1
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Kok DN, Zhou D, Tsourkas PK, Hendrickson HL. Paenibacillus larvae and their phages; a community science approach to discovery and initial testing of prophylactic phage cocktails against American Foulbrood in New Zealand. Microbiome Res Rep 2023; 2:30. [PMID: 38045927 PMCID: PMC10688787 DOI: 10.20517/mrr.2023.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/05/2023] [Accepted: 07/15/2023] [Indexed: 12/05/2023]
Abstract
Background: American foulbrood (AFB) is a devastating disease of the European honey bee (Apis mellifera) and is found throughout the world. AFB is caused by the bacterium Paenibacillus larvae (P. larvae). Treatment with antibiotics is strictly forbidden in many regions, including New Zealand. Safe and natural prophylactic solutions to protect honey bees from AFB are needed. Bacteriophages are a well-studied alternative to antibiotics and have been shown to be effective against P. larvae in other countries. Methods: We employed a community science approach to obtaining samples from around New Zealand to discover novel bacteriophages. Standard isolation approaches were employed for both bacteria and bacteriophages. Host range testing was performed by agar overlay spot tests, and cocktail formulation and in vitro testing were performed in 96-well plate assays, followed by sub-sampling and CFU visualization on agar plates. Results: Herein, we describe the discovery and isolation of eight P. larvae bacterial isolates and 26 P. larvae bacteriophages that are novel and native to New Zealand. The phage genomes were sequenced and annotated, and their genomes were compared to extant sequenced P. larvae phage genomes. We test the host ranges of the bacteriophages and formulate cocktails to undertake in vitro testing on a set of representative bacterial strains. These results form the basis of a promising solution for protecting honey bees in New Zealand from AFB.
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Affiliation(s)
- Danielle N. Kok
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Diana Zhou
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Philippos K. Tsourkas
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53792, USA
| | - Heather L. Hendrickson
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
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2
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Kok DN, Turnbull J, Takeuchi N, Tsourkas PK, Hendrickson HL. In Vitro Evolution to Increase the Titers of Difficult Bacteriophages: RAMP-UP Protocol. Phage (New Rochelle) 2023; 4:68-81. [PMID: 37350994 PMCID: PMC10282794 DOI: 10.1089/phage.2023.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Background Bacteriophages are becoming increasingly important in the race to find alternatives to antibiotics. Unfortunately, bacteriophages that might otherwise be useful are sometimes discarded due to low titers making them unsuitable for downstream applications. Methods Here, we present two distinct approaches used to experimentally evolve novel New Zealand Paenibacillus larvae bacteriophages. The first approach uses the traditional agar-overlay method, whereas the other was a 96-well plate liquid infection protocol that improved phage titers in as little as four days. We also used a mathematical model to probe the parameters and limits of the RAMP-UP approach to rapidly select mutants that improve bacteriophage titers. Results Both experimental approaches resulted in an increase in plaque-forming units (PFU/mL). The liquid infection approach developed here, which we call RAMP-UP for Rapid Adaptive Mutation of Phage - UP, was significantly faster and simpler, and allowed us to evolve high titer bacteriophages in as little as four days. Titers were increased from 100-100,000-fold relative to their ancestors. The resultant titers were sufficient to extract and sequence DNA from these bacteriophages. An analysis of these phage genomes is provided. Conclusion The RAMP-UP protocol is an effective method for experimentally evolving previously intractable bacteriophages in a high-throughput and expeditious manner.
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Affiliation(s)
- Danielle N. Kok
- School of Natural Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Joanne Turnbull
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Nobuto Takeuchi
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Philippos K. Tsourkas
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Heather L. Hendrickson
- School of Natural Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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3
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Kok DN, Hendrickson HL. Save our bees: bacteriophages to protect honey bees against the pathogen causing American foulbrood in New Zealand. New Zealand Journal of Zoology 2023. [DOI: 10.1080/03014223.2022.2157847] [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] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Danielle N. Kok
- School of Natural Sciences, Massey University, Auckland, New Zealand
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4
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Hanauer DI, Graham MJ, Arnold RJ, Ayuk MA, Balish MF, Beyer AR, Butela KA, Byrum CA, Chia CP, Chung HM, Clase KL, Conant S, Coomans RJ, D’Elia T, Diaz J, Diaz A, Doty JA, Edgington NP, Edwards DC, Eivazova E, Emmons CB, Fast KM, Fisher EJ, Fleischacker CL, Frederick GD, Freise AC, Gainey MD, Gissendanner CR, Golebiewska UP, Guild NA, Hendrickson HL, Herren CD, Hopson-Fernandes MS, Hughes LE, Jacobs-Sera D, Johnson AA, Kirkpatrick BL, Klyczek KK, Koga AP, Kotturi H, LeBlanc-Straceski J, Lee-Soety JY, Leonard JE, Mastropaolo MD, Merkhofer EC, Michael SF, Mitchell JC, Mohan S, Monti DL, Noutsos C, Nsa IY, Peters NT, Plymale R, Pollenz RS, Porter ML, Rinehart CA, Rosas-Acosta G, Ross JF, Rubin MR, Scherer AE, Schroeder SC, Shaffer CD, Sprenkle AB, Sunnen CN, Swerdlow SJ, Tobiason D, Tolsma SS, Tsourkas PK, Ward RE, Ware VC, Warner MH, Washington JM, Westover KM, White SJ, Whitefleet-Smith JL, Williams DC, Wolyniak MJ, Zeilstra-Ryalls JH, Asai DJ, Hatfull GF, Sivanathan V. Instructional Models for Course-Based Research Experience (CRE) Teaching. CBE Life Sci Educ 2022; 21:ar8. [PMID: 34978921 PMCID: PMC9250372 DOI: 10.1187/cbe.21-03-0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.
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Affiliation(s)
- David I. Hanauer
- Department of English, Indiana University of Pennsylvania, Indiana, PA 15705
| | - Mark J. Graham
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511
| | - Rachel J. Arnold
- Salish Sea Research Center, Northwest Indian College, Bellingham, WA 98229
| | - Mary A. Ayuk
- Biology, Howard University, Washington, DC 20059
| | | | - Andrea R. Beyer
- Department of Biology, Virginia State University, Petersburg, VA 23806
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | - Catherine P. Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Hui-Min Chung
- Biology, University of West Florida, Pensacola, FL 32514
| | - Kari L. Clase
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907
| | - Stephanie Conant
- Department of Biology, University of Detroit Mercy, Detroit, MI 48221
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411
| | - Tom D’Elia
- Department of Biology, Indian River State College, Fort Pierce, FL 34981
| | - Jason Diaz
- Integrated Science, Business, and Technology, La Salle University, Philadelphia, PA 19141
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, CA 92505
| | - Jean A. Doty
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938
| | | | - Dustin C. Edwards
- Biological Sciences, Tarleton State University, Stephenville, TX 76402
| | - Elvira Eivazova
- Biology Department, Columbia State Community College, Columbia, Tennessee 38401
| | | | - Kayla M. Fast
- Biological and Environmental Sciences, University of West Alabama, Livingston, AL 35470
| | - Emily J. Fisher
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | | | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, TX 75602
| | - Amanda C. Freise
- Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90025
| | - Maria D. Gainey
- Chemistry and Physics, Western Carolina University, Cullowhee, NC 28723
| | | | | | - Nancy A. Guild
- Molecular Cellular and Developmental Biology (MCDB), University of Colorado, Boulder, CO 80309
| | - Heather L. Hendrickson
- School of Natural and Computational Science, Massey University, Auckland 0632, New Zealand
| | | | | | - Lee E. Hughes
- Biological Sciences, University of North Texas, Denton, TX 76203
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Allison A. Johnson
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284
| | | | - Karen K. Klyczek
- Biology Department, University of Wisconsin-River Falls, River Falls, WI 54022
| | - Ann P. Koga
- Department of Biology, College of Idaho, Caldwell, ID 83605
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034
| | | | - Julia Y. Lee-Soety
- Department of Biology, Saint Joseph’s University, Philadelphia, PA 19131
| | | | - Matthew D. Mastropaolo
- Mathematics and Sciences, School of Arts and Sciences, Neumann University, Aston, PA 19014
| | | | - Scott F. Michael
- Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965
| | - Jon C. Mitchell
- Department of Science and Mathematics, Northern State University, Aberdeen, SD 57401
| | - Swarna Mohan
- College of Computer, Mathematical, and Natural Sciences, University of Maryland College Park, College Park, MD 20742
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35223
| | | | - Imade Y. Nsa
- Microbiology, University of Lagos, Lagos 101017, Nigeria
| | - Nick T. Peters
- Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011
| | - Ruth Plymale
- Department of Biology, Ouachita Baptist University, Arkadelphia, AR 71998
| | - Richard S. Pollenz
- Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620
| | - Megan L. Porter
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI 96822
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101
| | - German Rosas-Acosta
- Department of Biological Sciences, University of Texas at El Paso (UTEP), El Paso, TX 79968
| | - Joseph F. Ross
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125
| | - Michael R. Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | | | | | - C. Nicole Sunnen
- Biological Sciences, University of the Sciences, Philadelphia, PA 19104
| | | | | | - Sara S. Tolsma
- Department of Biology, Northwestern College, Orange City, IA 51041
| | | | - Robert E. Ward
- Biology, Case Western Reserve University, Cleveland, OH 44106
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, PA 18015
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | | | | | - Simon J. White
- Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | | | | | | | | | - David J. Asai
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Viknesh Sivanathan
- Science Education, Howard Hughes Medical Institute, Chevy Chase, MD 20815
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5
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Abstract
Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being.
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Affiliation(s)
- Michele Zuppi
- The Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Heather L. Hendrickson
- The School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Justin M. O’Sullivan
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Tommi Vatanen
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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6
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Davies CG, Reilly K, Altermann E, Hendrickson HL. PLAN-M; Mycobacteriophage Endolysins Fused to Biodegradable Nanobeads Mitigate Mycobacterial Growth in Liquid and on Surfaces. Front Microbiol 2021; 12:562748. [PMID: 33981289 DOI: 10.3389/fmicb.2021.562748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
The Mycobacteria are a genus of Actinobacteria that include human pathogens such as Mycobacterium tuberculosis (TB). Active TB disease can spread by airborne transmission to healthcare workers and to their community. The HHMI SEA-PHAGES program has contributed to discovering bacteriophages that are able to infect M. smegmatis MC2 155, a close relative of M. tuberculosis. This collection of diverse Mycobacteriophages is an excellent resource for trialling bacteriophage-sourced enzymes in novel applications. Herein we measured the ability Mycobacteriophage endolysins to lyse their host strain when functionally fused to biodegradable polyhydroxyalkanoate (PHA) nanobeads. PHA nanobeads facilitate both the expression and the application of enzymes to surfaces and have been demonstrated to stabilize a wide array of proteins for practical applications whilst eliminating the challenges of traditional protein purification. We selected two Lysin A and six Lysin B homologs to be functionally fused to the polyhydroxyalkanoate synthase C (PhaC). Expression of these constructs resulted in functional lysins displayed on the surface of PHA nanobeads. The lysins thus directionally displayed on nanobeads lysed up to 79% of the M. smegmatis MC2 155 population using 80 mg/mL of nanobeads in pure culture. In order to determine whether the nanobeads would be effective as a protective layer in PPE we adapted a fabric-based test and observed a maximum of 1 log loss of the cell population after 5 h of exposure on a textile (91% cell lysis). Lysin B enzymes performed better than the Lysin A enzymes as a protective barrier on textiles surface assays. These results suggest that bacterial endolysins are efficient in their action when displayed on PHA nanobeads and can cause significant population mortality in as little as 45 min. Our results provide the proof-of-principle that Mycobacteriophage endolysins can be used on functionalized nanobeads where they can protect surfaces such as personal protective equipment (PPE) that routinely come into contact with aerosolised bacteria.
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Affiliation(s)
- Courtney G Davies
- Massey Phage Whānau, School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | | | - Eric Altermann
- AgResearch Ltd., Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Heather L Hendrickson
- Massey Phage Whānau, School of Natural and Computational Sciences, Massey University, Auckland, New Zealand.,Infectious Disease Research Centre, Massey University, Palmerston North, New Zealand
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7
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Shao J, Subedi S, Pepper K, Badgett S, Christensen PA, Hendrickson HL, Thomas JS, Olsen RJ, Li Z. Identifying possible germline variants from tumor-only sequencing of hematological malignancies. Leuk Lymphoma 2020; 62:482-485. [PMID: 33054462 DOI: 10.1080/10428194.2020.1832665] [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: 10/23/2022]
Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Kristi Pepper
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sabrina Badgett
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Weill Cornell Medical College, Cornell University, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Weill Cornell Medical College, Cornell University, Houston, Texas
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Weill Cornell Medical College, Cornell University, Houston, Texas
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8
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Jacobs-Sera D, Abad LA, Alvey RM, Anders KR, Aull HG, Bhalla SS, Blumer LS, Bollivar DW, Bonilla JA, Butela KA, Coomans RJ, Cresawn SG, D'Elia T, Diaz A, Divens AM, Edgington NP, Frederick GD, Gainey MD, Garlena RA, Grant KW, Gurney SMR, Hendrickson HL, Hughes LE, Kenna MA, Klyczek KK, Kotturi H, Mavrich TN, McKinney AL, Merkhofer EC, Moberg Parker J, Molloy SD, Monti DL, Pape-Zambito DA, Pollenz RS, Pope WH, Reyna NS, Rinehart CA, Russell DA, Shaffer CD, Sivanathan V, Stoner TH, Stukey J, Sunnen CN, Tolsma SS, Tsourkas PK, Wallen JR, Ware VC, Warner MH, Washington JM, Westover KM, Whitefleet-Smith JL, Wiersma-Koch HI, Williams DC, Zack KM, Hatfull GF. Genomic diversity of bacteriophages infecting Microbacterium spp. PLoS One 2020; 15:e0234636. [PMID: 32555720 PMCID: PMC7302621 DOI: 10.1371/journal.pone.0234636] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/29/2020] [Indexed: 11/19/2022] Open
Abstract
The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.
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Affiliation(s)
- Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lawrence A. Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Richard M. Alvey
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - Kirk R. Anders
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Haley G. Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Suparna S. Bhalla
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Lawrence S. Blumer
- Department of Biology, Morehouse College, Atlanta, Georgia, United States of America
| | - David W. Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - J. Alfred Bonilla
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Tom D'Elia
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, California, United States of America
| | - Ashley M. Divens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicholas P. Edgington
- Department of Biology, Southern Connecticut State University, New Haven, Connecticut, United States of America
| | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, Texas, United States of America
| | - Maria D. Gainey
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kenneth W. Grant
- Department of Pathology, Wake Forest Baptist Health, Winston-Salem, North Carolina, United States of America
| | - Susan M. R. Gurney
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | | | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Margaret A. Kenna
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Karen K. Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, Oklahoma, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Angela L. McKinney
- Department of Biology, Nebraska Wesleyan University, Lincoln, Nebraska, United States of America
| | - Evan C. Merkhofer
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Sally D. Molloy
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, United States of America
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Dana A. Pape-Zambito
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard S. Pollenz
- Department Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan S. Reyna
- Department of Biology, Ouachita Baptist University, Arkadelphia, Arkansas, United States of America
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher D. Shaffer
- Department of Biology, University of Washington in St. Louis, St. Louis, Missouri, United States of America
| | - Viknesh Sivanathan
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Ty H. Stoner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph Stukey
- Biology Department, Hope College, Holland, Michigan, United States of America
| | - C. Nicole Sunnen
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Sara S. Tolsma
- Biology Department, Northwestern College, Orange City, Iowa, United States of America
| | - Philippos K. Tsourkas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, United States of America
| | - Jamie R. Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Kristi M. Westover
- Department of Biology, Winthrop University, Rock Hill, South Carolina, United States of America
| | - JoAnn L. Whitefleet-Smith
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Helen I. Wiersma-Koch
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Daniel C. Williams
- Department of Biology, Coastal Carolina University, Conway, South Carolina, United States of America
| | - Kira M. Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Christensen PA, Subedi S, Pepper K, Hendrickson HL, Li Z, Thomas JS, Long SW, Olsen RJ. Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data. JAMIA Open 2020; 3:299-305. [PMID: 32734171 PMCID: PMC7382636 DOI: 10.1093/jamiaopen/ooaa004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 11/13/2022] Open
Abstract
Objectives Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV). Materials and Methods We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3. Results We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments. Discussion and Conclusion Validation of each HMVV update was performed according to expert guidelines. We enabled an 8× reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.
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Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Kristi Pepper
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
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Affiliation(s)
- Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Heather L Hendrickson
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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Abstract
It is widely assumed that there is a clear distinction between eukaryotes, with cell nuclei, and prokaryotes, which lack nuclei. This suggests the evolution of nuclear compartmentation is a singular event. However, emerging knowledge of the diversity of bacterial internal cell structures suggests the picture may not be as black-and-white as previously thought. For instance, some members of the bacterial PVC superphylum appear to have nucleus-like compartmentation, where transcription and translation are physically separated, and some jumbophages have recently been shown to create nucleus-like structures within their Pseudomonad hosts. Moreover, there is also tantalizing metagenomic identification of new Archaea that carry homologs of genes associated with internal cell membrane structure in eukaryotes. All these cases invite comparison with eukaryote cell biology. While the bacterial cases of genetic compartmentation are likely convergent, and thus viewed by many as not germane to the question of eukaryote origins, we argue here that, in addressing the broader question of the evolution of compartmentation, other instances are at least as important: they provide us with a point of comparison which is critical for a more general understanding of both the conditions favoring the emergence of intracellular compartmentation of DNA and the evolutionary consequences of such cellular architecture. Finally, we consider three classes of explanation for the emergence of compartmentation: physical protection, crosstalk avoidance and nonadaptive origins.
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Affiliation(s)
- Heather L. Hendrickson
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Anthony M. Poole
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
- Te Ao Mârama/Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Hendrickson HL, Barbeau D, Ceschin R, Lawrence JG. Chromosome architecture constrains horizontal gene transfer in bacteria. PLoS Genet 2018; 14:e1007421. [PMID: 29813058 PMCID: PMC5993296 DOI: 10.1371/journal.pgen.1007421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 01/20/2018] [Revised: 06/08/2018] [Accepted: 05/16/2018] [Indexed: 11/19/2022] Open
Abstract
Despite significant frequencies of lateral gene transfer between species, higher taxonomic groups of bacteria show ecological and phenotypic cohesion. This suggests that barriers prevent panmictic dissemination of genes via lateral gene transfer. We have proposed that most bacterial genomes have a functional architecture imposed by Architecture IMparting Sequences (AIMS). AIMS are defined as 8 base pair sequences preferentially abundant on leading strands, whose abundance and strand-bias are positively correlated with proximity to the replication terminus. We determined that inversions whose endpoints lie within a single chromosome arm, which would reverse the polarity of AIMS in the inverted region, are both shorter and less frequent near the replication terminus. This distribution is consistent with the increased selection on AIMS function in this region, thus constraining DNA rearrangement. To test the hypothesis that AIMS also constrain DNA transfer between genomes, AIMS were identified in genomes while ignoring atypical, potentially laterally-transferred genes. The strand-bias of AIMS within recently acquired genes was negatively correlated with the distance of those genes from their genome’s replication terminus. This suggests that selection for AIMS function prevents the acquisition of genes whose AIMS are not found predominantly in the permissive orientation. This constraint has led to the loss of at least 18% of genes acquired by transfer in the terminus-proximal region. We used completely sequenced genomes to produce a predictive road map of paths of expected horizontal gene transfer between species based on AIMS compatibility between donor and recipient genomes. These results support a model whereby organisms retain introgressed genes only if the benefits conferred by their encoded functions outweigh the detriments incurred by the presence of foreign DNA lacking genome-wide architectural information. The potential success of horizontal gene transfer events is historically equated to the benefits conferred by encoded products. Here we show that gene transfer events are observed less frequently if the introduced genes disrupt important patterns of genomic information, suggesting that this disruption would confer an unacceptable cost. As a result, gene transfer events are less likely to be successful if the potential donor genomes have incompatible genome architecture. Because more distantly-related genes are less compatible, chromosome architecture serves as a mechanism to bias gene transfer events to those involving closer relatives, thereby providing a mechanism for the genotypic and phenotypic cohesion of higher taxonomic groups.
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Affiliation(s)
- Heather L. Hendrickson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Dominique Barbeau
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robin Ceschin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey G. Lawrence
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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13
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Christensen PA, Ni Y, Bao F, Hendrickson HL, Greenwood M, Thomas JS, Long SW, Olsen RJ. Houston Methodist Variant Viewer: An Application to Support Clinical Laboratory Interpretation of Next-generation Sequencing Data for Cancer. J Pathol Inform 2017; 8:44. [PMID: 29226007 PMCID: PMC5719586 DOI: 10.4103/jpi.jpi_48_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/12/2017] [Indexed: 01/17/2023] Open
Abstract
Introduction Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist. Although commercial tools for NGS data analysis and interpretation are available, they are often costly, lack key functionality or cannot be customized by the end user. Methods To facilitate NGS data analysis in our clinical molecular diagnostics laboratory, we created a custom bioinformatics tool termed Houston Methodist Variant Viewer (HMVV). HMVV is a Java-based solution that integrates sequencing instrument output, bioinformatics analysis, storage resources and end user interface. Results Compared to the predicate method used in our clinical laboratory, HMVV markedly simplifies the bioinformatics workflow for the molecular technologist and facilitates the variant review by the molecular pathologist. Importantly, HMVV reduces time spent researching the biological significance of the variants detected, standardizes the online resources used to perform the variant investigation and assists generation of the annotated report for the electronic medical record. HMVV also maintains a searchable variant database, including the variant annotations generated by the pathologist, which is useful for downstream quality improvement and research projects. Conclusions HMVV is a clinical grade, low-cost, feature-rich, highly customizable platform that we have made available for continued development by the pathology informatics community.
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Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Yunyun Ni
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA.,Helix, San Carlos, California 94070, USA
| | - Feifei Bao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Michael Greenwood
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
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Hendrickson HL. DNA replication can still spring surprises. Genome Biol 2008; 9:317. [PMID: 18710594 PMCID: PMC2575508 DOI: 10.1186/gb-2008-9-8-317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A report of the first EMBO conference in a biennial series 'Replication and Segregation of Chromosomes', Geilo, Norway, 16-20 June 2008. A report of the first EMBO conference in a biennial series 'Replication and Segregation of Chromosomes', Geilo, Norway, 16-20 June 2008.
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