Novel Metrics for Quantifying Bacterial Genome Composition Skews
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Ehrlichiosis in Dogs Animal Veterinary Associations Borne Diseases
21 Working ECAVA F F A E V C A A C V Group on E A F F A E V C Canine A FECAVA Federation of European Companion vector Ehrlichiosis in dogs Animal Veterinary Associations borne diseases WERSJA POPRAWIONA A Ehrlichia spp. !! Ehrlichiosis is a tick-borne disease caused by Ehrlichia spp, an obligate intracellular gram-negative bacterium of the Anaplasmataceae family. In Europe, Ehrlichia canis causes canine monocytic ehrlichiosis ! (CME) The tick Rhipicephalus sanguineus is its main vector in Europe. Dogs and wild canids act as reservoirs. The disease has a subclinical, acute asymptomatic phase and chronic phase. The prognosis for chronically sick dogs is poor, ! !! The incubation period is 1-4 weeks. German Shepherds and Siberian Huskies appear to be more susceptible to clinical ehrlichiosis with more severe clinical !! presentations than other breeds. When to suspect infection? Origin / travelling history Clinical signs o Dogs that live in, originate from or have travelled to countries where the parasite is endemic are at risk. Weight loss, anorexia, lethargy, fever o Dogs in countries not currently considered endemic Bleeding disorders: petechiae/ecchymoses of the skin, mucous o o should not be considered free of risk. membranes and conjunctivas, hyphaema, epistaxis Lymphadenomegaly o How can it be confirmed? o Splenomegaly o Ocular signs: conjunctivitis, uveitis, corneal oedema Blood smear: Visualisation of intracellular bacteria on blood o Neurological signs (less common): seizures, ataxia, paresis, smears stained with Giemsa or similar. Sensitivity is poor: hyperaesthesia, cranial nerve deficits E. canis morulae in monocytes are visualised in only 4% (meningitis/meninigoencephalitis) cases of acute infections. -
Ehrlichiosis and Anaplasmosis Are Tick-Borne Diseases Caused by Obligate Anaplasmosis: Intracellular Bacteria in the Genera Ehrlichia and Anaplasma
Ehrlichiosis and Importance Ehrlichiosis and anaplasmosis are tick-borne diseases caused by obligate Anaplasmosis: intracellular bacteria in the genera Ehrlichia and Anaplasma. These organisms are widespread in nature; the reservoir hosts include numerous wild animals, as well as Zoonotic Species some domesticated species. For many years, Ehrlichia and Anaplasma species have been known to cause illness in pets and livestock. The consequences of exposure vary Canine Monocytic Ehrlichiosis, from asymptomatic infections to severe, potentially fatal illness. Some organisms Canine Hemorrhagic Fever, have also been recognized as human pathogens since the 1980s and 1990s. Tropical Canine Pancytopenia, Etiology Tracker Dog Disease, Ehrlichiosis and anaplasmosis are caused by members of the genera Ehrlichia Canine Tick Typhus, and Anaplasma, respectively. Both genera contain small, pleomorphic, Gram negative, Nairobi Bleeding Disorder, obligate intracellular organisms, and belong to the family Anaplasmataceae, order Canine Granulocytic Ehrlichiosis, Rickettsiales. They are classified as α-proteobacteria. A number of Ehrlichia and Canine Granulocytic Anaplasmosis, Anaplasma species affect animals. A limited number of these organisms have also Equine Granulocytic Ehrlichiosis, been identified in people. Equine Granulocytic Anaplasmosis, Recent changes in taxonomy can make the nomenclature of the Anaplasmataceae Tick-borne Fever, and their diseases somewhat confusing. At one time, ehrlichiosis was a group of Pasture Fever, diseases caused by organisms that mostly replicated in membrane-bound cytoplasmic Human Monocytic Ehrlichiosis, vacuoles of leukocytes, and belonged to the genus Ehrlichia, tribe Ehrlichieae and Human Granulocytic Anaplasmosis, family Rickettsiaceae. The names of the diseases were often based on the host Human Granulocytic Ehrlichiosis, species, together with type of leukocyte most often infected. -
Ehrlichiosis in Brazil
Review Article Rev. Bras. Parasitol. Vet., Jaboticabal, v. 20, n. 1, p. 1-12, jan.-mar. 2011 ISSN 0103-846X (impresso) / ISSN 1984-2961 (eletrônico) Ehrlichiosis in Brazil Erliquiose no Brasil Rafael Felipe da Costa Vieira1; Alexander Welker Biondo2,3; Ana Marcia Sá Guimarães4; Andrea Pires dos Santos4; Rodrigo Pires dos Santos5; Leonardo Hermes Dutra1; Pedro Paulo Vissotto de Paiva Diniz6; Helio Autran de Morais7; Joanne Belle Messick4; Marcelo Bahia Labruna8; Odilon Vidotto1* 1Departamento de Medicina Veterinária Preventiva, Universidade Estadual de Londrina – UEL 2Departamento de Medicina Veterinária, Universidade Federal do Paraná – UFPR 3Department of Veterinary Pathobiology, University of Illinois 4Department of Veterinary Comparative Pathobiology, Purdue University, Lafayette 5Seção de Doenças Infecciosas, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul – UFRGS 6College of Veterinary Medicine, Western University of Health Sciences 7Department of Clinical Sciences, Oregon State University 8Departamento de Medicina Veterinária Preventiva e Saúde Animal, Universidade de São Paulo – USP Received June 21, 2010 Accepted November 3, 2010 Abstract Ehrlichiosis is a disease caused by rickettsial organisms belonging to the genus Ehrlichia. In Brazil, molecular and serological studies have evaluated the occurrence of Ehrlichia species in dogs, cats, wild animals and humans. Ehrlichia canis is the main species found in dogs in Brazil, although E. ewingii infection has been recently suspected in five dogs. Ehrlichia chaffeensis DNA has been detected and characterized in mash deer, whereas E. muris and E. ruminantium have not yet been identified in Brazil. Canine monocytic ehrlichiosis caused by E. canis appears to be highly endemic in several regions of Brazil, however prevalence data are not available for several regions. -
Tick-Borne Disease Working Group 2020 Report to Congress
2nd Report Supported by the U.S. Department of Health and Human Services • Office of the Assistant Secretary for Health Tick-Borne Disease Working Group 2020 Report to Congress Information and opinions in this report do not necessarily reflect the opinions of each member of the Working Group, the U.S. Department of Health and Human Services, or any other component of the Federal government. Table of Contents Executive Summary . .1 Chapter 4: Clinical Manifestations, Appendices . 114 Diagnosis, and Diagnostics . 28 Chapter 1: Background . 4 Appendix A. Tick-Borne Disease Congressional Action ................. 8 Chapter 5: Causes, Pathogenesis, Working Group .....................114 and Pathophysiology . 44 The Tick-Borne Disease Working Group . 8 Appendix B. Tick-Borne Disease Working Chapter 6: Treatment . 51 Group Subcommittees ...............117 Second Report: Focus and Structure . 8 Chapter 7: Clinician and Public Appendix C. Acronyms and Abbreviations 126 Chapter 2: Methods of the Education, Patient Access Working Group . .10 to Care . 59 Appendix D. 21st Century Cures Act ...128 Topic Development Briefs ............ 10 Chapter 8: Epidemiology and Appendix E. Working Group Charter. .131 Surveillance . 84 Subcommittees ..................... 10 Chapter 9: Federal Inventory . 93 Appendix F. Federal Inventory Survey . 136 Federal Inventory ....................11 Chapter 10: Public Input . 98 Appendix G. References .............149 Minority Responses ................. 13 Chapter 11: Looking Forward . .103 Chapter 3: Tick Biology, Conclusion . 112 Ecology, and Control . .14 Contributions U.S. Department of Health and Human Services James J. Berger, MS, MT(ASCP), SBB B. Kaye Hayes, MPA Working Group Members David Hughes Walker, MD (Co-Chair) Adalbeto Pérez de León, DVM, MS, PhD Leigh Ann Soltysiak, MS (Co-Chair) Kevin R. -
Canine Ehrliciosis in Australia
Canine ehrlichiosis in Australia Fact sheet Introductory statement Australia was previously believed to be free of Ehrlichia canis. During 2020, the organism was detected in Australian dogs for the first time. Infection with E. canis (ehrlichiosis) is a notifiable disease in Australia. If you suspect ehrlichiosis in Australia, call the Emergency Animal Disease hotline on 1800 675 888. The disease is also known as canine monocytic ehrlichiosis and can cause serious illness and death in dogs. Aetiology The organism Ehrlichia canis, is an obligate gram negative intracellular rickettsial bacterium belonging to the family Anaplasmataceae. It is transmitted through tick bites, in particular the bite of the brown dog tick (Rhipicephalus sanguineus). Natural hosts Dogs (Canis lupus familiaris) are considered the natural hosts of the organism. Other canids such as foxes and wolves are known to become infected with the bacterium (Santoro et al. 2016). It is assumed that dingos, a uniquely Australian ancient dog breed which some people consider a different species to domestic and wild dogs, may also become infected, and may be susceptible to disease from E. canis. On rare occasions, humans or cats can become infected from a tick bite (Stich et al. 2008; Day 2011). World distribution E. canis occurs worldwide, particularly in tropical and subtropical regions. It was, until recently, considered to be absent from Australia. Occurrences in Australia In 2020, E. canis was detected in Western Australia and the Northern Territory. It was first detected in a small number of domesticated dogs in the Kimberly region of WA in May 2020. This was the first detection of ehrlichiosis in dogs in Australia outside of dogs that had been imported from overseas. -
Canine Ehrlichiosis: Update
Canine Ehrlichiosis: Update Barbara Qurollo, MS, DVM ([email protected]) Vector-Borne Disease Diagnostic Laboratory Dep. Clinical Sciences-College of Veterinary Medicine North Carolina State University Overview Ehrlichia species are tick-transmitted, obligate intracellular bacteria that can cause granulocytic or monocytic ehrlichiosis. Ehlrichia species that have been detected in the blood and tissues of clinically ill dogs in North America include Ehrlichia canis, E. chaffeenis, E. ewingii, E. muris and Panola Mountain Ehrlichia species (Table 1). Clinicopathologic abnormalities reported in dogs with ehrlichiosis vary depending on the species of Ehrlichia, strain variances and the immune or health status of the dog. The course of disease may present as subclinical, acute, chronic or even result in death (Table 1). E. canis and E. ewingii are the most prevalent and frequently described Ehrlichia infections in dogs. E. canis: Transmitted by Rhipicephalus sanguineus, E. canis is found world-wide. Within North America, the highest seroprevalence rates have been reported in the Southern U. S.2, 12 E. canis typically infects canine mononuclear cells. Canine monocytic ehrlichiosis (CME) is characterized by 3 stages: acute, subclinical and chronic. Following an incubation period of 1-3 weeks, infected dogs may remain subclinical or present with nonspecific signs including fever, lethargy, lymphadenopathy, splenomegaly, lameness, edema, bleeding disorders and mucopurulent ocular discharge. Less commonly reported nonspecific signs include vomiting, diarrhea, coughing and dyspnea. Bleeding disorders can include epistaxis, petechiae, ecchymoses, gingival bleeding and melena. Ocular abnormalities identified in E. canis infected dogs have included anterior uveitis, corneal opacity, retinal hemorrhage, hyphema, chorioretinal lesions and tortuous retinal vessels.8 Following an acute phase (2-4 weeks), clinical signs may resolve without treatment and the dog could remain subclinically infected indefinitely or naturally clear the pathogen. -
Distinct Distributions of Genomic Features of the 5' and 3' Partners Of
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 40), pp: 66769-66783 Research Paper Distinct distributions of genomic features of the 5’ and 3’ partners of coding somatic cancer gene fusions: arising mechanisms and functional implications Yongzhong Zhao1,2, Won-Min Song1,2, Fan Zhang3, Ming-Ming Zhou4, Weijia Zhang3, Martin J. Walsh1,4,5 and Bin Zhang1,2 1Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY 10029, USA 2Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, NY 10029, USA 3Department of Medicine, Icahn School of Medicine at Mount Sinai, NY 10029, USA 4Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, NY 10029, USA 5Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA Correspondence to: Bin Zhang, email: [email protected] Keywords: cancer somatic gene fusions, gene age, GC skew, DNA-RNA R-loops, somatic amplification Received: April 02, 2016 Accepted: June 06, 2016 Published: July 20, 2016 Copyright: Zhao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT The genomic features and arising mechanisms of coding cancer somatic gene fusions (CSGFs) largely remain elusive. In this study, we show the gene origin stratification pattern of CSGF partners that fusion partners in human cancers are significantly enriched for genes with the gene age of Euteleostomes and with the gene family age of Bilateria. -
New Views on Strand Asymmetry in Insect Mitochondrial Genomes Shu-Jun Wei Zhejiang University, China
University of Kentucky UKnowledge Entomology Faculty Publications Entomology 9-15-2010 New views on strand asymmetry in insect mitochondrial genomes Shu-Jun Wei Zhejiang University, China Min Shi Zhejiang University, China Xue-Xin Chen Zhejiang University, China Michael J. Sharkey University of Kentucky, [email protected] Cornelis van Achterberg Nationaal Natuurhistorisch Museum, Netherlands See next page for additional authors Right click to open a feedback form in a new tab to let us know how this document benefits oy u. Follow this and additional works at: https://uknowledge.uky.edu/entomology_facpub Part of the Entomology Commons Repository Citation Wei, Shu-Jun; Shi, Min; Chen, Xue-Xin; Sharkey, Michael J.; van Achterberg, Cornelis; Ye, Gong-Yin; and He, Jun-Hua, "New views on strand asymmetry in insect mitochondrial genomes" (2010). Entomology Faculty Publications. 27. https://uknowledge.uky.edu/entomology_facpub/27 This Article is brought to you for free and open access by the Entomology at UKnowledge. It has been accepted for inclusion in Entomology Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. Authors Shu-Jun Wei, Min Shi, Xue-Xin Chen, Michael J. Sharkey, Cornelis van Achterberg, Gong-Yin Ye, and Jun- Hua He New views on strand asymmetry in insect mitochondrial genomes Notes/Citation Information Published in PLoS ONE, v. 5, no. 9, e12708. © 2010 Wei et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. -
Evolutionary Advantage of a Broken Symmetry in Autocatalytic Polymers Tentatively Explains Fundamental Properties of DNA
Evolutionary advantage of a broken symmetry in autocatalytic polymers tentatively explains fundamental properties of DNA Hemachander Subramanian1∗, Robert A. Gatenby1;2 1 Integrated Mathematical Oncology Department, 2Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. ∗To whom correspondence should be addressed; E-mail: hemachander.subramanian@moffitt.org. August 17, 2018 Abstract The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, in- cluding homochirality or mirror image asymmetry and 30-50 directionality, that are invariant across all life forms. The evolutionary advantages of these broken symmetries remain unknown. Here we utilize a very simple model of hypothetical self-replicating polymers to show that asymmetric autocatalytic polymers are more successful in self-replication compared to their symmetric counterparts in the Darwinian competition for space and common substrates. This broken-symmetry property, called asym- metric cooperativity, arises with the maximization of a replication poten- tial, where the catalytic influence of inter-strand bonds on their left and right neighbors is unequal. Asymmetric cooperativity also leads to ten- tative, qualitative and simple evolution-based explanations for a number of other properties of DNA that include four nucleotide alphabet, three nucleotide codons, circular genomes, helicity, anti-parallel double-strand orientation, heteromolecular base-pairing, asymmetric base compositions, and palindromic instability, apart from the structural asymmetries men- tioned above. Our model results and tentative explanations are consistent with multiple lines of experimental evidence, which include evidence for the presence of asymmetric cooperativity in DNA. arXiv:1605.00748v3 [q-bio.BM] 9 Mar 2017 Introduction Living systems, uniquely in nature, acquire, store and use information au- tonomously. -
DNA Replication and Strand Asymmetry in Prokaryotic and Mitochondrial Genomes
16 Current Genomics, 2012, 13, 16-27 DNA Replication and Strand Asymmetry in Prokaryotic and Mitochondrial Genomes Xuhua Xia*,1,2 1Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, P.O. Box 450, Station A, Ottawa, Ontario, Canada 2Ottawa Institute of Systems Biology, Ottawa, Canada Abstract: Different patterns of strand asymmetry have been documented in a variety of prokaryotic genomes as well as mitochondrial genomes. Because different replication mechanisms often lead to different patterns of strand asymmetry, much can be learned of replication mechanisms by examining strand asymmetry. Here I summarize the diverse patterns of strand asymmetry among different taxonomic groups to suggest that (1) the single-origin replication may not be universal among bacterial species as the endosymbionts Wigglesworthia glossinidia, Wolbachia species, cyanobacterium Synechocystis 6803 and Mycoplasma pulmonis genomes all exhibit strand asymmetry patterns consistent with the multiple origins of replication, (2) different replication origins in some archaeal genomes leave quite different patterns of strand asymmetry, suggesting that different replication origins in the same genome may be differentially used, (3) mitochondrial genomes from representative vertebrate species share one strand asymmetry pattern consistent with the strand- displacement replication documented in mammalian mtDNA, suggesting that the mtDNA replication mechanism in mammals may be shared among all vertebrate species, and (4) mitochondrial genomes from primitive forms of metazoans such as the sponge and hydra (representing Porifera and Cnidaria, respectively), as well as those from plants, have strand asymmetry patterns similar to single-origin or multi-origin replications observed in prokaryotes and are drastically different from mitochondrial genomes from other metazoans. -
Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus
viruses Article Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus Motohiro Akashi * and Masaharu Takemura Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Shinjuku, Tokyo 162-8601, Japan; [email protected] * Correspondence: [email protected] Received: 29 January 2019; Accepted: 14 March 2019; Published: 17 March 2019 Abstract: The detailed mechanisms of replication initiation, termination and segregation events were not yet known in Acanthamoeba polyphaga mimivirus (APMV). Here, we show detailed bioinformatics-based analyses of chromosomal replication in APMV from initiation to termination mediated by proteins bound to specific DNA sequences. Using GC/AT skew and coding sequence skew analysis, we estimated that the replication origin is located at 382 kb in the APMV genome. We performed homology-modeling analysis of the gamma domain of APMV-FtsK (DNA translocase coordinating chromosome segregation) related to FtsK-orienting polar sequences (KOPS) binding, suggesting that there was an insertion in the gamma domain which maintains the structure of the DNA binding motif. Furthermore, UvrD/Rep-like helicase in APMV was homologous to Bacillus subtilis AddA, while the chi-like quartet sequence 50-CCGC-30 was frequently found in the estimated ori region, suggesting that chromosomal replication of APMV is initiated via chi-like sequence recognition by UvrD/Rep-like helicase. Therefore, the replication initiation, -
Interplay Between DNA Sequence and Negative Superhelicity Drives R-Loop Structures
Interplay between DNA sequence and negative superhelicity drives R-loop structures Robert Stolza,b,1, Shaheen Sulthanaa,1, Stella R. Hartonoa, Maika Maliga,b, Craig J. Benhamc,d,e,2, and Frederic Chedina,e,2 aDepartment of Molecular and Cellular Biology, University of California, Davis, CA 95616; bIntegrative Genetics and Genomics Graduate Group, University of California, Davis, CA 95616; cDepartment of Mathematics, University of California, Davis, CA 95616; dDepartment of Biomedical Engineering, University of California, Davis, CA 95616; and eGenome Center, University of California, Davis, CA 95616 Edited by Philip C. Hanawalt, Stanford University, Stanford, CA, and approved February 4, 2019 (received for review November 13, 2018) R-loops are abundant three-stranded nucleic-acid structures that G clusters, in particular, were shown to be strong initiation form in cis during transcription. Experimental evidence suggests points for RNA strand invasion, leading to R-loop formation that R-loop formation is affected by DNA sequence and topology. upon extension (24, 25). However, the exact manner by which these factors interact to Experimental evidence suggests that R-loop formation is also determine R-loop susceptibility is unclear. To investigate this, we affected by DNA topology. In both Escherichia coli and yeast, developed a statistical mechanical equilibrium model of R-loop hypernegative supercoiling resulting from Topo1 inactivation formation in superhelical DNA. In this model, the energy involved leads to an increased frequency of R-loops in highly transcribed in forming an R-loop includes four terms—junctional and base- ribosomal regions (26–29). In human cells, transient knock- pairing energies and energies associated with superhelicity and down of Top1 also leads to R-loop gains at rDNA sequences with the torsional winding of the displaced DNA single strand and over long highly transcribed genes where supercoil dissi- around the RNA:DNA hybrid.