Metabolic Inactivation of the Circadian Transmitter, Pigment Dispersing Factor (PDF), by Neprilysin-Like Peptidases in Drosophila R
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Paul Hardin, Ph.D. John W
Department of Biology The College of Arts + Sciences | Indiana University Bloomington About Paul Hardin Distinguished Alumni Award Lecture Thu., Oct. 18, 2018 • 4 to 5 pm • Myers Hall 130 Paul Hardin, Ph.D. John W. Lyons Jr. ’59 Chair in Biology, Texas A&M University Genetic architecture underlying circadian clock initiation, maintenance, and output in Drosophila Circadian clocks drive daily rhythms in metabolism, physiology, and behavior in organisms ranging from cyanobacteria to humans. The identification and analysis of “clock genes” in Drosophila revealed that circadian timekeeping is based on a transcriptional feedback loop Paul Hardin studied the development of the sea in which CLOCK-CYCLE (CLK-CYC) heterodimers activate transcription of their feedback urchin embryo in William Klein’s lab at Indiana repressors PERIOD (PER) and TIMELESS (TIM). Subsequent studies revealed that similar University, from where he received his Ph.D. in transcriptional feedback loops keep circadian time in all eukaryotes and, in the case of 1987. He did his postdoctoral fellowship with animals, that these feedback loops are comprised of conserved components. The “core” Michael Rosbash at Brandeis University, working feedback loop described above operates in conjunction with an “interlocked” feedback on the circadian rhythms of the fruit fly, Drosophila loop in animals to drive rhythmic transcription of hundreds of genes that are maximally melanogaster. His work with Michael Rosbash and expressed at different phases of the circadian cycle. These feedback loops operate in many, Jeff Hall has been instrumental to our understanding but not all, tissues in flies including the brain pacemaker neurons that control rest:activity of how circadian rhythms affect a myriad of rhythms. -
Regulation of Drosophila Circadian Rhythms by Mirna Let-7 Is Mediated by a Regulatory Cycle
ARTICLE Received 10 Jul 2014 | Accepted 10 Oct 2014 | Published 24 Nov 2014 DOI: 10.1038/ncomms6549 Regulation of Drosophila circadian rhythms by miRNA let-7 is mediated by a regulatory cycle Wenfeng Chen1,*, Zhenxing Liu1,*, Tianjiao Li1, Ruifeng Zhang1, Yongbo Xue1, Yang Zhong1, Weiwei Bai1, Dasen Zhou1 & Zhangwu Zhao1 MicroRNA-mediated post-transcriptional regulations are increasingly recognized as important components of the circadian rhythm. Here we identify microRNA let-7, part of the Drosophila let-7-Complex, as a regulator of circadian rhythms mediated by a circadian regulatory cycle. Overexpression of let-7 in clock neurons lengthens circadian period and its deletion attenuates the morning activity peak as well as molecular oscillation. Let-7 regulates the circadian rhythm via repression of CLOCKWORK ORANGE (CWO). Conversely, upregulated cwo in cwo-expressing cells can rescue the phenotype of let-7-Complex overexpression. Moreover, circadian prothoracicotropic hormone (PTTH) and CLOCK- regulated 20-OH ecdysteroid signalling contribute to the circadian expression of let-7 through the 20-OH ecdysteroid receptor. Thus, we find a regulatory cycle involving PTTH, a direct target of CLOCK, and PTTH-driven miRNA let-7. 1 Department of Entomology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to Z.Z. (email: [email protected]). NATURE COMMUNICATIONS | 5:5549 | DOI: 10.1038/ncomms6549 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms6549 lmost all animals display a wide range of circadian bantam-dependent regulation of Clk expression is required for rhythms in behaviour and physiology, such as locomotor circadian rhythm. -
Distinct Visual Pathways Mediatedrosophilalarval Light
The Journal of Neuroscience, April 27, 2011 • 31(17):6527–6534 • 6527 Behavioral/Systems/Cognitive Distinct Visual Pathways Mediate Drosophila Larval Light Avoidance and Circadian Clock Entrainment Alex C. Keene,1 Esteban O. Mazzoni,1 Jamie Zhen,1 Meg A. Younger,1 Satoko Yamaguchi,1 Justin Blau,1 Claude Desplan,1 and Simon G. Sprecher1,2 1Department of Biology, Center for Developmental Genetics, New York University, New York, New York 10003-6688, and 2Department of Biology, Institute of Cell and Developmental Biology, University of Fribourg, 1700 Fribourg, Switzerland Visual organs perceive environmental stimuli required for rapid initiation of behaviors and can also entrain the circadian clock. The larval eye of Drosophila is capable of both functions. Each eye contains only 12 photoreceptors (PRs), which can be subdivided into two subtypes. Four PRs express blue-sensitive rhodopsin5 (rh5) and eight express green-sensitive rhodopsin6 (rh6). We found that either PR-subtype is sufficient to entrain the molecular clock by light, while only the Rh5-PR subtype is essential for light avoidance. Acetylcholine released from PRs confers both functions. Both subtypes of larval PRs innervate the main circadian pacemaker neurons of the larva, the neuropeptide PDF (pigment-dispersing factor)-expressing lateral neurons (LNs), providing sensory input to control circadian rhythms. How- ever, we show that PDF-expressing LNs are dispensable for light avoidance, and a distinct set of three clock neurons is required. Thus we have identifieddistinctsensoryandcentralcircuitryregulatinglightavoidancebehaviorandclockentrainment.Ourfindingsprovideinsightsintothe coding of sensory information for distinct behavioral functions and the underlying molecular and neuronal circuitry. Introduction sin6 (rh6) (Sprecher et al., 2007; Sprecher and Desplan, 2008). -
Genome Analysis and Knowledge
Dahary et al. BMC Medical Genomics (2019) 12:200 https://doi.org/10.1186/s12920-019-0647-8 SOFTWARE Open Access Genome analysis and knowledge-driven variant interpretation with TGex Dvir Dahary1*, Yaron Golan1, Yaron Mazor1, Ofer Zelig1, Ruth Barshir2, Michal Twik2, Tsippi Iny Stein2, Guy Rosner3,4, Revital Kariv3,4, Fei Chen5, Qiang Zhang5, Yiping Shen5,6,7, Marilyn Safran2, Doron Lancet2* and Simon Fishilevich2* Abstract Background: The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant genetic variations underlying a patient’s phenotypes and symptoms. The adoption of Whole Genome Sequencing requires novel capacities for interpretation of non-coding variants. Results: We present TGex, the Translational Genomics expert, a novel genome variation analysis and interpretation platform, with remarkable exome analysis capacities and a pioneering approach of non-coding variants interpretation. TGex’s main strength is combining state-of-the-art variant filtering with knowledge-driven analysis made possible by VarElect, our highly effective gene-phenotype interpretation tool. VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources. Access to such a comprehensive data compendium also facilitates TGex’s broad variant annotation, supporting evidence exploration, and decision making. TGex has an interactive, user-friendly, and easy adaptive interface, ACMG compliance, and an automated reporting system. Beyond comprehensive whole exome sequence capabilities, TGex encompasses innovative non-coding variants interpretation, towards the goal of maximal exploitation of whole genome sequence analyses in the clinical genetics practice. This is enabled by GeneCards’ recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters. -
Pololu Jrk USB Motor Controller User's Guide
Pololu Jrk USB Motor Controller User’s Guide © 2001–2019 Pololu Corporation Pololu Jrk USB Motor Controller User’s Guide https://www.pololu.com/docs/0J38/all Page 1 of 55 Pololu Jrk USB Motor Controller User’s Guide © 2001–2019 Pololu Corporation 1. Overview . 3 1.a. Module Pinout and Components . 6 1.b. Supported Operating Systems . 9 1.c. PID Calculation Overview . 10 2. Contacting Pololu . 12 3. Configuring the Motor Controller . 13 3.a. Installing Windows Drivers and the Configuration Utility . 13 3.b. Input Options . 18 3.c. Feedback Options . 20 3.d. PID Options . 22 3.e. Motor Options . 24 3.f. Error Response Options . 27 3.g. The Plots Window . 29 3.h. Upgrading Firmware . 30 4. Using the Serial Interface . 33 4.a. Serial Modes . 33 4.b. TTL Serial . 34 4.c. Command Protocols . 36 4.d. Cyclic Redundancy Check (CRC) Error Detection . 37 4.e. Motor Control Commands . 39 4.f. Error Reporting Commands . 41 4.g. Variable Reading Commands . 44 4.h. Daisy-Chaining . 46 4.i. Serial Example Code . 48 4.i.1. Cross-platform C . 48 4.i.2. Windows C . 50 5. Setting Up Your System . 51 6. Writing PC Software to Control the Jrk . 55 Page 2 of 55 Pololu Jrk USB Motor Controller User’s Guide © 2001–2019 Pololu Corporation 1. Overview The jrk family of versatile, general-purpose motor controllers supports a variety of interfaces, including USB. Analog voltage and tachometer (frequency) feedback options allow quick implementation of closed-loop servo systems, and a free configuration utility (for Windows) allows easy calibration and configuration through the USB port. -
PDF Cycling in the Dorsal Protocerebrum of the Drosophila Brain Is Not Necessary for Circadian Clock Function
PDF Cycling in the Dorsal Protocerebrum of the Drosophila Brain Is Not Necessary for Circadian Clock Function Elzbieta Kula,* Edwin S. Levitan,† Elzbieta Pyza,‡ and Michael Rosbash*,1 *Department of Biology-HHMI, Brandeis University, Waltham, MA, the †Department of Pharmacology, University of Pittsburgh, Pittsburgh, Pennsylvania, and the ‡Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, Krakow, Poland Abstract In Drosophila, the neuropeptide pigment-dispersing factor (PDF) is a likely circadian molecule, secreted by central pacemaker neurons (LNvs). PDF is expressed in both small and large LNvs (sLNvs and lLNvs), and there are striking circadian oscillations of PDF staining intensity in the small cell termini, which require a functional molecular clock. This cycling may be relevant to the proposed role of PDF as a synchronizer of the clock system or as an output signal connect- ing pacemaker cells to locomotor activity centers. In this study, the authors use a generic neuropeptide fusion protein (atrial natriuretic factor–green fluorescent protein [ANF-GFP]) and show that it can be expressed in the same neurons as PDF itself. Yet, ANF-GFP as well as PDF itself does not manifest any cyclical accumu- lation in sLNv termini in adult transgenic flies. Surprisingly, the absence of detectable PDF cycling is not accompanied by any detectable behavioral pheno- type, since these transgenic flies have normal morning and evening anticipation in a light-dark cycle (LD) and are fully rhythmic in constant darkness (DD). The molecular clock is also not compromised. The results suggest that robust PDF cycling in sLNv termini plays no more than a minor role in the Drosophila circa- dian system and is apparently not even necessary for clock output function. -
A Mutant Drosophila Homolog of Mammalian Clock Disrupts
Cell, Vol. 93, 791±804, May 29, 1998, Copyright 1998 by Cell Press AMutantDrosophila Homolog of Mammalian Clock Disrupts Circadian Rhythms and Transcription of period and timeless Ravi Allada,*²³§ Neal E. White,³ Aronson et al., 1994; Shearman et al., 1997; Sun et al., W. Venus So,²³ Jeffrey C. Hall,²³ 1997; Tei et al., 1997). ²³ and Michael Rosbash* k In Drosophila, there are two well-characterized clock *Howard Hughes Medical Institute genes: period (per) and timeless (tim). Protein levels, ² NSF, Center for Biological Timing RNA levels, and transcription rates of these two genes ³ Department of Biology undergo robust circadian oscillations (Zerr et al., 1990; Brandeis University Hardin et al., 1990, 1992; Hardin, 1994; Sehgal et al., Waltham, Massachusetts 02254 1995; So and Rosbash, 1997). In addition, mutations § Department of Pathology in the two proteins (PER and TIM) alter or abolish the Brigham and Women's Hospital periodicity and phase of these rhythms, demonstrating Boston, Massachusetts 02115 that both proteins regulate their own transcription (Har- din et al., 1990; Sehgal et al., 1995; Marrus et al., 1996). Although there is no evidence indicating that the effects Summary on transcription are direct, PER contains a PAS domain, which has been shown to mediate interactions between We report the identification, characterization, and transcription factors (Huang et al., 1993; Lindebro et cloning of a novel Drosophila circadian rhythm gene, al., 1995). Most of these PAS-containing transcription dClock. The mutant, initially called Jrk, manifests dom- factors also contain the well-characterized basic helix- inant effects: heterozygous flies have a period alter- loop-helix (bHLH) DNA-binding domains (Crews, 1998). -
Genes Controlling Essential Cell-Cycle Functions in Drosophila Melanogaster
Downloaded from genesdev.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Genes controlling essential cell-cycle functions in Drosophila melanogaster Maurizio Gatti I and Bruce S. Baker 2 ~Dipartimento de Genetica e Biologia Molecolare, Universit/l di Roma 'La Sapienza', 00185 Roma, Italy; 2Department of Biological Sciences, Stanford University, Stanford, California 94305 USA On the basis of the hypothesis that mutants in genes controlling essential cell cycle functions in Drosophila should survive up to the larval-pupal transition, 59 such 'late lethals' were screened for those mutants affecting cell division. Examination of mitosis in brain neuroblasts revealed that 30 of these lethals cause disruptions in mitotic chromosome behavior. These mutants identify genes whose wild-type functions are important for: (1) progression through different steps of interphase, (2) the maintenance of mitotic chromosome integrity, (3) chromosome condensation, (4) spindle formation and/or function, and (5) completion of cytokinesis or completion of chromosome segregation. The presence of mitotic defects in late lethal mutants is correlated tightly with the presence of defective imaginal discs. Thus, the phenotypes of late lethality and poorly developed imaginal discs are together almost diagnostic of mutations in essential cell-cycle functions. The terminal phenotypes exhibited by these Drosophila mitotic mutants are remarkably similar to those observed in mammalian cell-cycle mutants, suggesting that these diverse organisms use a common genetic logic to regulate and integrate the events of the cell cycle. [Key Words: Cell-cycle mutants; Drosophila; mitosis] Received November 30, 1988; revised version accepted February 7, 1989. The exquisitely precise cyclic changes that eukaryotic review, see Simchen 1978; Ling 1981; Oakley 1981; chromosomes and cells undergo during mitotic and Wissmger and Wang 1983; Marcus et al. -
The Human Genome Project
TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 Contents FOREWORD . 2 THE GENOME PROJECT—WHY THE DOE? . 4 A bold but logical step INTRODUCING THE HUMAN GENOME . 6 The recipe for life Some definitions . 6 A plan of action . 8 EXPLORING THE GENOMIC LANDSCAPE . 10 Mapping the terrain Two giant steps: Chromosomes 16 and 19 . 12 Getting down to details: Sequencing the genome . 16 Shotguns and transposons . 20 How good is good enough? . 26 Sidebar: Tools of the Trade . 17 Sidebar: The Mighty Mouse . 24 BEYOND BIOLOGY . 27 Instrumentation and informatics Smaller is better—And other developments . 27 Dealing with the data . 30 ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS . 32 An essential dimension of genome research Foreword T THE END OF THE ROAD in Little has been rapid, and it is now generally agreed Cottonwood Canyon, near Salt that this international project will produce Lake City, Alta is a place of the complete sequence of the human genome near-mythic renown among by the year 2005. A skiers. In time it may well And what is more important, the value assume similar status among molecular of the project also appears beyond doubt. geneticists. In December 1984, a conference Genome research is revolutionizing biology there, co-sponsored by the U.S. Department and biotechnology, and providing a vital of Energy, pondered a single question: Does thrust to the increasingly broad scope of the modern DNA research offer a way of detect- biological sciences. -
Chromosome.Pdf
Chromosomes What Exactly is a chromosome? Chromosomes are the rod-shaped, filamentous bodies present in the nucleus, which become visible during cell division. They are the carriers of the gene or unit of heredity. Chromosome are not visible in active nucleus due to their high water content, but are clearly seen during cell division. Chromosomes were first described by Strausberger in 1875. The term “Chromosome”, however was first used by Waldeyer in 1888. They were given the name chromosome (Chromo = colour; Soma = body) due to their marked affinity for basic dyes. Their number can be counted easily only during mitotic metaphase. Chromosomes are composed of thin chromatin threads called Chromatin fibers. These fibers undergo folding, coiling and supercoiling during prophase so that the chromosomes become progressively thicker and smaller. Therefore, chromosomes become readily observable under light microscope. At the end of cell division, on the other hand, the fibers uncoil and extend as fine chromatin threads, which are not visible at light microscope Number of chromosomes Normally, all the individuals of a species have the same number of chromosomes. Closely related species usually have similar chromosome numbers. Presence of a whole sets of chromosomes is called euploidy. It includes haploids, diploids, triploids, tetraploids etc. Gametes normally contain only one set of chromosome – this number is called Haploid Somatic cells usually contain two sets of chromosome - 2n : Diploid 3n – triploid 4n – tetraploid The condition in which the chromosomes sets are present in a multiples of “n” is Polyploidy When a change in the chromosome number does not involve entire sets of chromosomes, but only a few of the chromosomes - is Aneuploidy. -
Important for Jet-Lagged Circadian Loops Mary Harrington
Commentaries Location, location, location: important for jet-lagged circadian loops Mary Harrington Department of Psychology, Smith College, Northampton, Massachusetts, USA. It is now believed that frequent jet lag or shifts of daily rhythms caused by feedback signal inhibiting the activational rotating shift work can lead to deleterious health outcomes. Indeed, many drive of CLK and ARNTL that led to their serious health problems, including breast cancer, stroke, and cardiovascu- own production. After some time, period/ lar disease, have been linked to an occupational history of shift work. This cryptochrome inhibition is released, and has heightened interest in better understanding the biological responses to CLK and ARNTL are free to begin the cycle jet lag and shift work, with the hope that this will pave the way to developing again. This is a simplified example of the compounds that can help people avoid their negative health consequences. molecular mechanism underlying circadian In this context, a report in this issue of the JCI takes us to a new level of rhythms; there are several other genes play- understanding of the molecular control of the resetting of the multitude of ing feedback roles as well. For example, the internal biological clocks disrupted in a mouse model of jet lag. genes encoding nuclear receptor subfamily 1, group D, member 1 (NR1D1; also known Jet lag can seem like a minor discomfort, kept aligned with the cycles of the planet in as REV-ERBa) and RAR-related orphan but studies are now suggesting that fre- part by the regulatory influence of a small receptor a (RORa) mediate a feedback loop quent jet lag or shifts of daily rhythms as group of neurons in a region of the hypo- to provide rhythmic inhibitory and activat- a result of rotating shift work can lead to thalamus known as the suprachiasmatic ing drive, respectively, to Arntl. -
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.20 Document Published by the wwPDB This format complies with the PDB Exchange Dictionary (PDBx) http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Index/index.html. ©2008 wwPDB PDB File Format v. 3.2 Page i Table of Contents 1. Introduction................................................................................................................................... 1 Basic Notions of the Format Description ............................................................................................3 Record Format....................................................................................................................................5 Types of Records................................................................................................................................6 PDB Format Change Policy................................................................................................................9 Order of Records ..............................................................................................................................10 Sections of an Entry..........................................................................................................................12 Field Formats and Data Types .........................................................................................................14 2. Title Section...............................................................................................................................