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Schwartzman JA, Lebreton F, Salamzade R, Shea T, Martin MJ, Schaufler K, Urhan A, Abeel T, Camargo ILBC, Sgardioli BF, Prichula J, Guedes Frazzon AP, Giribet G, Van Tyne D, Treinish G, Innis CJ, Wagenaar JA, Whipple RM, Manson AL, Earl AM, Gilmore MS. Global diversity of enterococci and description of 18 previously unknown species. Proc Natl Acad Sci U S A 2024; 121:e2310852121. [PMID: 38416678 DOI: 10.1073/pnas.2310852121] [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: 07/10/2023] [Accepted: 12/06/2023] [Indexed: 03/01/2024] Open
Abstract
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.
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Affiliation(s)
- Julia A Schwartzman
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Biology, University of Southern California, Los Angeles, CA 90089
| | - Francois Lebreton
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Rauf Salamzade
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Melissa J Martin
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Katharina Schaufler
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- University of Greifswald, Institute of Pharmacy, Greifswald 17489, Germany
- Kiel University and University Medical Center Schleswig-Holstein, Institute of Infection Medicine, Kiel 24105, Germany
| | - Aysun Urhan
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Thomas Abeel
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Ilana L B C Camargo
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Bruna F Sgardioli
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Janira Prichula
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Federal University of Health Sciences of Porto Alegre, Porto Alegre - RS 90050-170, Brazil
| | - Ana Paula Guedes Frazzon
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre - RS, 90010-150, Brazil
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Daria Van Tyne
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburg, PA 15213
| | | | - Charles J Innis
- New England Aquarium, Animal Health Department and Anderson Cabot Center for Ocean Life, Boston, MA 02110
| | - Jaap A Wagenaar
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Ryan M Whipple
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Michael S Gilmore
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
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Coelho MA, David-Palma M, Shea T, Bowers K, McGinley-Smith S, Mohammad AW, Gnirke A, Yurkov AM, Nowrousian M, Sun S, Cuomo CA, Heitman J. Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion. bioRxiv 2024:2023.12.27.573464. [PMID: 38234769 PMCID: PMC10793447 DOI: 10.1101/2023.12.27.573464] [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] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
A large-scale comparative genomic analysis was conducted for the global human fungal pathogens within the Cryptococcus genus, compared to non-pathogenic Cryptococcus species, and related species from the sister genus Kwoniella. Chromosome-level genome assemblies were generated for multiple species of both genera, resulting in a dataset encompassing virtually all of their known diversity. Although Cryptococcus and Kwoniella have comparable genome sizes (about 19.2 and 22.9 Mb) and similar gene content, hinting at pre-adaptive pathogenic potential, our analysis found evidence in pathogenic Cryptococcus species of specific examples of gene gain (via horizontal gene transfer) and gene loss, which might represent evolutionary signatures of pathogenic development. Genome analysis also revealed a significant variation in chromosome number and structure between the two genera. By combining synteny analysis and experimental centromere validation, we found that most Cryptococcus species have 14 chromosomes, whereas most Kwoniella species have fewer (11, 8, 5 or even as few as 3). Reduced chromosome number in Kwoniella is associated with formation of giant chromosomes (up to 18 Mb) through repeated chromosome fusion events, each marked by a pericentric inversion and centromere loss. While similar chromosome inversion-fusion patterns were observed in all Kwoniella species with fewer than 14 chromosomes, no such pattern was detected in Cryptococcus. Instead, Cryptococcus species with less than 14 chromosomes, underwent chromosome reductions primarily through rearrangements associated with the loss of repeat-rich centromeres. Additionally, Cryptococcus genomes exhibited frequent interchromosomal translocations, including intercentromeric recombination facilitated by transposons shared between centromeres. Taken together, our findings advance our understanding of genomic changes possibly associated with pathogenicity in Cryptococcus and provide a foundation to elucidate mechanisms of centromere loss and chromosome fusion driving distinct karyotypes in closely related fungal species, including prominent global human pathogens.
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Affiliation(s)
- Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Katharine Bowers
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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Shea T, Mohabir JT, Kurbessoian T, Berdy B, Fontaine J, Gnirke A, Livny J, Stajich JE, Cuomo CA. Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen. Microbiol Resour Announc 2023:e0033823. [PMID: 37289095 DOI: 10.1128/mra.00338-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Lichtheimia ornata is an emerging opportunistic Mucorales pathogen that is associated with fatal infections in immunocompromised individuals. While these environmentally acquired infections have rarely been reported to date, cases were noted in a recent analysis of coronavirus disease 2019 (COVID-19)-associated mucormycosis in India. Here, we report the annotated genome sequence of the environmental isolate CBS 291.66.
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Affiliation(s)
- Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jason T Mohabir
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Tania Kurbessoian
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Brittany Berdy
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - James Fontaine
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andreas Gnirke
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Yorki S, Shea T, Cuomo CA, Walker BJ, LaRocque RC, Manson AL, Earl AM, Worby CJ. Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Brief Bioinform 2023; 24:bbad050. [PMID: 36804804 PMCID: PMC10025444 DOI: 10.1093/bib/bbad050] [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: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type's strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.
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Affiliation(s)
- Sosie Yorki
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruce J Walker
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Applied Invention, LLC, Cambridge, MA, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Colin J Worby
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Passer AR, Clancey SA, Shea T, David-Palma M, Averette AF, Boekhout T, Porcel BM, Nowrousian M, Cuomo CA, Sun S, Heitman J, Coelho MA. Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex. eLife 2022; 11:79114. [PMID: 35713948 PMCID: PMC9296135 DOI: 10.7554/elife.79114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
<title>eLife digest</title>. Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population. Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease. With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility. Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile. Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species. This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.
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Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Terrance Shea
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Márcia David-Palma
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity InstituteUtrechtNetherlands,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of AmsterdamAmsterdamNetherlands
| | - Betina M Porcel
- Génomique Métabolique, CNRS, University Evry, Université Paris-SaclayEvryFrance
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität BochumBochumGermany
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurhamUnited States
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Muñoz JF, Welsh RM, Shea T, Batra D, Gade L, Howard D, Rowe LA, Meis JF, Litvintseva AP, Cuomo CA. Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris. Genetics 2021; 218:iyab029. [PMID: 33769478 PMCID: PMC8128392 DOI: 10.1093/genetics/iyab029] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Candida auris is an emerging fungal pathogen of rising concern due to global spread, the ability to cause healthcare-associated outbreaks, and antifungal resistance. Genomic analyses revealed that early contemporaneously detected cases of C. auris were geographically stratified into four major clades. While Clades I, III, and IV are responsible for ongoing outbreaks of invasive and multidrug-resistant infections, Clade II, also termed the East Asian clade, consists primarily of cases of ear infection, is often susceptible to all antifungal drugs, and has not been associated with outbreaks. Here, we generate chromosome-level assemblies of twelve isolates representing the phylogenetic breadth of these four clades and the only isolate described to date from Clade V. This Clade V genome is highly syntenic with those of Clades I, III, and IV, although the sequence is highly divergent from the other clades. Clade II genomes appear highly rearranged, with translocations occurring near GC-poor regions, and large subtelomeric deletions in most chromosomes, resulting in a substantially different karyotype. Rearrangements and deletion lengths vary across Clade II isolates, including two from a single patient, supporting ongoing genome instability. Deleted subtelomeric regions are enriched in Hyr/Iff-like cell-surface proteins, novel candidate cell wall proteins, and an ALS-like adhesin. Cell wall proteins from these families and other drug-related genes show clade-specific signatures of selection in Clades I, III, and IV. Subtelomeric dynamics and the conservation of cell surface proteins in the clades responsible for global outbreaks causing invasive infections suggest an explanation for the different phenotypes observed between clades.
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Affiliation(s)
- José F Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rory M Welsh
- Mycotic Diseases Branch, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Dakota Howard
- Division of Scientific Resources, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Lori A Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
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Reyner L, Miller JE, Shea T. 0468 A Multiple Dose, Placebo-Controlled, Randomized Double-Blind, Multicenter Study to Investigate Triprolidine in the Treatment of Temporary Sleep Disturbance. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
American Association of Sleep Medicine guidelines states that the primary goals of the treatment of insomnia are to improve sleep quality and related daytime function. While H1 antihistamines have sedative effects, they are associated with residual daytime sleepiness and an effective dose range for hypnotic effect has hitherto not been established. Triprolidine a first generation antihistamine used to treat allergic rhinitis and the common cold has a mean half-life of 3.2 hours. We evaluated the effect of two doses of triprolodine compared with placebo on sleep onset latency and daytime sleepiness to determine the optimum dose in subjects with temporary sleep disturbance.
Methods
Multicenter, placebo-controlled, parallel group, double blind, multiple dose, randomized study of 178 patients aged 18 years or above with a primary diagnosis of temporary sleep disturbance. Patients were randomized to one of three groups. Group 1: 2 x placebo tablets; Group 2: 1 x placebo tablet + 1 x 2.5mg triprolidine tablet; Group 3: 2 x 2.5mg triprolodine tablets, taken 20 minutes before intended sleep on three consecutive evenings. Efficacy was measured objectively using the Sleep Disturbance Index using a wrist actimeter and subjectively using the Loughborough Sleep Log and Karolinska Sleepiness Scale.
Results
Both doses were statistically significantly superior to placebo in terms of quality and duration of sleep and sleep interruptions. No hangover effects or daytime sleepiness were observed with either dose compared to placebo. Patients on the 2.5 mg dose awoke more refreshed than the 5 mg dose. No serious adverse effects observed in any group and anticholinergic events i.e. dry mouth were very low.
Conclusion
Tripolidine is effective and safe in the treatment of temporary sleep disturbance. The optimum dose is 2.5mg.
Support
The study was sponsored by Boots Healthcare International.
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Affiliation(s)
- L Reyner
- Awake Ltd., Woodhouse Eaves, UNITED KINGDOM
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Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 2020; 180:816. [PMID: 32084344 PMCID: PMC7201975 DOI: 10.1016/j.cell.2020.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 2020; 180:263-277.e20. [PMID: 31955845 PMCID: PMC7197499 DOI: 10.1016/j.cell.2019.12.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022]
Abstract
Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 mya. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 million years through a process analogous to Darwinian evolution of the genome.
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Affiliation(s)
- Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Harold Pimentel
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ammar Nasif
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sophie Cook
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth Geinger
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert Lintner
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan K Pritchard
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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10
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Cuomo CA, Shea T, Nguyen T, Ashton P, Perfect J, Le T. Complete Genome Sequences for Two Talaromyces marneffei Clinical Isolates from Northern and Southern Vietnam. Microbiol Resour Announc 2020; 9:e01367-19. [PMID: 31919177 PMCID: PMC6952663 DOI: 10.1128/mra.01367-19] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 12/04/2019] [Indexed: 12/18/2022] Open
Abstract
Talaromyces marneffei is a thermally dimorphic fungus endemic in China and Southeast Asia that causes fatal infections in immunocompromised individuals, particularly in patients with advanced HIV disease. Here, we report the complete genome sequences of two clinical isolates from northern and southern Vietnam.
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Affiliation(s)
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Thu Nguyen
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Philip Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - John Perfect
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thuy Le
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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11
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Persinoti GF, Martinez DA, Li W, Döğen A, Billmyre RB, Averette A, Goldberg JM, Shea T, Young S, Zeng Q, Oliver BG, Barton R, Metin B, Hilmioğlu-Polat S, Ilkit M, Gräser Y, Martinez-Rossi NM, White TC, Heitman J, Cuomo CA. Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. Genetics 2018; 208:1657-1669. [PMID: 29467168 PMCID: PMC5887155 DOI: 10.1534/genetics.117.300573] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 11/29/2017] [Accepted: 02/07/2018] [Indexed: 11/18/2022] Open
Abstract
Dermatophytes include fungal species that infect humans, as well as those that also infect other animals or only grow in the environment. The dermatophyte species Trichophyton rubrum is a frequent cause of skin infection in immunocompetent individuals. While members of the T. rubrum species complex have been further categorized based on various morphologies, their population structure and ability to undergo sexual reproduction are not well understood. In this study, we analyze a large set of T. rubrum and T. interdigitale isolates to examine mating types, evidence of mating, and genetic variation. We find that nearly all isolates of T. rubrum are of a single mating type, and that incubation with T. rubrum "morphotype" megninii isolates of the other mating type failed to induce sexual development. While the region around the mating type locus is characterized by a higher frequency of SNPs compared to other genomic regions, we find that the population is remarkably clonal, with highly conserved gene content, low levels of variation, and little evidence of recombination. These results support a model of recent transition to asexual growth when this species specialized to growth on human hosts.
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Affiliation(s)
- Gabriela F Persinoti
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil 14049-900
| | - Diego A Martinez
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142
| | - Wenjun Li
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Aylin Döğen
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Turkey 33110
| | - R Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Anna Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Jonathan M Goldberg
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142
| | - Terrance Shea
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142
| | - Sarah Young
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142
| | - Qiandong Zeng
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142
| | - Brian G Oliver
- Center for Infectious Disease Research, Seattle, Washington 98109
| | - Richard Barton
- School of Molecular and Cellular Biology, University of Leeds, United Kingdom LS2 9JT
| | - Banu Metin
- Department of Food Engineering, Faculty of Engineering and Natural Sciences, Istanbul Sabahattin Zaim University, Turkey
| | | | - Macit Ilkit
- Division of Mycology, Department of Microbiology, Faculty of Medicine, University of Çukurova, Adana, Turkey 01330
| | - Yvonne Gräser
- Institute of Microbiology and Hygiene, University Medicine Berlin - Charité, Germany 12203
| | - Nilce M Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil 14049-900
| | - Theodore C White
- School of Biological Sciences, University of Missouri-Kansas City, Missouri 64110
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Christina A Cuomo
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142
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12
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Martin P, Jung SH, Pitcher B, Bartlett NL, Blum KA, Shea T, Hsi ED, Ruan J, Smith SE, Leonard JP, Cheson BD. A phase II trial of lenalidomide plus rituximab in previously untreated follicular non-Hodgkin's lymphoma (NHL): CALGB 50803 (Alliance). Ann Oncol 2017; 28:2806-2812. [PMID: 28945884 PMCID: PMC5789808 DOI: 10.1093/annonc/mdx496] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND This multicenter, phase II trial tested the tolerability and efficacy of lenalidomide plus rituximab in patients with previously untreated follicular lymphoma (FL). PATIENTS AND METHODS Patients with grade 1-3a FL, stage 3-4 or bulky stage 2, FL international prognostic index (FLIPI) 0-2, and no prior therapy were eligible to receive rituximab 375 mg/m2 weekly during cycle 1 and day 1 of cycles 4, 6, 8, and 10, plus lenalidomide 20-25 mg on days 1-21 for twelve 28-day cycles. The primary objectives were to evaluate response rates [complete (CR) and overall] and time to progression. Secondary objectives included toxicity, response according to polymorphisms in FcgR2A and FcgR3A, and changes in circulating pro-angiogenic cells. RESULTS From October 2010 to September 2011, 66 patients were enrolled. Median age was 53 years, 34 were female, 15 had bulky disease, 21 were FLIPI 0-1, 43 FLIPI 2, and 2 FLIPI 3. One patient withdrew before receiving treatment. Fifty-one patients completed 12 cycles of lenalidomide. Reasons for discontinuation included withdrawal (n = 6), adverse events (n = 6), progression (n = 2). Grade 3-4 hematologic toxicity included neutropenia (21%), lymphopenia (9%), and thrombocytopenia (2%), infection (11%), and rash (8%). Grade 1-2 toxicity included fatigue (78%), diarrhea (37%), rash (32%), and febrile neutropenia in one patient. The overall response rate was 95%; the CR rate was 72% (95% confidence interval, 60% to 83%). With a median follow-up of 5 years, the 2- and 5-year progression-free survival were 86% and 70%, respectively, and the 5-year overall survival was 100%. There was no association between CR rate or PFS and FLIPI, histological grade, bulky disease, FcgR2A/FcgR3A polymorphism, or change in circulating endothelial cell/hematopoietic progenitor cell. CONCLUSION Lenalidomide plus rituximab was associated with low rates of grade 3-4 toxicity, yielded a CR rate and PFS similar to chemotherapy-based treatment and may represent a reasonable alternative to immunochemotherapy in previously untreated FL. CLINICALTRIALS.GOV IDENTIFIER NCT01145495.
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Affiliation(s)
- P Martin
- Department of Medicine, Weill Cornell Medicine, New York.
| | - S-H Jung
- Alliance Statistics and Data Center, Duke University Medical Center, Durham
| | - B Pitcher
- Alliance Statistics and Data Center, Duke University Medical Center, Durham
| | - N L Bartlett
- Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis
| | - K A Blum
- The Ohio State University Medical Center, Columbus
| | - T Shea
- Oncology, University of North Carolina at Chapel Hill, Chapel Hill
| | - E D Hsi
- Clinical Pathology, Cleveland Clinic, Cleveland
| | - J Ruan
- Department of Medicine, Weill Cornell Medicine, New York
| | - S E Smith
- Alliance Protocol Office, University of Chicago, Chicago
| | - J P Leonard
- Department of Medicine, Weill Cornell Medicine, New York
| | - B D Cheson
- Hematology/Oncology, Georgetown University Hospital, Washington, USA
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13
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Martin P, Jung S, Pitcher B, Bartlett N, Blum K, Shea T, Ruan J, Smith S, Leonard J, Cheson B. FINAL RESULTS OF CALGB 50803 (ALLIANCE): A PHASE 2 TRIAL OF LENALIDOMIDE PLUS RITUXIMAB IN PATIENTS WITH PREVIOUSLY UNTREATED FOLLICULAR LYMPHOMA. Hematol Oncol 2017. [DOI: 10.1002/hon.2437_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- P. Martin
- Medicine; Weill Cornell Medicine; New York USA
| | - S. Jung
- Alliance Statistics and Data Center; Duke University Medical Center; Durham USA
| | - B. Pitcher
- Alliance Statistics and Data Center; Duke University Medical Center; Durham USA
| | - N.L. Bartlett
- Medicine; Washington University School of Medicine; St. Louis USA
| | - K.A. Blum
- Medicine; The Ohio State University; Columbus USA
| | - T. Shea
- Medicine; University of North Carolina at Chapel Hill; Chapel Hill USA
| | - J. Ruan
- Medicine; Weill Cornell Medicine; New York USA
| | - S.E. Smith
- Alliance Protocol Office; University of Chicago; Chicago USA
| | | | - B.D. Cheson
- Medicine; Georgetown University Hospital; Washington D.C. USA
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14
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Hamilton EP, Kapusta A, Huvos PE, Bidwell SL, Zafar N, Tang H, Hadjithomas M, Krishnakumar V, Badger JH, Caler EV, Russ C, Zeng Q, Fan L, Levin JZ, Shea T, Young SK, Hegarty R, Daza R, Gujja S, Wortman JR, Birren BW, Nusbaum C, Thomas J, Carey CM, Pritham EJ, Feschotte C, Noto T, Mochizuki K, Papazyan R, Taverna SD, Dear PH, Cassidy-Hanley DM, Xiong J, Miao W, Orias E, Coyne RS. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. eLife 2016; 5. [PMID: 27892853 PMCID: PMC5182062 DOI: 10.7554/elife.19090] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/14/2016] [Indexed: 12/30/2022] Open
Abstract
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena's germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.
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Affiliation(s)
- Eileen P Hamilton
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Piroska E Huvos
- Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, United States
| | | | - Nikhat Zafar
- J. Craig Venter Institute, Rockville, United States
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, United States
| | | | | | | | | | - Carsten Russ
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Qiandong Zeng
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Lin Fan
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Joshua Z Levin
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Terrance Shea
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sarah K Young
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Ryan Hegarty
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Riza Daza
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Sharvari Gujja
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jennifer R Wortman
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Bruce W Birren
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Chad Nusbaum
- Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Clayton M Carey
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Tomoko Noto
- Institute of Molecular Biotechnology, Vienna, Austria
| | | | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Eduardo Orias
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
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15
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Williams AH, Sharma M, Thatcher LF, Azam S, Hane JK, Sperschneider J, Kidd BN, Anderson JP, Ghosh R, Garg G, Lichtenzveig J, Kistler HC, Shea T, Young S, Buck SAG, Kamphuis LG, Saxena R, Pande S, Ma LJ, Varshney RK, Singh KB. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics 2016; 17:191. [PMID: 26945779 PMCID: PMC4779268 DOI: 10.1186/s12864-016-2486-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. RESULTS Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. CONCLUSIONS We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn't share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.
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Affiliation(s)
- Angela H Williams
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Louise F Thatcher
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Sarwar Azam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - James K Hane
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
- Department of Environment and Agriculture, Curtin Institute for Computation, and CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Perth, WA, 6102, Australia.
| | - Jana Sperschneider
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Brendan N Kidd
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Jonathan P Anderson
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Raju Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Gagan Garg
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Judith Lichtenzveig
- Department of Environment and Agriculture, Pulse Pathology and Genetics, Centre for Crop and Disease Management and Curtin Institute for Computation, Curtin University, Perth, WA, 6102, Australia.
| | - H Corby Kistler
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA.
| | | | - Sarah Young
- The Broad Institute, Cambridge, MA, 02141, USA.
| | - Sally-Anne G Buck
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Lars G Kamphuis
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Rachit Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Suresh Pande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Rajeev K Varshney
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Karam B Singh
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
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16
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Winglee K, Manson McGuire A, Maiga M, Abeel T, Shea T, Desjardins CA, Diarra B, Baya B, Sanogo M, Diallo S, Earl AM, Bishai WR. Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction. PLoS Negl Trop Dis 2016; 10:e0004332. [PMID: 26751217 PMCID: PMC4713829 DOI: 10.1371/journal.pntd.0004332] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/05/2015] [Indexed: 01/05/2023] Open
Abstract
Background Mycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC), causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal reservoir, a unique preference for hosts of West African ethnicity, and an inability to compete with other lineages outside of West Africa. These latter two hypotheses could be caused by loss of fitness or altered interactions with the host immune system. Methodology/Principal Findings We sequenced 92 MTC clinical isolates from Mali, including two lineage 5 and 24 lineage 6 strains. Our genome sequencing assembly, alignment, phylogeny and average nucleotide identity analyses enabled us to identify features that typify lineages 5 and 6 and made clear that these lineages do not constitute a distinct species within the MTC. We found that in Mali, lineage 6 and lineage 4 strains have similar levels of diversity and evolve drug resistance through similar mechanisms. In the process, we identified a putative novel streptomycin resistance mutation. In addition, we found evidence of person-to-person transmission of lineage 6 isolates and showed that lineage 6 is not enriched for mutations in virulence-associated genes. Conclusions This is the largest collection of lineage 5 and 6 whole genome sequences to date, and our assembly and alignment data provide valuable insights into what distinguishes these lineages from other MTC lineages. Lineages 5 and 6 do not appear to be geographically restricted due to an inability to transmit between West African hosts or to an elevated number of mutations in virulence-associated genes. However, lineage-specific mutations, such as mutations in cell wall structure, secretion systems and cofactor biosynthesis, provide alternative mechanisms that may lead to host specificity. Mycobacterium africanum consists of two lineages, lineages 5 and 6, within the Mycobacterium tuberculosis complex (MTC) that cause human tuberculosis in West Africa, but are found rarely outside of this region. Our analysis of the whole genome sequences of 26 lineage 5 and 6 isolates, and 66 isolates from other lineages within the MTC, reveal that M. africanum does not meet modern criteria to be considered an independent species. We analyzed drug resistance-associated genes and found that drug resistance evolves within these lineages through similar mechanisms as observed for the rest of the MTC in Mali. Though we did not see an elevated number of mutations in virulence-associated genes in these two lineages, we identified a number of lineage-specific mutations, pseudogenes and changes in gene content that may impact virulence and host specificity, and improve, overall, our understanding of what make these lineages unique.
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Affiliation(s)
- Kathryn Winglee
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Abigail Manson McGuire
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Mamoudou Maiga
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Thomas Abeel
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Terrance Shea
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Christopher A. Desjardins
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
| | - Bassirou Diarra
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Souleymane Diallo
- Project SEREFO (Centre de Recherche et de Formation sur le VIH/Sida et la Tuberculose)/University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ashlee M. Earl
- Genome Sequencing and Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (AME); (WRB)
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (AME); (WRB)
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17
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Velayati AA, Abeel T, Shea T, Konstantinovich Zhavnerko G, Birren B, Cassell GH, Earl AM, Hoffner S, Farnia P. Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization. Int J Mycobacteriol 2015; 5:66-73. [PMID: 26927992 DOI: 10.1016/j.ijmyco.2015.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE/BACKGROUND Mycobacterium tuberculosis (MTB) causes active tuberculosis (TB) in only a small percentage of infected people. In most cases, the infection is clinically latent, where bacilli can persist in human hosts for years without causing disease. Surprisingly, the biology of such persister cells is largely unknown. This study describes the isolation, identification, and whole-genome sequencing (WGS) of latent TB bacilli after 782days (26months) of latency (the ability of MTB bacilli to lie persistent). METHODS The in vitro double-stress model of latency (oxygen and nutrition) was designed for MTB culture. After 26months of latency, MTB cells that persisted were isolated and investigated under light and atomic force microscopy. Spoligotyping and WGS were performed to verify the identity of the strain. RESULTS We established a culture medium in which MTB bacilli arrest their growth, reduce their size (0.3-0.1μm), lose their acid fastness (85-90%) and change their shape. Spoligopatterns of latent cells were identical to original H37Rv, with differences observed at spacers two and 14. WGS revealed only a few genetic changes relative to the already published H37Rv reference genome. Among these was a large 2064-bp insertion (RvD6), which was originally detected in both H37Ra and CDC1551, but not H37Rv. CONCLUSION Here, we show cell-wall free cells of MTB bacilli in their latent state, and the biological adaptation of these cells was more phenotypic in nature than genomic. These cell-wall free cells represent a good model for understanding the nature of TB latency.
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Affiliation(s)
- Ali Akbar Velayati
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Thomas Abeel
- Genome Sequencing & Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, MA, USA; Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Terrance Shea
- Genome Sequencing & Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | | | - Bruce Birren
- Genome Sequencing & Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Gail H Cassell
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Ashlee M Earl
- Genome Sequencing & Analysis Program, The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Sven Hoffner
- Department of Microbiology, The Public Health Agency of Sweden, Solna, Sweden
| | - Parissa Farnia
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, Alm E. Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nat Biotechnol 2015; 33:1053-60. [PMID: 26368049 PMCID: PMC4720164 DOI: 10.1038/nbt.3329] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 07/28/2015] [Indexed: 01/21/2023]
Abstract
Analyses of metagenomic datasets that are sequenced to a depth of billions or trillions of bases can uncover hundreds of microbial genomes, but naive assembly of these data is computationally intensive, requiring hundreds of gigabytes to terabytes of RAM. We present latent strain analysis (LSA), a scalable, de novo pre-assembly method that separates reads into biologically informed partitions and thereby enables assembly of individual genomes. LSA is implemented with a streaming calculation of unobserved variables that we call eigengenomes. Eigengenomes reflect covariance in the abundance of short, fixed-length sequences, or k-mers. As the abundance of each genome in a sample is reflected in the abundance of each k-mer in that genome, eigengenome analysis can be used to partition reads from different genomes. This partitioning can be done in fixed memory using tens of gigabytes of RAM, which makes assembly and downstream analyses of terabytes of data feasible on commodity hardware. Using LSA, we assemble partial and near-complete genomes of bacterial taxa present at relative abundances as low as 0.00001%. We also show that LSA is sensitive enough to separate reads from several strains of the same species.
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Affiliation(s)
- Brian Cleary
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ilana Lauren Brito
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Katherine Huang
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Dirk Gevers
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Terrance Shea
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Sarah Young
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Eric Alm
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Schachtel B, Aspley S, Shephard A, Smith G, Sanner K, Savino L, Schachtel E, Lorton M, Shea T. The qualities of sore throat index (QUASTI): first use in a clinical trial testing the effects of Flurbiprofen 8.75 Mg lozenge on patient-reported qualities of throat pain. Clin Ther 2015. [DOI: 10.1016/j.clinthera.2015.05.271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Schachtel B, Shephard A, Aspley S, Smith G, Sanner K, Savino L, Schachtel E, Shea T. (363) Demonstration of clinically important relief and the percent change in pain intensity at the time of meaningful relief by flurbiprofen 8.75 mg lozenge. The Journal of Pain 2015. [DOI: 10.1016/j.jpain.2015.01.282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VLM, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DST, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MKN, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GWC, Tojo M, Topalis P, Tubio JMC, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MAT, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 2014; 347:1258522. [PMID: 25554792 DOI: 10.1126/science.1258522] [Citation(s) in RCA: 362] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.
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Affiliation(s)
- Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA.
| | - Robert M Waterhouse
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Mohammad R Abai
- Department of Medical Entomology and Vector Control, School of Public Health and Institute of Health Researches, Tehran University of Medical Sciences, Tehran, Iran
| | - Sergey S Aganezov
- George Washington University, Department of Mathematics and Computational Biology Institute, 45085 University Drive, Ashburn, VA 20147, USA
| | - Max A Alekseyev
- George Washington University, Department of Mathematics and Computational Biology Institute, 45085 University Drive, Ashburn, VA 20147, USA
| | - James E Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Amon
- National Vector Borne Disease Control Programme, Ministry of Health, Tafea Province, Vanuatu
| | - Bruno Arcà
- Department of Public Health and Infectious Diseases, Division of Parasitology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic-Pomona, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Gleb Artemov
- Tomsk State University, 36 Lenina Avenue, Tomsk, Russia
| | - Lauren A Assour
- Department of Computer Science and Engineering, Eck Institute for Global Health, 211B Cushing Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hamidreza Basseri
- Department of Medical Entomology and Vector Control, School of Public Health and Institute of Health Researches, Tehran University of Medical Sciences, Tehran, Iran
| | - Aaron Berlin
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Bruce W Birren
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Stephanie A Blandin
- Inserm, U963, F-67084 Strasbourg, France. CNRS, UPR9022, IBMC, F-67084 Strasbourg, France
| | - Andrew I Brockman
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Thomas R Burkot
- Faculty of Medicine, Health and Molecular Science, Australian Institute of Tropical Health Medicine, James Cook University, Cairns 4870, Australia
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Clara S Chan
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Joanna C Chiu
- Department of Entomology and Nematology, One Shields Avenue, University of California-Davis, Davis, CA 95616, USA
| | - Mikkel Christensen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlo Costantini
- Institut de Recherche pour le Développement, Unités Mixtes de Recherche Maladies Infectieuses et Vecteurs Écologie, Génétique, Évolution et Contrôle, 911, Avenue Agropolis, BP 64501 Montpellier, France
| | - Victoria L M Davidson
- Division of Biology, Kansas State University, 271 Chalmers Hall, Manhattan, KS 66506, USA
| | - Elena Deligianni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Nikolaou Plastira 100 GR-70013, Heraklion, Crete, Greece
| | - Tania Dottorini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Vicky Dritsou
- Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Stacey B Gabriel
- Genomics Platform, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou 01 BP 2208, Burkina Faso
| | - Andrew B Hall
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Mira V Han
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | - Thaung Hlaing
- Department of Medical Research, No. 5 Ziwaka Road, Dagon Township, Yangon 11191, Myanmar
| | - Daniel S T Hughes
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Adam M Jenkins
- Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
| | - Xiaofang Jiang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Evdoxia G Kakani
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - Maryam Kamali
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Petri Kemppainen
- Computational Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Ryan C Kennedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Ioannis K Kirmitzoglou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Bioinformatics Research Laboratory, Department of Biological Sciences, New Campus, University of Cyprus, CY 1678 Nicosia, Cyprus
| | - Lizette L Koekemoer
- Wits Research Institute for Malaria, Faculty of Health Sciences, and Vector Control Reference Unit, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, Johannesburg, South Africa
| | - Njoroge Laban
- National Museums of Kenya, P.O. Box 40658-00100, Nairobi, Kenya
| | - Nicholas Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mara K N Lawniczak
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Manolis Lirakis
- Department of Biology, University of Crete, 700 13 Heraklion, Greece
| | - Neil F Lobo
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert M MacCallum
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Chunhong Mao
- Virginia Bioinformatics Institute, 1015 Life Science Circle, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Charles Mbogo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Jenny McCarthy
- Department of Biological Sciences, California State Polytechnic-Pomona, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Kristin Michel
- Division of Biology, Kansas State University, 271 Chalmers Hall, Manhattan, KS 66506, USA
| | - Sara N Mitchell
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02115, USA
| | - Wendy Moore
- Department of Entomology, 1140 East South Campus Drive, Forbes 410, University of Arizona, Tucson, AZ 85721, USA
| | - Katherine A Murphy
- Department of Entomology and Nematology, One Shields Avenue, University of California-Davis, Davis, CA 95616, USA
| | - Anastasia N Naumenko
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Tony Nolan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Eva M Novoa
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Samantha O'Loughlin
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Chioma Oringanje
- Department of Entomology, 1140 East South Campus Drive, Forbes 410, University of Arizona, Tucson, AZ 85721, USA
| | - Mohammad A Oshaghi
- Department of Medical Entomology and Vector Control, School of Public Health and Institute of Health Researches, Tehran University of Medical Sciences, Tehran, Iran
| | - Nazzy Pakpour
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Philippos A Papathanos
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Ashley N Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Michael Povelones
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - Anil Prakash
- Regional Medical Research Centre NE, Indian Council of Medical Research, P.O. Box 105, Dibrugarh-786 001, Assam, India
| | - David P Price
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
| | - Ashok Rajaraman
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Lisa J Reimer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - David C Rinker
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Antonis Rokas
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37235, USA. Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Tanya L Russell
- Faculty of Medicine, Health and Molecular Science, Australian Institute of Tropical Health Medicine, James Cook University, Cairns 4870, Australia
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou 01 BP 2208, Burkina Faso
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Terrance Shea
- Genome Sequencing and Analysis Program, Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Frederic Simard
- Institut de Recherche pour le Développement, Unités Mixtes de Recherche Maladies Infectieuses et Vecteurs Écologie, Génétique, Évolution et Contrôle, 911, Avenue Agropolis, BP 64501 Montpellier, France
| | - Michel A Slotman
- Department of Entomology, Texas A&M University, College Station, TX 77807, USA
| | - Pradya Somboon
- Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Claudio J Struchiner
- Fundação Oswaldo Cruz, Avenida Brasil 4365, RJ Brazil. Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gregg W C Thomas
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Marta Tojo
- Department of Physiology, School of Medicine, Center for Research in Molecular Medicine and Chronic Diseases, Instituto de Investigaciones Sanitarias, University of Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Nikolaou Plastira 100 GR-70013, Heraklion, Crete, Greece
| | - José M C Tubio
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Maria F Unger
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA
| | - John Vontas
- Department of Biology, University of Crete, 700 13 Heraklion, Greece
| | - Catherine Walton
- Computational Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Craig S Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Judith H Willis
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Yi-Chieh Wu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Department of Computer Science, Harvey Mudd College, Claremont, CA 91711, USA
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, Hewitt Hall, Irvine, CA 92697, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Flaminia Catteruccia
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02115, USA. Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Perugia, Perugia, Italy
| | - George K Christophides
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Frank H Collins
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA
| | - Robert S Cornman
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK. Malaria Programme, Wellcome Trust Sanger Institute, Cambridge CB10 1SJ, UK
| | - Scott J Emrich
- Department of Computer Science and Engineering, Eck Institute for Global Health, 211B Cushing Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael C Fontaine
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA. Centre of Evolutionary and Ecological Studies (Marine Evolution and Conservation group), University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, Netherlands
| | - William Gelbart
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA. School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Immo A Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Molecular Biology Program, New Mexico State University, Las Cruces, NM 88003, USA
| | - Paul I Howell
- Centers for Disease Control and Prevention, 1600 Clifton Road NE MSG49, Atlanta, GA 30329, USA
| | - Fotis C Kafatos
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. The Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Daniel Lawson
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Christos Louis
- Department of Biology, University of Crete, 700 13 Heraklion, Greece. Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas, Nikolaou Plastira 100 GR-70013, Heraklion, Crete, Greece. Centre of Functional Genomics, University of Perugia, Perugia, Italy
| | - Shirley Luckhart
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Marc A T Muskavitch
- Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA. Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA
| | - José M Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, 12735 Twinbrook Parkway, Rockville, MD 20852, USA
| | - Michael A Riehle
- Department of Entomology, 1140 East South Campus Drive, Forbes 410, University of Arizona, Tucson, AZ 85721, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhijian Tu
- Program of Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Laurence J Zwiebel
- Departments of Biological Sciences and Pharmacology, Institutes for Chemical Biology, Genetics and Global Health, Vanderbilt University and Medical Center, Nashville, TN 37235, USA
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.
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Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963. [PMID: 25409509 PMCID: PMC4237348 DOI: 10.1371/journal.pone.0112963] [Citation(s) in RCA: 5076] [Impact Index Per Article: 507.6] [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: 08/25/2014] [Accepted: 10/16/2014] [Indexed: 02/06/2023] Open
Abstract
Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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Affiliation(s)
- Bruce J. Walker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (BJW); (AME)
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Margaret Priest
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Amr Abouelliel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sharadha Sakthikumar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jennifer Wortman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah K. Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ashlee M. Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (BJW); (AME)
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Hoeppner MP, Lundquist A, Pirun M, Meadows JRS, Zamani N, Johnson J, Sundström G, Cook A, FitzGerald MG, Swofford R, Mauceli E, Moghadam BT, Greka A, Alföldi J, Abouelleil A, Aftuck L, Bessette D, Berlin A, Brown A, Gearin G, Lui A, Macdonald JP, Priest M, Shea T, Turner-Maier J, Zimmer A, Lander ES, di Palma F, Lindblad-Toh K, Grabherr MG. An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One 2014; 9:e91172. [PMID: 24625832 PMCID: PMC3953330 DOI: 10.1371/journal.pone.0091172] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/08/2014] [Indexed: 12/22/2022] Open
Abstract
The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ∼175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ∼3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ∼20,700 high-confidence protein coding loci, we found ∼4,600 antisense transcripts overlapping exons of protein coding genes, ∼7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ∼11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts.
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Affiliation(s)
- Marc P. Hoeppner
- Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andrew Lundquist
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Mono Pirun
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Jennifer R. S. Meadows
- Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Neda Zamani
- Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Görel Sundström
- Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - April Cook
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Michael G. FitzGerald
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Evan Mauceli
- Boston Children's Hospital, Boston, Massachusetts, United States of America
| | | | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Amr Abouelleil
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Lynne Aftuck
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Daniel Bessette
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Aaron Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Gary Gearin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Annie Lui
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Margaret Priest
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Terrance Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jason Turner-Maier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Andrew Zimmer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Federica di Palma
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich, United Kingdom
| | - Kerstin Lindblad-Toh
- Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (KL-T); (MGG)
| | - Manfred G. Grabherr
- Science for Life Laboratories, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (KL-T); (MGG)
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24
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Mayer DK, Kinley T, Gerstel A, Jackson M, Shea T, Donald RL, Lawrence MB. Abstract P3-09-14: Using lean methods to increase access to support services in younger breast cancer survivors. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p3-09-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: A variety of ‘structured support services’ (services) are available to patients (e.g. genetics, fertility, counseling, physical functioning, nutrition). Many of these services have value for breast cancer survivors (survivors) as they are often likely to face issues regarding genetic factors, fertility, parenting, relationships, work, and financial hard-ships. As part of an ongoing CDC-funded initiative, we report about barriers to services use for survivors.
Methods: We used lean techniques to analyze system complexity including: process mapping; inventorying support services, providers/staff, and referral methods; stake holder leadership events; and Kaizen events to facilitate system improvements.
Results: We identified several barriers to patients getting services which reflect the complexity of cancer care delivery in an academic cancer center including: varying care pathways, lack of standard processes; lack of staff awareness of available service (hospital staff are located in 5 different clinics and include physicians, APPs, clinic nurses, nurse navigators, and patient schedulers); numerous different contact and referral methods to services (tribal knowledge of staff necessary to make SS referrals). We initially identified 7 and found 38 services through inventorying and mapping systems.
We implemented a number of systematic and non-systematic interventions to address these barriers. Systematic implementations include assisting in the development and piloting new patient orientation binders to include services, implementation of a revised scheduling form to streamline referrals, created and disseminated a quick reference referral guide to educate staff for how to make referrals. Non-systematic interventions included hosting services fair for breast cancer providers to meet and learn about them and advertising services on waiting room TVs.
Conclusions: Patients and providers both perceive many challenges accessing support services. Applying improvements in a complex health care system is difficult and incrementally addresses identified barriers. We will now be measuring the impact of these changes on the receipt of support services in breast cancer survivors.
Funding: CDC Grant 1U58DP003414 (PI Marks, L.).
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-09-14.
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Affiliation(s)
- DK Mayer
- UNC Lineberger Cancer Center, Chapel Hill, NC
| | - T Kinley
- UNC Lineberger Cancer Center, Chapel Hill, NC
| | - A Gerstel
- UNC Lineberger Cancer Center, Chapel Hill, NC
| | - M Jackson
- UNC Lineberger Cancer Center, Chapel Hill, NC
| | - T Shea
- UNC Lineberger Cancer Center, Chapel Hill, NC
| | - RL Donald
- UNC Lineberger Cancer Center, Chapel Hill, NC
| | - MB Lawrence
- UNC Lineberger Cancer Center, Chapel Hill, NC
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25
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Schachtel B, Aspley S, Berry P, Shephard A, Sanner K, Shea T, Smith G, Schachtel E. Chief Complaint: the therapeutogenic stimulus as the primary, individualized endpoint in clinical trials. The Journal of Pain 2012. [DOI: 10.1016/j.jpain.2012.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Walko C, Ivanova A, Whitley J, Rao K, Gabriel D, Serody J, Comeau T, Coghill J, Armistead P, Sarantopoulos S, Wood W, Shea T. Beneficial Effect of High-Dose Iv Busulfan (Bu) Delivered by Prolonged Continuous Infusion (CI) on Relapse Rate and Overall Survival (OS) in Matched Related and Unrelated Allogeneic Transplant Patients with Hematologic Malignancies. Biol Blood Marrow Transplant 2012. [DOI: 10.1016/j.bbmt.2011.12.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Liao L, Chen X, Dixon A, Munshaw S, Moody M, Zhang R, Nagel A, Foulger A, Derosa K, Parks R, Mcparland M, Whitesides J, Marshall D, Amos J, Yang Y, Gao F, Shea T, Margolis D, Shaw G, Markowitz M, Denny T, Kelsoe G, Tomaras G, Kepler T, Haynes B. P04-45. Characterization of the plasma cell repertoire in acute HIV-1 infection (AHI). Retrovirology 2009. [PMCID: PMC2767977 DOI: 10.1186/1742-4690-6-s3-p73] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Mueller K, Farmer A, Talbert G, Shea T. 436: Successful Integration of Complementary Therapies in a Combined Adult and Pediatric Bone Marrow Transplant Unit. Biol Blood Marrow Transplant 2008. [DOI: 10.1016/j.bbmt.2007.12.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Eron B, Marlow C, Coghill A, Talbert G, Shea T. 382: Making the leap. Biol Blood Marrow Transplant 2007. [DOI: 10.1016/j.bbmt.2007.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SMJ, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005; 438:803-19. [PMID: 16341006 DOI: 10.1038/nature04338] [Citation(s) in RCA: 1680] [Impact Index Per Article: 88.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 10/11/2005] [Indexed: 12/12/2022]
Abstract
Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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Affiliation(s)
- Kerstin Lindblad-Toh
- Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.
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Harvey RD, Shea T, Walko C, Krasnow C, Patel L, Serody J, Gabriel D, Comeau T, Lindley C. Intravenous busulfan test dose clearance comparison with first and thirteenth dose systemic exposure in allogenic bone marrow transplantation patients. J Clin Oncol 2005. [DOI: 10.1200/jco.2005.23.16_suppl.6658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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33
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Bensinger W, Weisdorf D, Gentile T, Cesano A, Elhardt D, Emmanouilides C, Erder M, Hansen K, Isitt J, Kewalramani T, McCarty J, Noga S, Rong A, Shea T, Spielberger R, Yanovich S, Stiff P. Palifermin reduces severe oral mucositis (OM), improves patient quality of life, and reduces health resource use in patients with hematologic malignancies receiving high-dose chemotherapy (HDCT) and total body irradiation (TBI) with autologous peripheral blood stem cell (PBSC) support: results from a phase III trial. Biol Blood Marrow Transplant 2004. [DOI: 10.1016/j.bbmt.2003.12.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Zhong Z, Toukdarian A, Helinski D, Knauf V, Sykes S, Wilkinson JE, O'Bryne C, Shea T, DeLoughery C, Caspi R. Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate. Appl Environ Microbiol 2001; 67:5771-9. [PMID: 11722934 PMCID: PMC93371 DOI: 10.1128/aem.67.12.5771-5779.2001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An agar-degrading marine bacterium identified as a Microscilla species was isolated from coastal California marine sediment. This organism harbored a single 101-kb circular DNA plasmid designated pSD15. The complete nucleotide sequence of pSD15 was obtained, and sequence analysis indicated a number of genes putatively encoding a variety of enzymes involved in polysaccharide utilization. The most striking feature was the occurrence of five putative agarase genes. Loss of the plasmid, which occurred at a surprisingly high frequency, was associated with loss of agarase activity, supporting the sequence analysis results.
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Affiliation(s)
- Z Zhong
- Division of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0322, USA
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35
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Zhang J, Martàsek P, Paschke R, Shea T, Siler Masters BS, Kim JJ. Crystal structure of the FAD/NADPH-binding domain of rat neuronal nitric-oxide synthase. Comparisons with NADPH-cytochrome P450 oxidoreductase. J Biol Chem 2001; 276:37506-13. [PMID: 11473123 DOI: 10.1074/jbc.m105503200] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitric-oxide synthase (NOS) is composed of a C-terminal, flavin-containing reductase domain and an N-terminal, heme-containing oxidase domain. The reductase domain, similar to NADPH-cytochrome P450 reductase, can be further divided into two different flavin-containing domains: (a) the N terminus, FMN-containing portion, and (b) the C terminus FAD- and NADPH-binding portion. The crystal structure of the FAD/NADPH-containing domain of rat neuronal nitric-oxide synthase, complexed with NADP(+), has been determined at 1.9 A resolution. The protein is fully capable of reducing ferricyanide, using NADPH as the electron donor. The overall polypeptide fold of the domain is very similar to that of the corresponding module of NADPH-cytochrome P450 oxidoreductase (CYPOR) and consists of three structural subdomains (from N to C termini): (a) the connecting domain, (b) the FAD-binding domain, and (c) the NADPH-binding domain. A comparison of the structure of the neuronal NOS FAD/NADPH domain and CYPOR reveals the strict conservation of the flavin-binding site, including the tightly bound water molecules, the mode of NADP(+) binding, and the aromatic residue that lies at the re-face of the flavin ring, strongly suggesting that the hydride transfer mechanisms in the two enzymes are very similar. In contrast, the putative FMN domain-binding surface of the NOS protein is less positively charged than that of its CYPOR counterpart, indicating a different nature of interactions between the two flavin domains and a different mode of regulation in electron transfer between the two flavins involving the autoinhibitory element and the C-terminal 33 residues, both of which are absent in CYPOR.
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Affiliation(s)
- J Zhang
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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36
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Berrey MM, Schacker T, Collier AC, Shea T, Brodie SJ, Mayers D, Coombs R, Krieger J, Chun TW, Fauci A, Self SG, Corey L. Treatment of primary human immunodeficiency virus type 1 infection with potent antiretroviral therapy reduces frequency of rapid progression to AIDS. J Infect Dis 2001; 183:1466-75. [PMID: 11319682 DOI: 10.1086/320189] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2000] [Revised: 02/02/2001] [Indexed: 11/03/2022] Open
Abstract
Immunologic data supporting immediate antiretroviral therapy in primary human immunodeficiency virus type 1 (HIV-1) infection are emerging; however, clinical benefit has not been demonstrated. The clinical and virologic course of 47 patients who were enrolled from September 1993 through June 1996 and who were not initially treated with potent therapy was compared with the course of 20 patients who immediately began therapy with zidovudine, lamivudine, and indinavir. Demographic and baseline laboratory data were comparable. During 78 weeks of follow-up, the early-treatment cohort showed a reduced frequency of opportunistic infections (5% vs. 21.3%; relative risk, 0.11; P=.02), less frequent progression to AIDS (13% vs. 0%), and significantly less frequent nonopportunistic mucocutaneous disorders and respiratory infections (P<.01). Plasma HIV-1 RNA levels were <50 copies/mL in all patients who continued therapy; however, after 9--12 months, HIV-1 remained detectable in latently infected CD4(+) T cells and in lymph node mononuclear cells. Combination antiretroviral therapy during primary HIV-1 infection demonstrated a decreased frequency of minor opportunistic infections, mucocutaneous disorders, and respiratory infections and reduced progression to AIDS.
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Affiliation(s)
- M M Berrey
- Department of Medicine, University of Washington, Seattle, WA, USA
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37
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Abstract
The techniques described herein have added to our repertoire of experimental approaches for the characterization of the NOSs. These procedures have reinforced our conviction that the NOSs are structurally suited to perform unique functions in their cellular milieux and that these differences have physiological consequences.
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Affiliation(s)
- P Martásek
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760, USA
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Chun TW, Engel D, Berrey MM, Shea T, Corey L, Fauci AS. Early establishment of a pool of latently infected, resting CD4(+) T cells during primary HIV-1 infection. Proc Natl Acad Sci U S A 1998; 95:8869-73. [PMID: 9671771 PMCID: PMC21169 DOI: 10.1073/pnas.95.15.8869] [Citation(s) in RCA: 636] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The presence of latently infected, resting CD4(+) T cells carrying replication-competent HIV-1 has been demonstrated in chronically infected individuals who are antiretroviral therapy naive as well as in those who are receiving highly active antiretroviral therapy (HAART). It is not clear, however, whether the establishment of a pool of latently infected CD4(+) T cells can be blocked by early initiation of HAART after primary infection. The present study demonstrates that initiation of HAART in infected individuals as early as 10 days after the onset of symptoms of primary HIV-1 infection did not prevent generation of latently infected, resting CD4(+) T cells carrying integrated HIV-1 DNA as well as infectious HIV-1 despite the successful control of plasma viremia shortly after institution of HAART. Furthermore, there was no correlation between either the duration of HAART at the time of study (range: 0.2-17 months) or the time of initiation of HAART after the onset of symptoms of primary HIV-1 infection (range: 0.3-4 months) and the frequencies of resting CD4(+) T cells carrying either integrated HIV-1 DNA or infectious virus. These results underscore the rapidity with which latent reservoirs are established in primary HIV-1 infection and indicate that it is unlikely that early treatment during primary infection can prevent establishment of a pool of latently infected, resting CD4(+) T cells as long as treatment is initiated after plasma viremia becomes evident.
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Affiliation(s)
- T W Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Abstract
OBJECTIVE Panic disorder with or without agoraphobia has a chronic relapsing course. Factors associated with poor outcome include early onset of illness and phobic avoidance. Several, but not all, authors have found a worse clinical course for women. Using observational, longitudinal data from the Harvard/Brown Anxiety Disorders Research Program, the authors analyzed remission and symptom recurrence rates in panic patients with respect to sex. METHOD Male and female patients (N = 412) in an episode of panic with or without agoraphobia were assessed by structured interview and prospectively followed for up to 5 years. Data on remission, symptom recurrence, and comorbid psychiatric conditions for each sex were compared. RESULTS There were no significant differences between men and women in panic symptoms or level of severity at baseline. Women were more likely to have panic with agoraphobia (85% versus 75%), while men were more likely to have uncomplicated panic (25% versus 15%). The rates of remission for panic with or without agoraphobia at 5 years were equivalent in men and women (39%). Of the subjects who achieved remission, 25% of the women and 15% of the men reexperienced symptoms by 6 months. Recurrence of panic symptoms continued to be higher in women (82%) than men (51%) during the follow-up period and was not influenced by concurrent agoraphobia. CONCLUSIONS This study extends previous findings by showing that not only are women more likely to have panic with concurrent agoraphobia, but they are more likely than men to suffer a recurrence of panic symptoms after remission of panic.
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Affiliation(s)
- K A Yonkers
- University of Texas Southwestern Medical Center at Dallas, TX 75235-9101, USA.
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Abstract
BACKGROUND The clinical events surrounding acute HIV-1 infection have been well described, but little is known about whether the virologic course of acute HIV-1 infection influences the subsequent progression of disease. OBJECTIVE To define the virologic natural history of acute and very early HIV infection. DESIGN Prospective, longitudinal cohort study. SETTING University of Washington Research Clinic PARTICIPANTS 74 adults enrolled soon after acquisition of HIV (mean, 69 days). MEASUREMENTS Plasma HIV-1 RNA levels; quantitative cell cultures; CD4 cell counts; and detailed clinical assessments done at study entry, biweekly for 1 month, monthly for 2 months, and quarterly thereafter. RESULTS In the first 30 days after acquisition of HIV, HIV-1 RNA levels varied greatly among participants (range, 27,200 to 1.6 x 10(6) copies per mL of plasma). Levels of HIV-1 RNA decreased by a mean of 6.5% per week for the first 120 days and then increased by a mean of 0.15% per week. CD4 cell counts decreased by a mean of 5.2 cells/mm3 per week for the first 160 days and by a mean of 1.9 cells/mm3 per week thereafter (P < 0.01). Disease progressed faster in participants who sought medical care for their acute seroconversion syndrome (P = 0.01) and those who had high plasma HIV-1 RNA levels 120 to 365 days after acquisition (P < 0.01). Peak levels in the first 120 days were not predictive of disease progression. CONCLUSIONS The variability in viral RNA levels associated with acute HIV-1 infection is greater than previously appreciated. Within 120 days of acquisition, plasma HIV RNA levels rapidly decrease to an inflection point, after which they gradually increase. Virus-host interactions soon after acquisition seem to have a major influence on the long-term outcome of HIV-1 disease.
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Affiliation(s)
- T W Schacker
- University of Washington and the Fred Hutchinson Cancer Research Center, Seattle 98104, USA
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Musey L, Hughes J, Schacker T, Shea T, Corey L, McElrath MJ. Cytotoxic-T-cell responses, viral load, and disease progression in early human immunodeficiency virus type 1 infection. N Engl J Med 1997; 337:1267-74. [PMID: 9345075 DOI: 10.1056/nejm199710303371803] [Citation(s) in RCA: 407] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Early in human immunodeficiency virus type 1 (HIV-1) infection there is a decline in viral replication that has been attributed to host immunity, but the components of this response, particularly the ability of cytotoxic T lymphocytes to control viral burden and influence the outcome of disease, are poorly understood. METHODS We prospectively studied 33 patients with primary HIV-1 infection for HIV-specific activated cytotoxic T lymphocytes and memory cytotoxic T lymphocytes and compared these lymphocyte responses with changes in viral load and clinical status over the subsequent 18 to 24 months. RESULTS Soon after infection, activated HIV-specific cytotoxic T lymphocytes, mediated primarily by CD8+ cells, were detected in 17 of 23 patients (74 percent). Memory cytotoxic T lymphocytes were found in 6 of 6 patients tested (100 percent) during the first three months of infection and in 17 of 21 patients (81 percent) tested during the first six months. The frequencies of memory cytotoxic T lymphocytes varied markedly over time, but overall they declined over the first 6 to 8 months and then stabilized over the next 12 to 18 months. The patients with higher frequencies of Env-specific memory cytotoxic T lymphocytes had a median level of plasma HIV-1 RNA about one third that of the patients with lower frequencies, (median number of RNA copies per milliliter, 22,000 vs. 62,000; P=0.006). Patients with low frequencies of Env-specific memory cytotoxic T lymphocytes (or none) in early infection had a more rapid decline to less than 300 CD4+ cells per cubic millimeter (P = 0.05). CONCLUSIONS In early HIV-1 infection, the induction of memory cytotoxic T lymphocytes, particularly those specific for Env, helps control viral replication and is associated with slower declines in CD4+ cell counts. Host cytolytic effector responses appear to delay the progression of HIV-1 disease.
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Affiliation(s)
- L Musey
- Department of Medicine, School of Medicine, University of Washington, Seattle, USA
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Abstract
BACKGROUND Though previous studies have clearly shown that lithium affords prophylaxis in bipolar affective disorder, these studies have not demonstrated the persistence of this prophylactic effect beyond the first year of recovery. METHODS One hundred and eighty-one patients with bipolar affective disorder recovered during 5 years of semi-annual follow-up. After 8 weeks of recovery, 139 were taking lithium prophylaxis and 42 were not. Analyses used drug status (lithium v. no-lithium) as a censoring variable to compare these two groups by interval-specific probabilities of recurrence. RESULTS Recurrence was initially less likely in the lithium group but interval-specific probabilities of recurrence did not consistently favour either group after the first 32 weeks of recovery. CONCLUSIONS Biases in treatment decisions may have both reduced the size and altered the specificity of the lithium effects seen here. Nevertheless, the apparent transience of lithium prophylactic effects is unexplained and may reflect important, physiological differences between relapse and recurrence. This possibility invites a controlled lithium discontinuation study, with gradual taper, of patients who have had at least 8 months of sustained euthymia.
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Affiliation(s)
- W Coryell
- Department of Psychiatry, University of Iowa College of Medicine, Iowa City, USA
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Abstract
BACKGROUND The acute clinical events surrounding the acquisition of human immunodeficiency virus (HIV) have not been well characterized. OBJECTIVE To further define the clinical and epidemiologic presentation of primary HIV infection. DESIGN Descriptive cohort study. SETTING University research clinic. PATIENTS 46 adults (43 men and 3 women) with primary HIV infection who enrolled in the study a median of 51 days after HIV seroconversion. MEASUREMENTS Documentation of recent HIV seroconversion. Standardized collection of demographic characteristics and sexual contact history, results of tests for HIV RNA, HIV culture, and T-cell subsets. RESULTS 41 of 46 patients (89%) developed an acute retroviral syndrome. Primary HIV infection was infrequently diagnosed at the initial medical encounter, even in persons enrolled in routine HIV screening programs. Median numbers of sexual partners 6 months and 1 month before acquisition of HIV were three and one, respectively; 21 patients (46%) reported having had only one partner in the month before seroconversion. Of the 12 patients who could identify the precise date of and activity leading to seroconversion, 4 reported having only oral-genital contact. CONCLUSIONS Primary HIV infection causes a recognizable clinical syndrome that is often underdiagnosed, even in persons enrolled in a program of routine surveillance for HIV infection. Frequency of sexual contact and overall numbers of sexual partners in this group of homosexual men who acquired HIV were markedly lower than those seen a decade ago. Acquisition of HIV does occur, even in persons with relatively few sexual partners. Increased attention to oral-genital contact as a means of acquiring HIV appears to be warranted.
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Wang M, Roberts DL, Paschke R, Shea T, Masters BSS, Kim JJP. Crystal structure of rat liver NADPH-cyctochrome P-450 reductase. Acta Crystallogr A 1996. [DOI: 10.1107/s010876739609455x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brecher ME, Sims L, Schmitz J, Shea T, Bentley SA. North American Multicenter Study on flow cytometric enumeration of CD34+ hematopoietic stem cells. J Hematother 1996; 5:227-36. [PMID: 8817389 DOI: 10.1089/scd.1.1996.5.227] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Transplant centers often rely on CD34+ cell quantitation by flow cytometry to ensure adequacy of hematopoietic progenitor cell collection. Because of variation in interpretation, a lack of interlaboratory proficiency studies, and no generally accepted methodology, comparison of CD34 data from site to site is difficult. Twenty-one samples from marrow and peripheral blood stem cell collections were shipped to 10 participating North American laboratories for analysis. Duplicate samples were included to assess reproducibility. Participants were surveyed for methodology. Three centers had previously attempted to standardize their methodology among themselves. The variability observed in the CD34 values ranged from a max/min. reported value per sample of 2.9 to 749 (median 76). Exclusion of two outlying sites reduced the variability of results to 1.2 to 27 (median 3.1). Variation among the three standardized sites ranged from 1.2 to 4.4 (median 1.6). Overall reproducibility (excluding the outlying sites B and G) ranged from a minimum of 0-16.5 (percent mean difference) for site C to a maximum of 4.1-133 for site H. Strategies for gating were found to largely influence results. We observed an alarming variation among the CD34 cell counts reported from different laboratories. Standardization substantially reduced observed variation. The need for standardized methodology, reporting, quality control, and proficiency testing is underscored by these findings.
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Affiliation(s)
- M E Brecher
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill 27514, USA
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Shea T, Graham M, Bernard S, Steagall A, Wiley J, Serody J, Brecher M, Bentley S, Johnston C, Vaisman A. A clinical and pharmacokinetic study of high-dose carboplatin, paclitaxel, granulocyte colony-stimulating factor, and peripheral blood stem cells in patients with unresectable or metastatic cancer. Semin Oncol 1995; 22:80-5. [PMID: 7481867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We have developed a regimen incorporating multiple cycles of high-dose carboplatin and fixed-dose paclitaxel (Taxol; Bristol-Myers Squibb Company, Princeton, NJ) with granulocyte colony-stimulating factor and peripheral blood stem cell support given every 21 days for up to four cycles. Our phase I study of this regimen has treated 26 patients with good performance status and histologically documented unresectable or metastatic carcinoma, sarcoma, or melanoma, 21 of whom received all planned courses every 21 days. Paclitaxel 250 mg/m2 was infused over 24 hours, followed by a 1-hour carboplatin infusion, with doses escalated between area under the concentration-time curve (AUC) targets of 8 and 20. Considering the carboplatin doses administered (two to three times those generally achieved with growth factor support), toxicity has been relatively modest. The median duration of grade 4 neutropenia and thrombocytopenia was not significantly different between the AUCs of 8 and 18, which proved to be the maximum tolerated carboplatin dose. Twelve courses were associated with hospitalization for neutropenic fever or catheter-related thrombophlebitis. One treatment-related death occurred, and severe toxicity caused withdrawal of two patients treated at the AUC of 20. Peripheral neuropathy was the most common serious nonhematologic complication. Pharmacokinetic analysis showed significantly lower measured versus predicted AUC values. Among 25 evaluable patients, preliminary results show one complete response (ovarian cancer) and 11 partial responses, including four in patients with non-small cell lung cancer. Additional issues to be addressed include the effect of a shorter (or longer) paclitaxel infusion on the carboplatin AUC (and the incidence of toxicity) and whether the discrepancy between actual and predicted AUCs (greater in our study than reported elsewhere) is due to the variability of creatinine clearance-determined glomerular filtration rate or to altered carboplatin pharmacokinetics when a short high-dose infusion follows paclitaxel. Additional patients are being accrued at the AUC of 18.
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Affiliation(s)
- T Shea
- Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill 27599, USA
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Abstract
OBJECTIVE This study sought to describe the characteristics and consequences of untreated major depressive disorder. METHOD As part of a family study of probands with major affective disorders, raters assessed 3,119 first-degree relatives, spouses, and comparison subjects. When 2,237 (71.7%) of these individuals were reassessed 6 years later, 547 had experienced episodes of major depressive disorder in the interval. Those who had sought any form of treatment for any episode of major depressive disorder in the interval were compared, by baseline demographic characteristics and clinical features of their worst episodes of major depressive disorder, to those who had not. Individuals who had had untreated major depressive disorder were then compared, by changes in socioeconomic status and by levels of psychosocial impairment at follow-up, to a matched group with no major depressive disorder in the interval. RESULTS The worst episodes of 313 treated individuals, compared to those of 234 untreated individuals, were characterized by older age, symptoms of the endogenous subtype, longer durations, and the presence of disruption in role function. Each of these factors contributed independently to the distinction between treated and untreated episodes. Untreated individuals experienced significant psychosocial impairment on follow-up but did not show the economic disadvantages shown elsewhere for probands who began follow-up as they sought treatment at tertiary medical centers. CONCLUSIONS These data suggest that illness characteristics and age determine the decision to seek treatment for major depressive disorder. Untreated depression is apparently associated with long-standing psychosocial difficulties but not with serious economic consequences.
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Affiliation(s)
- W Coryell
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
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