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Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manabe YC, Pekosz A, Smith RL, McManus DD, Brooke CB. Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection. J Virol 2024; 98:e0161823. [PMID: 38174928 PMCID: PMC10805032 DOI: 10.1128/jvi.01618-23] [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: 10/16/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.
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Affiliation(s)
- Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Michael A. Martin
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Laura L. Gibson
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kimberly K. O. Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J. Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Fadi G. Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H. Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C. Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca L. Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David D. McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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2
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Fujiwara R, Zhai SN, Liang D, Shah AP, Tracey M, Ma XK, Fields CJ, Mendoza-Figueroa MS, Meline MC, Tatomer DC, Yang L, Wilusz JE. IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol Cell 2023; 83:4445-4460.e7. [PMID: 37995689 PMCID: PMC10841813 DOI: 10.1016/j.molcel.2023.10.035] [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: 03/06/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
The metazoan-specific Integrator complex catalyzes 3' end processing of small nuclear RNAs (snRNAs) and premature termination that attenuates the transcription of many protein-coding genes. Integrator has RNA endonuclease and protein phosphatase activities, but it remains unclear if both are required for complex function. Here, we show IntS6 (Integrator subunit 6) over-expression blocks Integrator function at a subset of Drosophila protein-coding genes, although having no effect on snRNAs or attenuation of other loci. Over-expressed IntS6 titrates protein phosphatase 2A (PP2A) subunits, thereby only affecting gene loci where phosphatase activity is necessary for Integrator function. IntS6 functions analogous to a PP2A regulatory B subunit as over-expression of canonical B subunits, which do not bind Integrator, is also sufficient to inhibit Integrator activity. These results show that the phosphatase module is critical at only a subset of Integrator-regulated genes and point to PP2A recruitment as a tunable step that modulates transcription termination efficiency.
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Affiliation(s)
- Rina Fujiwara
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Si-Nan Zhai
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Aayushi P Shah
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew Tracey
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Christopher J Fields
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - María Saraí Mendoza-Figueroa
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michele C Meline
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
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3
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Harris NL, Fields CJ, Hokamp K, Just J, Khetani R, Maia J, Ménager H, Munoz-Torres MC, Unni D, Williams J. BOSC 2023, the 24th annual Bioinformatics Open Source Conference. F1000Res 2023; 12:1568. [PMID: 38076297 PMCID: PMC10704065 DOI: 10.12688/f1000research.143015.1] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
The 24th annual Bioinformatics Open Source Conference ( BOSC 2023) was part of the 2023i conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (ISMB/ECCB 2023). Launched in 2000 and held yearly since, BOSC is the premier meeting covering open-source bioinformatics and open science. Like ISMB 2022, the 2023 meeting was a hybrid conference, with the in-person component hosted in Lyon, France. ISMB/ECCB attracted a near-record number of attendees, with over 2100 in person and about 900 more online. Approximately 200 people participated in BOSC sessions. In addition to 43 talks and 49 posters, BOSC featured two keynotes: Sara El-Gebali, who spoke about "A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration", and Joseph Yracheta, who spoke about "The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution." Once again, a joint session brought together BOSC and the Bio-Ontologies COSI. The conference ended with a panel on Open and Ethical Data Sharing. As in prior years, BOSC was preceded by a CollaborationFest, a collaborative work event that brought together about 40 participants interested in synergistically combining ideas, shaping project plans, developing software, and more.
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Affiliation(s)
- Nomi L. Harris
- Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Christopher J. Fields
- Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College of Dublin, Dublin, D02 PN40, Ireland
| | - Jérémy Just
- Ecole Normale Superieure de Lyon, Lyon, Auvergne-Rhône-Alpes, 69364, France
| | - Radhika Khetani
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts, 02115, USA
| | - Jessica Maia
- BD Technologies and Innovation, Research Triangle Park, North Carolina, 27709, USA
| | | | | | - Deepak Unni
- Swiss Institute of Bioinformatics, Basel, 4051, Switzerland
| | - Jason Williams
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
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Arora D, Hernandez AG, Walden KKO, Fields CJ, Yan G. First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing. Int J Mol Sci 2023; 24:ijms24087311. [PMID: 37108472 PMCID: PMC10138993 DOI: 10.3390/ijms24087311] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Root-lesion nematodes (genus Pratylenchus) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to Pratylenchus genus is scarcely available. Here, we report the draft genome assembly of Pratylenchus scribneri generated on the PacBio Sequel IIe System using the ultra-low DNA input HiFi sequencing workflow. The final assembly created using 500 nematodes consisted of 276 decontaminated contigs, with an average contig N50 of 1.72 Mb and an assembled draft genome size of 227.24 Mb consisting of 51,146 predicted protein sequences. The benchmarking universal single-copy ortholog (BUSCO) analysis with 3131 nematode BUSCO groups indicated that 65.4% of the BUSCOs were complete, whereas 24.0%, 41.4%, and 1.8% were single-copy, duplicated, and fragmented, respectively, and 32.8% were missing. The outputs from GenomeScope2 and Smudgeplots converged towards a diploid genome for P. scribneri. The data provided here will facilitate future studies on host plant-nematode interactions and crop protection at the molecular level.
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Affiliation(s)
- Deepika Arora
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58105, USA
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Kimberly K O Walden
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Christopher J Fields
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Guiping Yan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58105, USA
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5
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Geary EL, Oba PM, Applegate CC, Clark LV, Fields CJ, Swanson KS. Effects of a mildly cooked human-grade dog diet on gene expression, skin and coat health measures, and fecal microbiota of healthy adult dogs. J Anim Sci 2022; 100:skac265. [PMID: 35965387 PMCID: PMC9527297 DOI: 10.1093/jas/skac265] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Purported benefits of human-grade pet foods include reduced inflammation, enhanced coat quality, and improved gut health, but research is scarce. Therefore, we compared gene expression, skin and coat health measures, and the fecal microbiome of dogs consuming a mildly cooked human-grade or extruded kibble diet. Twenty beagles (BW = 10.25 ± 0.82 kg; age = 3.85 ± 1.84 yr) were used in a completely randomized design. Test diets included: 1) chicken and brown rice recipe [feed-grade; extruded; blue buffalo (BB)]; and 2) chicken and white rice [human-grade; mildly cooked; Just Food for Dogs (JFFD)]. The study consisted of a 4-week baseline when all dogs ate BB, and a 12-week treatment phase when dogs were randomized to either diet (n = 10/group). After the baseline and treatment phases, fresh fecal samples were scored and collected for pH, dry matter (DM), and microbiome analysis; blood samples were collected for gene expression analysis; hair samples were microscopically imaged; and skin was analyzed for delayed-type hypersensitivity (DTH), sebum concentration, hydration status, and transepidermal water loss (TEWL). Data were analyzed as a change from baseline (CFB) using the Mixed Models procedure of SAS (version 9.4). At baseline, fecal pH was higher (P < 0.05) and hair surface score, superoxide dismutase (SOD) expression, and tumor necrosis factor-α (TNF-α) expression was lower (P < 0.05) in dogs allotted to JFFD. The decrease in CFB fecal pH and DM was greater (P < 0.05) in dogs fed JFFD, but fecal scores were not different. The increase in CFB hair surface score was higher (P < 0.05) in dogs fed JFFD. The decrease in CFB TEWL (back region) was greater (P < 0.05) in dogs fed JFFD, but TEWL (inguinal and ear regions), hydration status, and sebum concentrations in all regions were not different. Hair cortex scores and DTH responses were not affected by diet. The increase in CFB gene expression of SOD, COX-2, and TNF-α was greater (P < 0.05) in dogs fed JFFD. PCoA plots based on Bray-Curtis distances of bacterial genera and species showed small shifts over time in dogs fed BB, but dramatic shifts in those fed JFFD. JFFD increased (adj. P < 0.05) relative abundances of 4 bacterial genera, 11 bacterial species, 68 KEGG pathways, and 167 MetaCyc pathways, and decreased (adj. P < 0.05) 16 genera, 25 species, 98 KEGG pathways, and 87 MetaCyc pathways. In conclusion, the JFFD diet dramatically shifted the fecal microbiome but had minor effects on skin and coat measures and gene expression.
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Affiliation(s)
- Elizabeth L Geary
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Patrícia M Oba
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Catherine C Applegate
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- The Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lindsay V Clark
- High Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher J Fields
- High Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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6
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Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Zhou R, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution. Open Forum Infect Dis 2022; 9:ofac192. [PMID: 35791353 PMCID: PMC9047214 DOI: 10.1093/ofid/ofac192] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023] Open
Abstract
Background The global effort to vaccinate people against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during an ongoing pandemic has raised questions about how vaccine breakthrough infections compare with infections in immunologically naive individuals and the potential for vaccinated individuals to transmit the virus. Methods We examined viral dynamics and infectious virus shedding through daily longitudinal sampling in 23 adults infected with SARS-CoV-2 at varying stages of vaccination, including 6 fully vaccinated individuals. Results The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. Conclusions Vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.
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Affiliation(s)
- Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Chad J Achenbach
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sally McFall
- Center for Innovation in Point-of-Care Technologies for HIV/AIDS at Northwestern University, Evanston, Illinois, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, USA
| | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua Jacob
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Etienne Dembele
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Camille Bundy
- Institute for Sexual and Gender Minority Health and Wellbeing, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lacy M Simons
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A Ozer
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Judd F Hultquist
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ramon Lorenzo-Redondo
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Anita K Opdycke
- Department of Health Service, Northwestern University, Evanston, Illinois, USA
| | - Claudia Hawkins
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert L Murphy
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Junko Jarrett
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - John Broach
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- UMass Memorial Medical Center, Worcester, Massachusetts, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Matthew L Robinson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C Manabe
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - David D McManus
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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7
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Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Zhou R, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nat Microbiol 2022; 7:640-652. [PMID: 35484231 PMCID: PMC9084242 DOI: 10.1038/s41564-022-01105-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [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: 08/06/2021] [Accepted: 03/15/2022] [Indexed: 02/07/2023]
Abstract
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
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Affiliation(s)
- Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junko Jarrett
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kimberly K O Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Darci C Edmonson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shannon Bradley
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stacy L Gloss
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Crystal Reinhart
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jagadeesh Yedetore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica Quicksall
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Broach
- UMass Memorial Medical Center, Worcester, MA, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Heetderks
- National Institute for Biomedical Imaging and Bioengineering, Bethesda, MD, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David D McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Ellis JL, Wang M, Fu X, Fields CJ, Donovan SM, Booth SL. Feeding Practice and Delivery Mode Are Determinants of Vitamin K in the Infant Gut: An Exploratory Analysis. Curr Dev Nutr 2022; 6:nzac019. [PMID: 35295713 PMCID: PMC8921654 DOI: 10.1093/cdn/nzac019] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 02/02/2023] Open
Abstract
Background Infants have low stores of vitamin K at birth. Dietary intake of phylloquinone (PK) differs dramatically by infant feeding practice, but the contribution of microbially produced vitamin K (menaquinones) to infant vitamin K status is not well understood. Objectives The objective of this study was to investigate determinants of infant fecal vitamin K profiles in mother-infant dyads at 6 wk postpartum. Methods Fecal and breast milk samples were collected from a subsample of breastfeeding (n = 23) or formula-feeding (n = 23) mother and infant dyads, delivered vaginally (n = 26) or by cesarean section (CS) (n = 20) in the Synergistic Theory and Research on Nutrition and Growth (STRONG) Kids 2 cohort. Vitamin K concentrations in breast milk and feces were analyzed by LC/MS and/or HPLC. Fecal bacterial metagenomes were analyzed to derive taxonomy and vitamin K biosynthetic genes. Multivariate linear modeling was used to assess effects of delivery and feeding modes on infant fecal vitamin K. Results Breast milk contained 1.3 ± 0.2 ng/mL PK, and formula was reported to contain 52 ng/mL PK. Fecal PK was 38-times higher (P < 0.001) in formula-fed than breastfed infants. Infant fecal menaquinones (MKn) MK6, MK7, MK12, and MK13 were higher (P < 0.001) in formula-fed than breastfed infants, whereas MK8 predominated in breastfed and was 5-times higher than formula-fed infants. Total MKn were greater (P < 0.001) in vaginally delivered than CS infants. Relative abundances of 33 bacterial species were affected by feeding mode, 2 by delivery mode, and 4 by both (P < 0.05). Bacterial gene content of 5/12 vitamin K biosynthetic genes were greater (P < 0.05) in breastfed compared with formula-fed infants, and 1 differed by delivery mode. Conclusions Feeding practice and delivery mode influence bacterial vitamin K production in the infant gut. High concentrations of unmetabolized PK in feces of formula-fed infants suggests formula PK content exceeds the absorptive capacity of the infant gut.
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Affiliation(s)
- Jessie L Ellis
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Mei Wang
- Department of Food Science & Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xueyan Fu
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Christopher J Fields
- High Performance Biological Computing Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sharon M Donovan
- Department of Food Science & Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sarah L Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
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9
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Fields CJ, Li L, Hiers NM, Li T, Sheng P, Huda T, Shan J, Gay L, Gu T, Bian J, Kilberg MS, Renne R, Xie M. Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PLoS Genet 2021; 17:e1009934. [PMID: 34914716 PMCID: PMC8675727 DOI: 10.1371/journal.pgen.1009934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/25/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNA) are short non-coding RNAs widely implicated in gene regulation. Most metazoan miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis does not require Drosha. The functional importance of the TSS-miRNA biogenesis is uncertain. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (AGO-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without DROSHA knockout. We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by AGO-qCLASH. Targets for miR-320a are enriched for the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and antagomir- transfected cells, differentially expressed gene products are associated with eIF2 signaling. Within the AGO-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone calnexin as a direct miR-320a down-regulated target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. In summary, our study investigates the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.
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Affiliation(s)
- Christopher J. Fields
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Nicholas M. Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Taha Huda
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Jixiu Shan
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lauren Gay
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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10
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Oh SH, Schliep K, Isenhower A, Rodriguez-Bobadilla R, Vuong VM, Fields CJ, Hernandez AG, Hoyer LL. Using Genomics to Shape the Definition of the Agglutinin-Like Sequence ( ALS) Family in the Saccharomycetales. Front Cell Infect Microbiol 2021; 11:794529. [PMID: 34970511 PMCID: PMC8712946 DOI: 10.3389/fcimb.2021.794529] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 10/13/2021] [Accepted: 11/09/2021] [Indexed: 01/09/2023] Open
Abstract
The Candida albicans agglutinin-like sequence (ALS) family is studied because of its contribution to cell adhesion, fungal colonization, and polymicrobial biofilm formation. The goal of this work was to derive an accurate census and sequence for ALS genes in pathogenic yeasts and other closely related species, while probing the boundaries of the ALS family within the Order Saccharomycetales. Bioinformatic methods were combined with laboratory experimentation to characterize 47 novel ALS loci from 8 fungal species. AlphaFold predictions suggested the presence of a conserved N-terminal adhesive domain (NT-Als) structure in all Als proteins reported to date, as well as in S. cerevisiae alpha-agglutinin (Sag1). Lodderomyces elongisporus, Meyerozyma guilliermondii, and Scheffersomyces stipitis were notable because each species had genes with C. albicans ALS features, as well as at least one that encoded a Sag1-like protein. Detection of recombination events between the ALS family and gene families encoding other cell-surface proteins such as Iff/Hyr and Flo suggest widespread domain swapping with the potential to create cell-surface diversity among yeast species. Results from the analysis also revealed subtelomeric ALS genes, ALS pseudogenes, and the potential for yeast species to secrete their own soluble adhesion inhibitors. Information presented here supports the inclusion of SAG1 in the ALS family and yields many experimental hypotheses to pursue to further reveal the nature of the ALS family.
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Affiliation(s)
- Soon-Hwan Oh
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Klaus Schliep
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Allyson Isenhower
- Department of Biology, Millikin University, Decatur, IL, United States
| | | | - Vien M. Vuong
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Christopher J. Fields
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Lois L. Hoyer
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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11
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Li L, Sheng P, Li T, Fields CJ, Hiers NM, Wang Y, Li J, Guardia CM, Licht JD, Xie M. Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins. Genes Dev 2021; 35:1595-1609. [PMID: 34819352 PMCID: PMC8653786 DOI: 10.1101/gad.348874.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 07/29/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022]
Abstract
Binding of microRNAs (miRNAs) to mRNAs normally results in post-transcriptional repression of gene expression. However, extensive base-pairing between miRNAs and target RNAs can trigger miRNA degradation, a phenomenon called target RNA-directed miRNA degradation (TDMD). Here, we systematically analyzed Argonaute-CLASH (cross-linking, ligation, and sequencing of miRNA-target RNA hybrids) data and identified numerous candidate TDMD triggers, focusing on their ability to induce nontemplated nucleotide addition at the miRNA 3' end. When exogenously expressed in various cell lines, eight triggers induce degradation of corresponding miRNAs. Both the TDMD base-pairing and surrounding sequences are essential for TDMD. CRISPR knockout of endogenous trigger or ZSWIM8, a ubiquitin ligase essential for TDMD, reduced miRNA degradation. Furthermore, degradation of miR-221 and miR-222 by a trigger in BCL2L11, which encodes a proapoptotic protein, enhances apoptosis. Therefore, we uncovered widespread TDMD triggers in target RNAs and demonstrated an example that could functionally cooperate with the encoded protein.
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Affiliation(s)
- Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Yuzhi Wang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jianping Li
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Casey M Guardia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jonathan D Licht
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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12
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Harris NL, Cock PJA, Fields CJ, Hokamp K, Maia J, Munoz-Torres M, Sharan M, Williams J. BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference. F1000Res 2021; 10. [PMID: 34721839 PMCID: PMC8524300 DOI: 10.12688/f1000research.74074.1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
The 22nd annual Bioinformatics Open Source Conference (BOSC 2021, open-bio.org/events/bosc-2021/) was held online as a track of the 2021 Intelligent Systems for Molecular Biology / European Conference on Computational Biology (ISMB/ECCB) conference. Launched in 2000 and held every year since, BOSC is the premier meeting covering topics related to open source software and open science in bioinformatics. In 2020, BOSC partnered with the Galaxy Community Conference to form the Bioinformatics Community Conference (BCC2020); that was the first BOSC to be held online. This year, BOSC returned to its roots as part of ISMB/ECCB 2021. As in 2020, the Covid-19 pandemic made it impossible to hold the conference in person, so ISMB/ECCB 2021 took place as an online meeting attended by over 2000 people from 79 countries. Nearly 200 people participated in BOSC sessions, which included 27 talks reviewed and selected from submitted abstracts, and three invited keynote talks representing a range of global perspectives on the role of open science and open source in driving research and inclusivity in the biosciences, one of which was presented in French with English subtitles.
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Affiliation(s)
- Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter J A Cock
- Information and Computational Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Christopher J Fields
- Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, D02 PN40, Ireland
| | | | - Monica Munoz-Torres
- Biochemistry and Molecular Genetics Department, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | | | - Jason Williams
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
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13
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Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Zhou R, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Longitudinal analysis of SARS-CoV-2 vaccine breakthrough infections reveal limited infectious virus shedding and restricted tissue distribution. medRxiv 2021:2021.08.30.21262701. [PMID: 34494028 PMCID: PMC8423226 DOI: 10.1101/2021.08.30.21262701] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global effort to vaccinate people against SARS-CoV-2 in the midst of an ongoing pandemic has raised questions about the nature of vaccine breakthrough infections and the potential for vaccinated individuals to transmit the virus. These questions have become even more urgent as new variants of concern with enhanced transmissibility, such as Delta, continue to emerge. To shed light on how vaccine breakthrough infections compare with infections in immunologically naive individuals, we examined viral dynamics and infectious virus shedding through daily longitudinal sampling in a small cohort of adults infected with SARS-CoV-2 at varying stages of vaccination. The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. These data indicate that vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.
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14
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Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. medRxiv 2021. [PMID: 34282424 DOI: 10.1101/2021.07.12.21260208] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimate viral reproduction and clearance rates, and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to superspreading. Viral genome load often peaked days earlier in saliva than in nasal swabs, indicating strong compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of B.1.1.7 and non-B.1.1.7 viruses in nasal swabs were indistinguishable, however B.1.1.7 exhibited a significantly slower pre-peak growth rate in saliva. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
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Stribling D, Lei Y, Guardia CM, Li L, Fields CJ, Nowialis P, Opavsky R, Renne R, Xie M. A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor. RNA 2021; 27:694-709. [PMID: 33795480 PMCID: PMC8127991 DOI: 10.1261/rna.078694.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/26/2021] [Accepted: 03/24/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that function as critical posttranscriptional regulators in various biological processes. While most miRNAs are generated from processing of long primary transcripts via sequential Drosha and Dicer cleavage, some miRNAs that bypass Drosha cleavage can be transcribed as part of another small noncoding RNA. Here, we develop the target-oriented miRNA discovery (TOMiD) bioinformatic analysis method to identify Drosha-independent miRNAs from Argonaute crosslinking and sequencing of hybrids (Ago-CLASH) data sets. Using this technique, we discovered a novel miRNA derived from a primate specific noncoding RNA, the small NF90 associated RNA A (snaR-A). The miRNA derived from snaR-A (miR-snaR) arises independently of Drosha processing but requires Exportin-5 and Dicer for biogenesis. We identify that miR-snaR is concurrently up-regulated with the full snaR-A transcript in cancer cells. Functionally, miR-snaR associates with Ago proteins and targets NME1, a key metastasis inhibitor, contributing to snaR-A's role in promoting cancer cell migration. Our findings suggest a functional link between a novel miRNA and its precursor noncoding RNA.
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Affiliation(s)
- Daniel Stribling
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- UF Informatics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Yi Lei
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Casey M Guardia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Pawel Nowialis
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Rene Opavsky
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- UF Informatics Institute, University of Florida, Gainesville, Florida 32611, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
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16
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Harris NL, Cock PJA, Fields CJ, Hokamp K, Maia J, Munoz-Torres M, Taschuk M, Yehudi Y. The 21st annual Bioinformatics Open Source Conference (BOSC 2020, part of BCC2020). F1000Res 2020; 9. [PMID: 32983415 PMCID: PMC7506190 DOI: 10.12688/f1000research.26498.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/14/2020] [Indexed: 11/24/2022] Open
Abstract
Launched in 2000 and held every year since, the Bioinformatics Open Source Conference (BOSC) is a volunteer-run meeting coordinated by the Open Bioinformatics Foundation (OBF) that covers open source software development and open science in bioinformatics. Most years, BOSC has been part of the Intelligent Systems for Molecular Biology (ISMB) conference, but in 2018, and again in 2020, BOSC partnered with the Galaxy Community Conference (GCC). This year’s combined BOSC + GCC conference was called the Bioinformatics Community Conference (BCC2020, bcc2020.github.io). Originally slated to take place in Toronto, Canada, BCC2020 was moved online due to COVID-19. The meeting started with a wide array of training sessions; continued with a main program of keynote presentations, talks, posters, Birds of a Feather, and more; and ended with four days of collaboration (CoFest). Efforts to make the meeting accessible and inclusive included very low registration fees, talks presented twice a day, and closed captioning for all videos. More than 800 people from 61 countries registered for at least one part of the meeting, which was held mostly in the Remo.co video-conferencing platform.
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Affiliation(s)
- Nomi L Harris
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter J A Cock
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Christopher J Fields
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, D02 PN40, Ireland
| | | | - Monica Munoz-Torres
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - Morgan Taschuk
- Ontario Institute for Cancer Research, Toronto, Ontario, M5G 0A3, Canada
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17
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Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR. The ' in vivo lifestyle' of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. Gut Microbes 2020; 11:381-404. [PMID: 31177942 PMCID: PMC7524365 DOI: 10.1080/19490976.2019.1618173] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [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: 02/03/2023] Open
Abstract
The formation of secondary bile acids by gut microbes is a current topic of considerable biomedical interest. However, a detailed understanding of the biology of anaerobic bacteria in the genus Clostridium that are capable of generating secondary bile acids is lacking. We therefore sought to determine the transcriptional responses of two prominent secondary bile acid producing bacteria, Clostridium hylemonae and Clostridium hiranonis to bile salts (in vitro) and the cecal environment of gnotobiotic mice. The genomes of C. hylemonae DSM 15053 and C. hiranonis DSM 13275 were closed, and found to encode 3,647 genes (3,584 protein-coding) and 2,363 predicted genes (of which 2,239 are protein-coding), respectively, and 1,035 orthologs were shared between C. hylemonae and C. hiranonis. RNA-Seq analysis was performed in growth medium alone, and in the presence of cholic acid (CA) and deoxycholic acid (DCA). Growth with CA resulted in differential expression (>0.58 log2FC; FDR < 0.05) of 197 genes in C. hiranonis and 118 genes in C. hylemonae. The bile acid-inducible operons (bai) from each organism were highly upregulated in the presence of CA but not DCA. We then colonized germ-free mice with human gut bacterial isolates capable of metabolizing taurine-conjugated bile acids. This consortium included bile salt hydrolase-expressing Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Parabacteroides distasonis DSM 20701, as well as taurine-respiring Bilophila wadsworthia DSM 11045, and deoxycholic/lithocholic acid generating Clostridium hylemonae DSM 15053 and Clostridium hiranonis DSM 13275. Butyrate and iso-bile acid-forming Blautia producta ATCC 27340 was also included. The Bacteroidetes made up 84.71% of 16S rDNA cecal reads, B. wadsworthia, constituted 14.7%, and the clostridia made up <.75% of 16S rDNA cecal reads. Bile acid metabolomics of the cecum, serum, and liver indicate that the synthetic community were capable of functional bile salt deconjugation, oxidation/isomerization, and 7α-dehydroxylation of bile acids. Cecal metatranscriptome analysis revealed expression of genes involved in metabolism of taurine-conjugated bile acids. The in vivo transcriptomes of C. hylemonae and C. hiranonis suggest fermentation of simple sugars and utilization of amino acids glycine and proline as electron acceptors. Genes predicted to be involved in trimethylamine (TMA) formation were also expressed.
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Affiliation(s)
- Jason M. Ridlon
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA,CONTACT Jason M. Ridlon, Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
| | - Saravanan Devendran
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - João Mp Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Heidi Doden
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patricia G. Wolf
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gabriel V. Pereira
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lindsey Ly
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa Volland
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Meguro-Ku, Tokyo, Japan
| | | | - Tsuyoshi Murai
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - Takao Kurosawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - George E. Chlipala
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Stefan J. Green
- UIC Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Alvaro G. Hernandez
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J. Fields
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christy L. Wright
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Genta Kakiyama
- Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Isaac Cann
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Purna Kashyap
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Vance McCracken
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA,Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL, USA
| | - H. Rex Gaskins
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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18
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Giordano R, Donthu RK, Zimin AV, Julca Chavez IC, Gabaldon T, van Munster M, Hon L, Hall R, Badger JH, Nguyen M, Flores A, Potter B, Giray T, Soto-Adames FN, Weber E, Marcelino JAP, Fields CJ, Voegtlin DJ, Hill CB, Hartman GL. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochem Mol Biol 2020; 120:103334. [PMID: 32109587 DOI: 10.1016/j.ibmb.2020.103334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 02/10/2020] [Indexed: 05/12/2023]
Abstract
The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number of these duplicated genes. An Illumina GoldenGate assay of 2380 SNPs was used to determine the world-wide population structure of Ap. Glycines. China and South Korean aphids are the closest to those in North America. China is the likely origin of other Asian aphid populations. The most distantly related aphids to those in North America are from Australia. The diversity of Ap. glycines in North America has decreased over time since its arrival. The genetic diversity of Ap. glycines North American population sampled shortly after its first detection in 2001 up to 2012 does not appear to correlate with geography. However, aphids collected on soybean Rag experimental varieties in Minnesota (MN), Iowa (IA), and Wisconsin (WI), closer to high density Rhamnus cathartica stands, appear to have higher capacity to colonize resistant soybean plants than aphids sampled in Ohio (OH), North Dakota (ND), and South Dakota (SD). Samples from the former states have SNP alleles with high FST values and frequencies, that overlap with genes involved in iron metabolism, a crucial metabolic pathway that may be affected by the Rag-associated soybean plant response. The Ap. glycines Biotype 1 genome will provide needed information for future analyses of mechanisms of aphid virulence and pesticide resistance as well as facilitate comparative analyses between aphids with differing natural history and host plant range.
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Affiliation(s)
- Rosanna Giordano
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Ravi Kiran Donthu
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Irene Consuelo Julca Chavez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
| | - Toni Gabaldon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Manuella van Munster
- CIRAD-INRA-Montpellier SupAgro, TA A54/K, Campus International de Baillarguet, Montpellier, France
| | | | | | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, DHHS, Bethesda, MD, USA
| | - Minh Nguyen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandra Flores
- College of Liberal Arts and Sciences, School of Molecular and Cellular Biology, University of Illinois, Urbana, IL, USA
| | - Bruce Potter
- University of Minnesota, Southwest Research and Outreach Center, Lamberton, MN, USA
| | - Tugrul Giray
- Department of Biology, University of Puerto Rico, San Juan, PR, USA
| | - Felipe N Soto-Adames
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Entomology, Gainesville, FL, USA
| | | | - Jose A P Marcelino
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA; Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Christopher J Fields
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, USA
| | - David J Voegtlin
- Illinois Natural History Survey, University of Illinois, Urbana, IL, USA
| | | | - Glen L Hartman
- USDA-ARS and Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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19
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Tabatabaei SK, Wang B, Athreya NBM, Enghiad B, Hernandez AG, Fields CJ, Leburton JP, Soloveichik D, Zhao H, Milenkovic O. DNA punch cards for storing data on native DNA sequences via enzymatic nicking. Nat Commun 2020; 11:1742. [PMID: 32269230 PMCID: PMC7142088 DOI: 10.1038/s41467-020-15588-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 08/05/2019] [Accepted: 03/17/2020] [Indexed: 11/22/2022] Open
Abstract
Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all known platforms suffer from high cost, read-write latency and error-rates that render them noncompetitive with modern storage devices. One means to avoid the above problems is using readily available native DNA. As the sequence content of native DNA is fixed, one can modify the topology instead to encode information. Here, we introduce DNA punch cards, a macromolecular storage mechanism in which data is written in the form of nicks at predetermined positions on the backbone of native double-stranded DNA. The platform accommodates parallel nicking on orthogonal DNA fragments and enzymatic toehold creation that enables single-bit random-access and in-memory computations. We use Pyrococcus furiosus Argonaute to punch files into the PCR products of Escherichia coli genomic DNA and accurately reconstruct the encoded data through high-throughput sequencing and read alignment. Current synthetic DNA-based data storage systems have high recording costs, read-write latency and error-rates that make them uncompetitive compared to traditional digital storage. The authors use nicks in native DNA to encode data in parallel and create access sites for in-memory computations.
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Affiliation(s)
- S Kasra Tabatabaei
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Boya Wang
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Nagendra Bala Murali Athreya
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Behnam Enghiad
- Department of Chemical and Biomolecular engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alvaro Gonzalo Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher J Fields
- High Performance Computing in Biology (HPCBio), Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jean-Pierre Leburton
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - David Soloveichik
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Huimin Zhao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Chemical and Biomolecular engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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20
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Harris NL, Cock PJA, Fields CJ, Greshake Tzovaras B, Heuer M, Hokamp K, Munoz-Torres M, Peltzer A, Rieck B, Wiencko H, Yehudi Y. BOSC 2019, the 20th annual Bioinformatics Open Source Conference. F1000Res 2020; 8. [PMID: 32025286 PMCID: PMC6971845 DOI: 10.12688/f1000research.21568.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 11/20/2022] Open
Abstract
The Bioinformatics Open Source Conference is a volunteer-organized meeting that covers open source software development and open science in bioinformatics. Launched in 2000, BOSC has been held every year since. BOSC 2019, the 20th annual BOSC, took place as one of the Communities of Special Interest (COSIs) at the Intelligent Systems for Molecular Biology meeting (ISMB/ECCB 2019). The two-day meeting included a total of 46 talks and 55 posters, as well as eight Birds of a Feather interest groups. The keynote speaker was University of Cape Town professor Dr. Nicola Mulder, who spoke on “Building infrastructure for responsible open science in Africa”. Immediately after BOSC 2019, about 50 people participated in the two-day CollaborationFest (CoFest for short), an open and free community-driven event at which participants work together to contribute to bioinformatics software, documentation, training materials, and use cases.
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Affiliation(s)
- Nomi L Harris
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter J A Cock
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Christopher J Fields
- Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Michael Heuer
- University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Monica Munoz-Torres
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, 97331, USA
| | - Alexander Peltzer
- Quantitative Biology Center, University of Tübingen, Tübingen, 72074, Germany
| | - Bastian Rieck
- Machine Learning & Computational Biology Lab, ETH Zürich, Zürich, Switzerland
| | | | - Yo Yehudi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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21
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Dong Y, Sanford RA, Inskeep WP, Srivastava V, Bulone V, Fields CJ, Yau PM, Sivaguru M, Ahrén D, Fouke KW, Weber J, Werth CR, Cann IK, Keating KM, Khetani RS, Hernandez AG, Wright C, Band M, Imai BS, Fried GA, Fouke BW. Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats. Astrobiology 2019; 19:1442-1458. [PMID: 31038352 PMCID: PMC6918859 DOI: 10.1089/ast.2018.1965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.
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Affiliation(s)
- Yiran Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Robert A. Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William P. Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
- Division School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Christopher J. Fields
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Peter M. Yau
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dag Ahrén
- Microbial Ecology Group, Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Lund, Sweden
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
| | - Kyle W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology and Environmental Sciences, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Joseph Weber
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Charles R. Werth
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Civil, Architectural and Environmental Engineering, University of Texas Austin, Texas, USA
| | - Isaac K. Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kathleen M. Keating
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Radhika S. Khetani
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Chris Wright
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mark Band
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Brian S. Imai
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Glenn A. Fried
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bruce W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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22
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Tchouassi DP, Muturi EJ, Arum SO, Kim CH, Fields CJ, Torto B. Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya. PLoS Negl Trop Dis 2019; 13:e0007361. [PMID: 31173595 PMCID: PMC6584011 DOI: 10.1371/journal.pntd.0007361] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/19/2019] [Accepted: 04/04/2019] [Indexed: 12/14/2022] Open
Abstract
The composition and structure of microbial communities associated with mosquitoes remain poorly understood despite their important role in host biology and potential to be harnessed as novel strategies for mosquito-borne disease control. We employed MiSeq sequencing of the 16S rRNA gene amplicons to characterize the bacterial flora of field-collected populations of Aedes mcintoshi and Aedes ochraceus, the primary vectors of Rift Valley fever (RVF) virus in Kenya. Proteobacteria (53.5%), Firmicutes (22.0%) and Actinobacteria (10.0%) were the most abundant bacterial phyla accounting for 85.5% of the total sequences. Non-metric multi-dimensional scaling plots based on Bray-Curtis dissimilarities revealed a clear grouping of the samples by mosquito species, indicating that the two mosquito species harbored distinct microbial communities. Microbial diversity, richness and composition was strongly influenced by the site of mosquito collection and overall, Ae. ochraceus had significantly higher microbial diversity and richness than Ae. mcintoshi. Our findings suggest that host species and site of collection are important determinants of bacterial community composition and diversity in RVF virus vectors and these differences likely contribute to the spatio-temporal transmission dynamics of RVF virus. Knowledge of the microbial communities associated with disease vectors can be exploited for symbiotic control of vector-borne diseases. Here, we characterized and compared the bacterial communities of field-caught populations of Aedes mcintoshi and Aedes ochraceus, the primary vectors of Rift Valley fever (RVF) virus in Kenya. We show that the two mosquito species harbor distinct microbial communities whose diversity and richness are heavily influenced by the site of collection. Because some bacterial species are known to influence vector susceptibility to pathogens, differences in bacterial communities between the two mosquito species is likely one of the primary factors accounting for the spatial and temporal variation in transmission dynamics of RVF virus.
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Affiliation(s)
- David P. Tchouassi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- * E-mail:
| | - Ephantus J. Muturi
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois, United States of America
| | - Samwel O. Arum
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Chang-Hyun Kim
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Christopher J. Fields
- High Performance Computing in Biology (HPCBio), Roy J Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Illinois, United States of America
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
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23
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Alnaji FG, Holmes JR, Rendon G, Vera JC, Fields CJ, Martin BE, Brooke CB. Sequencing Framework for the Sensitive Detection and Precise Mapping of Defective Interfering Particle-Associated Deletions across Influenza A and B Viruses. J Virol 2019; 93:e00354-19. [PMID: 30867305 PMCID: PMC6532088 DOI: 10.1128/jvi.00354-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 11/20/2022] Open
Abstract
The mechanisms and consequences of defective interfering particle (DIP) formation during influenza virus infection remain poorly understood. The development of next-generation sequencing (NGS) technologies has made it possible to identify large numbers of DIP-associated sequences, providing a powerful tool to better understand their biological relevance. However, NGS approaches pose numerous technical challenges, including the precise identification and mapping of deletion junctions in the presence of frequent mutation and base-calling errors, and the potential for numerous experimental and computational artifacts. Here, we detail an Illumina-based sequencing framework and bioinformatics pipeline capable of generating highly accurate and reproducible profiles of DIP-associated junction sequences. We use a combination of simulated and experimental control data sets to optimize pipeline performance and demonstrate the absence of significant artifacts. Finally, we use this optimized pipeline to reveal how the patterns of DIP-associated junction formation differ between different strains and subtypes of influenza A and B viruses and to demonstrate how these data can provide insight into mechanisms of DIP formation. Overall, this work provides a detailed roadmap for high-resolution profiling and analysis of DIP-associated sequences within influenza virus populations.IMPORTANCE Influenza virus defective interfering particles (DIPs) that harbor internal deletions within their genomes occur naturally during infection in humans and during cell culture. They have been hypothesized to influence the pathogenicity of the virus; however, their specific function remains elusive. The accurate detection of DIP-associated deletion junctions is crucial for understanding DIP biology but is complicated by an array of technical issues that can bias or confound results. Here, we demonstrate a combined experimental and computational framework for detecting DIP-associated deletion junctions using next-generation sequencing (NGS). We detail how to validate pipeline performance and provide the bioinformatics pipeline for groups interested in using it. Using this optimized pipeline, we detect hundreds of distinct deletion junctions generated during infection with a diverse panel of influenza viruses and use these data to test a long-standing hypothesis concerning the molecular details of DIP formation.
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Affiliation(s)
- Fadi G Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jessica R Holmes
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - J Cristobal Vera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brigitte E Martin
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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24
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Abstract
Northern blot analysis detects RNA molecules immobilized on nylon membranes through hybridization with radioactive 32P-labeled DNA or RNA oligonucleotide probes. Alternatively, nonradioactive northern blot relies on chemiluminescent reactions triggered by horseradish peroxidase (HRP) conjugated probes. The use of regulated radioactive material and the complexity of chemiluminescent reactions and detection have hampered the adoption of northern blot techniques by the wider biomedical research community. Here, we describe a sensitive and straightforward nonradioactive northern blot method, which utilizes near-infrared (IR) fluorescent dye-labeled probes (irNorthern). We found that irNorthern has a detection limit of ∼0.05 femtomoles (fmol), which is slightly less sensitive than 32P-Northern. However, we found that the IR dye-labeled probe maintains the sensitivity after multiple usages as well as long-term storage. We also present alternative irNorthern methods using a biotinylated DNA probe, a DNA probe labeled by terminal transferase, or an RNA probe labeled during in vitro transcription. Furthermore, utilization of different IR dyes allows multiplex detection of different RNA species. Therefore, irNorthern represents a more convenient and versatile tool for RNA detection compared to traditional northern blot analysis.
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Affiliation(s)
- Bret R Miller
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Tianqi Wei
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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25
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Muturi EJ, Lagos-Kutz D, Dunlap C, Ramirez JL, Rooney AP, Hartman GL, Fields CJ, Rendon G, Kim CH. Mosquito microbiota cluster by host sampling location. Parasit Vectors 2018; 11:468. [PMID: 30107817 PMCID: PMC6092830 DOI: 10.1186/s13071-018-3036-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022] Open
Abstract
Background Microbial communities that inhabit the mosquito body play an import role in host biology and may have potential for mosquito control. However, the forces that shape these microbial communities are poorly understood. Methods To gain a better understanding of how host location influences the composition and diversity of mosquito microbiota, we performed a survey of microbial communities in mosquito samples collected from six USA states using HiSeq sequencing of the 16S rRNA gene. Results A total of 284 bacterial operational taxonomic units (OTUs) belonging to 14 phyla were detected in nine mosquito species, with Proteobacteria, Firmicutes and Actinobacteria accounting for 95% of total sequences. OTU richness varied markedly within and between mosquito species. The microbial composition and diversity was heavily influenced by the site of mosquito collection, suggesting that host location plays an important role in shaping the mosquito microbiota. Conclusions Variation in microbial composition and diversity between mosquitoes from different locations may have important implications on vector competence and transmission dynamics of mosquito-borne pathogens. Future studies should investigate the environmental factors responsible for these variations and the role of key bacteria characterized in this study on mosquito biology and their potential application in symbiotic control of mosquito-borne diseases. Electronic supplementary material The online version of this article (10.1186/s13071-018-3036-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ephantus J Muturi
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL, 61604, USA.
| | - Doris Lagos-Kutz
- National Soybean Research Center, Agricultural Research Service,U.S. Department of Agriculture, 1101 W. Peabody Dr., Urbana, IL, 61801, USA
| | - Christopher Dunlap
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL, 61604, USA
| | - Jose L Ramirez
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL, 61604, USA
| | - Alejandro P Rooney
- Crop Bioprotection Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University St., Peoria, IL, 61604, USA
| | - Glen L Hartman
- National Soybean Research Center, Agricultural Research Service,U.S. Department of Agriculture, 1101 W. Peabody Dr., Urbana, IL, 61801, USA
| | - Christopher J Fields
- High Performance Biological Computing (HPCBio), Roy J Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr., Urbana, IL, 61801, USA
| | - Gloria Rendon
- High Performance Biological Computing (HPCBio), Roy J Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr., Urbana, IL, 61801, USA
| | - Chang-Hyun Kim
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign, IL, 61820, USA
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26
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Showmaker KC, Walden KKO, Fields CJ, Lambert KN, Hudson ME. Genome Sequence of the Soybean Cyst Nematode (Heterodera glycines) Endosymbiont "Candidatus Cardinium hertigii" Strain cHgTN10. Genome Announc 2018; 6:e00624-18. [PMID: 29954916 PMCID: PMC6025951 DOI: 10.1128/genomea.00624-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/02/2018] [Indexed: 02/01/2023]
Abstract
In this study, we present the genome sequence of the "Candidatus Cardinium hertigii" strain cHgTN10, an endosymbiotic bacterium of the plant-parasitic nematode Heterodera glycines This is the first genome assembly reported for an endosymbiont directly sequenced from a tylenchid nematode.
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Affiliation(s)
- Kurt C Showmaker
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kimberly K O Walden
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kris N Lambert
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Matthew E Hudson
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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27
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Harris SC, Devendran S, Méndez- García C, Mythen SM, Wright CL, Fields CJ, Hernandez AG, Cann I, Hylemon PB, Ridlon JM. Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243 T. Gut Microbes 2018; 9:523-539. [PMID: 29617190 PMCID: PMC6287680 DOI: 10.1080/19490976.2018.1458180] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [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: 02/03/2023] Open
Abstract
Strains of Eggerthella lenta are capable of oxidation-reduction reactions capable of oxidizing and epimerizing bile acid hydroxyl groups. Several genes encoding these enzymes, known as hydroxysteroid dehydrogenases (HSDH) have yet to be identified. It is also uncertain whether the products of E. lenta bile acid metabolism are further metabolized by other members of the gut microbiota. We characterized a novel human fecal isolate identified as E. lenta strain C592. The complete genome of E. lenta strain C592 was sequenced and comparative genomics with the type strain (DSM 2243) revealed high conservation, but some notable differences. E. lenta strain C592 falls into group III, possessing 3α, 3β, 7α, and 12α-hydroxysteroid dehydrogenase (HSDH) activity, as determined by mass spectrometry of thin layer chromatography (TLC) separated metabolites of primary and secondary bile acids. Incubation of E. lenta oxo-bile acid and iso-bile acid metabolites with whole-cells of the high-activity bile acid 7α-dehydroxylating bacterium, Clostridium scindens VPI 12708, resulted in minimal conversion of oxo-derivatives to lithocholic acid (LCA). Further, Iso-chenodeoxycholic acid (iso-CDCA; 3β,7α-dihydroxy-5β-cholan-24-oic acid) was not metabolized by C. scindens. We then located a gene encoding a novel 12α-HSDH in E. lenta DSM 2243, also encoded by strain C592, and the recombinant purified enzyme was characterized and substrate-specificity determined. Genomic analysis revealed genes encoding an Rnf complex (rnfABCDEG), an energy conserving hydrogenase (echABCDEF) complex, as well as what appears to be a complete Wood-Ljungdahl pathway. Our prediction that by changing the gas atmosphere from nitrogen to hydrogen, bile acid oxidation would be inhibited, was confirmed. These results suggest that E. lenta is an important bile acid metabolizing gut microbe and that the gas atmosphere may be an important and overlooked regulator of bile acid metabolism in the gut.
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Affiliation(s)
- Spencer C. Harris
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,McGuire Veterans Affairs, Richmond, VA, USA
| | - Saravanan Devendran
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Sean M. Mythen
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chris L. Wright
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J. Fields
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alvaro G. Hernandez
- Keck Center for Biotechnology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Isaac Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Phillip B. Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,McGuire Veterans Affairs, Richmond, VA, USA
| | - Jason M. Ridlon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Cancer Center of Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA,CONTACT Jason M. Ridlon Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL USA
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28
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Herb BR, Shook MS, Fields CJ, Robinson GE. Defense against territorial intrusion is associated with DNA methylation changes in the honey bee brain. BMC Genomics 2018; 19:216. [PMID: 29580210 PMCID: PMC5870497 DOI: 10.1186/s12864-018-4594-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to specific environmental conditions, and may thus be a neuromolecular regulator of both of these processes. A previous study reported DNA methylation differences between aggressive Africanized and gentle European honey bees. We investigated whether threat-induced aggression altered DNA methylation profiles in the honey bee brain in response to a behavioral stimulus (aggression-provoking intruder bee or inert control). We sampled five minutes and two hours after stimulus exposure to examine the effect of time on epigenetic profiles of aggression. RESULTS There were DNA methylation differences between aggressive and control bees for individual cytosine-guanine dinucleotides (CpGs) across the genome. Eighteen individual CpG sites showed significant difference between aggressive and control bees 120 min post stimulus. For clusters of CpGs, we report four genomic regions differentially methylated between aggressive and control bees at the 5-min time point, and 50 regions differentially methylated at the120-minute time point following intruder exposure. Differential methylation occurred at genes involved in neural plasticity, chromatin remodeling and hormone signaling. Additionally, there was a significant overlap of differential methylation with previously published epigenetic differences that distinguish aggressive Africanized and gentle European honey bees, suggesting an evolutionarily conserved use of brain DNA methylation in the regulation of aggression. Lastly, we identified individually statistically suggestive CpGs that as a group were significantly associated with differentially expressed genes underlying aggressive behavior and also co-localize with binding sites of transcription factors involved in neuroplasticity or neurodevelopment. CONCLUSIONS There were DNA methylation differences in the brain associated with response to an intruder. These differences increased in number a few hours after the initial exposure and overlap with previously reported aggression-associated genes and neurobiologically relevant transcription factor binding sites. Many DNA methylation differences that occurred in association with the expression of aggression in real time also exist between Africanized bees and European bees, suggesting an evolutionarily conserved role for epigenetic regulation in aggressive behavior.
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Affiliation(s)
- Brian R Herb
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Molly S Shook
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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29
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Avalos A, Pan H, Li C, Acevedo-Gonzalez JP, Rendon G, Fields CJ, Brown PJ, Giray T, Robinson GE, Hudson ME, Zhang G. A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee. Nat Commun 2017; 8:1550. [PMID: 29142254 PMCID: PMC5688081 DOI: 10.1038/s41467-017-01800-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 06/12/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait. Africanized honey bees (AHB) are notoriously aggressive, but in Puerto Rico they have a ‘gentle’ phenotype. Here, Avalos et al. show that there has been a soft selective sweep at several loci in the Puerto Rican AHB population and suggest a role in the rapid evolution of gentle behaviour.
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Affiliation(s)
- Arian Avalos
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hailin Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Cai Li
- China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | | | - Gloria Rendon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Patrick J Brown
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tugrul Giray
- Departamento de Biología, Universidad de Puerto Rico, Río Piedras, PR, 00931, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Matthew E Hudson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China. .,China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China. .,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark.
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30
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Abstract
The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC (
http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.
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Affiliation(s)
- Nomi L Harris
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Brad Chapman
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christopher J Fields
- High Performance Computing in Biology Group, Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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31
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Sun J, Zhang Y, Xu T, Zhang Y, Mu H, Zhang Y, Lan Y, Fields CJ, Hui JHL, Zhang W, Li R, Nong W, Cheung FKM, Qiu JW, Qian PY. Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes. Nat Ecol Evol 2017; 1:121. [PMID: 28812709 DOI: 10.1038/s41559-017-0121] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/16/2017] [Indexed: 01/08/2023]
Abstract
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro-benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.
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Affiliation(s)
- Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.,Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Science, Shenzhen University, Shenzhen, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yi Lan
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Christopher J Fields
- High Performance Computing in Biology, Roy J. Carver Biotechnology Centre, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jerome Ho Lam Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Wenyan Nong
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Fiona Ka Man Cheung
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.,HKUST-CAS Joint Laboratory, Sanya Institute of Deep Sea Science and Engineering, Sanya 572000, China
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32
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Muturi EJ, Donthu RK, Fields CJ, Moise IK, Kim CH. Effect of pesticides on microbial communities in container aquatic habitats. Sci Rep 2017; 7:44565. [PMID: 28300212 PMCID: PMC5353589 DOI: 10.1038/srep44565] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/09/2017] [Indexed: 11/25/2022] Open
Abstract
Container aquatic habitats support a specialized community of macroinvertebrates (e.g. mosquitoes) that feed on microbial communities associated with decaying organic matter. These aquatic habitats are often embedded within and around agricultural lands and are frequently exposed to pesticides. We used a microcosm approach to examine the single and combined effects of two herbicides (atrazine, glyphosate), and three insecticides (malathion, carbaryl, permethrin) on microbial communities of container aquatic habitats. MiSeq sequencing of the V4 region of both bacterial and archaeal 16S rRNA gene was used to characterize the microbial communities of indoor microcosms that were either exposed to each pesticide alone, a mix of herbicides, a mix of insecticides, or a mix of all five insecticides. Individual insecticides but not herbicides reduced the microbial diversity and richness and two insecticides, carbaryl and permethrin, also altered the microbial community structure. A mixture of herbicides had no effect on microbial diversity or structure but a mixture of insecticides or all five pesticides reduced microbial diversity and altered the community structure. These findings suggest that exposure of aquatic ecosystems to individual pesticides or their mixtures can disrupt aquatic microbial communities and there is need to decipher how these changes affect resident macroinvertebrate communities.
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Affiliation(s)
- Ephantus J. Muturi
- Crop Bioprotection Research Unit, USDA, ARS, 1815 N. University St., Peoria, IL. 61604, USA
| | - Ravi Kiran Donthu
- High Performance Biological Computing (HPCBio), Roy J Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr. Urbana, IL. 61801, USA
| | - Christopher J. Fields
- High Performance Biological Computing (HPCBio), Roy J Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr. Urbana, IL. 61801, USA
| | - Imelda K. Moise
- Department of Geography and Regional Studies, University of Miami, 1300 Campo Sano Ave., Coral Gables, FL. 33146, USA
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, USA
| | - Chang-Hyun Kim
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, 1816 S. Oak St., Champaign IL 61820, USA
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33
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Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. Plant Cell 2016; 28:2700-2714. [PMID: 27803309 PMCID: PMC5155341 DOI: 10.1105/tpc.16.00353] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/19/2016] [Accepted: 10/31/2016] [Indexed: 05/18/2023]
Abstract
Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.
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Affiliation(s)
- Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Megan J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ilya Soifer
- Calico Labs, San Francisco, California 94080
| | | | | | | | - Fei Lu
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Christopher J Fields
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Chris L Wright
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | | | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Edward Buckler
- Instiute for Genome Diversity, Cornell University, Ithaca, New York 14850
- U.S. Department of Agriculture/Agricultural Research Services, Ithaca, New York 14850
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- DOE Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706
- DOE Great Lakes Bioenergy Research Center, Madison, Wisconsin 53706
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Center for Genomics-Enabled Plant Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Mark A Mikel
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
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34
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Abstract
Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual
ISMB conference. The
17th annual BOSC (
http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.
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Affiliation(s)
- Nomi L Harris
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Brad Chapman
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Christopher J Fields
- High Performance Computing in Biology Group, Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
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35
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Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Yeoman CJ, Miller MEB, Fields CJ, Terrapon N, Le Bourvellec C, Renard CMGC, Henrissat B, White BA, Mosoni P. Erratum to: Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics 2016; 17:426. [PMID: 27267263 PMCID: PMC4896027 DOI: 10.1186/s12864-016-2758-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jordane Despres
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, Saint-Genès Champanelle, 63122, France
| | - Evelyne Forano
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, Saint-Genès Champanelle, 63122, France
| | - Pascale Lepercq
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, Saint-Genès Champanelle, 63122, France
| | - Sophie Comtet-Marre
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, Saint-Genès Champanelle, 63122, France
| | - Grégory Jubelin
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, Saint-Genès Champanelle, 63122, France
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, 59718, USA
| | - Margret E Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, Marseille, 13288, France.,INRA, USC 1408 AFMB, Marseille, 13288, France
| | - Carine Le Bourvellec
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, Avignon, F-84000, France.,Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, Avignon, F-84000, France
| | - Catherine M G C Renard
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, Avignon, F-84000, France.,Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, Avignon, F-84000, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, Marseille, 13288, France.,INRA, USC 1408 AFMB, Marseille, 13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bryan A White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pascale Mosoni
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, Saint-Genès Champanelle, 63122, France.
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36
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Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Chambon C, Yeoman CJ, Berg Miller ME, Fields CJ, Martens E, Terrapon N, Henrissat B, White BA, Mosoni P. Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level. BMC Genomics 2016; 17:326. [PMID: 27142817 PMCID: PMC4855328 DOI: 10.1186/s12864-016-2680-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/28/2016] [Indexed: 11/16/2022] Open
Abstract
Background Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1AT. Results Transcriptomic analyses of B. xylanisolvens XB1AT grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70. Conclusion This study shows that xylan degradation by B. xylanisolvens XB1AT is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens XB1AT has specialized in the degradation of xylans of low complexity. This functional feature may provide a niche to all xylanolytic bacteria harboring similar PULs. Further functional and ecological studies on fibrolytic Bacteroides species are needed to better understand their role in dietary fiber degradation and their impact on intestinal health. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2680-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jordane Despres
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Evelyne Forano
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Pascale Lepercq
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Sophie Comtet-Marre
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Gregory Jubelin
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France
| | - Christophe Chambon
- INRA, Plate-forme d'Exploration du Métabolisme, 63122, Saint-Genès Champanelle, France
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, 59718, USA
| | - Margaret E Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France.,INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France.,INRA, USC 1408 AFMB, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bryan A White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pascale Mosoni
- Institut National de la recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand-Theix, 63122, Saint-Genès-Champanelle, France.
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37
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Despres J, Forano E, Lepercq P, Comtet-Marre S, Jubelin G, Yeoman CJ, Miller MEB, Fields CJ, Terrapon N, Le Bourvellec C, Renard CMGC, Henrissat B, White BA, Mosoni P. Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis. BMC Genomics 2016; 17:147. [PMID: 26920945 PMCID: PMC4769552 DOI: 10.1186/s12864-016-2472-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 07/03/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background Diet and particularly dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Pectin is a highly consumed dietary fibre found in fruits and vegetables and is also a widely used additive in the food industry. Yet there is no information on the effect of pectin on the human gut microbiome. Likewise, little is known on gut pectinolytic bacteria and their enzyme systems. This study was undertaken to investigate the mechanisms of pectin degradation by the prominent human gut symbiont Bacteroides xylanisolvens. Results Transcriptomic analyses of B. xylanisolvens XB1A grown on citrus and apple pectins at mid- and late-log phases highlighted six polysaccharide utilization loci (PUL) that were overexpressed on pectin relative to glucose. The PUL numbers used in this report are those given by Terrapon et al. (Bioinformatics 31(5):647-55, 2015) and found in the PUL database: http://www.cazy.org/PULDB/. Based on their CAZyme composition, we propose that PUL 49 and 50, the most overexpressed PULs on both pectins and at both growth phases, are involved in homogalacturonan (HG) and type I rhamnogalacturonan (RGI) degradation, respectively. PUL 13 and PUL 2 could be involved in the degradation of arabinose-containing side chains and of type II rhamnogalacturonan (RGII), respectively. Considering that HG is the most abundant moiety (>70 %) within pectin, the importance of PUL 49 was further investigated by insertion mutagenesis into the susC-like gene. The insertion blocked transcription of the susC-like and the two downstream genes (susD-like/FnIII). The mutant showed strong growth reduction, thus confirming that PUL 49 plays a major role in pectin degradation. Conclusion This study shows the existence of six PULs devoted to pectin degradation by B. xylanisolvens, one of them being particularly important in this function. Hence, this species deploys a very complex enzymatic machinery that probably reflects the structural complexity of pectin. Our findings also highlight the metabolic plasticity of B. xylanisolvens towards dietary fibres that contributes to its competitive fitness within the human gut ecosystem. Wider functional and ecological studies are needed to understand how dietary fibers and especially plant cell wall polysaccharides drive the composition and metabolism of the fibrolytic and non-fibrolytic community within the gut microbial ecosystem. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2472-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jordane Despres
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Evelyne Forano
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Pascale Lepercq
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Sophie Comtet-Marre
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Grégory Jubelin
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, 59718, USA.
| | - Margret E Berg Miller
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Christopher J Fields
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France. .,INRA, USC 1408 AFMB, 13288, Marseille, France.
| | - Carine Le Bourvellec
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France. .,Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France.
| | - Catherine M G C Renard
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France. .,Université d'Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d'Origine Végétale, F-84000, Avignon, France.
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France. .,INRA, USC 1408 AFMB, 13288, Marseille, France. .,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Bryan A White
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Pascale Mosoni
- Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, 63122, Saint-Genès Champanelle, France.
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Lugli G, Cohen AM, Bennett DA, Shah RC, Fields CJ, Hernandez AG, Smalheiser NR. Plasma Exosomal miRNAs in Persons with and without Alzheimer Disease: Altered Expression and Prospects for Biomarkers. PLoS One 2015; 10:e0139233. [PMID: 26426747 PMCID: PMC4591334 DOI: 10.1371/journal.pone.0139233] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [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: 06/10/2015] [Accepted: 09/10/2015] [Indexed: 12/20/2022] Open
Abstract
To assess the value of exosomal miRNAs as biomarkers for Alzheimer disease (AD), the expression of microRNAs was measured in a plasma fraction enriched in exosomes by differential centrifugation, using Illumina deep sequencing. Samples from 35 persons with a clinical diagnosis of AD dementia were compared to 35 age and sex matched controls. Although these samples contained less than 0.1 microgram of total RNA, deep sequencing gave reliable and informative results. Twenty miRNAs showed significant differences in the AD group in initial screening (miR-23b-3p, miR-24-3p, miR-29b-3p, miR-125b-5p, miR-138-5p, miR-139-5p, miR-141-3p, miR-150-5p, miR-152-3p, miR-185-5p, miR-338-3p, miR-342-3p, miR-342-5p, miR-548at-5p, miR-659-5p, miR-3065-5p, miR-3613-3p, miR-3916, miR-4772-3p, miR-5001-3p), many of which satisfied additional biological and statistical criteria, and among which a panel of seven miRNAs were highly informative in a machine learning model for predicting AD status of individual samples with 83–89% accuracy. This performance is not due to over-fitting, because a) we used separate samples for training and testing, and b) similar performance was achieved when tested on technical replicate data. Perhaps the most interesting single miRNA was miR-342-3p, which was a) expressed in the AD group at about 60% of control levels, b) highly correlated with several of the other miRNAs that were significantly down-regulated in AD, and c) was also reported to be down-regulated in AD in two previous studies. The findings warrant replication and follow-up with a larger cohort of patients and controls who have been carefully characterized in terms of cognitive and imaging data, other biomarkers (e.g., CSF amyloid and tau levels) and risk factors (e.g., apoE4 status), and who are sampled repeatedly over time. Integrating miRNA expression data with other data is likely to provide informative and robust biomarkers in Alzheimer disease.
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Affiliation(s)
- Giovanni Lugli
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Aaron M. Cohen
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University, Chicago, Illinois, United States of America
| | - Raj C. Shah
- Rush Alzheimer’s Disease Center, Rush University, Chicago, Illinois, United States of America
| | | | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology Center, Urbana, Illinois, United States of America
| | - Neil R. Smalheiser
- Department of Psychiatry and Psychiatric Institute, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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39
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Chu CC, Zavala JA, Spencer JL, Curzi MJ, Fields CJ, Drnevich J, Siegfried BD, Seufferheld MJ. Patterns of differential gene expression in adult rotation-resistant and wild-type western corn rootworm digestive tracts. Evol Appl 2015; 8:692-704. [PMID: 26240606 PMCID: PMC4516421 DOI: 10.1111/eva.12278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/21/2015] [Indexed: 01/03/2023] Open
Abstract
The western corn rootworm (WCR,Diabrotica virgifera virgifera LeConte) is an important pest of corn. Annual crop rotation between corn and soybean disrupts the corn-dependent WCR life cycle and is widely adopted to manage this pest. This strategy selected for rotation-resistant (RR) WCR with reduced ovipositional fidelity to corn. Previous studies revealed that RR-WCR adults exhibit greater tolerance of soybean diets, different gut physiology, and host-microbe interactions compared to rotation-susceptible wild types (WT). To identify the genetic mechanisms underlying these phenotypic changes, a de novo assembly of the WCR adult gut transcriptome was constructed and used for RNA-sequencing analyses of RNA libraries from different WCR phenotypes fed with corn or soybean diets. Global gene expression profiles of WT- and RR-WCR were similar when feeding on corn diets, but different when feeding on soybean. Using network-based methods, we identified gene modules transcriptionally correlated with the RR phenotype. Gene ontology enrichment analyses indicated that the functions of these modules were related to metabolic processes, immune responses, biological adhesion, and other functions/processes that appear to correlate to documented traits in RR populations. These results suggest that gut transcriptomic divergence correlated with brief soybean feeding and other physiological traits may exist between RR- and WT-WCR adults.
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Affiliation(s)
- Chia-Ching Chu
- Department of Crop Sciences, University of Illinois Urbana, IL, USA
| | - Jorge A Zavala
- Facultad de Agronomía, Cátedra de Bioquímica INBA-CONICET, University of Buenos Aires-CONICET Buenos Aires, Argentina
| | - Joseph L Spencer
- Illinois Natural History Survey, University of Illinois Champaign, IL, USA
| | | | - Christopher J Fields
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center Urbana, IL, USA
| | - Jenny Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center Urbana, IL, USA
| | | | - Manfredo J Seufferheld
- Department of Entomology, University of Illinois Urbana, IL, USA ; Illinois Natural History Survey, University of Illinois Champaign, IL, USA
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Wingfield BD, Ades PK, Al-Naemi FA, Beirn LA, Bihon W, Crouch JA, de Beer ZW, De Vos L, Duong TA, Fields CJ, Fourie G, Kanzi AM, Malapi-Wight M, Pethybridge SJ, Radwan O, Rendon G, Slippers B, Santana QC, Steenkamp ET, Taylor PW, Vaghefi N, van der Merwe NA, Veltri D, Wingfield MJ. IMA Genome-F 4: Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata. IMA Fungus 2015; 6:233-48. [PMID: 26203426 PMCID: PMC4500086 DOI: 10.5598/imafungus.2015.06.01.15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 12/15/2022] Open
Abstract
The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Peter K. Ades
- Department of Forest and Ecosystem Science, The University of Melbourne, Victoria, 3010, Australia
| | - Fatima A. Al-Naemi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Lisa A. Beirn
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Wubetu Bihon
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
- Agricultural Research Council, Vegetable and Ornamental Plant Institute, P. Bag X293, Pretoria 0001, South Africa
| | - Jo Anne Crouch
- Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, MD 20705, USA
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
| | - Lieschen De Vos
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Christopher J. Fields
- High Performance Biological Computing Group, Roy J. Carver Biotechnology Center/W.M. Keck Center, University of Illinois at Urbana-Champaign, IL, USA
| | - Gerda Fourie
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
| | - Aquillah M. Kanzi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Martha Malapi-Wight
- Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, MD 20705, USA
| | - Sarah J. Pethybridge
- School of Integrative Plant Sciences, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Osman Radwan
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, IL, USA and Department of Plant Production, College of Technology, Zagazig University, Sharkia, Egypt
| | - Gloria Rendon
- High Performance Biological Computing Group, Roy J. Carver Biotechnology Center/W.M. Keck Center, University of Illinois at Urbana-Champaign, IL, USA
| | - Bernard Slippers
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Quentin C. Santana
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
| | - Paul W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, 3010, Australia
| | - Niloofar Vaghefi
- School of Integrative Plant Sciences, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Nicolaas A. van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Daniel Veltri
- Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, MD 20705, USA
- Oak Ridge Laboratories ARS Research Participation Program, USDA-ARS, Beltsville, MD 20705, USA
| | - Michael J. Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015; 16:395. [PMID: 25986459 PMCID: PMC4437557 DOI: 10.1186/s12864-015-1627-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 05/11/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015. [PMID: 25986459 DOI: 10.1186/s12864‐015‐1627‐9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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Abstract
Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. Contact:f.angly@uq.edu.au Supplementary information:Supplementary data are available at Bioinformatics online
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Affiliation(s)
- Florent E Angly
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive
- MC-195, Urbana, IL 61801, USA
| | - Christopher J Fields
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive
- MC-195, Urbana, IL 61801, USA
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive
- MC-195, Urbana, IL 61801, USA
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Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2009; 38:1767-71. [PMID: 20015970 PMCID: PMC2847217 DOI: 10.1093/nar/gkp1137] [Citation(s) in RCA: 917] [Impact Index Per Article: 61.1] [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: 11/20/2022] Open
Abstract
FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.
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Jørgensen CM, Fields CJ, Chander P, Watt D, Burgner JW, Smith JL, Switzer RL. pyr RNA binding to the Bacillus caldolyticus PyrR attenuation protein - characterization and regulation by uridine and guanosine nucleotides. FEBS J 2008; 275:655-70. [PMID: 18190533 DOI: 10.1111/j.1742-4658.2007.06227.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The PyrR protein regulates expression of pyrimidine biosynthetic (pyr) genes in many bacteria. PyrR binds to specific sites in the 5' leader RNA of target operons and favors attenuation of transcription. Filter binding and gel mobility assays were used to characterize the binding of PyrR from Bacillus caldolyticus to RNA sequences (binding loops) from the three attenuation regions of the B. caldolyticus pyr operon. Binding of PyrR to the three binding loops and modulation of RNA binding by nucleotides was similar for all three RNAs. The apparent dissociation constants at 0 degrees C were in the range 0.13-0.87 nm in the absence of effectors; dissociation constants were decreased by three- to 12-fold by uridine nucleotides and increased by 40- to 200-fold by guanosine nucleotides. The binding data suggest that pyr operon expression is regulated by the ratio of intracellular uridine nucleotides to guanosine nucleotides; the effects of nucleoside addition to the growth medium on aspartate transcarbamylase (pyrB) levels in B. subtilis cells in vivo supported this conclusion. Analytical ultracentrifugation established that RNA binds to dimeric PyrR, even though the tetrameric form of unbound PyrR predominates in solution at the concentrations studied.
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Abstract
Regulation of pyrimidine biosynthetic (pyr) genes by a transcription attenuation mechanism that is mediated by the PyrR mRNA-binding regulatory protein has been demonstrated for numerous gram-positive bacteria. Mycobacterial genomes specify pyrR genes and contain obvious PyrR-binding sequences in the initially transcribed regions of their pyr operons, but transcription antiterminator and attenuation terminator sequences are absent from their pyr 5' leader regions. This work demonstrates that repression of pyr operon expression in Mycobacterium smegmatis by exogenous uracil requires the pyrR gene and the pyr leader RNA sequence for binding of PyrR. Plasmids containing the M. smegmatis pyr promoter-leader region translationally fused to lacZ also displayed pyrR-dependent repression, but transcriptional fusions of the same sequences to a lacZ gene that retained the lacZ ribosome-binding site were not regulated by PyrR plus uracil. We propose that PyrR regulates pyr expression in M. smegmatis, other mycobacteria, and probably in numerous other bacteria by a translational repression mechanism in which nucleotide-regulated binding of PyrR occludes the first ribosome-binding site of the pyr operon.
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Affiliation(s)
- Christopher J Fields
- Department of Biochemistry, University of Illinois, 600 South Mathews, Urbana, IL 61801, USA
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Chander P, Halbig KM, Miller JK, Fields CJ, Bonner HKS, Grabner GK, Switzer RL, Smith JL. Structure of the nucleotide complex of PyrR, the pyr attenuation protein from Bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides. J Bacteriol 2005; 187:1773-82. [PMID: 15716449 PMCID: PMC1064020 DOI: 10.1128/jb.187.5.1773-1782.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [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] [Indexed: 11/20/2022] Open
Abstract
PyrR is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (pyr genes) in many bacteria. PyrR acts by binding to specific sequences on pyr mRNA and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. PyrR from Bacillus subtilis has been purified and extensively studied. In this work, we describe the purification to homogeneity and characterization of recombinant PyrR from the thermophile Bacillus caldolyticus and the crystal structures of unliganded PyrR and a PyrR-nucleotide complex. The B. caldolyticus pyrR gene was previously shown to restore normal regulation of the B. subtilis pyr operon in a pyrR deletion mutant. Like B. subtilis PyrR, B. caldolyticus PyrR catalyzes the uracil phosphoribosyltransferase reaction but with maximal activity at 60 degrees C. Crystal structures of B. caldolyticus PyrR reveal a dimer similar to the B. subtilis PyrR dimer and, for the first time, binding sites for nucleotides. UMP and GMP, accompanied by Mg2+, bind specifically to PyrR active sites. Nucleotide binding to PyrR is similar to other phosphoribosyltransferases, but Mg2+ binding differs. GMP binding was unexpected. The protein bound specific sequences of pyr RNA 100 to 1,000 times more tightly than B. subtilis PyrR, depending on the RNA tested and the assay method; uridine nucleotides enhanced RNA binding, but guanosine nucleotides antagonized it. The new findings of specific GMP binding and its antagonism of RNA binding suggest cross-regulation of the pyr operon by purines.
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Affiliation(s)
- Preethi Chander
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
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