Genes Controlling Essential Cell-Cycle Functions in Drosophila Melanogaster
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Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
Transposable Elements Drive Reorganisation of 3D Chromatin
bioRxiv preprint doi: https://doi.org/10.1101/523712; this version posted January 17, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis Kai Kruse1, Noelia Díaz1, §, Rocio Enriquez-Gasca1, §, Xavier Gaume2, 4, Maria-Elena Torres-Padilla2, 3 and Juan M. Vaquerizas1, * 1. Max Planck Institute for Molecular Biomedicine, Roentgenstrasse 20, 48149 Muenster, Germany. 2. Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Marchioninistraße 25, 81377 Munich, Germany. 3. Faculty of Biology, Ludwig Maximilians Universität, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany. 4. Present address: Cancer Research Center of Lyon, 28 Rue Laennec, Lyon 69008, France. §. These authors have contributed equally to this work. *. Correspondence to J.M.V. ([email protected], @vaquerizasjm) Keywords: Chromosome conformation capture; low-input Hi-C; early embryonic development; totipotency; transposable elements; MERVL; TAds; 2-cell embryo; 2-cell-like cells; zygotic genome activation; CAF-1; dux. Transposable elements are abundant genetic components of eukaryotic genomes with important regulatory features affecting transcription, splicing, and recombination, among others. Here we demonstrate that the Murine Endogenous Retroviral Element (MuERV-L/MERVL) family of transposable elements drives the 3D reorganisation of the genome in the early mouse embryo. By generating Hi-C data in 2-cell-like cells, we show that MERLV elements promote the formation of insulating domain boundaries through- out the genome in vivo and in vitro. -
Review Cell Division from a Genetic Perspective
REVIEW CELL DIVISION FROM A GENETIC PERSPECTIVE LELAND H. HARTWELL From the Department of Genetics, University of Washington, Seattle, Washington 98195 Recently, a number of laboratories have begun to incubation at the restrictive condition for that study mutant cells that are defective in specific mutation, whereas mutants with defects in one of stages of the eukaryotic cell cycle. The long-range the continuously required functions will arrest at goals of this work are to identify the genes that the restrictive temperature with cells at a variety code for division-related proteins, to define the of positions in the cell cycle. roles that these gene products play and to investi- Classes of mutants may be distinguished from gate the hierarchies of order that assure their one another and the roles of their products delim- coordinated activity. It is my intent in this brief ited by determining the stage-specific event at review to discuss the strategies employed in this which they arrest. It is convenient to have a genetic approach and to enumerate some of the designation for the first landmark of the cell cycle new conclusions that have come to light. A recent that is blocked in a particular mutant, and I shall review on the genetics of meiosis (2) complements call it the diagnostic landmark for that mutant. this review on mitosis. Mutants of Saccharomyces cerevisiae have been identified that have diagnostic landmarks at spin- MUTANTS dle pole body (SPB) duplication, SPB separation, Mutations that inactivate gene products essential initiation of DNA synthesis, DNA replication, for division would be lethal. -
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. -
L. Lacey Knowles
Curriculum Vitae L. Lacey Knowles Department of Ecology and Evolutionary Biology E-mail: [email protected] Museum of Zoology, University of Michigan Orcid ID: 0000-0002-6567-4853 Ann Arbor, MI 48109-1079 POSITIONS 2015-present, Robert B. Payne Collegiate Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan 2012-2015, Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan 2008-2012, Associate Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan 2003-2008, Assistant Professor, Department of Ecology and Evolutionary Biology, Curator of Insects, Museum of Zoology, University of Michigan ACADEMIC APPOINTMENTS: Science Communication Fellow, Museum of Natural History, University of Michigan Member, Center for statistical Genetics, University of Michigan NIH Training Program in Genome Sciences, University of Michigan EDUCATION 2001-2002 NIH Postdoctoral Fellowship (PERT: Postdoctoral Excellence in Research and Teaching) awarded through the Center for Insect Science at the University of Arizona 1999-2001 Postdoctoral Fellowship from the National Science Foundation Research Training Group in the Analysis of Biological Diversification at the University of Arizona 1999 Ph.D., Ecology and Evolution, State University of New York at Stony Brook Dissertation title: Genealogical portraits of Pleistocene speciation and diversity patterns in montane grasshoppers 1993 M.S., Zoology, University of South Florida. Thesis title: Effects of habitat structure on community assemblages of epifaunal macroinvertebrates in seagrass systems. 1989 B.S., cum laude with honors in Marine Biology, University of North Carolina, Wilmington RESEARCH INTERESTS Speciation and processes that promote divergence Phylogenomics and statistical phylogeography Evolutionary consequences of climate change HONORS AND AWARDS *Fulbright U.S. -
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. -
Cell Division and Cycle
Name: _______________________ Date:_____________ Period_________ Subject: ________ Cell Division and Cycle Read the phase to answer the questions 1 through 10. Living organisms are constantly making new cells. They make new cells in order to grow and also to replace old dead cells. The process by which new cells are made is called cell division. Cell division is occurring all the time. Around two trillion cell divisions occur in the average human body every day! Types of Cell Division There are three main types of cell division: binary fission, mitosis, and meiosis. Binary fission is used by simple organisms like bacteria. More complex organisms gain new cells by either mitosis or meiosis. Mitosis Mitosis is used when a cell needs to be replicated into exact copies of itself. Everything in the cell is duplicated. The two new cells have the same DNA, functions, and genetic code. The original cell is called the mother cell and the two new cells are called daughter cells. The full process, or cycle, of mitosis is described in more detail below. Examples of cells that are produced through mitosis include cells in the human body for the skin, blood, and muscles. Cell Cycle for Mitosis Cells go through different phases called the cell cycle. The "normal" state of a cell is called the "interphase". The genetic material is duplicated during the interphase stage of the cell. When a cell gets the signal that it is to duplicate, it will enter the first state of mitosis called the "prophase". Prophase - During this phase the chromatin condenses into chromosomes and the nuclear membrane and nucleolus break down. -
Mitosis Vs. Meiosis
Mitosis vs. Meiosis In order for organisms to continue growing and/or replace cells that are dead or beyond repair, cells must replicate, or make identical copies of themselves. In order to do this and maintain the proper number of chromosomes, the cells of eukaryotes must undergo mitosis to divide up their DNA. The dividing of the DNA ensures that both the “old” cell (parent cell) and the “new” cells (daughter cells) have the same genetic makeup and both will be diploid, or containing the same number of chromosomes as the parent cell. For reproduction of an organism to occur, the original parent cell will undergo Meiosis to create 4 new daughter cells with a slightly different genetic makeup in order to ensure genetic diversity when fertilization occurs. The four daughter cells will be haploid, or containing half the number of chromosomes as the parent cell. The difference between the two processes is that mitosis occurs in non-reproductive cells, or somatic cells, and meiosis occurs in the cells that participate in sexual reproduction, or germ cells. The Somatic Cell Cycle (Mitosis) The somatic cell cycle consists of 3 phases: interphase, m phase, and cytokinesis. 1. Interphase: Interphase is considered the non-dividing phase of the cell cycle. It is not a part of the actual process of mitosis, but it readies the cell for mitosis. It is made up of 3 sub-phases: • G1 Phase: In G1, the cell is growing. In most organisms, the majority of the cell’s life span is spent in G1. • S Phase: In each human somatic cell, there are 23 pairs of chromosomes; one chromosome comes from the mother and one comes from the father. -
Metabolic Inactivation of the Circadian Transmitter, Pigment Dispersing Factor (PDF), by Neprilysin-Like Peptidases in Drosophila R
4465 The Journal of Experimental Biology 210, 4465-4470 Published by The Company of Biologists 2007 doi:10.1242/jeb.012088 Metabolic inactivation of the circadian transmitter, pigment dispersing factor (PDF), by neprilysin-like peptidases in Drosophila R. Elwyn Isaac1,*, Erik C. Johnson2, Neil Audsley3 and Alan D. Shirras4 1Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK, 2Department of Biology, Wake Forest University, NC, USA, 3Central Science Laboratory, Sand Hutton, York, YO41 1LZ, UK and 4Department of Biological Sciences, University of Lancaster, LA1 4YQ, UK *Author for correspondence (e-mail: [email protected]) Accepted 4 October 2007 Summary Recent studies have firmly established pigment confirming that such cleavage results in PDF inactivation. dispersing factor (PDF), a C-terminally amidated The Ser7–Leu8 peptide bond was also the principal octodecapeptide, as a key neurotransmitter regulating cleavage site when PDF was incubated with membranes rhythmic circadian locomotory behaviours in adult prepared from heads of adult Drosophila. This Drosophila melanogaster. The mechanisms by which PDF endopeptidase activity was inhibited by the neprilysin –1 functions as a circadian peptide transmitter are not fully inhibitors phosphoramidon (IC50, 0.15·mol·l ) and –1 understood, however; in particular, nothing is known thiorphan (IC50, 1.2·mol·l ). We propose that cleavage by about the role of extracellular peptidases in terminating a member of the Drosophila neprilysin family of PDF signalling at synapses. In this study we show that PDF endopeptidases is the most likely mechanism for is susceptible to hydrolysis by neprilysin, an endopeptidase inactivating synaptic PDF and that neprilysin might have that is enriched in synaptic membranes of mammals and an important role in regulating PDF signals within insects. -
Hypothesis As an Alternative. the Distribution Of
Heredity (1976), 36 (3), 293-304 REASSOCIATIONPATTERNS AMONG SEGMENTAL INTERCHANGES IN MAIZE D.B. WALDEN and R. C. JANCEY Department of Plant Sciences,Universityof WesternOntario,London, Ontario N6A 3K7 Received2.iv.75 SUMMARY Data from Longley (1961) and Burnham (1969) on the cytological position of the break-points in chrornosomal rearrangements in maize were re-expressed in terms of segment lengths and analysed. After correction for the deviation of the distribution of break-points from an equidistribution, it was shown that highly significant excesses and deficits occurred among some but not all segment length classes. It was concluded that the pattern of reassociation shows: (i) that reassociation involves non-homologues whose interstitial segments are of similar length more frequently than expected; (ii) that the two interchange segments involved in a translocation are of similar length more frequently than expected. 1. INTRODUCTION AN extensive literature exists on the genetic effects and consequences of exposure to radiation and radiomimetic and radiochemical compounds. The origin of chromosomal aberrations had long been considered to be the consequence of" breakage and reunion" until Revell (1955) proposed an "exchange" hypothesis as an alternative. The distribution of the "breakage" or "exchange" events has been approximately determined in several species, with a" random "distribution being claimed by some workers and a "non-random" distribution favoured by several recent investigators (e.g. Caspersson et al., 1972). It is important for the present communication to note that most of the studies record observations made one or a few cell generations after exposure to the mutagen and that only limited information is available about the survival of the aberrations so induced. -
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. -
Effects of Gut-Associated Yeasts on Drosophila Melanogaster Performance
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 12-6-2016 12:00 AM Effects of gut-associated yeasts on Drosophila melanogaster performance Yanira Jiménez Padilla The University of Western Ontario Supervisor Brent Sinclair The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Yanira Jiménez Padilla 2016 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Biology Commons Recommended Citation Jiménez Padilla, Yanira, "Effects of gut-associated yeasts on Drosophila melanogaster performance" (2016). Electronic Thesis and Dissertation Repository. 4285. https://ir.lib.uwo.ca/etd/4285 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract I used Drosophila melanogaster as a model to study the role of the gut microbiota, specifically yeasts, in animal physiology. I used Saccharomyces cerevisiae, the yeast commonly included in Drosophila diet, and Lachancea kluyveri, isolated from some Drosophila in the wild, and generated axenic (germ-free) and gnotobiotic (yeast-fed) flies. I found that L. kluyveri persists in the crop, as ascospores and vegetative cells, longer than S. cerevisiae. Some L. kluyveri vegetative cells survive passage through the gut. Egg to adult development time is reduced by 14% in vials containing live L. kluyveri or S. cerevisiae, whereas heat-killed yeasts reduced development time by 3.5-4.5%.