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Conyers LE, Saunders BM. Treatment for non-tuberculous mycobacteria: challenges and prospects. Front Microbiol 2024; 15:1394220. [PMID: 38887711 PMCID: PMC11180805 DOI: 10.3389/fmicb.2024.1394220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Non-Tuberculous mycobacteria (NTM) are opportunistic environmental bacteria. Globally, NTM incidence is increasing and modeling suggests that, without new interventions, numbers will continue to rise. Effective treatments for NTM infections remain suboptimal. Standard therapy for Mycobacterium avium complex, the most commonly isolated NTM, requires a 3-drug regime taken for approximately 18 months, with rates of culture conversion reported between 45 and 70%, and high rates of relapse or reinfection at up to 60%. New therapeutic options for NTM treatment are urgently required. A survey of ongoing clinical trials for new NTM therapy listed on ClinicalTrials.Gov using the terms 'Mycobacterium avium', 'Mycobacterium abscessus', 'Mycobacterium intracellulare', 'Non tuberculous Mycobacteria' and 'Nontuberculous Mycobacteria' and a selection criterion of interventional studies using antibiotics demonstrates that most trials involve dose and combination therapy of the guideline based therapy or including one or more of; Amikacin, Clofazimine, Azithromycin and the anti-TB drugs Bedaquiline and Linezolid. The propensity of NTMs to form biofilms, their unique cell wall and expression of both acquired and intrinsic resistance, are all hampering the development of new anti-NTM therapy. Increased investment in developing targeted treatments, specifically for NTM infections is urgently required.
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Allers S, O'Connell KA, Carlson T, Belardo D, King BL. Reusable tutorials for using cloud-based computing environments for the analysis of bacterial gene expression data from bulk RNA sequencing. Brief Bioinform 2024; 25:bbae301. [PMID: 38997128 DOI: 10.1093/bib/bbae301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024] Open
Abstract
This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on RNA sequencing (RNAseq) data analysis in an interactive format that uses appropriate cloud resources for data access and analyses. Biomedical research is increasingly data-driven, and dependent upon data management and analysis methods that facilitate rigorous, robust, and reproducible research. Cloud-based computing resources provide opportunities to broaden the application of bioinformatics and data science in research. Two obstacles for researchers, particularly those at small institutions, are: (i) access to bioinformatics analysis environments tailored to their research; and (ii) training in how to use Cloud-based computing resources. We developed five reusable tutorials for bulk RNAseq data analysis to address these obstacles. Using Jupyter notebooks run on the Google Cloud Platform, the tutorials guide the user through a workflow featuring an RNAseq dataset from a study of prophage altered drug resistance in Mycobacterium chelonae. The first tutorial uses a subset of the data so users can learn analysis steps rapidly, and the second uses the entire dataset. Next, a tutorial demonstrates how to analyze the read count data to generate lists of differentially expressed genes using R/DESeq2. Additional tutorials generate read counts using the Snakemake workflow manager and Nextflow with Google Batch. All tutorials are open-source and can be used as templates for other analysis.
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Affiliation(s)
- Steven Allers
- Department of Molecular and Biomedical Sciences, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, United States
| | - Kyle A O'Connell
- Center for Information Technology, National Institutes of Health, 6555 Rock Spring Dr, Bethesda, MD 20817, United States
- Health Data and AI, Deloitte Consulting LLP, 1919 N. Lynn St, Arlington, VA 22203, United States
| | - Thad Carlson
- Center for Information Technology, National Institutes of Health, 6555 Rock Spring Dr, Bethesda, MD 20817, United States
- Health Data and AI, Deloitte Consulting LLP, 1919 N. Lynn St, Arlington, VA 22203, United States
| | - David Belardo
- Google Cloud, Google, 1900 Reston Metro Plaza, Reston, VA 20190, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, United States
- Maine Institutional Development Award Network of Biomedical Research Excellence (INBRE) Data Science Core, MDI Biological Laboratory, 159 Old Bar Harbor Rd, Bar Harbor, ME 04609, United States
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, United States
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Poulton NC, DeJesus MA, Munsamy-Govender V, Kanai M, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: The whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. Cell Chem Biol 2024; 31:669-682.e7. [PMID: 38266648 PMCID: PMC11031301 DOI: 10.1016/j.chembiol.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/13/2023] [Accepted: 12/23/2023] [Indexed: 01/26/2024]
Abstract
Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. The conserved whiB7 stress response reduces the effectiveness of antibiotic therapy by activating several intrinsic antibiotic resistance mechanisms. Despite our comprehensive biochemical understanding of WhiB7, the complex set of signals that induce whiB7 expression remain less clear. We employed a reporter-based, genome-wide CRISPRi epistasis screen to identify a diverse set of 150 mycobacterial genes whose inhibition results in constitutive whiB7 expression. We show that whiB7 expression is determined by the amino acid composition of the 5' regulatory uORF, thereby allowing whiB7 to sense amino acid starvation. Although deprivation of many amino acids can induce whiB7, whiB7 specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme, aspC. These findings describe a metabolic function for whiB7 and help explain its evolutionary conservation across mycobacterial species occupying diverse ecological niches.
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Affiliation(s)
- Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | | | - Mariko Kanai
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Karl Matthew Lin
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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Glauser KG, Kelley RE, Leonard WJ, Hendrix J, Petri S, Tong EI, Chan YL, Lipner EM, Dawrs SN, Honda JR. Common Features of Environmental Mycobacterium chelonae from Colorado Using Partial and Whole Genomic Sequence Analyses. Curr Microbiol 2024; 81:69. [PMID: 38238596 PMCID: PMC10796651 DOI: 10.1007/s00284-023-03589-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024]
Abstract
Nontuberculous mycobacteria (NTM) are environmentally acquired opportunistic pathogens that cause chronic lung disease in susceptible individuals. While presumed to be ubiquitous in built and natural environments, NTM environmental studies are limited. While environmental sampling campaigns have been performed in geographic areas of high NTM disease burden, NTM species diversity is less defined among areas of lower disease burden like Colorado. In Colorado, metals such as molybdenum have been correlated with increased risk for NTM infection, yet environmental NTM species diversity has not yet been widely studied. Based on prior regression modeling, three areas of predicted high, moderate, and low NTM risk were identified for environmental sampling in Colorado. Ice, plumbing biofilms, and sink tap water samples were collected from publicly accessible freshwater sources. All samples were microbiologically cultured and NTM were identified using partial rpoB gene sequencing. From these samples, areas of moderate risk were more likely to be NTM positive. NTM recovery from ice was more common than recovery from plumbing biofilms or tap water. Overall, nine different NTM species were identified, including clinically important Mycobacterium chelonae. MinION technology was used to whole genome sequence and compare mutational differences between six M. chelonae genomes, representing three environmental isolates from this study and three other M. chelonae isolates from other sources. Drug resistance genes and prophages were common findings among environmentally derived M. chelonae, promoting the need for expanded environmental sampling campaigns to improve our current understanding of NTM species abundance while opening new avenues for improved targeted drug therapies.
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Affiliation(s)
- Kayden G Glauser
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - Reagan E Kelley
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - William J Leonard
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - Jo Hendrix
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Suzanne Petri
- Department of Science, Principles of Experimental Design in Biotechnology, Rock Canyon High School, Littleton, CO, 80124, USA
| | - Eric I Tong
- Aina Informatics Network, 'Iolani School, Honolulu, HI, 96826, USA
| | - Yvonne L Chan
- Aina Informatics Network, 'Iolani School, Honolulu, HI, 96826, USA
| | - Ettie M Lipner
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Stephanie N Dawrs
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, 80206, USA
| | - Jennifer R Honda
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX, 75708, USA.
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Abad L, Gauthier CH, Florian I, Jacobs-Sera D, Hatfull GF. The heterogenous and diverse population of prophages in Mycobacterium genomes. mSystems 2023; 8:e0044623. [PMID: 37791767 PMCID: PMC10654092 DOI: 10.1128/msystems.00446-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/18/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mycobacterium species include several human pathogens and mycobacteriophages show potential for therapeutic use to control Mycobacterium infections. However, phage infection profiles vary greatly among Mycobacterium abscessus clinical isolates and phage therapies must be personalized for individual patients. Mycobacterium phage susceptibility is likely determined primarily by accessory parts of bacterial genomes, and we have identified the prophage and phage-related genomic regions across sequenced Mycobacterium strains. The prophages are numerous and diverse, especially in M. abscessus genomes, and provide a potentially rich reservoir of new viruses that can be propagated lytically and used to expand the repertoire of therapeutically useful phages.
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Affiliation(s)
- Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christian H. Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Isabella Florian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Davies-Bolorunduro OF, Jaemsai B, Ruangchai W, Phumiphanjarphak W, Aiewsakun P, Palittapongarnpim P. Analysis of whiB7 in Mycobacterium tuberculosis reveals novel AT-hook deletion mutations. Sci Rep 2023; 13:13324. [PMID: 37587174 PMCID: PMC10432532 DOI: 10.1038/s41598-023-40152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023] Open
Abstract
Mutations in whiB7 have been associated with both hypersusceptibility and resistance to various antibiotics in Mycobacterium tuberculosis (Mtb). Unlocking the secrets of antibiotic resistance in the bacterium, we examined mutations in the coding sequences of whiB7 of over 40,000 diverse Mtb isolates. Our results unveil the dominant c.191delG (Gly64delG) mutation, present in all members of the lineage L1.2.2 and its impact on WhiB7's conserved GVWGG-motif, causing conformational changes and deletion of the C-terminal AT-hook. Excitingly, we discovered six unique mutations associated with partial or total deletion of the AT-hook, specific to certain sublineages. Our findings suggest the selective pressures driving these mutations, underlining the potential of genomics to advance our understanding of Mtb's antibiotic resistance. As tuberculosis remains a global health threat, our study offers valuable insights into the diverse nature and functional consequences of whiB7 mutations, paving the way for the development of novel therapeutic interventions.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Center for Tuberculosis Research, Microbiology Department, Nigerian Institute of Medical Research, 6 Edmund Crescent, P.M.B 2013, Yaba, 101012, Lagos, Nigeria
| | - Bharkbhoom Jaemsai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
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7
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Poulton NC, DeJesus MA, Munsamy-Govender V, Roberts CG, Azadian ZA, Bosch B, Lin KM, Li S, Rock JM. Beyond antibiotic resistance: the whiB7 transcription factor coordinates an adaptive response to alanine starvation in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543512. [PMID: 37333137 PMCID: PMC10274678 DOI: 10.1101/2023.06.02.543512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. These bacteria are highly intrinsically drug resistant, making infections challenging to treat. The conserved whiB7 stress response is a key contributor to mycobacterial intrinsic drug resistance. Although we have a comprehensive structural and biochemical understanding of WhiB7, the complex set of signals that activate whiB7 expression remain less clear. It is believed that whiB7 expression is triggered by translational stalling in an upstream open reading frame (uORF) within the whiB7 5' leader, leading to antitermination and transcription into the downstream whiB7 ORF. To define the signals that activate whiB7, we employed a genome-wide CRISPRi epistasis screen and identified a diverse set of 150 mycobacterial genes whose inhibition results in constitutive whiB7 activation. Many of these genes encode amino acid biosynthetic enzymes, tRNAs, and tRNA synthetases, consistent with the proposed mechanism for whiB7 activation by translational stalling in the uORF. We show that the ability of the whiB7 5' regulatory region to sense amino acid starvation is determined by the coding sequence of the uORF. The uORF shows considerable sequence variation among different mycobacterial species, but it is universally and specifically enriched for alanine. Providing a potential rationalization for this enrichment, we find that while deprivation of many amino acids can activate whiB7 expression, whiB7 specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme, aspC. Our results provide a holistic understanding of the biological pathways that influence whiB7 activation and reveal an extended role for the whiB7 pathway in mycobacterial physiology, beyond its canonical function in antibiotic resistance. These results have important implications for the design of combination drug treatments to avoid whiB7 activation, as well as help explain the conservation of this stress response across a wide range of pathogenic and environmental mycobacteria.
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Affiliation(s)
- Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Vanisha Munsamy-Govender
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Cameron G Roberts
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Karl Matthew Lin
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
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8
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Cote J, Welch C, Kimble M, Archambault D, Ross JC, Orellana H, Amero K, Bourett C, Daigle A, Hutchison KW, Molloy SD. Characterization of the cluster MabR prophages of Mycobacterium abscessus and Mycobacterium chelonae. G3 GENES|GENOMES|GENETICS 2022; 12:6650627. [PMID: 35894699 PMCID: PMC9434293 DOI: 10.1093/g3journal/jkac188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022]
Abstract
Mycobacterium abscessus is an emerging pathogen of concern in cystic fibrosis and immunocompromised patients and is considered one of the most drug-resistant mycobacteria. The majority of clinical Mycobacterium abscessus isolates carry 1 or more prophages that are hypothesized to contribute to virulence and bacterial fitness. The prophage McProf was identified in the genome of the Bergey strain of Mycobacterium chelonae and is distinct from previously described prophages of Mycobacterium abscessus. The McProf genome increases intrinsic antibiotic resistance of Mycobacterium chelonae and drives expression of the intrinsic antibiotic resistance gene, whiB7, when superinfected by a second phage. The prevalence of McProf-like genomes was determined in sequenced mycobacterial genomes. Related prophage genomes were identified in the genomes of 25 clinical isolates of Mycobacterium abscessus and assigned to the novel cluster, MabR. They share less than 10% gene content with previously described prophages; however, they share features typical of prophages, including polymorphic toxin–immunity systems.
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Affiliation(s)
- Jacob Cote
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
| | - Colin Welch
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
- The Honors College, University of Maine , Orono, ME 04469, USA
| | - Madeline Kimble
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
- The Honors College, University of Maine , Orono, ME 04469, USA
| | - Dakota Archambault
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
- The Honors College, University of Maine , Orono, ME 04469, USA
| | - John Curtis Ross
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
| | - Hector Orellana
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
| | - Katelyn Amero
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
- The Honors College, University of Maine , Orono, ME 04469, USA
| | - Claire Bourett
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
- The Honors College, University of Maine , Orono, ME 04469, USA
| | - Andre Daigle
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
| | - Keith W Hutchison
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
- The Honors College, University of Maine , Orono, ME 04469, USA
| | - Sally D Molloy
- Department of Molecular and Biomedical Sciences, University of Maine , Orono, ME 04469, USA
- The Honors College, University of Maine , Orono, ME 04469, USA
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