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Brumwell A, Sutton G, Lantos PM, Hoffman K, Ruffin F, Brinkac L, Clarke TH, Adams MD, Fowler VG, Fouts DE, Thaden JT. Escherichia coli ST131 Associated with Increased Mortality in Bloodstream Infections from Urinary Tract Source. J Clin Microbiol 2023; 61:e0019923. [PMID: 37338371 PMCID: PMC10358158 DOI: 10.1128/jcm.00199-23] [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: 02/11/2023] [Accepted: 05/18/2023] [Indexed: 06/21/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone, although its clinical impact on patients with bloodstream infection (BSI) is incompletely understood. This study aims to further define the risk factors, clinical outcomes, and bacterial genetics associated with ST131 BSI. A prospectively enrolled cohort study of adult inpatients with E. coli BSI was conducted from 2002 to 2015. Whole-genome sequencing was performed with the E. coli isolates. Of the 227 patients with E. coli BSI in this study, 88 (39%) were infected with ST131. Patients with E. coli ST131 BSI and those with non-ST131 BSI did not differ with respect to in-hospital mortality (17/82 [20%] versus 26/145 [18%]; P = 0.73). However, in patients with BSI from a urinary tract source, ST131 was associated with a numerically higher in-hospital mortality than patients with non-ST131 BSI (8/42 [19%] versus 4/63 [6%]; P = 0.06) and increased mortality in an adjusted analysis (odds ratio of 5.85; 95% confidence interval of 1.44 to 29.49; P = 0.02). Genomic analyses showed that ST131 isolates primarily had an H4:O25 serotype, had a higher number of prophages, and were associated with 11 flexible genomic islands as well as virulence genes involved in adhesion (papA, kpsM, yfcV, and iha), iron acquisition (iucC and iutA), and toxin production (usp and sat). In patients with E. coli BSI from a urinary tract source, ST131 was associated with increased mortality in an adjusted analysis and contained a distinct repertoire of genes influencing pathogenesis. These genes could contribute to the higher mortality observed in patients with ST131 BSI.
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Affiliation(s)
- Amanda Brumwell
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland, USA
- Noblis, Inc., Washington, DC, USA
| | - Paul M. Lantos
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kate Hoffman
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - Felicia Ruffin
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | | | | | - Mark D. Adams
- J. Craig Venter Institute, Rockville, Maryland, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Vance G. Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Clinical Research Institute, Durham, North Carolina, USA
| | | | - Joshua T. Thaden
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
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2
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Clarke TH, Greco C, Brinkac L, Nelson KE, Singh H. MPrESS: An R-Package for Accurately Predicting Power for Comparisons of 16S rRNA Microbiome Taxa Distributions including Simulation by Dirichlet Mixture Modeling. Microorganisms 2023; 11:1166. [PMID: 37317139 DOI: 10.3390/microorganisms11051166] [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: 02/27/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
Deep sequencing has revealed that the 16S rRNA gene composition of the human microbiome can vary between populations. However, when existing data are insufficient to address the desired study questions due to limited sample sizes, Dirichlet mixture modeling (DMM) can simulate 16S rRNA gene predictions from experimental microbiome data. We examined the extent to which simulated 16S rRNA gene microbiome data can accurately reflect the diversity within that identified from experimental data and calculate the power. Even when experimental and simulated datasets differed by less than 10%, simulation by DMM consistently overestimates power, except when using only highly discriminating taxa. Admixtures of DMM with experimental data performed poorly compared to pure simulation and did not show the same correlation with experimental data p-value and power values. While multiple replications of random sampling remain the favored method of determining the power, when the estimated sample size required to achieve a certain power exceeds the sample number, then simulated samples based on DMM can be used. We introduce an R-Package, MPrESS, to assist in power calculation and sample size estimation for a 16S rRNA gene microbiome dataset to detect a difference between populations. MPrESS can be downloaded from GitHub.
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Affiliation(s)
- Thomas H Clarke
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
| | - Chris Greco
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
| | - Lauren Brinkac
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
- Noblis, Reston, VA 20191, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
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3
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Correa-Garhwal SM, Baker RH, Clarke TH, Ayoub NA, Hayashi CY. The evolutionary history of cribellate orb-weaver capture thread spidroins. BMC Ecol Evol 2022; 22:89. [PMID: 35810286 PMCID: PMC9270836 DOI: 10.1186/s12862-022-02042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Background Spiders have evolved two types of sticky capture threads: one with wet adhesive spun by ecribellate orb-weavers and another with dry adhesive spun by cribellate spiders. The evolutionary history of cribellate capture threads is especially poorly understood. Here, we use genomic approaches to catalog the spider-specific silk gene family (spidroins) for the cribellate orb-weaver Uloborus diversus. Results We show that the cribellar spidroin, which forms the puffy fibrils of cribellate threads, has three distinct repeat units, one of which is conserved across cribellate taxa separated by ~ 250 Mya. We also propose candidates for a new silk type, paracribellar spidroins, which connect the puffy fibrils to pseudoflagelliform support lines. Moreover, we describe the complete repeat architecture for the pseudoflagelliform spidroin (Pflag), which contributes to extensibility of pseudoflagelliform axial fibers. Conclusions Our finding that Pflag is closely related to Flag, supports homology of the support lines of cribellate and ecribellate capture threads. It further suggests an evolutionary phase following gene duplication, in which both Flag and Pflag were incorporated into the axial lines, with subsequent loss of Flag in uloborids, and increase in expression of Flag in ecribellate orb-weavers, explaining the distinct mechanical properties of the axial lines of these two groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02042-5.
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Chaw RC, Clarke TH, Arensburger P, Ayoub NA, Hayashi CY. Gene expression profiling reveals candidate genes for defining spider silk gland types. Insect Biochem Mol Biol 2021; 135:103594. [PMID: 34052321 DOI: 10.1016/j.ibmb.2021.103594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/07/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Molecular studies of the secretory glands involved in spider silk production have revealed candidate genes for silk synthesis and a complicated history of spider silk gene evolution. However, differential gene expression profiles of the multiple silk gland types within an individual orb-web weaving spider are lacking. Each of these gland types produces a functionally distinct silk type. Comparison of gene expression among spider silk gland types would provide insight into the genes that define silk glands generally from non-silk gland tissues, and the genes that define silk glands from each other. Here, we perform 3' tag digital gene expression profiling of the seven silk gland types of the silver garden orb weaver Argiope argentata. Five of these gland types produce silks that are non-adhesive fibers, one silk includes both fibers and glue-like adhesives, and one silk is exclusively glue-like. We identify 1275 highly expressed, significantly upregulated, and tissue specific silk gland specific transcripts (SSTs). These SSTs include seven types of spider silk protein encoding genes known as spidroin genes. We find that the fiber-producing major ampullate and minor ampullate silk glands have more similar expression profiles than any other pair of glands. We also find that a subset of the SSTs is enriched for transmembrane transport and oxidoreductases, and that these transcripts highlight differences and similarities among the major ampullate, minor ampullate, and aggregate silk glands. Furthermore, we show that the wet glue-producing aggregate glands have the most unique SSTs, but still share some SSTs with fiber producing glands. Aciniform glands were the only gland type to share a majority of SSTs with other silk gland types, supporting previous hypotheses that duplication of aciniform glands and subsequent divergence of the duplicates gave rise to the multiple silk gland types within an individual spider.
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Affiliation(s)
- R Crystal Chaw
- University of California, Riverside, Department of Evolution, Ecology, and Organismal Biology, 2710 Life Science Building, Riverside, CA, 92521, USA.
| | - Thomas H Clarke
- Washington and Lee University, Department of Biology, Howe Hall, Lexington, VA, 24450, USA.
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, 91768, USA.
| | - Nadia A Ayoub
- Washington and Lee University, Department of Biology, Howe Hall, Lexington, VA, 24450, USA.
| | - Cheryl Y Hayashi
- University of California, Riverside, Department of Evolution, Ecology, and Organismal Biology, 2710 Life Science Building, Riverside, CA, 92521, USA.
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5
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Chan AP, Choi Y, Clarke TH, Brinkac LM, White RC, Jacobs MR, Bonomo RA, Adams MD, Fouts DE. AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates. J Antimicrob Chemother 2021; 75:2760-2768. [PMID: 32681170 PMCID: PMC7556812 DOI: 10.1093/jac/dkaa266] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 10/08/2019] [Revised: 05/01/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates. METHODS Using a combination of long and short reads generated from the Oxford Nanopore and Illumina platforms, contiguous chromosomes and plasmid sequences were determined. BLAST-based analysis was used to identify the RI insertion target. RESULTS Genomes of four multiply antibiotic-resistant A. baumannii clinical strains, from a US hospital system, belonging to prevalent MLST ST2 (Pasteur scheme) and ST281 (Oxford scheme) clade F isolates were sequenced to completion. A class 1 integron carrying aadB (tobramycin resistance) and aadA2 (streptomycin/spectinomycin resistance) was identified. The class 1 integron was 6.8 kb, bounded by IS26 at both ends, and embedded in a new target location between an α/β-hydrolase and a reductase. Due to its novel insertion site and unique RI composition, we suggest naming this novel RI AbGRI4. Molecular analysis of global A. baumannii isolates identified multiple AbGRI4 RI variants in non-ST2 clonal lineages, including variations in the resistance gene cassettes, integron backbone and insertion breakpoints at the hydrolase gene. CONCLUSIONS A novel RI insertion target harbouring a class 1 integron was identified in a subgroup of ST2/ST281 clinical isolates. Variants of the RI suggested evolution and horizontal transfer of the RI across clonal lineages. Long- and short-read hybrid assembly technology completely resolved the genomic context of IS-bounded RIs, which was not possible using short reads alone.
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Affiliation(s)
| | | | | | | | | | - Michael R Jacobs
- Department of Pathology, University Hospitals Cleveland Medical Center and Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
| | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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6
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Inman JM, Sutton GG, Beck E, Brinkac LM, Clarke TH, Fouts DE. Large-scale comparative analysis of microbial pan-genomes using PanOCT. Bioinformatics 2019; 35:1049-1050. [PMID: 30165579 PMCID: PMC6419995 DOI: 10.1093/bioinformatics/bty744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 06/16/2018] [Accepted: 08/22/2018] [Indexed: 12/04/2022] Open
Abstract
Summary The JCVI pan-genome pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (pan-genome ortholog clustering tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes and generate figures, tables and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used. Availability and implementation Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.
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Affiliation(s)
- Jason M Inman
- Department of Informatics, J. Craig Venter Institute, Rockville, MD, USA
| | - Granger G Sutton
- Department of Informatics, J. Craig Venter Institute, Rockville, MD, USA
| | - Erin Beck
- Department of Informatics, J. Craig Venter Institute, Rockville, MD, USA
| | - Lauren M Brinkac
- Department of Informatics, J. Craig Venter Institute, Rockville, MD, USA
| | - Thomas H Clarke
- Department of Informatics, J. Craig Venter Institute, Rockville, MD, USA
| | - Derrick E Fouts
- Department of Informatics, J. Craig Venter Institute, Rockville, MD, USA
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7
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Duan Y, Llorente C, Lang S, Brandl K, Chu H, Jiang L, White RC, Clarke TH, Nguyen K, Torralba M, Shao Y, Liu J, Hernandez-Morales A, Lessor L, Rahman IR, Miyamoto Y, Ly M, Gao B, Sun W, Kiesel R, Hutmacher F, Lee S, Ventura-Cots M, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Bataller R, Tu XM, Eckmann L, van der Donk WA, Young R, Lawley TD, Stärkel P, Pride D, Fouts DE, Schnabl B. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature 2019; 575:505-511. [PMID: 31723265 PMCID: PMC6872939 DOI: 10.1038/s41586-019-1742-x] [Citation(s) in RCA: 429] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022]
Abstract
Chronic liver disease due to alcohol use disorder contributes markedly to the global burden of disease and mortality1–3. Alcoholic hepatitis is a severe and life-threatening form of alcohol-associated liver disease. The gut microbiota promotes ethanol-induced liver disease in mice4, but little is known about microbial factors responsible for this process. We identified cytolysin, a two-subunit exotoxin secreted by Enterococcus faecalis (E. faecalis)5,6, to cause hepatocyte death and liver injury. Compared with controls, patients with alcoholic hepatitis have increased fecal numbers of E. faecalis. The presence of cytolysin-positive (cytolytic) E. faecalis correlated with liver disease severity and mortality in patients with alcoholic hepatitis. Using humanized mice colonized with bacteria from feces of patients with alcoholic hepatitis, we investigated the therapeutic effects of bacteriophages that target cytolytic E. faecalis. We found these phages to decrease cytolysin in the liver and abolish ethanol-induced liver disease in humanized mice. Our findings link cytolysin-positive E. faecalis with worse clinical outcomes and mortality in patients with alcoholic hepatitis. We show that bacteriophages can specifically target cytolytic E. faecalis, providing a method to precisely edit the intestinal microbiota. A prospective clinical trial with a larger cohort is required to validate human relevance of our findings and to test whether this new therapeutic approach is effective for patients with alcoholic hepatitis.
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Affiliation(s)
- Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Cristina Llorente
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Sonja Lang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Katharina Brandl
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Huikuan Chu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lu Jiang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | | | | | | | | | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Jinyuan Liu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | | | - Lauren Lessor
- Center for Phage Technology, Texas A & M AgriLife Research and Texas A & M University, College Station, TX, USA
| | - Imran R Rahman
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yukiko Miyamoto
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Melissa Ly
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Bei Gao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Weizhong Sun
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roman Kiesel
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Felix Hutmacher
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Suhan Lee
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Meritxell Ventura-Cots
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh Liver Research Center, Pittsburgh, PA, USA
| | - Francisco Bosques-Padilla
- Hospital Universitario, Departamento de Gastroenterología, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Elizabeth C Verna
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Juan G Abraldes
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Robert S Brown
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA
| | - Victor Vargas
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Jose Altamirano
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Caballería
- Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.,Liver Unit, Hospital Clinic, Barcelona, Spain
| | - Debbie L Shawcross
- Liver Sciences, Department of Inflammation Biology, School of Infectious Diseases and Microbial Sciences, King's College London, London, UK
| | - Samuel B Ho
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Alexandre Louvet
- Service des Maladies de L'appareil Digestif et Unité INSERM, Hôpital Huriez, Lille, France
| | - Michael R Lucey
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Philippe Mathurin
- Service des Maladies de L'appareil Digestif et Unité INSERM, Hôpital Huriez, Lille, France
| | - Guadalupe Garcia-Tsao
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA.,Section of Digestive Diseases, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Ramon Bataller
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh Liver Research Center, Pittsburgh, PA, USA
| | - Xin M Tu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Lars Eckmann
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, TX, USA.,Center for Phage Technology, Texas A & M AgriLife Research and Texas A & M University, College Station, TX, USA
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Peter Stärkel
- St Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - David Pride
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Pathology, University of California San Diego, La Jolla, CA, USA.,Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA
| | | | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA. .,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA. .,Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA.
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Clarke TH, Brinkac LM, Sutton G, Fouts DE. GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models. Bioinformatics 2019; 34:3032-3034. [PMID: 29668840 PMCID: PMC6129299 DOI: 10.1093/bioinformatics/bty300] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/12/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation The vast number of available sequenced bacterial genomes occasionally exceeds the facilities of comparative genomic methods or is dominated by a single outbreak strain, and thus a diverse and representative subset is required. Generation of the reduced subset currently requires a priori supervised clustering and sequence-only selection of medoid genomic sequences, independent of any additional genome metrics or strain attributes. Results The Gaussian Genome Representative Selector with Prioritization (GGRaSP) R-package described below generates a reduced subset of genomes that prioritizes maintaining genomes of interest to the user as well as minimizing the loss of genetic variation. The package also allows for unsupervised clustering by modeling the genomic relationships using a Gaussian mixture model to select an appropriate cluster threshold. We demonstrate the capabilities of GGRaSP by generating a reduced list of 315 genomes from a genomic dataset of 4600 Escherichia coli genomes, prioritizing selection by type strain and by genome completeness. Availability and implementaion GGRaSP is available at https://github.com/JCVenterInstitute/ggrasp/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Lauren M Brinkac
- J. Craig Venter Institute, Rockville, MD, USA.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
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9
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Correa-Garhwal SM, Clarke TH, Janssen M, Crevecoeur L, McQuillan BN, Simpson AH, Vink CJ, Hayashi CY. Spidroins and Silk Fibers of Aquatic Spiders. Sci Rep 2019; 9:13656. [PMID: 31541123 PMCID: PMC6754431 DOI: 10.1038/s41598-019-49587-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 01/15/2019] [Accepted: 08/24/2019] [Indexed: 12/21/2022] Open
Abstract
Spiders are commonly found in terrestrial environments and many rely heavily on their silks for fitness related tasks such as reproduction and dispersal. Although rare, a few species occupy aquatic or semi-aquatic habitats and for them, silk-related specializations are also essential to survive in aquatic environments. Most spider silks studied to date are from cob-web and orb-web weaving species, leaving the silks from many other terrestrial spiders as well as water-associated spiders largely undescribed. Here, we characterize silks from three Dictynoidea species: the aquatic spiders Argyroneta aquatica and Desis marina as well as the terrestrial Badumna longinqua. From silk gland RNA-Seq libraries, we report a total of 47 different homologs of the spidroin (spider fibroin) gene family. Some of these 47 spidroins correspond to known spidroin types (aciniform, ampullate, cribellar, pyriform, and tubuliform), while other spidroins represent novel branches of the spidroin gene family. We also report a hydrophobic amino acid motif (GV) that, to date, is found only in the spidroins of aquatic and semi-aquatic spiders. Comparison of spider silk sequences to the silks from other water-associated arthropods, shows that there is a diversity of strategies to function in aquatic environments.
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Affiliation(s)
- Sandra M Correa-Garhwal
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92591, USA.
| | - Thomas H Clarke
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92591, USA
- J. Craig Venter Institute, Rockville, MD, 28050, USA
| | | | - Luc Crevecoeur
- Limburg Dome for Nature Study, Provincial Nature Center, Genk, 3600, Belgium
| | | | | | - Cor J Vink
- Canterbury Museum, Christchurch, 8013, New Zealand
| | - Cheryl Y Hayashi
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92591, USA
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
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10
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Correa-Garhwal SM, Chaw RC, Dugger T, Clarke TH, Chea KH, Kisailus D, Hayashi CY. Semi-aquatic spider silks: transcripts, proteins, and silk fibres of the fishing spider, Dolomedes triton (Pisauridae). Insect Mol Biol 2019; 28:35-51. [PMID: 30059178 DOI: 10.1111/imb.12527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To survive in terrestrial and aquatic environments, spiders often rely heavily on their silk. The vast majority of silks that have been studied are from orb-web or cob-web weaving species, leaving the silks of water-associated spiders largely undescribed. We characterize transcripts, proteins, and silk fibres from the semi-aquatic spider Dolomedes triton. From silk gland RNAseq libraries, we report 18 silk transcripts representing four categories of known silk protein types: aciniform, ampullate, pyriform, and tubuliform. Proteomic and structural analyses (scanning electron microscopy, energy dispersive X-ray spectrometry, contact angle) of the D. triton submersible egg sac reveal similarities to silks from aquatic caddisfly larvae. We identified two layers in D. triton egg sacs, notably a highly hydrophobic outer layer with a different elemental composition compared to egg sacs of terrestrial spiders. These features may provide D. triton egg sacs with their water repellent properties.
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Affiliation(s)
- S M Correa-Garhwal
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - R C Chaw
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
- Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - T Dugger
- Materials Science and Engineering Program, University of California, Riverside, CA, USA
| | - T H Clarke
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
- J. Craig Venter Institute, Rockville, MD, USA
| | - K H Chea
- Materials Science and Engineering Program, University of California, Riverside, CA, USA
| | - D Kisailus
- Materials Science and Engineering Program, University of California, Riverside, CA, USA
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - C Y Hayashi
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Collin MA, Clarke TH, Ayoub NA, Hayashi CY. Genomic perspectives of spider silk genes through target capture sequencing: Conservation of stabilization mechanisms and homology-based structural models of spidroin terminal regions. Int J Biol Macromol 2018; 113:829-840. [DOI: 10.1016/j.ijbiomac.2018.02.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/06/2018] [Indexed: 11/30/2022]
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12
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Clarke TH, Brinkac LM, Inman JM, Sutton G, Fouts DE. PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes. BMC Bioinformatics 2018; 19:246. [PMID: 29945570 PMCID: PMC6020400 DOI: 10.1186/s12859-018-2250-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 09/08/2017] [Accepted: 06/14/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to locate and analyze these regions. Multiple software packages are available to visualize pan-genomes, but currently their ability to address these concerns are limited by using only pre-computed data sets, prioritizing core over variable gene clusters, or by not accounting for pan-chromosome positioning in the viewer. RESULTS We introduce PanACEA (Pan-genome Atlas with Chromosome Explorer and Analyzer), which utilizes locally-computed interactive web-pages to view ordered pan-genome data. It consists of multi-tiered, hierarchical display pages that extend from pan-chromosomes to both core and variable regions to single genes. Regions and genes are functionally annotated to allow for rapid searching and visual identification of regions of interest with the option that user-supplied genomic phylogenies and metadata can be incorporated. PanACEA's memory and time requirements are within the capacities of standard laptops. The capability of PanACEA as a research tool is demonstrated by highlighting a variable region important in differentiating strains of Enterobacter hormaechei. CONCLUSIONS PanACEA can rapidly translate the results of pan-chromosome programs into an intuitive and interactive visual representation. It will empower researchers to visually explore and identify regions of the pan-chromosome that are most biologically interesting, and to obtain publication quality images of these regions.
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Affiliation(s)
| | - Lauren M Brinkac
- J. Craig Venter Institute, Rockville, MD, 20850, USA
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Jason M Inman
- J. Craig Venter Institute, Rockville, MD, 20850, USA
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13
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Brinkac L, Clarke TH, Singh H, Greco C, Gomez A, Torralba MG, Frank B, Nelson KE. Spatial and Environmental Variation of the Human Hair Microbiota. Sci Rep 2018; 8:9017. [PMID: 29899411 PMCID: PMC5997989 DOI: 10.1038/s41598-018-27100-1] [Citation(s) in RCA: 21] [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: 11/10/2017] [Accepted: 05/18/2018] [Indexed: 02/07/2023] Open
Abstract
The skin is a complex living ecosystem harboring diverse microbial communities. Its highly variable properties and influence of intrinsic and extrinsic factors creates unique microenvironments where niche-specific microbes thrive. As part of the skin, hair supports its own microbial habitat that is also intra and inter-personal variable. This little explored substrate has significant potential in forensics microbiome research due to the unique signatures that are available on an individual. To further investigate this, we explored the hair microbiota from scalp and pubic regions in healthy adults to investigate how the hair shaft microenvironment varies microbially. Our results suggest that there are distinct differences between the microbial communities identified on hair shafts originating from different parts of the body. The taxonomic composition of the communities from different hair sources are most reminiscent of those identified from their associated cutaneous region. We further demonstrate that the hair microbiota varies by geographical origin and has the potential to be used to predict the source location of the hair.
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Affiliation(s)
- Lauren Brinkac
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD, 20850, USA.
| | - Thomas H Clarke
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD, 20850, USA
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD, 20850, USA
| | - Chris Greco
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD, 20850, USA
| | - Andres Gomez
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.,Department of Animal Science, University of Minnesota-Twin Cities, St Paul, MN, 55108, USA
| | | | - Bryan Frank
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD, 20850, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD, 20850, USA
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14
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Sutton GG, Brinkac LM, Clarke TH, Fouts DE. Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. F1000Res 2018; 7:521. [PMID: 30430006 PMCID: PMC6097438 DOI: 10.12688/f1000research.14566.2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/27/2018] [Indexed: 12/22/2022] Open
Abstract
Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp. oharae, E. hormaechei subsp. steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E. hormaechei subsp. hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.
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15
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Sutton GG, Brinkac LM, Clarke TH, Fouts DE. Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. F1000Res 2018; 7:521. [PMID: 30430006 PMCID: PMC6097438 DOI: 10.12688/f1000research.14566.1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2018] [Indexed: 07/24/2023] Open
Abstract
Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp. oharae, E. hormaechei subsp. steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E. hormaechei subsp. hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.
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16
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Correa-Garhwal SM, Chaw RC, Clarke TH, Ayoub NA, Hayashi CY. Silk gene expression of theridiid spiders: implications for male-specific silk use. ZOOLOGY 2017; 122:107-114. [PMID: 28536006 DOI: 10.1016/j.zool.2017.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 01/15/2023]
Abstract
Spiders (order Araneae) rely on their silks for essential tasks, such as dispersal, prey capture, and reproduction. Spider silks are largely composed of spidroins, members of a protein family that are synthesized in silk glands. As needed, silk stored in silk glands is extruded through spigots on the spinnerets. Nearly all studies of spider silks have been conducted on females; thus, little is known about male silk biology. To shed light on silk use by males, we compared silk gene expression profiles of mature males to those of females from three cob-web weaving species (Theridiidae). We de novo assembled species-specific male transcriptomes from Latrodectus hesperus, Latrodectus geometricus, and Steatoda grossa followed by differential gene expression analyses. Consistent with their complement of silk spigots, male theridiid spiders express appreciable amounts of aciniform, major ampullate, minor ampullate, and pyriform spidroin genes but not tubuliform spidroin genes. The relative expression levels of particular spidroin genes varied between sexes and species. Because mature males desert their prey-capture webs and become cursorial in their search for mates, we anticipated that major ampullate (dragline) spidroin genes would be the silk genes most highly expressed by males. Indeed, major ampullate spidroin genes had the highest expression in S. grossa males. However, minor ampullate spidroin genes were the most highly expressed spidroin genes in L. geometricus and L. hesperus males. Our expression profiling results suggest species-specific adaptive divergence of silk use by male theridiids.
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Affiliation(s)
| | - R Crystal Chaw
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Thomas H Clarke
- Department of Biology, University of California, Riverside, CA 92521, USA; Department of Biology, Washington and Lee University, Lexington, VA 24450, USA; J. Craig Venter Institute, Rockville, MD 20850, USA.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA.
| | - Cheryl Y Hayashi
- Department of Biology, University of California, Riverside, CA 92521, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
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17
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Vienneau-Hathaway JM, Brassfield ER, Lane AK, Collin MA, Correa-Garhwal SM, Clarke TH, Schwager EE, Garb JE, Hayashi CY, Ayoub NA. Duplication and concerted evolution of MiSp-encoding genes underlie the material properties of minor ampullate silks of cobweb weaving spiders. BMC Evol Biol 2017; 17:78. [PMID: 28288560 PMCID: PMC5348893 DOI: 10.1186/s12862-017-0927-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 08/24/2016] [Accepted: 02/24/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Orb-web weaving spiders and their relatives use multiple types of task-specific silks. The majority of spider silk studies have focused on the ultra-tough dragline silk synthesized in major ampullate glands, but other silk types have impressive material properties. For instance, minor ampullate silks of orb-web weaving spiders are as tough as draglines, due to their higher extensibility despite lower strength. Differences in material properties between silk types result from differences in their component proteins, particularly members of the spidroin (spider fibroin) gene family. However, the extent to which variation in material properties within a single silk type can be explained by variation in spidroin sequences is unknown. Here, we compare the minor ampullate spidroins (MiSp) of orb-weavers and cobweb weavers. Orb-web weavers use minor ampullate silk to form the auxiliary spiral of the orb-web while cobweb weavers use it to wrap prey, suggesting that selection pressures on minor ampullate spidroins (MiSp) may differ between the two groups. RESULTS We report complete or nearly complete MiSp sequences from five cobweb weaving spider species and measure material properties of minor ampullate silks in a subset of these species. We also compare MiSp sequences and silk properties of our cobweb weavers to published data for orb-web weavers. We demonstrate that all our cobweb weavers possess multiple MiSp loci and that one locus is more highly expressed in at least two species. We also find that the proportion of β-spiral-forming amino acid motifs in MiSp positively correlates with minor ampullate silk extensibility across orb-web and cobweb weavers. CONCLUSIONS MiSp sequences vary dramatically within and among spider species, and have likely been subject to multiple rounds of gene duplication and concerted evolution, which have contributed to the diverse material properties of minor ampullate silks. Our sequences also provide templates for recombinant silk proteins with tailored properties.
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Affiliation(s)
| | | | - Amanda Kelly Lane
- Department of Biology, Washington and Lee University, Lexington, VA USA
| | | | | | - Thomas H. Clarke
- Department of Biology, Washington and Lee University, Lexington, VA USA
- Department of Biology, University of California, Riverside, CA USA
| | - Evelyn E. Schwager
- Department of Biological Sciences, University of Massachusetts, Lowell, MA USA
| | - Jessica E. Garb
- Department of Biological Sciences, University of Massachusetts, Lowell, MA USA
| | | | - Nadia A. Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA USA
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18
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Chaw RC, Arensburger P, Clarke TH, Ayoub NA, Hayashi CY. Candidate egg case silk genes for the spider Argiope argentata from differential gene expression analyses. Insect Mol Biol 2016; 25:757-768. [PMID: 27500384 DOI: 10.1111/imb.12260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Orb-web weaving spiders produce a variety of task-specific silks from specialized silk glands. The genetics underlying the synthesis of specific silk types are largely unknown, and transcriptome analysis could be a powerful approach for identifying candidate genes. However, de novo assembly and expression profiling of silk glands with RNA-sequencing (RNAseq) are problematic because the few known gene transcripts for silk proteins are extremely long and highly repetitive. To identify candidate genes for tubuliform (egg case) silk synthesis by the orb-weaver Argiope argentata (Araneidae), we estimated transcript abundance using two sequencing methods: RNAseq reads from throughout the length of mRNA molecules, and 3' digital gene expression reads from the 3' region of mRNA molecules. Both analyses identified similar sets of genes as differentially expressed when comparing tubuliform and nonsilk gland tissue. However, incompletely assembled silk gene transcripts were identified as differentially expressed because of RNAseq read alignments to highly repetitive regions, confounding interpretation of RNAseq results. Homologues of egg case silk protein (ECP) genes were upregulated in tubuliform glands. This discovery is the first description of ECP homologues in an araneid. We also propose additional candidate genes involved in synthesis of tubuliform or other silk types.
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Affiliation(s)
- R C Chaw
- Department of Biology, University of California, Riverside, CA, USA
| | - P Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA
| | - T H Clarke
- Department of Biology, University of California, Riverside, CA, USA
- Department of Biology, Washington and Lee University, Lexington, VA, USA
| | - N A Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA, USA
| | - C Y Hayashi
- Department of Biology, University of California, Riverside, CA, USA
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19
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Collin MA, Clarke TH, Ayoub NA, Hayashi CY. Evidence from Multiple Species that Spider Silk Glue Component ASG2 is a Spidroin. Sci Rep 2016; 6:21589. [PMID: 26875681 PMCID: PMC4753498 DOI: 10.1038/srep21589] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Spiders in the superfamily Araneoidea produce viscous glue from aggregate silk glands. Aggregate glue coats prey-capture threads and hampers the escape of prey from webs, thereby increasing the foraging success of spiders. cDNAs for Aggregate Spider Glue 1 (ASG1) and 2 (ASG2) have been previously described from the golden orb-weaver, Nephila clavipes, and Western black widow, Latrodectus hesperus. To further investigate aggregate glues, we assembled ASG1 and ASG2 from genomic target capture libraries constructed from three species of cob-web weavers and three species of orb-web weavers, all araneoids. We show that ASG1 is unlikely to be a glue, but rather is part of a widespread arthropod gene family, the peritrophic matrix proteins. For ASG2, we demonstrate its remarkable architectural and sequence similarities to spider silk fibroins, indicating that ASG2 is a member of the spidroin gene family. Thus, spidroins have diversified into glues in addition to task-specific, high performance fibers.
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Affiliation(s)
- Matthew A Collin
- University of California, Riverside, Department of Biology, Riverside, California 92521, United States
| | - Thomas H Clarke
- University of California, Riverside, Department of Biology, Riverside, California 92521, United States.,Washington and Lee University, Department of Biology, Lexington, Virginia 24450, United States
| | - Nadia A Ayoub
- Washington and Lee University, Department of Biology, Lexington, Virginia 24450, United States
| | - Cheryl Y Hayashi
- University of California, Riverside, Department of Biology, Riverside, California 92521, United States
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20
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Haney RA, Clarke TH, Gadgil R, Fitzpatrick R, Hayashi CY, Ayoub NA, Garb JE. Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders. Genome Biol Evol 2016; 8:228-42. [PMID: 26733576 PMCID: PMC4758249 DOI: 10.1093/gbe/evv253] [Citation(s) in RCA: 33] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. By assembling and analyzing multitissue transcriptomes from the Western black widow spider and two closely related species with distinct venom toxicity phenotypes, we do not find that gene duplication and duplicate retention is greater in gene families with venom gland biased expression in comparison with broadly expressed families. Positive selection has acted on some venom toxin families, but does not appear to be in excess for families with venom gland biased expression. Moreover, we find 309 distinct gene families that have single transcripts with venom gland biased expression, suggesting that the switching of genes to venom gland expression in numerous unrelated gene families has been a dominant mode of evolution. We also find ample variation in protein sequences of venom gland–specific transcripts, lineage-specific family sizes, and ortholog expression among species. This variation might contribute to the variable venom toxicity of these species.
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Affiliation(s)
- Robert A Haney
- Department of Biological Sciences, University of Massachusetts, Lowell
| | - Thomas H Clarke
- Department of Biology, Washington and Lee University Department of Biology, University of California, Riverside
| | - Rujuta Gadgil
- Department of Biological Sciences, University of Massachusetts, Lowell
| | - Ryan Fitzpatrick
- Department of Biological Sciences, University of Massachusetts, Lowell
| | | | - Nadia A Ayoub
- Department of Biology, Washington and Lee University
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts, Lowell
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21
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Abstract
![]()
Spider
silk research has largely focused on spidroins, proteins
that are the primary components of spider silk fibers. Although a
number of spidroins have been characterized, other types of proteins
associated with silk synthesis are virtually unknown. Previous analyses
of tissue-specific RNA-seq libraries identified 647 predicted genes
that were differentially expressed in silk glands of the Western black
widow, Latrodectus hesperus. Only ∼5%
of these silk-gland specific transcripts (SSTs) encode spidroins;
although the remaining predicted genes presumably encode other proteins
associated with silk production, this is mostly unverified. Here,
we used proteomic analysis of multiple silk glands and dragline silk
fiber to investigate the translation of the differentially expressed
genes. We find 48 proteins encoded by the differentially expressed
transcripts in L. hesperus major ampullate,
minor ampullate, and tubuliform silk glands and detect 17 SST encoded
proteins in major ampullate silk fibers. The observed proteins include
known silk-related proteins, but most are uncharacterized, with no
annotation. These unannotated proteins likely include novel silk-associated
proteins. Major and minor ampullate glands have the highest overlap
of identified proteins, consistent with their shared, distinctive
ampullate shape and the overlapping functions of major and minor ampullate
silks. Our study substantiates and prioritizes predictions from differential
expression analysis of spider silk gland transcriptomes.
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Affiliation(s)
- Ro Crystal Chaw
- Department of Biology, University of California , Riverside, California 92521, United States
| | - Sandra M Correa-Garhwal
- Department of Biology, University of California , Riverside, California 92521, United States
| | - Thomas H Clarke
- Department of Biology, Washington and Lee University , Lexington, Virginia 24450, United States
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University , Lexington, Virginia 24450, United States
| | - Cheryl Y Hayashi
- Department of Biology, University of California , Riverside, California 92521, United States
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22
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Clarke TH, Garb JE, Hayashi CY, Arensburger P, Ayoub NA. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution. Genome Biol Evol 2015; 7:1856-70. [PMID: 26058392 PMCID: PMC4524477 DOI: 10.1093/gbe/evv110] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [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] [Indexed: 12/15/2022] Open
Abstract
The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae).
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Affiliation(s)
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts, Lowell
| | | | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona
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Haney RA, Ayoub NA, Clarke TH, Hayashi CY, Garb JE. Dramatic expansion of the black widow toxin arsenal uncovered by multi-tissue transcriptomics and venom proteomics. BMC Genomics 2014; 15:366. [PMID: 24916504 PMCID: PMC4058007 DOI: 10.1186/1471-2164-15-366] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [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: 12/30/2013] [Accepted: 05/08/2014] [Indexed: 12/22/2022] Open
Abstract
Background Animal venoms attract enormous interest given their potential for pharmacological discovery and understanding the evolution of natural chemistries. Next-generation transcriptomics and proteomics provide unparalleled, but underexploited, capabilities for venom characterization. We combined multi-tissue RNA-Seq with mass spectrometry and bioinformatic analyses to determine venom gland specific transcripts and venom proteins from the Western black widow spider (Latrodectus hesperus) and investigated their evolution. Results We estimated expression of 97,217 L. hesperus transcripts in venom glands relative to silk and cephalothorax tissues. We identified 695 venom gland specific transcripts (VSTs), many of which BLAST and GO term analyses indicate may function as toxins or their delivery agents. ~38% of VSTs had BLAST hits, including latrotoxins, inhibitor cystine knot toxins, CRISPs, hyaluronidases, chitinase, and proteases, and 59% of VSTs had predicted protein domains. Latrotoxins are venom toxins that cause massive neurotransmitter release from vertebrate or invertebrate neurons. We discovered ≥ 20 divergent latrotoxin paralogs expressed in L. hesperus venom glands, significantly increasing this biomedically important family. Mass spectrometry of L. hesperus venom identified 49 proteins from VSTs, 24 of which BLAST to toxins. Phylogenetic analyses showed venom gland specific gene family expansions and shifts in tissue expression. Conclusions Quantitative expression analyses comparing multiple tissues are necessary to identify venom gland specific transcripts. We present a black widow venom specific exome that uncovers a trove of diverse toxins and associated proteins, suggesting a dynamic evolutionary history. This justifies a reevaluation of the functional activities of black widow venom in light of its emerging complexity. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-366) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts, Lowell, MA 01854, USA.
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Liu N, Wu S, Van Houten J, Wang Y, Ding B, Fei Z, Clarke TH, Reed JW, van der Knaap E. Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato. J Exp Bot 2014; 65:2507-20. [PMID: 24723401 PMCID: PMC4036516 DOI: 10.1093/jxb/eru141] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Auxin regulates the expression of diverse genes that affect plant growth and development. This regulation requires AUXIN RESPONSE FACTORS (ARFs) that bind to the promoter regions of these genes. ARF6 and ARF8 in Arabidopsis thaliana are required to promote inflorescence stem elongation and late stages of petal, stamen, and gynoecium development. All seed plants studied thus far have ARF6 and ARF8 orthologues as well as the microRNA miR167, which targets ARF6 and ARF8. Whether these genes have broadly conserved roles in flower development is not known. To address this question, the effects of down-regulation of ARF6 and ARF8 were investigated through transgenic expression of Arabidopsis MIR167a in tomato, which diverged from Arabidopsis before the radiation of dicotyledonous plants approximately 90-112 million years ago. The transgenic tomato plants overexpressing MIR167a exhibited reductions in leaf size and internode length as well as shortened petals, stamens, and styles. More significantly, the transgenic plants were female-sterile as a result of failure of wild-type pollen to germinate on the stigma surface and/or to grow through the style. RNA-Seq analysis identified many genes with significantly altered expression patterns, including those encoding products with functions in 'transcription regulation', 'cell wall' and 'lipid metabolism' categories. Putative orthologues of a subset of these genes were also differentially expressed in Arabidopsis arf6 arf8 mutant flowers. These results thus suggest that ARF6 and ARF8 have conserved roles in controlling growth and development of vegetative and flower organs in dicots.
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Affiliation(s)
- Ning Liu
- The Ohio State University, Ohio Agricultural Research and Development Center, Department of Horticulture and Crop Science, Wooster, OH 44691, USA
| | - Shan Wu
- The Ohio State University, Ohio Agricultural Research and Development Center, Department of Horticulture and Crop Science, Wooster, OH 44691, USA
| | - Jason Van Houten
- The Ohio State University, Ohio Agricultural Research and Development Center, Department of Horticulture and Crop Science, Wooster, OH 44691, USA
| | - Ying Wang
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA
| | - Biao Ding
- The Ohio State University, Department of Molecular Genetics, Columbus, OH 43210, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Thomas H Clarke
- University of North Carolina, Department of Biology, Chapel Hill, NC 27599-3280, USA
| | - Jason W Reed
- University of North Carolina, Department of Biology, Chapel Hill, NC 27599-3280, USA
| | - Esther van der Knaap
- The Ohio State University, Ohio Agricultural Research and Development Center, Department of Horticulture and Crop Science, Wooster, OH 44691, USA
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Clarke TH, Garb JE, Hayashi CY, Haney RA, Lancaster AK, Corbett S, Ayoub NA. Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit. BMC Genomics 2014; 15:365. [PMID: 24916340 PMCID: PMC4200122 DOI: 10.1186/1471-2164-15-365] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/30/2014] [Indexed: 01/13/2023] Open
Abstract
Background Spiders (Order Araneae) are essential predators in every terrestrial ecosystem largely because they have evolved potent arsenals of silk and venom. Spider silks are high performance materials made almost entirely of proteins, and thus represent an ideal system for investigating genome level evolution of novel protein functions. However, genomic level resources remain limited for spiders. Results We de novo assembled a transcriptome for the Western black widow (Latrodectus hesperus) from deeply sequenced cDNAs of three tissue types. Our multi-tissue assembly contained ~100,000 unique transcripts, of which > 27,000 were annotated by homology. Comparing transcript abundance among the different tissues, we identified 647 silk gland-specific transcripts, including the few known silk fiber components (e.g. six spider fibroins, spidroins). Silk gland specific transcripts are enriched compared to the entire transcriptome in several functions, including protein degradation, inhibition of protein degradation, and oxidation-reduction. Phylogenetic analyses of 37 gene families containing silk gland specific transcripts demonstrated novel gene expansions within silk glands, and multiple co-options of silk specific expression from paralogs expressed in other tissues. Conclusions We propose a transcriptional program for the silk glands that involves regulating gland specific synthesis of silk fiber and glue components followed by protecting and processing these components into functional fibers and glues. Our black widow silk gland gene repertoire provides extensive expansion of resources for biomimetic applications of silk in industry and medicine. Furthermore, our multi-tissue transcriptome facilitates evolutionary analysis of arachnid genomes and adaptive protein systems. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-365) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, Lexington, VA 24450, USA.
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Brunschwig A, Clarke TH, Van Prohaska J, Schmitz R. A GASTRIC SECRETORY DEPRESSANT IN EXTRACTS OF ACHLORHYDRIC CARCINOMATOUS STOMACHS. Ann Surg 2007; 113:41-6. [PMID: 17857713 PMCID: PMC1385652 DOI: 10.1097/00000658-194101000-00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Brunschwig A, Van Prohaska J, Clarke TH, Kandel E. A SECRETORY DEPRESSANT IN GASTRIC JUICE OF PATIENTS WITH PERNICIOUS ANEMIA. J Clin Invest 2006; 18:415-22. [PMID: 16694675 PMCID: PMC434888 DOI: 10.1172/jci101056] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- A Brunschwig
- Department of Surgery, and the Douglas Smith Foundation, The University of Chicago, Chicago
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Abstract
Ciliated protozoa have two kinds of nuclei: Macronuclei (MAC) and Micronuclei (MIC). In some ciliate classes, such as spirotrichs, most genes undergo several layers of DNA rearrangement during macronuclear development. Because of such processes, these organisms provide ideal systems for studying mechanisms of recombination and gene rearrangement. Here, we describe a database that contains all spirotrich genes for which both MAC and MIC versions are sequenced, with consistent annotation and easy access to all the features. An interface to query the database is available at http://oxytricha.princeton.edu/dimorphism/database.htm.
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Affiliation(s)
- Andre R O Cavalcanti
- Department of Ecology and Evolutionary Biology, Princeton University, NJ 08544, USA
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Clarke TH. A ship built together. J Am Podiatry Assoc 1979; 69:522-6. [PMID: 469167 DOI: 10.7547/87507315-69-8-522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Clarke TH. Growing pains--maturation or decline...? J Am Podiatry Assoc 1979; 69:392-3. [PMID: 448039 DOI: 10.7547/87507315-69-6-392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Clarke TH. From the nail groove to the sinus tarsi--how did we get here? Where are we going? J Am Podiatry Assoc 1978; 68:515-7. [PMID: 353122 DOI: 10.7547/87507315-68-7-515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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