Bimm 120 – Week 5

Total Page：16

File Type：pdf, Size：1020Kb

BIMM 120 – WEEK 5 11/02/20 Sections A03 and A04 IA: Jaxon Wagner ([email protected]) QUIZ 2 CLASS STATISTICS LECTURE 8 REVIEW! J Ø Lecture 8 part II o Horizontal Gene Transfer o Transformation o Transduction o Conjugation Ø Homework o Have Homework Grade by Tomorrow Ø Election Tomorrow! o https://www.sos.ca.gov/elections/polling-place GENE EVOLUTION HOMOLOGOUS RECOMBINATION BY RECA Splices Patches Does not cause complete Causes complete integration of new integration of new DNA! DNA! (Single or Double crossover) HORIZONTAL GENE TRANSFER (HGT) Vertical transfer of genetic material from parent to offspring Horizontal transfer of genetic material Chinmay Kalluraya Significance of HGT in Nature Dr. Lynn Margulis Endosymbiotic Theory Reference: Andrew Z. Colvin - Barth F. Smets, Ph.D. HORIZONTAL GENE TRANSFER • Movement of genetic material other than by parents to offspring. • HGT established method for bacterial evolution. • Mechanisms : transformation transduction conjugation Reference: https://courses.lumenlearning.com/microbiology/ TRANSFORMATION – PLASMIDS • Competent cells can take up external DNA • DNA can be either be integrated into the chromosome via RecA recombinase, or can stay and replicate independently as a plasmid • Plasmids usually do not encode for their own integration • Most plasmids do not get integrated or recombined at all (they stay as plasmids) • If they are integrated, this is usually done by RecA, which is on the chromosome TRANSDUCTION – LYTIC AND LYSOGENIC PHAGES Infection & Injection Some signals (like UV stress) cause Phage DNA to excise from chromosome Lytic Cycle Lysogenic Cycle (All phages) (Only lysogenic phages) Circulization of phage DNA Phage DNA replicates with cell Cell lyses, releasing virions (getting a free ride!) Integration of phage DNA Host chromosome is degraded and phage into chromosome (prophage) DNA is packaged into new virions GENERALIZED TRANSDUCTION USING THE LYTIC CYCLE AND HOPING YOU GET LUCKY (RANDOM) Infection & Injection Circulization of phage DNA Host chromosome degraded, DNA is packaged randomly, phage DNA replicated, some only get host DNA (white) phage parts assembled Cell lyses, releasing virions Infection & Injection Bacterial DNA from another cell is recombined SPECIALIZED TRANSDUCTION LYSOGENIC PHAGES SPECIFICALLY GRAB DNA NEAR THE PROPHAGE Integration of phage DNA Circulization of phage DNA Phage DNA is packaged into new virions Infection & Injection into chromosome (prophage, blue) – some phage DNA has (into new host) near gene of interest (fuschia) Gene Fuschia (%that have Gene Fuschia ~ linkage strength) Linkage: How close your prophage is to your gene of interest Closer (fewer base pairs between) = tighter linkage = higher % of new phage particles that have the gene of interest (can be up to nearly 100%!) CONJUGATION – SEX PILUS AND F- PLASMIDS • Transfer of a conjugation plasmid (F-plasmid) via sex pilus • F-plasmids contain a conjugation sequence and tra genes for pili formation • F-plasmids often encode virulence factors or antibiotic resistances • Plasmids transferred by conjugation can either be replicated as a plasmid or integrated into the new host chromosome via RecA • Don’t sweat the details J.

Copy Link

Recommended publications

Bacteria Definitions.Pdf
Antibiotic -- a type of antimicrobial substance active against bacteria Archae-bacteria -- microorganisms that are similar to bacteria in size and simplicity of structure but radically different in molecular organization Bacilli -- a taxonomic class of bacteria that includes two orders, Bacillales and Lactobacillales Bacillus anthracis -- the cause of anthrax Bacteria – ubiquitous one-celled organisms involved in fermentation, putrefaction, infectious diseases, and nitrogen fixation Bacteriophage -- a virus that infects and replicates within bacteria and archaea Binary fission -- the process that bacteria use to carry out cell division Capsid – structure that encloses a virus’ nucleic acid Chemo-heterotroph -- an organism that derives its energy from chemicals, and needs to consume other organisms in order to live Class -- A taxonomic group comprised of organisms that share a common attribute Cocci – spherical bacteria Conjugation – temporary union of two bacteria Coronavirus -- when viewed under an electron microscopic each virion in this type of virus is surrounded by a halo Domain -- the highest taxonomic rank of organisms Endospore – spore formed within a cell of a rod-shaped organism Eubacteria -- single-celled prokaryotic microorganisms that have a range of characteristics and are found in various conditions throughout all parts of the world. All types of bacteria fall under this title, except for archaebacteria Eykaryote -- organisms whose cells have a nucleus enclosed within a nuclear envelope Family -- A taxonomic rank in the
[Show full text]
Phylogenomic Networks Reveal Limited Phylogenetic Range of Lateral Gene Transfer by Transduction
The ISME Journal (2017) 11, 543–554 OPEN © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction Ovidiu Popa1, Giddy Landan and Tal Dagan Institute of General Microbiology, Christian-Albrechts University of Kiel, Kiel, Germany Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage- mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species.
[Show full text]
Management of Animal Botulism Outbreaks: from Clinical Suspicion to Practical Countermeasures to Prevent Or Minimize Outbreaks
Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science Volume 11, Supplement 1, 2013 ª Mary Ann Liebert, Inc. DOI: 10.1089/bsp.2012.0089 Management of Animal Botulism Outbreaks: From Clinical Suspicion to Practical Countermeasures to Prevent or Minimize Outbreaks Fabrizio Anniballi, Alfonsina Fiore, Charlotta Lo¨fstro¨m, Hanna Skarin, Bruna Auricchio, Ce´dric Woudstra, Luca Bano, Bo Segerman, Miriam Koene, Viveca Ba˚verud, Trine Hansen, Patrick Fach, Annica Tevell A˚berg, Mikael Hedeland, Eva Olsson Engvall, and Dario De Medici Botulism is a severe neuroparalytic disease that affects humans, all warm-blooded animals, and some fishes. The disease is caused by exposure to toxins produced by Clostridium botulinum and other botulinum toxin–producing clostridia. Botulism in animals represents a severe environmental and economic concern because of its high mortality rate. Moreover, meat or other products from affected animals entering the food chain may result in a publichealthproblem.Tothisend,earlydiagnosisiscrucialto define and apply appropriate veterinary public health measures. Clinical diagnosis is based on clinical findings eliminating other causes of neuromuscular disorders and on the absence of internal lesions observed during postmortem examination. Since clinical signs alone are often insufficient to make a definitive diagnosis, laboratory confirmation is required. Botulinum antitoxin administration and supportive therapies are used to treat sick animals. Once the diagnosis has been made, euthanasia is frequently advisable. Vaccine administration is subject to health authorities’ permission, and it is restricted to a small number of animal species. Several measures can be adopted to prevent or minimize outbreaks. In this article we outline all phases of management of animal botulism outbreaks occurring in wet wild birds, poultry, cattle, horses, and fur farm animals.
[Show full text]
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut Hiroki Nishiyama, Hisashi Endo, Romain Blanc-Mathieu, Hiroyuki Ogata
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut Hiroki Nishiyama, Hisashi Endo, Romain Blanc-Mathieu, Hiroyuki Ogata To cite this version: Hiroki Nishiyama, Hisashi Endo, Romain Blanc-Mathieu, Hiroyuki Ogata. Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Microorganisms, MDPI, 2020, 8 (11), pp.1663. 10.3390/microorganisms8111663. hal-03078511 HAL Id: hal-03078511 https://hal.archives-ouvertes.fr/hal-03078511 Submitted on 16 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License microorganisms Article Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut Hiroki Nishiyama 1 , Hisashi Endo 1 , Romain Blanc-Mathieu 2 and Hiroyuki Ogata 1,* 1 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan; [email protected] (H.N.); [email protected] (H.E.) 2 Laboratoire de Physiologie Cellulaire & Végétale, CEA, CNRS, INRA, IRIG, Université Grenoble Alpes, 38000 Grenoble, France; [email protected] * Correspondence: [email protected]; Tel.: +81-774-38-3270 Received: 30 September 2020; Accepted: 23 October 2020; Published: 27 October 2020 Abstract: The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD).
[Show full text]
The Lysogenic Cycle the Lytic Cycle
CAMPBELL TENTH BIOLOGY EDITION Reece • Urry • Cain • Wasserman • Minorsky • Jackson 19 Viruses Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick © 2014 Pearson Education, Inc. A Borrowed Life • A virus is an infectious particle consisting of genes packaged in a protein coat • Viruses are much simpler in structure than even prokaryotic cells • Viruses cannot reproduce or carry out metabolism outside of a host cell Figure 19.1 Figure 19.1a Concept 19.1: A virus consists of a nucleic acid surrounded by a protein coat • Viruses were detected indirectly long before they were actually seen The Discovery of Viruses: Scientific Inquiry • Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration • In the late 1800s, some researchers hypothesized that a particle smaller than bacteria caused the disease • In 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV) Experiment Figure 19.2 1 Extracted sap 2 Passed sap 3 Rubbed filtered from tobacco through a sap on healthy plant with porcelain filter tobacco plants tobacco mosaic known to trap disease bacteria 4 Healthy plants became infected Figure 19.2a Figure 19.2b Figure 19.2c Structure of Viruses • Viruses are not cells • A virus is a very small infectious particle consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope Viral Genomes • Viral genomes may consist of either • Double- or single-stranded DNA, or • Double- or single-stranded
[Show full text]
The Diversification of Microbial Gene Repertoires by Phage-Mediated Horizontal Gene Transfer Marie Touchon, Jorge Moura De Sousa, Eduardo Rocha
Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer Marie Touchon, Jorge Moura de Sousa, Eduardo Rocha To cite this version: Marie Touchon, Jorge Moura de Sousa, Eduardo Rocha. Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Current Opinion in Microbi- ology, Elsevier, 2017, 38, pp.66-73. 10.1016/j.mib.2017.04.010. pasteur-03111100 HAL Id: pasteur-03111100 https://hal-pasteur.archives-ouvertes.fr/pasteur-03111100 Submitted on 15 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer Marie Touchon a,b, Jorge A Moura de Sousa a,b, Eduardo P.C. Rocha a,b,* aMicrobial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France bCNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France *Author for correspondence: Telephone +33 (0) 1 40 61 33 53. Email: [email protected] Short title: Phage-mediated horizontal gene transfer Keywords: Bacteriophages; horizontal gene transfer; bacterial evolution; mobile genetic elements; transduction.
[Show full text]
Viruses and Bacteria
Name___________________________________________________ 21 CRITICAL THINKING REVIEW Viruses and Bacteria “Work-Alikes” In the space provided, write the letter of the term or phrase that best describes how each numbered item functions. 1. virus envelope a. security guards get sick and die 2. bacteriophage b. door key 3. HIV infection c. a rumor being spread among people 4. influenza d. a hypodermic needle Cause and Effect In the space provided, write the letter of the term or phrase that best matches each cause or effect given below. Cause Effect 5. viruses do not grow, do a. lysogenic cycle not have homeostasis, and b. specificity of viruses do not metabolize c. resistant bacteria 6. host cell not destroyed survive and reproduce 7. escape of fragments of d. they are not alive host cell genes 8. resistance to antibiotics T rade-offs In the space provided, write the letter of the bad news item that best matches each numbered good news item below. “Good News” “Bad News” 9. Those infected with HIV do not develop a. They are not truly AIDS for years. multicellular. b. They feel healthy while 10. Some bacteria adhere to each other spreading the virus to to form strands. others. Copyright © by Holt, Rinehart and Winston. All rights reserved. 11. Bacteria perform several different kinds c. A species of of anaerobic and aerobic respiration. Staphylococcus causes food poisoning. 12. Streptomyces bacteria produce d. Eukaryotes are mostly an antibiotic. limited to aerobic metabolism. Linkages In the spaces provided, write the letters of the two terms or phrases that are linked together by the term or phrase in the middle.
[Show full text]
A Theoretical Model of Temperate Phages As Mediators of Gut Microbiome Dysbiosis [Version 1; Peer Review: 2 Approved] Derek M
F1000Research 2019, 8(F1000 Faculty Rev):997 Last updated: 17 JUL 2019 REVIEW A theoretical model of temperate phages as mediators of gut microbiome dysbiosis [version 1; peer review: 2 approved] Derek M. Lin 1, Henry C. Lin1,2 1Medicine Service, New Mexico VA Health Care System, Albuquerque, New Mexico, USA 2Department of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, New Mexico, USA First published: 01 Jul 2019, 8(F1000 Faculty Rev):997 ( Open Peer Review v1 https://doi.org/10.12688/f1000research.18480.1) Latest published: 01 Jul 2019, 8(F1000 Faculty Rev):997 ( https://doi.org/10.12688/f1000research.18480.1) Reviewer Status Abstract Invited Reviewers Bacteriophages are the most prominent members of the gut microbiome, 1 2 outnumbering their bacterial hosts by a factor of 10. Phages are bacteria-specific viruses that are gaining attention as highly influential version 1 regulators of the gut bacterial community. Dysregulation of the gut bacterial published community contributes to dysbiosis, a microbiome disorder characterized 01 Jul 2019 by compositional and functional changes that contribute to disease. A role for phages in gut microbiome dysbiosis is emerging with evidence that the gut phage community is altered in dysbiosis-associated disorders such as F1000 Faculty Reviews are written by members of colorectal cancer and inflammatory bowel disease. Several recent studies the prestigious F1000 Faculty. They are have linked successful fecal microbiota transplantation to uptake of the commissioned and are peer reviewed before donor’s gut phage community, offering some insight into why some publication to ensure that the final, published version recipients respond to treatment whereas others do not.
[Show full text]
A New Perspective on Lysogeny: Prophages As Active Regulatory
PERSPECTIVES that do enter the lysogenic cycle, sponta- OPINION neous induction of lytic production can still occur in the absence of an obvious A new perspective on lysogeny: stressor13,14. Phage genome excision and integration prophages as active regulatory are crucial steps in the onset of the lytic and lysogenic cycles, respectively. These events are mediated by phage-encoded DNA switches of bacteria recombinases, such as integrases and excisio- nases, and take place at a specific attachment Ron Feiner, Tal Argov, Lev Rabinovich, Nadejda Sigal, Ilya Borovok and site in the bacterial genome (attB), which is Anat A. Herskovits identical to an attachment site (attP) in the phage genome15. Although these sequences Abstract | Unlike lytic phages, temperate phages that enter lysogeny maintain a determine the phage specificity to the bacte- long-term association with their bacterial host. In this context, mutually beneficial rial genome, secondary sites can be used if interactions can evolve that support efficient reproduction of both phages and the original attB site is lost, as was shown 16 bacteria. Temperate phages are integrated into the bacterial chromosome as with Escherichia coli phage λ . Moreover, some phages integrate randomly within their large DNA insertions that can disrupt gene expression, and they may pose a host genome, such as phage Mu, and thus fitness burden on the cell. However, they have also been shown to benefit their increase variation and possible mutations bacterial hosts by providing new functions in a bacterium–phage
[Show full text]
BIO281 Microbiology 2019
Cape Cod Community College Departmental Syllabus Prepared by the Department of Natural Sciences & Applied Technology Date of Department Approval: January 17, 2019 Date of Approval by Curriculum and Programs: March 27, 2019 Effective: Fall 2019 1. Course Number: BIO281 and BIO 281L Course Title: Microbiology and Microbiology Laboratory 2. Description: An introduction to microorganisms and their activities, for health-related majors. The topics cover cell structure, classification, metabolism, methods of control, antimicrobial drugs, genetics, microbial and host defenses, immunology and applications, representative infectious diseases, and food and industrial microbiology. Independent study is encouraged. The laboratory component introduces basic procedures of handling, growing, and identifying microorganisms. (3 class hours/ 2 laboratory hours per week) 3. Student Learning Outcomes (instructional objectives; intellectual skills): Upon successful completion of the course, students are able to do the following: • Explain the structure and function of cellular components in eukaryotes and prokaryotes. • Describe the properties of representative Archaea, Bacteria, Fungi, Algae, Protozoa, with emphasis on animal and human pathogens. • Explain the structure and life cycle of Viruses, Viroids, and Prions, with respect to transmission and pathogenesis. • Describe the major processes of microbial metabolism, energy generation, and cellular growth. • Define the basic processes of sterilization, disinfection, and antisepsis, with examples from physical and chemical methods of control. • Describe the properties and regulation of prokaryotic and eukaryotic genes, and mutations as the basis of cancer development. • Describe mechanisms of microbial pathogenicity, and components of the innate and induced immune system in humans. • Relate the impact of microbiology on public health and control of disease in the human population.
[Show full text]
Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma
microorganisms Article Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma Tianli Ma 1,2,†, Jinlong Ru 1,2,† , Jinling Xue 1,2, Sarah Schulz 1,2 , Mohammadali Khan Mirzaei 1,2 , Klaus-Peter Janssen 3, Michael Quante 4,5,* and Li Deng 1,2,* 1 Helmholtz Centre Munich—German Research Center for Environmental Health, Institute of Virology, 85764 Neuherberg, Germany; [email protected] (T.M.); [email protected] (J.R.); [email protected] (J.X.); [email protected] (S.S.); [email protected] (M.K.M.) 2 Institute of Virology, Technical University of Munich, 81675 Munich, Germany 3 Department of Surgery, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich, Germany; [email protected] 4 II. Medizinische Klinik, Klinikum Rechts der Isar, Technische Universität München, 81675 Munich, Germany 5 Innere Medizin II, Universitätsklinik Freiburg, Universität Freiburg, 79106 Freiburg, Germany * Correspondence: [email protected] (M.Q.); [email protected] (L.D.) † These authors contributed equally to this work. Abstract: The relationship between viruses (dominated by bacteriophages or phages) and lower gastrointestinal (GI) tract diseases has been investigated, whereas the relationship between gut bacteriophages and upper GI tract diseases, such as esophageal diseases, which mainly include Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC), remains poorly described. This study aimed to reveal the gut bacteriophage community and their behavior in the progression of esophageal diseases. In total, we analyzed the gut phage community of sixteen samples from patients Citation: Ma, T.; Ru, J.; Xue, J.; with esophageal diseases (six BE patients and four EAC patients) as well as six healthy controls.
[Show full text]
Lysogeny and Prophage Induction in Coastal and Offshore Bacterial Communities
AQUATIC MICROBIAL ECOLOGY Vol. 18: 217-225. 1999 Published August 20 Aquat Microb Ecol - p-- p --p- -- - - Lysogeny and prophage induction in coastal and offshore bacterial communities Markus G. Weinbauerl, Curtis A. Suttle2.* 'National Research Centre for Biotechnology, Division of Microbiology, Mascheroder Weg 1. D-38124 Braunschweig, Germany 'Departments of Earth and Ocean Sciences (Oceanography). Botany and Microbiology & Immunology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia V6T 124, Canada ABSTRACT: The influence of solar radiation and hydrogen peroxide on induction of lysogens, and the resulting effect on bacteriophage production and bacterial mortality was investigated for coastal and oceanic manne bacterial conlmunities at 6 stations in the western Gulf of Mexico. The percentage of lysogenic cells induced by mitomycin C was also determined. Solar radiation and hydrogen peroxide were not as effective as mitomycin C at inducing phage production. The burst size of cells induced by mitomycin C was estimated by transmission electron microscopy, assuming that cells completely filled with viral particles were on the verge of bursting. The smallest estimates of burst size were associated with oligotrophic oceanic stations and ranged from 15 to 28 viruses produced per lyhc event, whde in more productive coastal waters the estimated burst sizes ranged from 33 to 64. The mitomycin C- induced phage production and burst size were used to estimate the number of lysogenic bacterial cells. On average, the percentage of inducible lysogens was higher at offshore (1.5 to 11.4 %) than at coastal (0.8 to 2.2 %) stations. However, with the exception of 1 station, less than 5 % of the bacteria could be induced to produce phage, suggesting that lysogens only occasionally comprised a significant compo- nent of these bacterial communities.
[Show full text]