topics and developments in the field, which has made tremendous strides since the publication of the second edition in 2004. Many novel techniques based on Next Generation Sequencing have sped up the analysis of fungi and major advances have been made in genome editing, leading to a deeper understanding of the genetics underlying cellular processes as well as their applicability. At the same time, the relevance of fungi is unbroken, both due to the serious threats to human health and welfare posed by fungal pests and pathogens, and to the many benefits that fungal biotechnology can offer for diverse emerging markets and processes that form the basis of the modern bioeconomy. With regard to these advances, the first section of this volume, Genetics, illustrates the basic genetic processes underlying inheritance, cell biology, metabolism and “lifestyles” of fungi. The second section, Biotechnology, addresses the applied side of fungal genetics, ranging from new tools for synthetic biology to the biotechnological potential of fungi from diverse environments. Gathering chapters written by reputed scientists, the book represents an invaluable reference guide for fungal biologists, geneticists and biotechnologists alike.

Download or read book Pharmacoepigenetics written by and published by Academic Press. This book was released on 2019-06-04 with total page 983 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pharmacoepigenetics, Volume Eleven provides a comprehensive volume on the role of epigenetics and epigenomics in drug discovery and development, providing a detailed, but accessible, view of the field, from basic principles, to applications in disease therapeutics. Leading international researchers from across academia, clinical settings and the pharmaceutical industry discuss the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, and treatment, current epigenetic drugs, and the application of epigenetic procedures in drug development. Throughout the book, chapter authors offer a balanced and objective discussion of the future of pharmacoepigenetics and its crucial contribution to the growth of precision and personalized medicine. Fully examines the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, treatment, current epigenetic drugs and the application of epigenetic procedures in drug development Features chapter contributions from leading international researchers in academia, clinical settings and the pharmaceutical industry Instructs researchers, students and clinicians on how to better interpret and employ pharmacoepigenetics in drug development, efficiency and safety Provides a balanced and objective discussion of the future of pharmacoepigenetics and its crucial role in precision medicine

Download or read book Suprachiasmatic Nucleus written by David C. Klein and published by Oxford University Press, USA. This book was released on 1991 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: Based on a conference funded by the National Institutes of Health, this timely book is the most up-to-date and definitive reference on the suprachiasmatic nucleus (SCN), the part of the brain that controls circadian rhythms in mammals. These biological rhythms range from daily fluctuations in metabolism to seasonal and annual cycles. This book comprehensive and incisive review of the SCN covers anatomy and physiology, intrinsic SCN rhythms, circadian rhythms, neuropharmacology, transplants, and development.

Download or read book Proteins Advances in Research and Application 2011 Edition written by and published by ScholarlyEditions. This book was released on 2012-01-09 with total page 1746 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins: Advances in Research and Application: 2011 Edition is a ScholarlyEditions™ eBook that delivers timely, authoritative, and comprehensive information about Amino Acids, Peptides, and Proteins. The editors have built Proteins: Advances in Research and Application: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Amino Acids, Peptides, and Proteins in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Proteins: Advances in Research and Application: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.

Download or read book RNA Metabolism in Neurodegenerative Diseases written by Rita Sattler and published by Springer. This book was released on 2018-06-18 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has become evident over the last years that abnormalities in RNA processing play a fundamental part in the pathogenesis of neurodegenerative diseases. Cellular viability depends on proper regulation of RNA metabolism and subsequent protein synthesis, which requires the interplay of many processes including transcription, pre--‐mRNA splicing, mRNA editing as well as mRNA stability, transport and translation. Dysfunction in any of these processes, often caused by mutations in the coding and non--‐ coding RNAs, can be very destructive to the cellular environment and consequently impair neural viability. The result of this RNA toxicity can lead to a toxic gain of function or a loss of function, depending on the nature of the mutation. For example, in repeat expansion disorders, such as the newly discovered hexanucleotide repeat expansion in theC9orf72 gene found in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), a toxic gain of function leads to the formation of RNA foci and the sequestration of RNA binding proteins (RBPs). This in return leads to a loss of function of those RBPs, which is hypothesized to play a significant part in the disease progression of ALS and FTD. Other toxicities arising from repeat expansions are the formation of RNA foci, bi--‐directional transcription and production of repeat associated non--‐ATG (RAN) translation products. This book will touch upon most of these disease mechanisms triggered by aberrant RNA metabolism and will therefore provide a broad perspective of the role of RNA processing and its dysfunction in a variety of neurodegenerative disorders, including ALS, FTD, Alzheimer’s disease, Huntington’s disease, spinal muscular atrophy, myotonic dystrophy and ataxias. The proposed authors are leading scientists in the field and are expected to not only discuss their own work, but to be inclusive of historic as well as late breaking discoveries. The compiled chapters will therefore provide a unique collection of novel studies and hypotheses aimed to describe the consequences of altered RNA processing events and its newest molecular players and pathways.

Download or read book Molecular Biology of Fungal Development written by Heinz D. Osiewacz and published by CRC Press. This book was released on 2002-05-07 with total page 592 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text gives an overview of the fundamental aspects of molecular fungal development in one comprehensive volume, highlighting different elements in the maturational and reproductive cycles of selected fungal taxa.

Download or read book Data Fitting and Uncertainty written by Tilo Strutz and published by Springer Vieweg. This book was released on 2015-12-16 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The subject of data fitting bridges many disciplines, especially those traditionally dealing with statistics like physics, mathematics, engineering, biology, economy, or psychology, but also more recent fields like computer vision. This book addresses itself to engineers and computer scientists or corresponding undergraduates who are interested in data fitting by the method of least-squares approximation, but have no or only limited pre-knowledge in this field. Experienced readers will find in it new ideas or might appreciate the book as a useful work of reference. Familiarity with basic linear algebra is helpful though not essential as the book includes a self-contained introduction and presents the method in a logical and accessible fashion. The primary goal of the text is to explain how data fitting via least squares works. The reader will find that the emphasis of the book is on practical matters, not on theoretical problems. In addition, the book enables the reader to design own software implementations with application-specific model functions based on the comprehensive discussion of several examples. The text is accompanied with working source code in ANSI-C for fitting with weighted least squares including outlier detection. Among others the book covers following topics * fitting of linear and nonlinear functions with one- or multi-dimensional variables * weighted least-squares * outlier detection * evaluation of the fitting results * different optimisation strategies * combined fitting of different model functions * total least-squares approach with multi-dimensional conditions

Download or read book Military Strategies for Sustainment of Nutrition and Immune Function in the Field written by Institute of Medicine and published by National Academies Press. This book was released on 1999-05-13 with total page 722 pages. Available in PDF, EPUB and Kindle. Book excerpt: Every aspect of immune function and host defense is dependent upon a proper supply and balance of nutrients. Severe malnutrition can cause significant alteration in immune response, but even subclinical deficits may be associated with an impaired immune response, and an increased risk of infection. Infectious diseases have accounted for more off-duty days during major wars than combat wounds or nonbattle injuries. Combined stressors may reduce the normal ability of soldiers to resist pathogens, increase their susceptibility to biological warfare agents, and reduce the effectiveness of vaccines intended to protect them. There is also a concern with the inappropriate use of dietary supplements. This book, one of a series, examines the impact of various types of stressors and the role of specific dietary nutrients in maintaining immune function of military personnel in the field. It reviews the impact of compromised nutrition status on immune function; the interaction of health, exercise, and stress (both physical and psychological) in immune function; and the role of nutritional supplements and newer biotechnology methods reported to enhance immune function. The first part of the book contains the committee's workshop summary and evaluation of ongoing research by Army scientists on immune status in special forces troops, responses to the Army's questions, conclusions, and recommendations. The rest of the book contains papers contributed by workshop speakers, grouped under such broad topics as an introduction to what is known about immune function, the assessment of immune function, the effect of nutrition, and the relation between the many and varied stresses encountered by military personnel and their effect on health.

Download or read book Circadian Rhythms in Bacteria and Microbiomes written by Carl Hirschie Johnson and published by Springer Nature. This book was released on 2021-06-21 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses multiple aspects of biological clocks in prokaryotes. The first part of the book deals with the circadian clock system in cyanobacteria, i.e. the pioneer of bacterial clocks. Starting with the history and background of cyanobacteria and circadian rhythms in microorganisms, the topics range from the molecular basis, structure and evolution of the circadian clock to modelling approaches, Kai systems in cyanobacteria and biotechnological applications. In the second part, emergent timekeeping properties of bacteria in microbiomes and bacteria other than cyanobacteria are discussed. Since the discovery of circadian rhythms in cyanobacteria in the late 1980s, the field has exploded with new information. The cyanobacterial model system for studying circadian rhythms (Synechococcus elongatus), has allowed a detailed genetic dissection of the bacterial clock due to state-of-the-art methods in molecular, structural, and evolutionary biology. Cutting-edge research spanning from cyanobacteria and circadian phenomena in other kinds of bacteria, to microbiomes has now given the field another major boost. This book is aimed at junior and senior researchers alike. Students or researchers new to the field of biological clocks in prokaryotes will get a comprehensive overview, while more experienced researchers will get an update on the latest developments.

Download or read book Protein Phosphatases and Stress Management in Plants written by Girdhar K. Pandey and published by Springer Nature. This book was released on 2020-09-26 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: The regulation of the phosphorylation/dephosphorylation process, resulting in “cellular switches” that monitor normal plant physiology, growth and development, has immense potential in crop systems. With much of the information in the nascent stages, coming largely from Arabidopsis and rice particularly, the use of cell biology, genetic screens, biochemical approaches aided by an omics approach should help unravel the detail functional information available about signaling pathways in plants. The regulation could be exploited to develop crop varieties better equipped to handle changing environments and enhance agricultural productivity. In the post-genomic era, one of the major challenges is investigation and understanding of multiple genes and gene families regulating a particular physiological and developmental aspect of plant life cycle. One of the important physiological processes is regulation of stress response, which leads to adaptation or adjustment in response to adverse stimuli. With the holistic understanding of the signaling pathways involving phosphatases, one gene family or multiple genes or gene families, plant biologist can lay a foundation for designing and generating future crops, which can withstand the higher degree of environmental stresses. Especially abiotic stresses, which are the major cause of crop loss throughout the world without losing crop yield and productivity. This book incorporates the contributions from leading plant biologists in the field of stress-mediated dephosphorylation by phosphatases as an important task to elucidate the aspects of stress signaling by functional genomic approaches.

Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1089 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that