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Rogers MB, Harner A, Buhay M, Firek B, Methé B, Morris A, Palmer OMP, Promes SB, Sherwin RL, Southerland L, Vieira AR, Yende S, Morowitz MJ, Huang DT. The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study. PLoS One 2024; 19:e0290062. [PMID: 38206940 PMCID: PMC10783762 DOI: 10.1371/journal.pone.0290062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/01/2023] [Indexed: 01/13/2024] Open
Abstract
The human microbiome contributes to health and disease, but the oral microbiota is understudied relative to the gut microbiota. The salivary microbiota is easily accessible, underexplored, and may provide insight into response to infections. We sought to determine the composition, association with clinical features, and heterogeneity of the salivary microbiota in patients with acute lower respiratory tract infection (LRTI). We conducted a multicenter prospective cohort study of 147 adults with acute LRTI presenting to the emergency department of seven hospitals in three states (Pennsylvania, Michigan, and Ohio) between May 2017 and November 2018. Salivary samples were collected in the emergency department, at days 2-5 if hospitalized, and at day 30, as well as fecal samples if patients were willing. We compared salivary microbiota profiles from patients to those of healthy adult volunteers by sequencing and analyzing bacterial 16-rRNA. Compared to healthy volunteers, the salivary microbiota of patients with LRTI was highly distinct and strongly enriched with intestinal anaerobes such as Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae (e.g., mean 10% relative abundance of Bacteroides vs < 1% in healthy volunteers). Within the LRTI population, COPD exacerbation was associated with altered salivary microbiota composition compared to other LRTI conditions. The largest determinant of microbiota variation within the LRTI population was geography (city in which the hospital was located).
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Affiliation(s)
- Matthew B. Rogers
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ashley Harner
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Megan Buhay
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Brian Firek
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Barbara Methé
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison Morris
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Susan B. Promes
- Pennsylvania State University, State College, Pennsylvania, United States of America
| | | | - Lauren Southerland
- The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Alexandre R. Vieira
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sachin Yende
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michael J. Morowitz
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - David T. Huang
- University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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2
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Francis ME, Jansen EB, Yourkowski A, Selim A, Swan CL, MacPhee BK, Thivierge B, Buchanan R, Lavender KJ, Darbellay J, Rogers MB, Lew J, Gerdts V, Falzarano D, Skowronski DM, Sjaarda C, Kelvin AA. Previous infection with seasonal coronaviruses does not protect male Syrian hamsters from challenge with SARS-CoV-2. Nat Commun 2023; 14:5990. [PMID: 37752151 PMCID: PMC10522707 DOI: 10.1038/s41467-023-41761-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
SARS-CoV-2 variants and seasonal coronaviruses continue to cause disease and coronaviruses in the animal reservoir pose a constant spillover threat. Importantly, understanding of how previous infection may influence future exposures, especially in the context of seasonal coronaviruses and SARS-CoV-2 variants, is still limited. Here we adopted a step-wise experimental approach to examine the primary immune response and subsequent immune recall toward antigenically distinct coronaviruses using male Syrian hamsters. Hamsters were initially inoculated with seasonal coronaviruses (HCoV-NL63, HCoV-229E, or HCoV-OC43), or SARS-CoV-2 pango B lineage virus, then challenged with SARS-CoV-2 pango B lineage virus, or SARS-CoV-2 variants Beta or Omicron. Although infection with seasonal coronaviruses offered little protection against SARS-CoV-2 challenge, HCoV-NL63-infected animals had an increase of the previously elicited HCoV-NL63-specific neutralizing antibodies during challenge with SARS-CoV-2. On the other hand, primary infection with HCoV-OC43 induced distinct T cell gene signatures. Gene expression profiling indicated interferon responses and germinal center reactions to be induced during more similar primary infection-challenge combinations while signatures of increased inflammation as well as suppression of the antiviral response were observed following antigenically distant viral challenges. This work characterizes and analyzes seasonal coronaviruses effect on SARS-CoV-2 secondary infection and the findings are important for pan-coronavirus vaccine design.
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Affiliation(s)
- Magen E Francis
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ethan B Jansen
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Yourkowski
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Alaa Selim
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Cynthia L Swan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brian K MacPhee
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brittany Thivierge
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rachelle Buchanan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kerry J Lavender
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joseph Darbellay
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matthew B Rogers
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada
| | - Danuta M Skowronski
- BC Centre for Disease Control, Immunization Programs and Vaccine Preventable Diseases Service, Vancouver, BC, Canada
- University of British Columbia, School of Population and Public Health, Vancouver, BC, Canada
| | - Calvin Sjaarda
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
- Queen's Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Centre, Kingston, ON, Canada
| | - Alyson A Kelvin
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
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3
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. bioRxiv 2023:2023.09.13.557637. [PMID: 37745602 PMCID: PMC10515900 DOI: 10.1101/2023.09.13.557637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.
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Affiliation(s)
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan E. Pekar
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B. Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P. G. Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Florence Débarre
- Institut d’Écologie et des Sciences de l’Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France
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Novak EA, Crawford EC, Mentrup HL, Griffith BD, Fletcher DM, Flanagan MR, Schneider C, Firek B, Rogers MB, Morowitz MJ, Piganelli JD, Wang Q, Mollen KP. Epithelial NAD + depletion drives mitochondrial dysfunction and contributes to intestinal inflammation. Front Immunol 2023; 14:1231700. [PMID: 37744380 PMCID: PMC10512956 DOI: 10.3389/fimmu.2023.1231700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction We have previously demonstrated that a pathologic downregulation of peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC1α) within the intestinal epithelium contributes to the pathogenesis of inflammatory bowel disease (IBD). However, the mechanism underlying downregulation of PGC1α expression and activity during IBD is not yet clear. Methods Mice (male; C57Bl/6, Villincre/+;Pgc1afl/fl mice, and Pgc1afl/fl) were subjected to experimental colitis and treated with nicotinamide riboside. Western blot, high-resolution respirometry, nicotinamide adenine dinucleotide (NAD+) quantification, and immunoprecipitation were used to in this study. Results We demonstrate a significant depletion in the NAD+ levels within the intestinal epithelium of mice undergoing experimental colitis, as well as humans with ulcerative colitis. While we found no decrease in the levels of NAD+-synthesizing enzymes within the intestinal epithelium of mice undergoing experimental colitis, we did find an increase in the mRNA level, as well as the enzymatic activity, of the NAD+-consuming enzyme poly(ADP-ribose) polymerase-1 (PARP1). Treatment of mice undergoing experimental colitis with an NAD+ precursor reduced the severity of colitis, restored mitochondrial function, and increased active PGC1α levels; however, NAD+ repletion did not benefit transgenic mice that lack PGC1α within the intestinal epithelium, suggesting that the therapeutic effects require an intact PGC1α axis. Discussion Our results emphasize the importance of PGC1α expression to both mitochondrial health and homeostasis within the intestinal epithelium and suggest a novel therapeutic approach for disease management. These findings also provide a mechanistic basis for clinical trials of nicotinamide riboside in IBD patients.
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Affiliation(s)
- Elizabeth A. Novak
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Erin C. Crawford
- Division of Gastroenterology, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Heather L. Mentrup
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Brian D. Griffith
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI, United States
| | - David M. Fletcher
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | | | - Corinne Schneider
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Matthew B. Rogers
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Jon D. Piganelli
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Qian Wang
- Department of Pathology, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Kevin P. Mollen
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
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Rogers MB, Simon D, Firek B, Silfies L, Fabio A, Bell MJ, Yeh A, Azar J, Cheek R, Kochanek PM, Peddada SD, Morowitz MJ. Temporal and Spatial Changes in the Microbiome Following Pediatric Severe Traumatic Brain Injury. Pediatr Crit Care Med 2022; 23:425-434. [PMID: 35283451 PMCID: PMC9203870 DOI: 10.1097/pcc.0000000000002929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES The microbiome may be affected by trauma and critical illness. Many studies of the microbiome in critical illness are restricted to a single body site or time point and confounded by preexisting conditions. We report temporal and spatial alterations in the microbiome of previously healthy children with severe traumatic brain injury (TBI). DESIGN We collected oral, rectal, and skin swabs within 72 hours of admission and then twice weekly until ICU discharge. Samples were analyzed by 16S rRNA gene amplicon sequencing. Children undergoing elective outpatient surgery served as controls. Alpha and beta diversity comparisons were performed with Phyloseq, and differentially abundant taxa were predicted using Analysis of Composition of Microbiomes. SETTING Five quaternary-care PICUs. PATIENTS Patients less than 18 years with severe TBI requiring placement of an intracranial pressure monitor. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Three hundred twenty-seven samples were analyzed from 23 children with severe TBI and 35 controls. The community composition of initial oral (F = 3.2756, R2 = 0.0535, p = 0.012) and rectal (F = 3.0702, R2 = 0.0649, p = 0.007) samples differed between TBI and control patients. Rectal samples were depleted of commensal bacteria from Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae families and enriched in Staphylococcaceae after TBI (p < 0.05). In exploratory analyses, antibiotic exposure, presence of an endotracheal tube, and occurrence of an infection were associated with greater differences of the rectal and oral microbiomes between TBI patients and healthy controls, whereas enteral nutrition was associated with smaller differences (p < 0.05). CONCLUSIONS The microbiome of children with severe TBI is characterized by early depletion of commensal bacteria, loss of site specificity, and an enrichment of potential pathogens. Additional studies are needed to determine the impact of these changes on clinical outcomes.
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Affiliation(s)
- Matthew B. Rogers
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dennis Simon
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC Children’s Hospital of Pittsburgh Neuroscience Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Laurie Silfies
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Anthony Fabio
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Michael J. Bell
- Division of Critical Care Medicine, Children’s National Medical Center, Washington, DC, USA
| | - Andrew Yeh
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Justin Azar
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Richard Cheek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patrick M. Kochanek
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC Children’s Hospital of Pittsburgh Neuroscience Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Shyamal D. Peddada
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Microbiome and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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6
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Opeyemi OM, Rogers MB, Firek BA, Janesko-Feldman K, Vagni V, Mullett SJ, Wendell SG, Nelson BP, New LA, Mariño E, Kochanek PM, Bayır H, Clark RS, Morowitz MJ, Simon DW. Sustained Dysbiosis and Decreased Fecal Short-Chain Fatty Acids after Traumatic Brain Injury and Impact on Neurologic Outcome. J Neurotrauma 2021; 38:2610-2621. [PMID: 33957773 PMCID: PMC8403202 DOI: 10.1089/neu.2020.7506] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Traumatic brain injury (TBI) alters microbial populations present in the gut, which may impact healing and tissue recovery. However, the duration and impact of these changes on outcome from TBI are unknown. Short-chain fatty acids (SCFAs), produced by bacterial fermentation of dietary fiber, are important signaling molecules in the microbiota gut-brain axis. We hypothesized that TBI would lead to a sustained reduction in SCFA producing bacteria, fecal SCFAs concentration, and administration of soluble SCFAs would improve functional outcome after TBI. Adult mice (n = 10) had the controlled cortical impact (CCI) model of TBI performed (6 m/sec, 2-mm depth, 50-msec dwell). Stool samples were collected serially until 28 days after CCI and analyzed for SCFA concentration by high-performance liquid chromatography-mass spectrometry/mass spectrometry and microbiome analyzed by 16S gene sequencing. In a separate experiment, mice (n = 10/group) were randomized 2 weeks before CCI to standard drinking water or water supplemented with the SCFAs acetate (67.5 mM), propionate (25.9 mM), and butyrate (40 mM). Morris water maze performance was assessed on post-injury Days 14-19. Alpha diversity remained stable until 72 h, at which point a decline in diversity was observed without recovery out to 28 days. The taxonomic composition of post-TBI fecal samples demonstrated depletion of bacteria from Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae families, and enrichment of bacteria from the Verrucomicrobiaceae family. Analysis from paired fecal samples revealed a reduction in total SCFAs at 24 h and 28 days after TBI. Acetate, the most abundant SCFA detected in the fecal samples, was reduced at 7 days and 28 days after TBI. SCFA administration improved spatial learning after TBI versus standard drinking water. In conclusion, TBI is associated with reduced richness and diversity of commensal microbiota in the gut and a reduction in SCFAs detected in stool. Supplementation of soluble SCFAs improves spatial learning after TBI.
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Affiliation(s)
| | - Matthew B. Rogers
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian A. Firek
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Keri Janesko-Feldman
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Vincent Vagni
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven J. Mullett
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stacy G. Wendell
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brittany P. Nelson
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lee Ann New
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eliana Mariño
- Department of Biochemistry, Monash University, Melbourne, Victoria, Australia
| | - Patrick M. Kochanek
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC Children's Hospital of Pittsburgh Neuroscience Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Hülya Bayır
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC Children's Hospital of Pittsburgh Neuroscience Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Robert S.B. Clark
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC Children's Hospital of Pittsburgh Neuroscience Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Microbiome and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Dennis W. Simon
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC Children's Hospital of Pittsburgh Neuroscience Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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7
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Holder-Murray J, Yeh A, Rogers MB, Firek B, Mahler B, Medich D, Celebrezze J, Morowitz MJ. Time-dependent displacement of commensal skin microbes by pathogens at the site of colorectal surgery. Clin Infect Dis 2020; 73:e2754-e2762. [PMID: 33097951 DOI: 10.1093/cid/ciaa1615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the healthy human skin microbiome has been the subject of recent studies, it is not known whether alterations among commensal microbes contribute to surgical site infections (SSIs). The objective of this study was to characterize temporal and spatial variation in the skin microbiota of patients undergoing colorectal surgery and to determine if dysbiosis contributes to SSIs. METHODS Sixty (60) adults scheduled to undergo elective colon or rectal resection were identified by convenience sampling. By analyzing bacterial 16S rRNA gene sequences isolated from clinical samples, we used a culture-independent strategy to monitor perioperative changes in microbial diversity of fecal samples and the skin. RESULTS 990 samples were analyzed from 60 patients. Alpha diversity on the skin decreased after surgery but later recovered at the postoperative clinic visit. In most patients, we observed a transient postoperative loss of skin commensals (Corynebacterium and Propionibacterium) at the surgical site, which were replaced by potential pathogens and intestinal anaerobes (e.g. Enterobacteriaceae). These changes were not observed on skin that was uninvolved in the surgical incision (chest wall). One patient developed a wound infection. Incisional skin swabs from this patient demonstrated a sharp postoperative increase in the abundance of Enterococcus, which was also cultured from wound drainage. CONCLUSION We observed reproducible perioperative changes in the skin microbiome following surgery. The low incidence of SSIs in this cohort precluded analysis of associations between dysbiosis and infection. We postulate that real time monitoring of the skin microbiome could provide actionable findings about the pathogenesis of SSIs.
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Affiliation(s)
- Jennifer Holder-Murray
- Division of Colon & Rectal Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA.,Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew Yeh
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Matthew B Rogers
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brian Firek
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brandon Mahler
- Division of Colon & Rectal Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - David Medich
- Division of Colon & Rectal Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA.,Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - James Celebrezze
- Division of Colon & Rectal Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA.,Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael J Morowitz
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Division of Pediatric General and Thoracic Surgery, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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8
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Simon DW, Rogers MB, Gao Y, Vincent G, Firek BA, Janesko-Feldman K, Vagni V, Kochanek PM, Ozolek JA, Mollen KP, Clark RSB, Morowitz MJ. Depletion of gut microbiota is associated with improved neurologic outcome following traumatic brain injury. Brain Res 2020; 1747:147056. [PMID: 32798452 DOI: 10.1016/j.brainres.2020.147056] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/20/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Signaling between intestinal microbiota and the brain influences neurologic outcome in multiple forms of brain injury. The impact of gut microbiota following traumatic brain injury (TBI) has not been well established. Our objective was to compare TBI outcomes in specific pathogen-free mice with or without depletion of intestinal bacteria. Adult male C57BL6/J SPF mice (n = 6/group) were randomized to standard drinking water or ampicillin (1 g/L), metronidazole (1 g/L), neomycin (1 g/L), and vancomycin (0.5 g/L) (AMNV) containing drinking water 14 days prior to controlled cortical impact (CCI) model of TBI. 16S rRNA gene sequencing of fecal pellets was performed and alpha and beta diversity determined. Hippocampal neuronal density and microglial activation was assessed 72 h post-injury by immunohistochemistry. In addition, mice (n = 8-12/group) were randomized to AMNV or no treatment initiated immediately after CCI and memory acquisition (fear conditioning) and lesion volume assessed. Mice receiving AMNV had significantly reduced alpha diversity (p < 0.05) and altered microbiota community composition compared to untreated mice (PERMANOVA: p < 0.01). Mice receiving AMNV prior to TBI had increased CA1 hippocampal neuronal density (15.2 ± 1.4 vs. 8.8 ± 2.1 cells/0.1 mm; p < 0.05) and a 26.6 ± 6.6% reduction in Iba-1 positive cells (p < 0.05) at 72 h. Mice randomized to AMNV immediately after CCI had attenuated associative learning deficit on fear conditioning test (%freeze Cue: 63.7 ± 2.7% vs. 41.0 ± 5.1%, p < 0.05) and decreased lesion volume (27.2 ± 0.8 vs. 24.6 ± 0.7 mm3, p < 0.05). In conclusion, depletion of intestinal microbiota was consistent with a neuroprotective effect whether initiated before or after injury in a murine model of TBI. Further investigations of the role of gut microbiota in TBI are warranted.
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Affiliation(s)
- Dennis W Simon
- Departments of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Matthew B Rogers
- Departments of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yuan Gao
- Departments of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Garret Vincent
- Departments of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Brian A Firek
- Departments of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Keri Janesko-Feldman
- Departments of Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vincent Vagni
- Departments of Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patrick M Kochanek
- Departments of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John A Ozolek
- Department of Pathology, Anatomy, and Laboratory Medicine, West Virginia University, Morgantown, WV, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kevin P Mollen
- Departments of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert S B Clark
- Departments of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Clinical and Translational Science Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Safar Center for Resuscitation Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael J Morowitz
- Departments of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Center for Microbiome and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Departments of Environmental and Occupational Health, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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9
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Foster JM, Grote A, Mattick J, Tracey A, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A, Holroyd N, Korlach J, Li Y, Libro S, Lustigman S, Michalski ML, Paulini M, Rogers MB, Teigen L, Twaddle A, Welch L, Berriman M, Dunning Hotopp JC, Ghedin E. Sex chromosome evolution in parasitic nematodes of humans. Nat Commun 2020; 11:1964. [PMID: 32327641 PMCID: PMC7181701 DOI: 10.1038/s41467-020-15654-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/20/2020] [Indexed: 11/09/2022] Open
Abstract
Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.
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Affiliation(s)
- Jeremy M Foster
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Alexandra Grote
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - John Mattick
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Matthew Chung
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Adam Geber
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Yichao Li
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Silvia Libro
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Michelle L Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Matthew B Rogers
- Department of Surgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, 15224, USA
| | - Laura Teigen
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Alan Twaddle
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julie C Dunning Hotopp
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
- Department of Epidemiology, School of Global Public Health, New York University, New York, NY, 10003, USA.
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10
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Wan Y, White C, Robert N, Rogers MB, Szabo-Rogers HL. Localization of Tfap2β, Casq2, Penk, Zic1, and Zic3 Expression in the Developing Retina, Muscle, and Sclera of the Embryonic Mouse Eye. J Histochem Cytochem 2019; 67:863-871. [PMID: 31638440 DOI: 10.1369/0022155419885112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Optic development involves sequential interactions between several different tissue types, including the overlying ectoderm, adjacent mesoderm, and neural crest mesenchyme and the neuroectoderm. In an ongoing expression screen, we identified that Tfap2β, Casq2, Penk, Zic1, and Zic3 are expressed in unique cell types in and around the developing eye. Tfap2β, Zic1, and Zic3 are transcription factors, Casq2 is a calcium binding protein and Penk is a neurotransmitter. Tfap2β, Zic1, and Zic3 have reported roles in brain and craniofacial development, while Casq2 and Penk have unknown roles. These five genes are expressed in the major tissue types in the eye, including the muscles, nerves, cornea, and sclera. Penk expression is found in the sclera and perichondrium. At E12.5 and E15.5, the extra-ocular muscles express Casq2, the entire neural retina expresses Zic1, and Zic3 is expressed in the optic disk and lip of the optic cup. The expression of Tfap2β expanded from corneal epithelium to the neural retina between E12.5 to E15.5. These genes are expressed in similar domains as Hedgehog (Gli1, and Ptch1) and the Wnt (Lef1) pathways. The expression patterns of these five genes warrant further study to determine their role in eye morphogenesis.
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Affiliation(s)
- Yong Wan
- Center for Craniofacial Regeneration, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Casey White
- Center for Craniofacial Regeneration, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Nadine Robert
- Center for Craniofacial Regeneration, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Matthew B Rogers
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Heather L Szabo-Rogers
- Center for Craniofacial Regeneration, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA.,McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA
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11
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Yeh A, Conners EM, Ramos-Jimenez RG, Firek B, Novak EA, Rogers MB, Cheek R, Ozolek J, Mollen KP, Morowitz MJ. Plant-based Enteral Nutrition Modifies the Gut Microbiota and Improves Outcomes in Murine Models of Colitis. Cell Mol Gastroenterol Hepatol 2019; 7:872-874.e6. [PMID: 30716421 PMCID: PMC6522637 DOI: 10.1016/j.jcmgh.2019.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 12/10/2022]
Affiliation(s)
- Andrew Yeh
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Eric M. Conners
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Rafael G. Ramos-Jimenez
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brian Firek
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Elizabeth A. Novak
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Matthew B. Rogers
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Richard Cheek
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - John Ozolek
- Department of Pathology, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Kevin P. Mollen
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania,Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Michael J. Morowitz
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania,Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania,Corresponding author:
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12
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Río Bártulos C, Rogers MB, Williams TA, Gentekaki E, Brinkmann H, Cerff R, Liaud MF, Hehl AB, Yarlett NR, Gruber A, Kroth PG, van der Giezen M. Mitochondrial Glycolysis in a Major Lineage of Eukaryotes. Genome Biol Evol 2018; 10:2310-2325. [PMID: 30060189 PMCID: PMC6198282 DOI: 10.1093/gbe/evy164] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/21/2022] Open
Abstract
The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host’s metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.
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Affiliation(s)
- Carolina Río Bártulos
- Institut für Genetik, Technische Universität Braunschweig.,Fachbereich Biologie, Universität Konstanz, Germany
| | - Matthew B Rogers
- Biosciences, University of Exeter, United Kingdom.,Rangos Research Center, University of Pittsburgh, Children's Hospital, Pittsburgh, PA
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Eleni Gentekaki
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,School of Science and Human Gut Microbiome for Health Research Unit, Mae Fah Luang University, Chiang Rai, Thailand
| | - Henner Brinkmann
- Département de Biochimie, Université de Montréal C.P. 6128, Montréal, Quebec, Canada.,Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Rüdiger Cerff
- Institut für Genetik, Technische Universität Braunschweig
| | | | - Adrian B Hehl
- Institute of Parasitology, University of Zürich, Switzerland
| | - Nigel R Yarlett
- Department of Chemistry and Physical Sciences, Pace University
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, Germany.,Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
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13
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Kerr PJ, Cattadori IM, Rogers MB, Fitch A, Geber A, Liu J, Sim DG, Boag B, Eden JS, Ghedin E, Read AF, Holmes EC. Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia. PLoS Pathog 2017; 13:e1006252. [PMID: 28253375 PMCID: PMC5349684 DOI: 10.1371/journal.ppat.1006252] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/14/2017] [Accepted: 02/20/2017] [Indexed: 11/19/2022] Open
Abstract
The co-evolution of myxoma virus (MYXV) and the European rabbit occurred independently in Australia and Europe from different progenitor viruses. Although this is the canonical study of the evolution of virulence, whether the genomic and phenotypic outcomes of MYXV evolution in Europe mirror those observed in Australia is unknown. We addressed this question using viruses isolated in the United Kingdom early in the MYXV epizootic (1954-1955) and between 2008-2013. The later UK viruses fell into three distinct lineages indicative of a long period of separation and independent evolution. Although rates of evolutionary change were almost identical to those previously described for MYXV in Australia and strongly clock-like, genome evolution in the UK and Australia showed little convergence. The phenotypes of eight UK viruses from three lineages were characterized in laboratory rabbits and compared to the progenitor (release) Lausanne strain. Inferred virulence ranged from highly virulent (grade 1) to highly attenuated (grade 5). Two broad disease types were seen: cutaneous nodular myxomatosis characterized by multiple raised secondary cutaneous lesions, or an amyxomatous phenotype with few or no secondary lesions. A novel clinical outcome was acute death with pulmonary oedema and haemorrhage, often associated with bacteria in many tissues but an absence of inflammatory cells. Notably, reading frame disruptions in genes defined as essential for virulence in the progenitor Lausanne strain were compatible with the acquisition of high virulence. Combined, these data support a model of ongoing host-pathogen co-evolution in which multiple genetic pathways can produce successful outcomes in the field that involve both different virulence grades and disease phenotypes, with alterations in tissue tropism and disease mechanisms.
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Affiliation(s)
- Peter J. Kerr
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
- CSIRO Health and Biosecurity, Canberra, Australian Capital Territory 2601, Australia
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States of America
| | - Matthew B. Rogers
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States of America
| | - Adam Fitch
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States of America
| | - Adam Geber
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, New York 10003, United States of America
| | - June Liu
- CSIRO Health and Biosecurity, Canberra, Australian Capital Territory 2601, Australia
| | - Derek G. Sim
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States of America
| | - Brian Boag
- The James Hutton Institute, Invergowrie, DD2 5DA, United Kingdom
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elodie Ghedin
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, New York 10003, United States of America
| | - Andrew F. Read
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States of America
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States of America
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
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14
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Rogers MB, Aveson V, Firek B, Yeh A, Brooks B, Brower-Sinning R, Steve J, Banfield JF, Zureikat A, Hogg M, Boone BA, Zeh HJ, Morowitz MJ. Disturbances of the Perioperative Microbiome Across Multiple Body Sites in Patients Undergoing Pancreaticoduodenectomy. Pancreas 2017; 46:260-267. [PMID: 27846140 PMCID: PMC5235958 DOI: 10.1097/mpa.0000000000000726] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The goals of this study were to characterize bacterial communities within fecal samples, pancreatic fluid, bile, and jejunal contents from patients undergoing pancreaticoduodenectomy (PD) and to identify associations between microbiome profiles and clinical variables. METHODS Fluid was collected from the pancreas, common bile duct, and proximal jejunum from 50 PD patients. Postoperative fecal samples were also collected. The microbial burden within samples was quantified with droplet digital polymerase chain reaction. Bacterial 16S ribosomal RNA gene sequences were amplified, sequenced, and analyzed. Data from fecal samples were compared with publicly available data obtained from volunteers. RESULTS Droplet digital polymerase chain reaction confirmed the presence of bacteria in all sample types, including pancreatic fluid. Relative to samples from the American Gut Project, fecal samples from PD patients were enriched with Klebsiella and Bacteroides and were depleted of anaerobic taxa (eg, Roseburia and Faecalibacterium). Similar patterns were observed within PD pancreas, bile, and jejunal samples. Postoperative fecal samples from patients with a pancreatic fistula contained increased abundance of Klebsiella and decreased abundance of commensal anaerobes, for example, Ruminococcus. CONCLUSIONS This study confirms the presence of altered bacterial populations within samples from PD patients. Future research must validate these findings and may evaluate targeted microbiome modifications to improve outcomes in PD patients.
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Affiliation(s)
| | - Victoria Aveson
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Brian Firek
- Division of Pediatric General and Thoracic Surgery, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA
| | - Andrew Yeh
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Brandon Brooks
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA
| | | | - Jennifer Steve
- Division of GI Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA
| | - Amer Zureikat
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA,Division of GI Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Melissa Hogg
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA,Division of GI Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Brian A. Boone
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA,Division of GI Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Herbert J. Zeh
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA,Division of GI Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Michael J. Morowitz
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA,Division of Pediatric General and Thoracic Surgery, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA,Address Correspondence to: Michael J. Morowitz, MD, Division of Pediatric Surgery, Children’s Hospital of Pittsburgh of UPMC, 4401 Penn Avenue, 7th Floor Faculty Pavilion, Pittsburgh, PA 15244, , phone 412-692-7282, fax 412-692-8299
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15
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Rogers MB, Firek B, Shi M, Yeh A, Brower-Sinning R, Aveson V, Kohl BL, Fabio A, Carcillo JA, Morowitz MJ. Disruption of the microbiota across multiple body sites in critically ill children. Microbiome 2016; 4:66. [PMID: 28034303 PMCID: PMC5200963 DOI: 10.1186/s40168-016-0211-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/24/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets. RESULTS Bacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs. The mean age of the PICU patients was 2.9 years (range 1-9 years), and many were chronically ill children that had previously been hospitalized in the PICU. Relative to healthy adults and children, alpha diversity was decreased in PICU GI and tongue but not skin samples. Measures of beta diversity indicated differences in community membership at each body site between PICU, adult, and pediatric groups. Taxonomic alterations in the PICU included enrichment of gut pathogens such as Enterococcus and Staphylococcus at multiple body sites and depletion of commensals such as Faecalibacterium and Ruminococcus from GI samples. Alpha and beta diversity were unstable over time in patients followed longitudinally. We observed the frequent presence of "dominant" pathogens in PICU samples at relative abundance >50%. PICU samples were characterized by loss of site specificity, with individual taxa commonly present simultaneously at three sample sites on a single individual. Some pathogens identified by culture of tracheal aspirates were commonly observed in skin samples from the same patient. CONCLUSIONS We conclude that the microbiota in critically ill children differs sharply from the microbiota of healthy children and adults. Acknowledgement of dysbiosis associated with critical illness could provide opportunities to modulate the microbiota with precision and thereby improve patient outcomes.
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Affiliation(s)
- Matthew B. Rogers
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Brian Firek
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Min Shi
- Division of Pediatric General and Thoracic Surgery, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
| | - Andrew Yeh
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Rachel Brower-Sinning
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Victoria Aveson
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Brittany L. Kohl
- Division of Pediatric Critical Care Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
| | - Anthony Fabio
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Joseph A. Carcillo
- Division of Pediatric Critical Care Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Michael J. Morowitz
- Division of Pediatric Surgery, Children’s Hospital of Pittsburgh of UPMC, 4401 Penn Avenue, 7th Floor Faculty Pavilion, Pittsburgh, PA 15244 USA
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16
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Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JCD, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JMC, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S. The genome of Onchocerca volvulus, agent of river blindness. Nat Microbiol 2016; 2:16216. [PMID: 27869790 PMCID: PMC5310847 DOI: 10.1038/nmicrobiol.2016.216] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/26/2016] [Indexed: 01/08/2023]
Abstract
Human onchocerciasis is a serious neglected tropical disease caused by the filarial nematode Onchocerca volvulus that can lead to blindness and chronic disability. Control of the disease relies largely on mass administration of a single drug, and the development of new drugs and vaccines depends on a better knowledge of parasite biology. Here, we describe the chromosomes of O. volvulus and its Wolbachia endosymbiont. We provide the highest-quality sequence assembly for any parasitic nematode to date, giving a glimpse into the evolution of filarial parasite chromosomes and proteomes. This resource was used to investigate gene families with key functions that could be potentially exploited as targets for future drugs. Using metabolic reconstruction of the nematode and its endosymbiont, we identified enzymes that are likely to be essential for O. volvulus viability. In addition, we have generated a list of proteins that could be targeted by Federal-Drug-Agency-approved but repurposed drugs, providing starting points for anti-onchocerciasis drug development.
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Affiliation(s)
- James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Alexandra Grote
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Bhavana Harsha
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Alan Tracey
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Robin Beech
- Institute of Parasitology, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Stephen R Doyle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Matthew Dunn
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Taisei Kikuchi
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Olivia Lambert
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Amruta Mhashilkar
- Global Health Infectious Disease Research Program, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida 33612, USA
| | - Prudence Mutowo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Nirvana Nursimulu
- Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada.,Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Jose M C Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Matthew B Rogers
- Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224, USA
| | - Eleanor Stanley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lakshmipuram S Swapna
- Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Thomas R Unnasch
- Global Health Infectious Disease Research Program, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida 33612, USA
| | - Denis Voronin
- New York Blood Center, New York, New York 10065, USA
| | - John Parkinson
- Department of Computer Science, University of Toronto, Toronto M5S 3G4, Canada.,Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Departments of Biochemistry and Molecular Genetics, University of Toronto, M5S 1A8, Canada
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA.,College of Global Public Health, New York University, New York, New York 10003, USA
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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17
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Rogers MB, Brower-Sinning R, Firek B, Zhong D, Morowitz MJ. Acute Appendicitis in Children Is Associated With a Local Expansion of Fusobacteria. Clin Infect Dis 2016; 63:71-78. [DOI: 10.1093/cid/ciw208] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/17/2016] [Indexed: 01/29/2023] Open
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18
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Cunningham KE, Vincent G, Sodhi CP, Novak EA, Ranganathan S, Egan CE, Stolz DB, Rogers MB, Firek B, Morowitz MJ, Gittes GK, Zuckerbraun BS, Hackam DJ, Mollen KP. Peroxisome Proliferator-activated Receptor-γ Coactivator 1-α (PGC1α) Protects against Experimental Murine Colitis. J Biol Chem 2016; 291:10184-200. [PMID: 26969166 DOI: 10.1074/jbc.m115.688812] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Indexed: 12/16/2022] Open
Abstract
Peroxisome proliferator-activated receptor-γ coactivator 1-α (PGC1α) is the primary regulator of mitochondrial biogenesis and was recently found to be highly expressed within the intestinal epithelium. PGC1α is decreased in the intestinal epithelium of patients with inflammatory bowel disease, but its role in pathogenesis is uncertain. We now hypothesize that PGC1α protects against the development of colitis and helps to maintain the integrity of the intestinal barrier. We selectively deleted PGC1α from the intestinal epithelium of mice by breeding a PGC1α(loxP/loxP) mouse with a villin-cre mouse. Their progeny (PGC1α(ΔIEC) mice) were subjected to 2% dextran sodium sulfate (DSS) colitis for 7 days. The SIRT1 agonist SRT1720 was used to enhance PGC1α activation in wild-type mice during DSS exposure. Mice lacking PGC1α within the intestinal epithelium were more susceptible to DSS colitis than their wild-type littermates. Pharmacologic activation of PGC1α successfully ameliorated disease and restored mitochondrial integrity. These findings suggest that a depletion of PGC1α in the intestinal epithelium contributes to inflammatory changes through a failure of mitochondrial structure and function as well as a breakdown of the intestinal barrier, which leads to increased bacterial translocation. PGC1α induction helps to maintain mitochondrial integrity, enhance intestinal barrier function, and decrease inflammation.
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Affiliation(s)
- Kellie E Cunningham
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - Garret Vincent
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - Chhinder P Sodhi
- the Department of Surgery, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Elizabeth A Novak
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - Sarangarajan Ranganathan
- the Department of Pathology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224, and
| | - Charlotte E Egan
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - Donna Beer Stolz
- the Center for Biologic Imaging, University or Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Matthew B Rogers
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - Brian Firek
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - Michael J Morowitz
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - George K Gittes
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - Brian S Zuckerbraun
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
| | - David J Hackam
- the Department of Surgery, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Kevin P Mollen
- the Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, From the Division of Pediatric Surgery, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224,
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19
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Poon LLM, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, Sebra R, Halpin RA, Guan Y, Twaddle A, DePasse JV, Stockwell TB, Wentworth DE, Holmes EC, Greenbaum B, Peiris JSM, Cowling BJ, Ghedin E. Quantifying influenza virus diversity and transmission in humans. Nat Genet 2016; 48:195-200. [PMID: 26727660 PMCID: PMC4731279 DOI: 10.1038/ng.3479] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/07/2015] [Indexed: 01/26/2023]
Abstract
Influenza A virus is characterized by high genetic diversity. However, most of what is known about influenza evolution has come from consensus sequences sampled at the epidemiological scale that only represent the dominant virus lineage within each infected host. Less is known about the extent of within-host virus diversity and what proportion of this diversity is transmitted between individuals. To characterize virus variants that achieve sustainable transmission in new hosts, we examined within-host virus genetic diversity in household donor-recipient pairs from the first wave of the 2009 H1N1 pandemic when seasonal H3N2 was co-circulating. Although the same variants were found in multiple members of the community, the relative frequencies of variants fluctuated, with patterns of genetic variation more similar within than between households. We estimated the effective population size of influenza A virus across donor-recipient pairs to be approximately 100-200 contributing members, which enabled the transmission of multiple lineages, including antigenic variants.
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Affiliation(s)
- Leo L M Poon
- Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Timothy Song
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
| | - Roni Rosenfeld
- School of Computer Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Xudong Lin
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Matthew B Rogers
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bin Zhou
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Yi Guan
- Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Alan Twaddle
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
| | - Jay V DePasse
- Pittsburgh Supercomputer Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | | | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Oncology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joseph S M Peiris
- Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Benjamin J Cowling
- Epidemiology and Biostatistics, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA.,College of Global Public Health, New York University, New York, New York, USA
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20
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Bolette DP, Cui L, Rogers MB. Enterobius (Enterobius) shriveri n. sp. (Nematoda: Oxyuridae: Enterobiinae) from Macaca fascicularis Raffles, 1821 (Primates: Cercopithecidae: Cercopithecinae) and Three Other Cercopitheciid Primate Species: With Additional Information on Enterobius (Enterobius) macaci Yen, 1973. COMP PARASITOL 2016. [DOI: 10.1654/1525-2647-83.1.54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- David P. Bolette
- University of Pittsburgh, Laboratory Animal Resources, S1040 Biomedical Science Tower, Pittsburgh, Pennsylvania 15261, U.S.A. (e-mail: )
| | - Lijia Cui
- University of Pittsburgh, Department of Computational and Systems Biology, Pittsburgh, Pennsylvania 15261, U.S.A. (e-mail: e-mail: )
- Tsinghua University, School of Medicine, Beijing, 100084 China (e-mail: )
| | - Matthew B. Rogers
- University of Pittsburgh, Department of Computational and Systems Biology, Pittsburgh, Pennsylvania 15261, U.S.A. (e-mail: e-mail: )
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21
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Cui L, Lucht L, Tipton L, Rogers MB, Fitch A, Kessinger C, Camp D, Kingsley L, Leo N, Greenblatt RM, Fong S, Stone S, Dermand JC, Kleerup EC, Huang L, Morris A, Ghedin E. Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease. Am J Respir Crit Care Med 2015; 191:932-42. [PMID: 25603113 DOI: 10.1164/rccm.201409-1583oc] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
RATIONALE Microbiome studies typically focus on bacteria, but fungal species are common in many body sites and can have profound effects on the host. Wide gaps exist in the understanding of the fungal microbiome (mycobiome) and its relationship to lung disease. OBJECTIVES To characterize the mycobiome at different respiratory tract levels in persons with and without HIV infection and in HIV-infected individuals with chronic obstructive pulmonary disease (COPD). METHODS Oral washes (OW), induced sputa (IS), and bronchoalveolar lavages (BAL) were collected from 56 participants. We performed 18S and internal transcribed spacer sequencing and used the neutral model to identify fungal species that are likely residents of the lung. We used ubiquity-ubiquity plots, random forest, logistic regression, and metastats to compare fungal communities by HIV status and presence of COPD. MEASUREMENTS AND MAIN RESULTS Mycobiomes of OW, IS, and BAL shared common organisms, but each also had distinct members. Candida was dominant in OW and IS, but BAL had 39 fungal species that were disproportionately more abundant than in the OW. Fungal communities in BAL differed significantly by HIV status and by COPD, with Pneumocystis jirovecii significantly overrepresented in both groups. Other fungal species were also identified as differing in HIV and COPD. CONCLUSIONS This study systematically examined the respiratory tract mycobiome in a relatively large group. By identifying Pneumocystis and other fungal species as overrepresented in the lung in HIV and in COPD, it is the first to determine alterations in fungal communities associated with lung dysfunction and/or HIV, highlighting the clinical relevance of these findings. Clinical trial registered with www.clinicaltrials.gov (NCT00870857).
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22
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Liu C, Voronin D, Poole CB, Bachu S, Rogers MB, Jin J, Ghedin E, Lustigman S, McReynolds LA, Unnasch TR. Functional analysis of microRNA activity in Brugia malayi. Int J Parasitol 2015; 45:579-83. [PMID: 26004246 DOI: 10.1016/j.ijpara.2015.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/22/2015] [Accepted: 04/24/2015] [Indexed: 01/20/2023]
Abstract
The complement of the Brugia malayi microRNA-71 was inserted into the 3' untranslated region of a reporter plasmid, resulting in a decrease in reporter activity. Mutation of the seed sequence restored activity. Insertion of the 3' untranslated regions from two algorithm-predicted putative target genes into the reporter resulted in a similar decrease in activity; mutation of the predicted target sequences restored activity. These experiments demonstrate that B. malayi microRNA targets may be predicted using current algorithms and describe a functional assay to confirm predicted targets.
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Affiliation(s)
- Canhui Liu
- Global Health Infectious Disease Research Program, Department of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Blvd, Suite 304, Tampa, FL 33612, USA
| | - Denis Voronin
- New York Blood Center, Lindsley F. Kimball Research Institute, 310 East 67th Street, New York, NY 10065, USA
| | | | - Saheed Bachu
- New York Blood Center, Lindsley F. Kimball Research Institute, 310 East 67th Street, New York, NY 10065, USA
| | - Matthew B Rogers
- Department of Surgery, University of Pittsburgh, Children's Hospital, Pittsburgh, USA
| | - Jingmin Jin
- New England Biolabs, 240 County Road, Ipswich, MA 01938-2723, USA
| | - Elodie Ghedin
- Department of Biology, Center for Genomics & Systems Biology, Global Institute of Public Health, New York University, New York, NY 10003, USA
| | - Sara Lustigman
- New York Blood Center, Lindsley F. Kimball Research Institute, 310 East 67th Street, New York, NY 10065, USA
| | | | - Thomas R Unnasch
- Global Health Infectious Disease Research Program, Department of Global Health, College of Public Health, University of South Florida, 3720 Spectrum Blvd, Suite 304, Tampa, FL 33612, USA.
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23
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Rogers MB, Cui L, Fitch A, Popov V, Travassos da Rosa APA, Vasilakis N, Tesh RB, Ghedin E. Whole genome analysis of sierra nevada virus, a novel mononegavirus in the family nyamiviridae. Am J Trop Med Hyg 2014; 91:159-64. [PMID: 24778199 DOI: 10.4269/ajtmh.14-0076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A novel mononegavirus was isolated in 1975 from ticks (Ornithodoros coriaceus) collected during investigation of an outbreak of epizootic bovine abortion (EBA) in northern California. It was originally designated "bovine abortion-tick virus" (BA-T virus). The EBA is now known to be associated with a deltaproteobacterium infection, and not a virus. The BA-T virus had remained uncharacterized until now. We have determined by electron microscopy, serology, and genome sequencing that the BA-T virus is a fourth member of the newly proposed family Nyamiviridae, and we have renamed it Sierra Nevada virus (SNVV). Although antigenically distinct, phylogenetically SNVV is basal to Nyamanini virus (NYMV) and Midway virus (MIDWV), two other tick-borne agents. Although NYMV was found to infect land birds, and MIDWV seabirds, it is presently unknown whether SNVV naturally infects birds or mammals.
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Affiliation(s)
- Matthew B Rogers
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Lijia Cui
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Adam Fitch
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Vsevolod Popov
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Amelia P A Travassos da Rosa
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Nikos Vasilakis
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Robert B Tesh
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Elodie Ghedin
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Tsinghua University School of Medicine, Beijing, China; Center for Biodefense and Emerging Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
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24
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Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodova M, Volf P, Berriman M, Cotton JA, Smith DF. Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. PLoS Genet 2014; 10:e1004092. [PMID: 24453988 PMCID: PMC3894156 DOI: 10.1371/journal.pgen.1004092] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 11/20/2013] [Indexed: 12/02/2022] Open
Abstract
Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Çukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. This observation allowed us to estimate the relative rates of sexual and asexual reproduction within this population, to our knowledge the first quantitative estimate of these events during the Leishmania life cycle. Sexual reproduction is predicted to be a rare event in Leishmania parasites, as evidenced by detection of rare parasite hybrids in natural populations using molecular methods. Recently, a sexual cycle has been detected experimentally in parasites within the sand fly vector (that transmits this pathogenic microorganism to mammalian species including man, causing human leishmaniasis). In this study, we have used whole genome sequencing to investigate genetic variation at the highest level of resolution in Leishmania parasites isolated from sand flies in a defined focus of leishmaniasis in southeast Turkey. Using a range of analytical tools, we show that variation in these parasites arose following a single cross between two diverse strains and subsequent recombination between the progeny, despite mainly clonal reproduction in the parasite population. We have thus been able to derive quantitative estimates of the relative rates of sexual and asexual reproduction during the Leishmania life cycle for the first time, information that will be critical to our understanding of the epidemiology and evolution of this genus.
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Affiliation(s)
- Matthew B. Rogers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom
| | - Tim Downing
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Barbara A. Smith
- Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom
| | - Hideo Imamura
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Milena Svobodova
- Department of Parasitology, Fac. Sci., Charles University, Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Fac. Sci., Charles University, Prague, Czech Republic
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - James A. Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- * E-mail: (JAC); (DFS)
| | - Deborah F. Smith
- Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom
- * E-mail: (JAC); (DFS)
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Douradinha B, Reis VCB, Rogers MB, Torres FAG, Evans JD, Marques Jr ETA. Novel insights in genetic transformation of the probiotic yeast Saccharomyces boulardii. Bioengineered 2014; 5:21-9. [PMID: 24013355 PMCID: PMC4008461 DOI: 10.4161/bioe.26271] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 02/04/2023] Open
Abstract
Saccharomyces boulardii (S. boulardii) is a probiotic yeast related to Saccharomyces cerevisiae (S. cerevisiae) but with distinct genetic, taxonomic and metabolic properties. S. cerevisiae has been used extensively in biotechnological applications. Currently, many strains are available, and multiple genetic tools have been developed, which allow the expression of several exogenous proteins of interest with applications in the fields of medicine, biofuels, the food industry, and scientific research, among others. Although S. boulardii has been widely studied due to its probiotic properties against several gastrointestinal tract disorders, very few studies addressed the use of this yeast as a vector for expression of foreign genes of interest with biotechnological applications. Here we show that, despite the similarity of the two yeasts, not all genetic tools used in S. cerevisiae can be applied in S. boulardii. While transformation of the latter could be obtained using a commercial kit developed for the former, consequent screening of successful transformants had to be optimized. We also show that several genes frequently used in genetic manipulation of S. cerevisiae (e.g., promoters and resistance markers) are present in S. boulardii. Sequencing revealed a high rate of homology (> 96%) between the orthologs of the two yeasts. However, we also observed some of them are not eligible to be targeted for transformation of S. boulardii. This work has important applications toward the potential of this probiotic yeast as an expression system for genes of interest.
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Affiliation(s)
- Bruno Douradinha
- Fondazione Ri.MED; Palermo, Italy
- University of Pittsburgh Center for Vaccine Research; Pittsburgh, PA USA
| | - Viviane CB Reis
- Centro de Biotecnologia Molecular; Instituto de Ciências Biológicas; Universidade de Brasília; Brasília, Brazil
| | - Matthew B Rogers
- University of Pittsburgh Center for Vaccine Research; Pittsburgh, PA USA
| | - Fernando AG Torres
- Centro de Biotecnologia Molecular; Instituto de Ciências Biológicas; Universidade de Brasília; Brasília, Brazil
| | - Jared D Evans
- University of Pittsburgh Center for Vaccine Research; Pittsburgh, PA USA
- Department of Microbiology and Molecular Genetics; School of Medicine; University of Pittsburgh; Pittsburgh, PA USA
| | - Ernesto TA Marques Jr
- University of Pittsburgh Center for Vaccine Research; Pittsburgh, PA USA
- Department of Infectious Diseases and Microbiology; School of Medicine; University of Pittsburgh; Pittsburgh, PA USA
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Ghedin E, Rogers MB, Widen SG, Guzman H, Travassos da Rosa APA, Wood TG, Fitch A, Popov V, Holmes EC, Walker PJ, Vasilakis N, Tesh RB. Kolente virus, a rhabdovirus species isolated from ticks and bats in the Republic of Guinea. J Gen Virol 2013; 94:2609-2615. [PMID: 24062532 DOI: 10.1099/vir.0.055939-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Kolente virus (KOLEV) is a rhabdovirus originally isolated from ticks and a bat in Guinea, West Africa, in 1985. Although tests at the time of isolation suggested that KOLEV is a novel rhabdovirus, it has remained largely uncharacterized. We assembled the complete genome sequence of the prototype strain DakAr K7292, which was found to encode the five canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORFs (>180 nt) in the P and L genes. Serologically, KOLEV exhibited a weak antigenic relationship with Barur and Fukuoka viruses in the Kern Canyon group. Phylogenetic analysis revealed that KOLEV represents a distinct and divergent lineage that shows no clear relationship to any rhabdovirus except Oita virus, although with limited phylogenetic resolution. In summary, KOLEV represents a novel species in the family Rhabdoviridae.
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Affiliation(s)
- Elodie Ghedin
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew B Rogers
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hilda Guzman
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Amelia P A Travassos da Rosa
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam Fitch
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vsevolod Popov
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Edward C Holmes
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.,Sydney Emerging Infections & Biosecurity Institute, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Peter J Walker
- CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Nikos Vasilakis
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Robert B Tesh
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G, McQuillan JA, Carver T, Aslett M, Olsen C, Subramanian S, Phan I, Farris C, Mitra S, Ramasamy G, Wang H, Tivey A, Jackson A, Houston R, Parkhill J, Holden M, Harb OS, Brunk BP, Myler PJ, Roos D, Carrington M, Smith DF, Hertz-Fowler C, Berriman M. GeneDB--an annotation database for pathogens. Nucleic Acids Res 2011; 40:D98-108. [PMID: 22116062 PMCID: PMC3245030 DOI: 10.1093/nar/gkr1032] [Citation(s) in RCA: 195] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.
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Affiliation(s)
- Flora J Logan-Klumpler
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA, Depledge DP, Harris D, Her Y, Herzyk P, Imamura H, Otto TD, Sanders M, Seeger K, Dujardin JC, Berriman M, Smith DF, Hertz-Fowler C, Mottram JC. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res 2011; 21:2129-42. [PMID: 22038252 DOI: 10.1101/gr.122945.111] [Citation(s) in RCA: 316] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated a reference genome for Leishmania mexicana and refined the reference genomes for Leishmania major, Leishmania infantum, and Leishmania braziliensis. This has allowed the identification of a remarkably low number of genes or paralog groups (2, 14, 19, and 67, respectively) unique to one species. These were found to be conserved in additional isolates of the same species. We have predicted allelic variation and find that in these isolates, L. major and L. infantum have a surprisingly low number of predicted heterozygous SNPs compared with L. braziliensis and L. mexicana. We used short read coverage to infer ploidy and gene copy numbers, identifying large copy number variations between species, with 200 tandem gene arrays in L. major and 132 in L. mexicana. Chromosome copy number also varied significantly between species, with nine supernumerary chromosomes in L. infantum, four in L. mexicana, two in L. braziliensis, and one in L. major. A significant bias against gene arrays on supernumerary chromosomes was shown to exist, indicating that duplication events occur more frequently on disomic chromosomes. Taken together, our data demonstrate that there is little variation in unique gene content across Leishmania species, but large-scale genetic heterogeneity can result through gene amplification on disomic chromosomes and variation in chromosome number. Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression in response to environmental conditions in the host, providing a genetic basis for disease tropism.
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Affiliation(s)
- Matthew B Rogers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
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Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, Gardner MJ, Gingle A, Grant G, Harb OS, Heiges M, Hertz-Fowler C, Houston R, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Logan FJ, Miller JA, Mitra S, Myler PJ, Nayak V, Pennington C, Phan I, Pinney DF, Ramasamy G, Rogers MB, Roos DS, Ross C, Sivam D, Smith DF, Srinivasamoorthy G, Stoeckert CJ, Subramanian S, Thibodeau R, Tivey A, Treatman C, Velarde G, Wang H. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res 2009; 38:D457-62. [PMID: 19843604 PMCID: PMC2808979 DOI: 10.1093/nar/gkp851] [Citation(s) in RCA: 687] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
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Affiliation(s)
- Martin Aslett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Puthiyaveetil S, Kavanagh TA, Cain P, Sullivan JA, Newell CA, Gray JC, Robinson C, van der Giezen M, Rogers MB, Allen JF. The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts. Proc Natl Acad Sci U S A 2008; 105:10061-6. [PMID: 18632566 PMCID: PMC2474565 DOI: 10.1073/pnas.0803928105] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Indexed: 11/18/2022] Open
Abstract
We describe a novel, typically prokaryotic, sensor kinase in chloroplasts of green plants. The gene for this chloroplast sensor kinase (CSK) is found in cyanobacteria, prokaryotes from which chloroplasts evolved. The CSK gene has moved, during evolution, from the ancestral chloroplast to the nuclear genomes of eukaryotic algae and green plants. The CSK protein is now synthesised in the cytosol of photosynthetic eukaryotes and imported into their chloroplasts as a protein precursor. In the model higher plant Arabidopsis thaliana, CSK is autophosphorylated and required for control of transcription of chloroplast genes by the redox state of an electron carrier connecting photosystems I and II. CSK therefore provides a redox regulatory mechanism that couples photosynthesis to gene expression. This mechanism is inherited directly from the cyanobacterial ancestor of chloroplasts, is intrinsic to chloroplasts, and is targeted to chloroplast genes.
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Affiliation(s)
- Sujith Puthiyaveetil
- *School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom
| | | | - Peter Cain
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - James A. Sullivan
- *School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Christine A. Newell
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom; and
| | - John C. Gray
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom; and
| | - Colin Robinson
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mark van der Giezen
- Centre for Eukaryotic Evolutionary Microbiology, School of Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Matthew B. Rogers
- Centre for Eukaryotic Evolutionary Microbiology, School of Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - John F. Allen
- *School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, United Kingdom
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Hamblin K, Standley DM, Rogers MB, Stechmann A, Roger AJ, Maytum R, van der Giezen M. Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Mol Microbiol 2008; 68:1395-405. [PMID: 18452512 PMCID: PMC2440562 DOI: 10.1111/j.1365-2958.2008.06228.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The anaerobic lifestyle of the intestinal parasite Blastocystis raises questions about the biochemistry and function of its mitochondria-like organelles. We have characterized the Blastocystis succinyl-CoA synthetase (SCS), a tricarboxylic acid cycle enzyme that conserves energy by substrate-level phosphorylation. We show that SCS localizes to the enigmatic Blastocystis organelles, indicating that these organelles might play a similar role in energy metabolism as classic mitochondria. Although analysis of residues inside the nucleotide-binding site suggests that Blastocystis SCS is GTP-specific, we demonstrate that it is ATP-specific. Homology modelling, followed by flexible docking and molecular dynamics simulations, indicates that while both ATP and GTP fit into the Blastocystis SCS active site, GTP is destabilized by electrostatic dipole interactions with Lys 42 and Lys 110, the side-chains of which lie outside the nucleotide-binding cavity. It has been proposed that residues in direct contact with the substrate determine nucleotide specificity in SCS. However, our results indicate that, in Blastocystis, an electrostatic gatekeeper controls which ligands can enter the binding site.
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Affiliation(s)
- Karleigh Hamblin
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
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Abstract
Background Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes. Results Here, we show that abundant marine cyanobacteria in the related genera Synechococcus and Prochlorococcus acquired a key Calvin cycle/glycolytic enzyme from a eukaryote. Two non-homologous forms of fructose bisphosphate aldolase (FBA) are characteristic of eukaryotes and prokaryotes respectively. However, a eukaryotic gene has been inserted immediately upstream of the ancestral prokaryotic gene in several strains (ecotypes) of Synechococcus and Prochlorococcus. In one lineage this new gene has replaced the ancestral gene altogether. The eukaryotic gene is most closely related to the plastid-targeted FBA from red algae. This eukaryotic-type FBA once replaced the plastid/cyanobacterial type in photosynthetic eukaryotes, hinting at a possible functional advantage in Calvin cycle reactions. The strains that now possess this eukaryotic FBA are scattered across the tree of Synechococcus and Prochlorococcus, perhaps because the gene has been transferred multiple times among cyanobacteria, or more likely because it has been selectively retained only in certain lineages. Conclusion A gene for plastid-targeted FBA has been transferred from red algae to cyanobacteria, where it has inserted itself beside its non-homologous, functional analogue. Its current distribution in Prochlorococcus and Synechococcus is punctate, suggesting a complex history since its introduction to this group.
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Affiliation(s)
- Matthew B Rogers
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Nicola J Patron
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
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Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ. The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. Mol Biol Evol 2006; 24:54-62. [PMID: 16990439 DOI: 10.1093/molbev/msl129] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chlorarachniophytes are amoeboflagellate cercozoans that acquired a plastid by secondary endosymbiosis. Chlorarachniophytes are the last major group of algae for which there is no completely sequenced plastid genome. Here we describe the 69.2-kbp chloroplast genome of the model chlorarachniophyte Bigelowiella natans. The genome is highly reduced in size compared with plastids of other photosynthetic algae and is closer in size to genomes of several nonphotosynthetic plastids. Unlike nonphotosynthetic plastids, however, the B. natans chloroplast genome has not sustained a massive loss of genes, and it retains nearly all of the functional photosynthesis-related genes represented in the genomes of other green algae. Instead, the genome is highly compacted and gene dense. The genes are organized with a strong strand bias, and several unusual rearrangements and inversions also characterize the genome; notably, an inversion in the small-subunit rRNA gene, a translocation of 3 genes in the major ribosomal protein operon, and the fragmentation of the cluster encoding the large photosystem proteins PsaA and PsaB. The chloroplast endosymbiont is known to be a green alga, but its evolutionary origin and relationship to other primary and secondary green plastids has been much debated. A recent hypothesis proposes that the endosymbionts of chlorarachniophytes and euglenids share a common origin (the Cabozoa hypothesis). We inferred phylogenies using individual and concatenated gene sequences for all genes in the genome. Concatenated gene phylogenies show a relationship between the B. natans plastid and the ulvophyte-trebouxiophyte-chlorophyte clade of green algae to the exclusion of Euglena. The B. natans plastid is thus not closely related to that of Euglena, which suggests that plastids originated independently in these 2 groups and the Cabozoa hypothesis is false.
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Affiliation(s)
- Matthew B Rogers
- Botany Department, University of British Columbia, British Columbia, Canada
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Abstract
BACKGROUND The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded. RESULTS Here, we test whether the phylogenetically distinct nucleomorph genomes of the cryptomonad, Guillardia theta, and the chlorarachniophyte, Bigelowiella natans, have experienced similar evolutionary pressures during their transformation to reduced organelles. We compared the evolutionary rates of genes from nuclear, nucleomorph, and plastid genomes, all of which encode proteins that function in the same cellular compartment, the plastid, and are thus subject to similar selection pressures. Furthermore, we investigated the divergence of nucleomorphs within cryptomonads by comparing G. theta and Rhodomonas salina. CONCLUSION Chlorarachniophyte nucleomorph genes have accumulated errors at a faster rate than other genomes within the same cell, regardless of the compartment where the gene product functions. In contrast, most nucleomorph genes in cryptomonads have evolved faster than genes in other genomes on average, but genes for plastid-targeted proteins are not overly divergent, and it appears that cryptomonad nucleomorphs are not presently evolving rapidly and have therefore stabilized. Overall, these analyses suggest that the forces at work in the two lineages are different, despite the similarities between the structures of their genomes.
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Affiliation(s)
- Nicola J Patron
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Matthew B Rogers
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
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Patron NJ, Rogers MB, Keeling PJ. Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Eukaryot Cell 2004; 3:1169-75. [PMID: 15470245 PMCID: PMC522617 DOI: 10.1128/ec.3.5.1169-1175.2004] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2004] [Accepted: 07/30/2004] [Indexed: 11/20/2022]
Abstract
Plastids (photosynthetic organelles of plants and algae) are known to have spread between eukaryotic lineages by secondary endosymbiosis, that is, by the uptake of a eukaryotic alga by another eukaryote. But the number of times this has taken place is controversial. This is particularly so in the case of eukaryotes with plastids derived from red algae, which are numerous and diverse. Despite their diversity, it has been suggested that all these eukaryotes share a recent common ancestor and that their plastids originated in a single endosymbiosis, the so-called "chromalveolate hypothesis." Here we describe a novel molecular character that supports the chromalveolate hypothesis. Fructose-1,6-bisphosphate aldolase (FBA) is a glycolytic and Calvin cycle enzyme that exists as two nonhomologous types, class I and class II. Red algal plastid-targeted FBA is a class I enzyme related to homologues from plants and green algae, and it would be predicted that the plastid-targeted FBA from algae with red algal secondary endosymbionts should be related to this class I enzyme. However, we show that plastid-targeted FBA of heterokonts, cryptomonads, haptophytes, and dinoflagellates (all photosynthetic chromalveolates) are class II plastid-targeted enzymes, completely unlike those of red algal plastids. The chromalveolate enzymes form a strongly supported group in FBA phylogeny, and their common possession of this unexpected plastid characteristic provides new evidence for their close relationship and a common origin for their plastids.
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Affiliation(s)
- Nicola J Patron
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia V6T 1Z4, Canada
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Abstract
Chlorarachniophytes are marine amoeboflagellate protists that have acquired their plastid (chloroplast) through secondary endosymbiosis with a green alga. Like other algae, most of the proteins necessary for plastid function are encoded in the nuclear genome of the secondary host. These proteins are targeted to the organelle using a bipartite leader sequence consisting of a signal peptide (allowing entry in to the endomembrane system) and a chloroplast transit peptide (for transport across the chloroplast envelope membranes). We have examined the leader sequences from 45 full-length predicted plastid-targeted proteins from the chlorarachniophyte Bigelowiella natans with the goal of understanding important features of these sequences and possible conserved motifs. The chemical characteristics of these sequences were compared with a set of 10 B. natans endomembrane-targeted proteins and 38 cytosolic or nuclear proteins, which show that the signal peptides are similar to those of most other eukaryotes, while the transit peptides differ from those of other algae in some characteristics. Consistent with this, the leader sequence from one B. natans protein was tested for function in the apicomplexan parasite, Toxoplasma gondii, and shown to direct the secretion of the protein.
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Affiliation(s)
- Matthew B Rogers
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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Archibald JM, Rogers MB, Toop M, Ishida KI, Keeling PJ. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc Natl Acad Sci U S A 2003; 100:7678-83. [PMID: 12777624 PMCID: PMC164647 DOI: 10.1073/pnas.1230951100] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2003] [Accepted: 04/18/2003] [Indexed: 02/01/2023] Open
Abstract
Chlorarachniophytes are amoeboflagellate algae that acquired photosynthesis secondarily by engulfing a green alga and retaining its plastid (chloroplast). An important consequence of secondary endosymbiosis in chlorarachniophytes is that most of the nuclear genes encoding plastid-targeted proteins have moved from the nucleus of the endosymbiont to the host nucleus. We have sequenced and analyzed 83 cDNAs encoding 78 plastid-targeted proteins from the model chlorarachniophyte Bigelowiella natans (formerly Chlorarachnion sp. CCMP621). Phylogenies inferred from the majority of these genes are consistent with a chlorophyte green algal origin. However, a significant number of genes ( approximately 21%) show signs of having been acquired by lateral gene transfer from numerous other sources: streptophyte algae, red algae (or algae with red algal endosymbionts), as well as bacteria. The chlorarachniophyte plastid proteome may therefore be regarded as a mosaic derived from various organisms in addition to the ancestral chlorophyte plastid. In contrast, the homologous genes from the chlorophyte Chlamydomonas reinhardtii do not show any indications of lateral gene transfer. This difference is likely a reflection of the mixotrophic nature of Bigelowiella (i.e., it is photosynthetic and phagotrophic), whereas Chlamydomonas is strictly autotrophic. These results underscore the importance of lateral gene transfer in contributing foreign proteins to eukaryotic cells and their organelles, and also suggest that its impact can vary from lineage to lineage.
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Affiliation(s)
- John M Archibald
- Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
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Abstract
Stem cells generate many differentiated, short-lived cell types, such as blood, skin, and sperm, throughout adult life. Stem cells maintain a long-term capacity to divide, producing daughter cells that either self-renew or initiate differentiation. Although the surrounding microenvironment or "niche" influences stem cell fate decisions, few signals that emanate from the niche to specify stem cell self-renewal have been identified. Here we demonstrate that the apical hub cells in the Drosophila testis act as a cellular niche that supports stem cell self-renewal. Hub cells express the ligand Unpaired (Upd), which activates the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway in adjacent germ cells to specify self-renewal and continual maintenance of the germ line stem cell population.
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Affiliation(s)
- A A Kiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
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39
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Abstract
During development, many cells are specifically eliminated. Therefore, programmed cell death must be understood to fully elucidate embryogenesis. Retinoic acid (RA) and bone morphogenetic protein (BMP) 4 induce rapidly dividing P19 embryonal carcinoma cells to undergo apoptosis. RA alone minimally induces apoptosis, while BMP4 alone induces none. RA and BMP4 exposure also elevates the number of cells in the G1 phase of the cell cycle. Because many cell cycle proteins control both proliferation and apoptosis, we determined the role of these proteins in inducing apoptosis. Although the mRNA levels of cyclins D1 and D2 are reduced in cells undergoing apoptosis, the protein levels are not. In contrast, RA and BMP4 induce the Cdk inhibitor p27. This protein binds Cdk4 in RA- and BMP4-treated cells and inhibits Cdk4-dependent kinase activity. We used p27 antisense oligonucleotides to rescue the P19 cells from RA and BMP4 apoptosis thus proving that p27 is necessary. The Cdk4 substrate, retinoblastoma (Rb) protein, is also induced in apoptotic cells. Consistent with the decreased kinase activity of the apoptotic cells, this Rb protein is hypophosphorylated and presumably active. These data support the hypothesis that RA and BMP4 together induce the p27 protein leading to Rb activation and ultimately apoptosis.
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Affiliation(s)
- M A Glozak
- Department of Biology, University of South Florida, BSF119, 4202 E. Fowler Avenue, Tampa, Florida 33620, USA
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Rogers MB. The banded Herbst appliance. J Clin Orthod 2001; 35:494-9. [PMID: 11589096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- M B Rogers
- Department of Orthodontics, School of Dentistry, Medical College of Georgia, Augusta, USA.
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Rogers MB. Virtual reality in psychotherapy: the MYTHSEEKER software. Stud Health Technol Inform 2001; 58:170-9. [PMID: 10350917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
This chapter outlines the use in psychotherapy and medical diagnosis of an intelligent software system that helps clients to explore Personal Myth within virtual reality environments. Patented MYTHSEEKER software will allow clients to work with mythic analogues of lifeshapes and aspirations. This can help to focus therapy directions, find ways to participate with the person's world, and allow a kind of personal expression not previously possible. The software phases of assessment, facilitation, and enaction are described by which the client is assisted to explore systems of mythology or spirituality (called Depth Systems) that are traditional, ancient or newly-arising. The client builds a Personal Depth System representing Personal Myth, based on experiencing other Depth Systems, which can itself be experienced in the virtual environment. This paper outlines our methodology and technology to realize these operations. Space limitations prevent further description in the present chapter of MYTHSEEKER software technology or psychotherapy scenarios of involvement.
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Affiliation(s)
- M B Rogers
- MYTHSEEKER Institute, Eagle Rock, California, USA
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42
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Abstract
Mutagenesis of Vibrio cholerae with TnphoA, followed by screening for fusions that were activated under low-iron conditions, led to the identification of seven independent fusion strains, each of which was deficient in the ability to utilize ferrichrome as a sole iron source for growth in a plate bioassay and had an insertion in genes encoding products homologous to Escherichia coli FhuA or FhuD. Expression of the gene fusions was independent of IrgB but regulated by Fur. We report here a map of the operon and the predicted amino acid sequence of FhuA, based on the nucleotide sequence. Unlike those of the E. coli fhu operon, the V. cholerae ferrichrome utilization genes are located adjacent and opposite in orientation to a gene encoding an ATP-binding cassette transporter homolog, but this gene, if disrupted, does not affect the utilization of ferrichrome in vitro.
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Affiliation(s)
- M B Rogers
- Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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Li Y, Glozak MA, Smith SM, Rogers MB. The expression and activity of D-type cyclins in F9 embryonal carcinoma cells: modulation of growth by RXR-selective retinoids. Exp Cell Res 1999; 253:372-84. [PMID: 10585260 DOI: 10.1006/excr.1999.4664] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The growth rate of malignant F9 embryonal carcinoma cells slows considerably following all-trans-retinoic acid-induced differentiation into benign parietal endoderm. To determine the mechanism of this process, we examined the expression of cyclins D1, D2, and D3 and the activity of their associated kinases. Cyclin D1 and D3 mRNA levels decreased during complete differentiation induced by all-trans-retinoic acid and dibutyryl cAMP, while the levels of cyclin D2 and the cyclin-dependent kinase (Cdk) inhibitor p27 mRNAs increased. Ultimately, terminally differentiated cells possessed 50% of the Cdk4-associated kinase activity observed in undifferentiated cells. Since numerous genes are differentially regulated during parietal endoderm differentiation, it is difficult to determine whether retinoic acid affects cell cycle gene expression directly or if these changes are caused by differentiation. We found that the retinoid X receptor (RXR)-selective agonists LG100153 and LG100268 significantly inhibited F9 cell growth without causing overt terminal differentiation as assessed by anchorage-independent growth and differentiation-associated gene expression. As seen in cells induced to differentiate by the RAR agonist all-trans-retinoic acid, RXR activation led to an increase in the number of cells in G1 phase. RXR agonists also sharply induced the levels of the Cdk regulatory subunits, cyclin D2 and D3. However, Cdk4-dependent kinase activity was reduced by RXR-selective retinoid treatment. These observations suggest that some retinoids can directly inhibit proliferation and regulate Cdk4-dependent kinase activity without inducing terminal differentiation.
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Affiliation(s)
- Y Li
- Department of Biology, University of South Florida, Tampa, 4202 E. Fowler Avenue, 33620, USA
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Lin W, Fullner KJ, Clayton R, Sexton JA, Rogers MB, Calia KE, Calderwood SB, Fraser C, Mekalanos JJ. Identification of a vibrio cholerae RTX toxin gene cluster that is tightly linked to the cholera toxin prophage. Proc Natl Acad Sci U S A 1999; 96:1071-6. [PMID: 9927695 PMCID: PMC15352 DOI: 10.1073/pnas.96.3.1071] [Citation(s) in RCA: 222] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/1998] [Indexed: 11/18/2022] Open
Abstract
We identify and characterize a gene cluster in El Tor Vibrio cholerae that encodes a cytotoxic activity for HEp-2 cells in vitro. This gene cluster contains four genes and is physically linked to the cholera toxin (CTX) element in the V. cholerae genome. We demonstrate by using insertional mutagenesis that this gene cluster is required for the cytotoxic activity. The toxin, RtxA, resembles members of the RTX (repeats in toxin) toxin family in that it contains a GD-rich repeated motif. Like other RTX toxins, its activity depends on an activator, RtxC, and an associated ABC transporter system, RtxB and RtxD. In V. cholerae strains of the classical biotype, a deletion within the gene cluster removes rtxC and eliminates cytotoxic activity. Other strains, including those of the current cholera pandemic, contain a functional gene cluster and display cytotoxic activity. Thus, the RTX gene cluster in El Tor O1 and O139 strains might have contributed significantly to their emergence. Furthermore, the RTX toxin of V. cholerae may be associated with residual adverse properties displayed by certain live, attenuated cholera vaccines.
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Affiliation(s)
- W Lin
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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Zwemer TJ, Fortson WM, Rogers MB. Howard W. Conley. Am J Orthod Dentofacial Orthop 1999; 115:223. [PMID: 9971931 DOI: 10.1016/s0889-5406(99)70164-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Heller LC, Li Y, Abrams KL, Rogers MB. Transcriptional regulation of the Bmp2 gene. Retinoic acid induction in F9 embryonal carcinoma cells and Saccharomyces cerevisiae. J Biol Chem 1999; 274:1394-400. [PMID: 9880512 DOI: 10.1074/jbc.274.3.1394] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bmp2, a highly conserved member of the transforming growth factor-beta gene family, is crucial for normal development. Retinoic acid, combined with cAMP analogs, sharply induces the Bmp2 mRNA during the differentiation of F9 embryonal carcinoma cells into parietal endoderm. Retinoic acid (RA) also induces the Bmp2 gene in chick limb buds. Since normal Bmp2 expression may require an endogenous retinoid signal and aberrant Bmp2 expression may cause some aspects of RA-induced teratogenesis, we studied the mechanism underlying the induction of Bmp2. Measurements of the Bmp2 mRNA half-life and nuclear run-on assays indicated that RA stimulated the transcription rate of the Bmp2 gene. The results of ribonuclease protection and primer extension assays indicated that Bmp2 transcription started 2,127 nucleotides upstream of the translation start site in F9 cells. To identify genetic elements controlling this transcription rate increase, upstream and downstream genomic sequences flanking the Bmp2 gene were screened using chloramphenicol acetyltransferase reporter genes in F9 cells and beta-galactosidase reporter genes in Saccharomyces cerevisiae that were cotransformed with retinoic acid receptor and retinoid X receptor expression plasmids. RA-dependent transcriptional activation was detected between base pairs -2,373 and -2,316 relative to the translation start site. We also identified a required Sp1 binding site between -2,308 and -2,298. The data indicate that Bmp2 is directly regulated by retinoic acid-bound receptors and Sp1.
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Affiliation(s)
- L C Heller
- Department of Biology, University of South Florida, Tampa, Florida 33620, USA
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Rogers MB. MYTHSEEKER Project Status Summary. Cyberpsychol Behav 1999; 2:375-379. [PMID: 19178235 DOI: 10.1089/cpb.1999.2.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This is a summary of the present status of The MYTHSEEKER Project. The first section provides a brief synopsis of the project's purpose and approach. The second section summarizes present activity in a number of directions-including decisions that are shaping development. The third section outlines the next steps for development programming, the initial software product, and a communications network of MYTHSEEKER Centers. Some extended viewpoints are mentioned.
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Affiliation(s)
- M B Rogers
- The MYTHSEEKER Institute, Eagle Rock, CA 90041, USA
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Glozak MA, Rogers MB. BMP4- and RA-induced apoptosis is mediated through the activation of retinoic acid receptor alpha and gamma in P19 embryonal carcinoma cells. Exp Cell Res 1998; 242:165-73. [PMID: 9665814 DOI: 10.1006/excr.1998.4075] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Some growth factors, for example, members of the transforming growth factor-beta family, can induce apoptosis in a variety of cells. Retinoic acid (RA) also causes apoptosis in several malignant cell types. We have previously demonstrated that, although BMP2 or BMP4 cannot induce apoptosis alone, BMP2 or BMP4 and RA synergize to induce apoptosis in 95% of P19 embryonal carcinoma cells within 4 days of treatment. Such treatment also prevents neuronal differentiation of these cells. Retinoids exert their many effects through any of six distinct nuclear receptors. These retinoid-activated transcription factors directly regulate genes involved in cellular response such as apoptosis. Complete understanding of how BMP and RA specifically induce cell death requires identification of the retinoid receptors controlling apoptosis. By using receptor-selective retinoid agonists and antagonists, we have obtained evidence suggesting that activation of RAR alpha or gamma is sufficient to induce apoptosis in BMP4-treated cells.
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Affiliation(s)
- M A Glozak
- Department of Biology, Pharmacology, University of South Florida, Tampa 33620, USA
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Li Y, MacLennan AJ, Rogers MB. A putative G-protein-coupled receptor, H218, is down-regulated during the retinoic acid-induced differentiation of F9 embryonal carcinoma cells. Exp Cell Res 1998; 239:320-5. [PMID: 9521849 DOI: 10.1006/excr.1997.3904] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have previously cloned a novel guanine nucleotide-binding protein (G-protein)-coupled receptor, H218, that has sequence similarity to a lysophosphatidic acid receptor, edg2. We present here Northern analysis indicating that the H218 mRNA is expressed in undifferentiated F9 embryonal carcinoma cells. The H218 message is down-regulated and its stability is decreased during retinoic acid- and dibutyryl cAMP-induced differentiation. Treatment by various receptor-selective retinoids indicated that retinoic acid receptor beta or gamma signaling, but not retinoid X receptor activation, is required for the down-regulation of H218 mRNA. Activation of the H218 receptor may contribute to the phenotype of undifferentiated F9 embryonal carcinoma cells.
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MESH Headings
- Animals
- Benzoates/pharmacology
- Bucladesine/pharmacology
- Carcinoma, Embryonal/pathology
- Cell Differentiation/drug effects
- Chromans/pharmacology
- Down-Regulation/drug effects
- GTP-Binding Proteins/physiology
- Gene Expression Regulation, Neoplastic/drug effects
- Mice
- Naphthalenes/pharmacology
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Phenotype
- RNA, Messenger/biosynthesis
- RNA, Neoplasm/biosynthesis
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Receptors, G-Protein-Coupled
- Receptors, Lysophospholipid
- Receptors, Retinoic Acid/classification
- Receptors, Retinoic Acid/drug effects
- Retinoids/pharmacology
- Signal Transduction/drug effects
- Tetrahydronaphthalenes/pharmacology
- Tretinoin/pharmacology
- Tumor Cells, Cultured/drug effects
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Affiliation(s)
- Y Li
- Department of Biology, University of South Florida, Tampa 33620, USA
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50
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Abstract
This review focuses on known genes whose expression may be perturbed by teratogens during early embryogenesis (preorganogenesis). Teratogens may disrupt embryogenesis by modifying positional information. Genes controlling positional information include those specifying the primary body axes: anterior-posterior, dorsal-ventral, or left-right. These genes often encode transcription factors, whose regulation or activation can stimulate aberrant tissue differentiation and morphogenesis. Alternatively, teratogens may directly affect cell differentiation, proliferation, or apoptosis. Hydrophilic signalling molecules such as growth factors and hydrophobic molecules such as retinoids regulate these processes. The signalling pathways activated often induce the coordinate regulation of tissue specific gene expression. In addition to modifying individual signalling pathways, teratogens can synergize with or antagonize the effects of other teratogens through inappropriate interactions between signal transduction pathways. Since teratogens may often directly or indirectly perturb the expression of known or as yet undescribed developmentally critical genes, this review also provides a short description of techniques to identify genes whose expression is altered by teratogens.
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Affiliation(s)
- M B Rogers
- Department of Biology, University of South Florida, Tampa 33620-5150, USA.
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