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Owen-Smith A, Porter J, Thomas CM, Clarke S, Ogrodnick MM, Hand LJ, Dawson-Hahn E, O'Connor MH, Feinberg I, Adde S, Desta R, Yubo Z, Chin A, Safi M. 'Getting control of Corona takes many angles': COVID-19 vaccine knowledge, attitudes and beliefs among refugee/immigrant/migrant communities in four US cities. Health Educ Res 2024; 39:182-196. [PMID: 38300230 DOI: 10.1093/her/cyae003] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
The objectives of the study were to (i) document refugee, immigrant and migrant (RIM) communities' knowledge, attitudes and beliefs (KABs) related to the Coronavirus disease (COVID-19) vaccine and (ii) identify best practices for developing and disseminating culturally and linguistically responsive health messaging addressing those KABs. Thirteen online focus groups (OFGs) in 10 languages were conducted. Each OFG was conducted in the participants' native language. OFGs were recorded, transcribed, translated and uploaded to qualitative software for coding. A thematic analysis was conducted. Results suggest that while there was some variation between different language groups (e.g. whether religious leaders were seen as trusted sources of information about COVID), there were also important commonalities. Most language groups (i) alluded to hearing about or having gaps in knowledge about COVID-19/the COVID-19 vaccine, (ii) reported hearing negative or conflicting stories about the vaccine and (iii) shared concerns about the negative side effects of the vaccine. There continues to be a need for health messaging in RIM communities that is culturally and linguistically concordant and follows health literacy guidelines. Message content about the COVID-19 vaccine should focus on vaccine importance, effectiveness and safety, should be multimodal and should be primarily delivered by healthcare professionals and community members who have already been vaccinated.
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Affiliation(s)
- A Owen-Smith
- Department of Health Policy and Behavioral Sciences, Georgia State University, School of Public Health, 140 Decatur Street, Atlanta, GA 30303, USA
| | - J Porter
- International Rescue Committee UK, 100 Wood Street, London EC2V 7AN, United Kingdom
| | - C M Thomas
- Department of Medicine, University of Minnesota, Division of Infectious Diseases and International Medicine, 401 East River Parkway, Minneapolis, MN 55455, USA
| | - S Clarke
- Society of Refugee Healthcare Providers, 172 Colby St, Spencerport, New York 14559
| | - M M Ogrodnick
- Department of Health Policy and Behavioral Sciences, Georgia State University, School of Public Health, 140 Decatur Street, Atlanta, GA 30303, USA
| | - L J Hand
- Department of Communication, Georgia State University, 800 Twenty Five Park Place NE, Atlanta, GA 30303, USA
- School of Communication and Media, Kennesaw State University, 1000 Chastain Road, Kennesaw, GA 30144, USA
| | - E Dawson-Hahn
- Department of Pediatrics, University of Washington, 4245 Roosevelt Way NE, Seattle, WA 98105, USA
| | - M H O'Connor
- Department of Health Policy and Behavioral Sciences, Georgia State University, School of Public Health, 140 Decatur Street, Atlanta, GA 30303, USA
| | - I Feinberg
- College of Education and Human Development, Georgia State University, 30 Pryor St. SW, Atlanta, GA 30303, USA
| | - S Adde
- Department of Health Policy and Behavioral Sciences, Georgia State University, School of Public Health, 140 Decatur Street, Atlanta, GA 30303, USA
| | - R Desta
- Department of Health Policy and Behavioral Sciences, Georgia State University, School of Public Health, 140 Decatur Street, Atlanta, GA 30303, USA
| | - Z Yubo
- Department of Health Policy and Behavioral Sciences, Georgia State University, School of Public Health, 140 Decatur Street, Atlanta, GA 30303, USA
| | - A Chin
- Department of Health Policy and Behavioral Sciences, Georgia State University, School of Public Health, 140 Decatur Street, Atlanta, GA 30303, USA
| | - M Safi
- International Rescue Committee UK, 100 Wood Street, London EC2V 7AN, United Kingdom
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Elg CA, Mack E, Rolfsmeier M, McLean TC, Kosterlitz O, Soderling E, Narum S, Rowley PA, Thomas CM, Top EM. Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost. bioRxiv 2024:2024.02.05.579024. [PMID: 38370613 PMCID: PMC10871194 DOI: 10.1101/2024.02.05.579024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Plasmids play a major role in bacterial evolution and rapid adaptation by facilitating the horizontal transfer of diverse genes. Understanding how plasmids are transferred and maintained in bacterial populations is important, especially given the increasing plasmid-mediated spread of antibiotic-resistance genes to human pathogens. We investigated why broad-host range plasmid pBP136, originally isolated from clinical samples of Bordetella pertussis, quickly became extinct in laboratory Escherichia coli populations. We found that the inactivation of a previously uncharacterized plasmid gene, upf31, drastically improved long-term maintenance of the plasmid in E. coli. Loss of this single gene was associated with decreased transcription of numerous genes in the plasmid korA, korB and korC regulons, as well as changes in many chromosomal genes primarily related to metabolism. This change in transcriptome is likely initiated by Upf31 interacting with one of these major plasmid regulators, KorB. Expression of upf31 in trans not only negatively affected the persistence of a pBP136 upf31 deletion mutant, but also of the closely related archetype IncPβ plasmid R751, which is stable in E. coli and natively encodes an internally truncated upf31 allele. This suggests that whereas the upf31 allele in pBP136 might advantageously modulate gene expression in its original host, B. pertussis, the same function can have harmful effects in E. coli. Thus, using multiple hosts to study the effects of knockouts in broad-host-range plasmid genes of unknown function may reveal unexpected mechanisms that determine the fate of that plasmid in bacterial communities.
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Affiliation(s)
- Clinton A. Elg
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Erin Mack
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Michael Rolfsmeier
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Thomas C. McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Olivia Kosterlitz
- Biology Department, University of Washington, Seattle, Washington, USA
| | | | - Solana Narum
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | | | - Eva M. Top
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
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Thomas CM, de Cerff C, Maniel GAV, Oyatoye AE, Rocke E, Marco HG, Pillay D. Water filtration by endobenthic sandprawns enhances resilience against eutrophication under experimental global change conditions. Sci Rep 2023; 13:19067. [PMID: 37925538 PMCID: PMC10625564 DOI: 10.1038/s41598-023-46168-y] [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: 08/01/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023] Open
Abstract
Identifying processes that confer resilience against global change is a scientific challenge but is central to managing ecosystem functionality in future. Detecting resilience-enhancing mechanisms is especially relevant in coastal ecosystems, where multi-stressor interactions can drive degradation over time. Here, we quantify the resilience-conferring potential of endobenthic sandprawns against eutrophication, including under high temperatures. We show using a global change mesocosm experiment that sandprawn presence was associated with declines in phytoplankton biomass, particularly under eutrophic conditions, where sandprawns reduced phytoplankton biomass by approximately 74% and prevented a shift to extreme eutrophy. Eutrophic waters were nanophytoplankton-dominated, but sandprawn presence countered this, resulting in even contributions of pico- and nanophytoplankton. Our findings highlight the potential for sandprawns to increase resilience against eutrophication by limiting phytoplankton blooms, preventing extreme eutrophy and counteracting nanophytoplankton dominance. Incorporating endobenthic crustaceans into resilience-based management practices can assist in arresting future water quality declines in coastal ecosystems.
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Affiliation(s)
- C M Thomas
- Department of Biological Sciences, Marine and Antarctic Research Centre for Innovation and Sustainability, University of Cape Town, Cape Town, 7701, South Africa
| | - C de Cerff
- Department of Biological Sciences, Marine and Antarctic Research Centre for Innovation and Sustainability, University of Cape Town, Cape Town, 7701, South Africa
- Marine and Freshwater Research Centre, Atlantic Technological University, Galway, Ireland
| | - G A V Maniel
- Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA), Muséum national d'Histoire naturelle, 61 rue Buffon, 75005, Paris, France
| | - A E Oyatoye
- Department of Biological Sciences, Marine and Antarctic Research Centre for Innovation and Sustainability, University of Cape Town, Cape Town, 7701, South Africa
| | - E Rocke
- Department of Biological Sciences, Marine and Antarctic Research Centre for Innovation and Sustainability, University of Cape Town, Cape Town, 7701, South Africa
| | - H G Marco
- Department of Biological Sciences, Marine and Antarctic Research Centre for Innovation and Sustainability, University of Cape Town, Cape Town, 7701, South Africa
| | - D Pillay
- Department of Biological Sciences, Marine and Antarctic Research Centre for Innovation and Sustainability, University of Cape Town, Cape Town, 7701, South Africa.
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Abstract
This short primer is intended to give an overview of bacterial plasmids for those not yet familiar with these fascinating genetic elements. It covers their basic properties but does not attempt to cover the diversity of phenotypic properties that can be encoded by plasmids, and includes suggestions for further reading.
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Affiliation(s)
- Georgina S. Lloyd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Cook DP, Thomas CM, Wu AY, Rusznak M, Zhang J, Zhou W, Cephus JY, Gibson-Corley KN, Polosukhin VV, Norlander AE, Newcomb DC, Stoltz DA, Peebles RS. Cystic Fibrosis Reprograms Airway Epithelial IL-33 Release and Licenses IL-33-Dependent Inflammation. Am J Respir Crit Care Med 2023; 207:1486-1497. [PMID: 36952660 PMCID: PMC10263140 DOI: 10.1164/rccm.202211-2096oc] [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: 11/14/2022] [Accepted: 03/23/2023] [Indexed: 03/25/2023] Open
Abstract
Rationale: Type 2 inflammation has been described in people with cystic fibrosis (CF). Whether loss of CFTR (cystic fibrosis transmembrane conductance regulator) function contributes directly to a type 2 inflammatory response has not been fully defined. Objectives: The potent alarmin IL-33 has emerged as a critical regulator of type 2 inflammation. We tested the hypothesis that CFTR deficiency increases IL-33 expression and/or release and deletion of IL-33 reduces allergen-induced inflammation in the CF lung. Methods: Human airway epithelial cells (AECs) grown from non-CF and CF cell lines and Cftr+/+ and Cftr-/- mice were used in this study. Pulmonary inflammation in Cftr+/+ and Cftr-/- mice with and without IL-33 or ST2 (IL-1 receptor-like 1) germline deletion was determined by histological analysis, BAL, and cytokine analysis. Measurements and Main Results: After allergen challenge, both CF human AECs and Cftr-/- mice had increased IL-33 expression compared with control AECs and Cftr+/+ mice, respectively. DUOX1 (dual oxidase 1) expression was increased in CF human AECs and Cftr-/- mouse lungs compared with control AECs and lungs from Cftr+/+ mice and was necessary for the increased IL-33 release in Cftr-/- mice compared with Cftr+/+ mice. IL-33 stimulation of Cftr-/- CD4+ T cells resulted in increased type 2 cytokine production compared with Cftr+/+ CD4+ T cells. Deletion of IL-33 or ST2 decreased both type 2 inflammation and neutrophil recruitment in Cftr-/- mice compared with Cftr+/+ mice. Conclusions: Absence of CFTR reprograms airway epithelial IL-33 release and licenses IL-33-dependent inflammation. Modulation of the IL-33/ST2 axis represents a novel therapeutic target in CF type 2-high and neutrophilic inflammation.
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Affiliation(s)
| | | | | | | | | | | | | | - Katherine N. Gibson-Corley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Dawn C. Newcomb
- Department of Internal Medicine and
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David A. Stoltz
- Department of Internal Medicine and
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa; and
| | - R. Stokes Peebles
- Department of Internal Medicine and
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
- Tennessee Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, Tennessee
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Maurya AP, Lazdins A, Wilson H, Lloyd GS, Stephens ER, Haines AS, Thomas CM. Iteron control of oriV function in IncP-1 plasmid RK2. Plasmid 2023; 126:102681. [PMID: 36990191 DOI: 10.1016/j.plasmid.2023.102681] [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] [Received: 01/04/2023] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Replication control of many plasmids is mediated by the balance between the positive and negative effects of Rep protein binding repeated sequences (iterons) associated with the replication origin, oriV. Negative control is thought to be mediated by dimeric Rep protein linking iterons in a process termed "handcuffing". The well-studied oriV region of RK2 contains 9 iterons arranged as a singleton (iteron 1), a group of 3 (iterons 2-4) and a group of 5 (iterons 5-9), but only iterons 5 to 9 are essential for replication. An additional iteron (iteron 10), oriented in the opposite direction, is also involved and reduces copy-number nearly two-fold. Since iterons 1 and 10 share an identical upstream hexamer (5' TTTCAT 3') it has been hypothesised that they form a TrfA-mediated loop facilitated by their inverted orientation. Here we report that contrary to the hypothesis, flipping one or other so they are in direct orientation results in marginally lower rather than higher copy-number. In addition, following mutagenesis of the hexamer upstream of iteron 10, we report that the Logo for the hexamer "upstream" of the regulatory iterons (1 to 4 and 10) differs from that of the essential iterons, suggesting functional differences in their interaction with TrfA.
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Affiliation(s)
- Anand P Maurya
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alessandro Lazdins
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Helen Wilson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Georgina S Lloyd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Abstract
The sympathetic nervous system (SNS) and parasympathetic nervous system (PNS) regulate the effector functions of group 2 innate lymphoid cells (ILC2s) through β2 adrenergic receptor (ADRB2) and nicotinic/muscarinic cholinergic receptor signaling, respectively. To further maintain the critical balance between host-protective and pathogenic type 2 inflammation in the lungs, neuropeptides neuromedin B (NMB) and neuromedin U (NMU) function to suppress or promote ILC2 responses in synergy with IL-33/IL-25, respectively. Additionally, the release of ATP into the extracellular environment in response to cell death caused by challenge to the airway epithelial barrier quickly becomes converted into adenosine, which helps keep the inflammatory response in check by suppressing ILC2 responses. Besides neurotransmitter and neuropeptides derived from other cells, ILC2s further regulate allergic airway inflammation through the production of acetylcholine (ACh) and calcitonin gene-related peptide (CGRP). In this article we review the neuromodulation of ILC2s through cholinergic and adrenergic signaling, neuropeptides, and adenosine and its role in allergic airway inflammation. Furthermore, we discuss the potential clinical utility of targeting these pathways for therapeutic goals and address directions for future research.
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Affiliation(s)
- Christopher M. Thomas
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - R. Stokes Peebles
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, United States,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States,Research Service, Tennessee Valley Healthcare System, United States Department of Veterans Affairs, Nashville, TN, United States,Correspondence: R. Stokes Peebles
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8
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Thomas CM, Peebles RS. Development and function of regulatory innate lymphoid cells. Front Immunol 2022; 13:1014774. [PMID: 36275689 PMCID: PMC9581395 DOI: 10.3389/fimmu.2022.1014774] [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: 08/08/2022] [Accepted: 09/20/2022] [Indexed: 01/12/2023] Open
Abstract
Innate lymphoid cells (ILCs) are a critical element of the innate immune system and are potent producers of pro-inflammatory cytokines. Recently, however, the production of the anti-inflammatory cytokine IL-10 has been observed in all ILC subtypes (ILC1s, ILC2s, and ILC3s) suggesting their ability to adopt a regulatory phenotype that serves to maintain lung and gut homeostasis. Other studies advocate a potential therapeutic role of these IL-10-expressing ILCs in allergic diseases such as asthma, colitis, and pancreatic islet allograft rejection. Herein, we review IL-10 producing ILCs, discussing their development, function, regulation, and immunotherapeutic potential through suppressing harmful inflammatory responses. Furthermore, we address inconsistencies in the literature regarding these regulatory IL-10 producing ILCs, as well as directions for future research.
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Affiliation(s)
- Christopher M. Thomas
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - R. Stokes Peebles
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, United States,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States,Research Service, Tennessee Valley Healthcare System, United States Department of Veterans Affairs, Nashville, TN, United States,*Correspondence: R. Stokes Peebles Jr,
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Thomas CM, Kumar D, Scheel RA, Ramarao B, Nomura CT. Production of Medium Chain Length polyhydroxyalkanoate copolymers from agro-industrial waste streams. Biocatalysis and Agricultural Biotechnology 2022. [DOI: 10.1016/j.bcab.2022.102385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Haines AS, Kendrew SG, Crowhurst N, Stephens ER, Connolly J, Hothersall J, Miller CE, Collis AJ, Huckle BD, Thomas CM. High quality genome annotation and expression visualisation of a mupirocin-producing bacterium. PLoS One 2022; 17:e0268072. [PMID: 35511780 PMCID: PMC9070926 DOI: 10.1371/journal.pone.0268072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/25/2021] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas strain NCIMB10586, in the P. fluorescens subgroup, produces the polyketide antibiotic mupirocin, and has potential as a host for industrial production of a range of valuable products. To underpin further studies on its genetics and physiology, we have used a combination of standard and atypical approaches to achieve a quality of the genome sequence and annotation, above current standards for automated pathways. Assembly of Illumina reads to a PacBio genome sequence created a retrospectively hybrid assembly, identifying and fixing 415 sequencing errors which would otherwise affect almost 5% of annotated coding regions. Our annotation pipeline combined automation based on related well-annotated genomes and stringent, partially manual, tests for functional features. The strain was close to P. synxantha and P. libaniensis and was found to be highly similar to a strain being developed as a weed-pest control agent in Canada. Since mupirocin is a secondary metabolite whose production is switched on late in exponential phase, we carried out RNAseq analysis over an 18 h growth period and have developed a method to normalise RNAseq samples as a group, rather than pair-wise. To review such data we have developed an easily interpreted way to present the expression profiles across a region, or the whole genome at a glance. At the 2-hour granularity of our time-course, the mupirocin cluster increases in expression as an essentially uniform bloc, although the mupirocin resistance gene stands out as being expressed at all the time points.
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Affiliation(s)
- Anthony S. Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Steve G. Kendrew
- Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom
| | - Nicola Crowhurst
- Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom
| | - Elton R. Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Jack Connolly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Claire E. Miller
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Andrew J. Collis
- Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom
| | - Benjamin D. Huckle
- Manufacturing Science and Technology, GlaxoSmithKline, Worthing, West Sussex, United Kingdom
| | - Christopher M. Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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Gamon J, Haller S, Giaume D, Robert C, Thomas CM, D'Alençon L, Buissette V, Le Mercier T, Barboux P. Aqueous-Based Low-Temperature Synthesis and Thin-Film Properties of Oxysulfide BiCuOS Nanoparticles. Chempluschem 2020; 85:634-640. [PMID: 32237226 DOI: 10.1002/cplu.201900733] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/05/2020] [Indexed: 11/10/2022]
Abstract
BiCuOS is a nontoxic p-type semiconductor that is a promising candidate for photoelectric applications. The formation of thin films with a good electronic transport at the grain boundaries, while avoiding thermal treatment detrimental to its chemical stability is a challenge. We have developed a chemical method for the direct synthesis of stable colloidal suspensions of BiCuOS nanoparticles from soluble precursors. These colloidal solutions were stabilized with a catechol functionalized poly-3-hexylthiophene that allows easy spin-coating deposition and favors electronic transport along the grain boundaries. Stacking of ZnO-BiCuOS layers were achieved, allowing preparation of n-p junctions. These act as rectifying diodes and are strongly photosensitive, with Iph /Idark =85 corresponding to an enhancement of the photocurrent of more than two orders of magnitude compared to that of BiCuOS alone. This energy-efficient and low-cost method is a further step in the development of new sulfide semiconductor devices.
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Affiliation(s)
- J Gamon
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, 75005, Paris, France.,Solvay, Research and Innovation Center Paris, 52 rue de La Haie Coq, 93308, Aubervilliers Cedex, France
| | - S Haller
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, 75005, Paris, France.,Solvay, Research and Innovation Center Paris, 52 rue de La Haie Coq, 93308, Aubervilliers Cedex, France
| | - D Giaume
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, 75005, Paris, France
| | - C Robert
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, 75005, Paris, France
| | - C M Thomas
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, 75005, Paris, France
| | - L D'Alençon
- Solvay, Research and Innovation Center Paris, 52 rue de La Haie Coq, 93308, Aubervilliers Cedex, France
| | - V Buissette
- Solvay, Research and Innovation Center Paris, 52 rue de La Haie Coq, 93308, Aubervilliers Cedex, France
| | - T Le Mercier
- Solvay, Research and Innovation Center Paris, 52 rue de La Haie Coq, 93308, Aubervilliers Cedex, France
| | - P Barboux
- Chimie ParisTech, PSL University, CNRS, Institut de Recherche de Chimie Paris, 75005, Paris, France
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Scheel RA, Fusi AD, Min BC, Thomas CM, Ramarao BV, Nomura CT. Increased Production of the Value-Added Biopolymers Poly( R-3-Hydroxyalkanoate) and Poly(γ-Glutamic Acid) From Hydrolyzed Paper Recycling Waste Fines. Front Bioeng Biotechnol 2019; 7:409. [PMID: 31921814 PMCID: PMC6930151 DOI: 10.3389/fbioe.2019.00409] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/27/2019] [Indexed: 11/25/2022] Open
Abstract
Reject fines, a waste stream of short lignocellulosic fibers produced from paper linerboard recycling, are a cellulose-rich paper mill byproduct that can be hydrolyzed enzymatically into fermentable sugars. In this study, the use of hydrolyzed reject fines as a carbon source for bacterial biosynthesis of poly(R-3-hydroxyalkanoate) (PHA) and poly(γ-glutamic acid) (PGA) was investigated. Recombinant Escherichia coli harboring PHA biosynthesis genes were cultivated with purified sugars or crude hydrolysate to produce both poly(R-3-hydroxybutyrate) (PHB) homopolymer and medium chain length-containing copolymer (PHB-co-MCL). Wild-type Bacillus licheniformis WX-02 were cultivated with crude hydrolysate to produce PGA. Both PHB and short chain-length-co-medium chain-length (SCL-co-MCL) PHA yields from crude hydrolysate were a 2-fold improvement over purified sugars, and the MCL monomer fraction was decreased slightly in copolymers produced from crude hydrolysate. PGA yield from crude hydrolysate was similarly increased 2-fold. The results suggest that sugars from hydrolyzed reject fines are a viable carbon source for PHA and PGA biosynthesis. The use of crude hydrolysate is not only possible but beneficial for biopolymer production, eliminating the need for costly separation and purification techniques. This study demonstrates the potential to divert a lignocellulosic waste stream into valuable biomaterials, mitigating the environmental impacts of solid waste disposal.
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Affiliation(s)
- Ryan A Scheel
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Alexander D Fusi
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Byeong C Min
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Christopher M Thomas
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Bandaru V Ramarao
- Department of Paper and Bioprocess Engineering, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Christopher T Nomura
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States.,Center for Applied Microbiology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
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13
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Crockett MP, Zhang H, Thomas CM, Byers JA. Adding diffusion ordered NMR spectroscopy (DOSY) to the arsenal for characterizing paramagnetic complexes. Chem Commun (Camb) 2019; 55:14426-14429. [PMID: 31730148 DOI: 10.1039/c9cc08229h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report the development of diffusion ordered NMR spectroscopy (DOSY) for its use to characterize metal complexes containing paramagnetic first row transition metal elements. This technique is capable of assessing the purity and speciation of paramagnetic complexes, and also provides a convenient method to provide qualitative and sometimes quantitative molecular weight data.
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Affiliation(s)
- M P Crockett
- Department of Chemistry, Boston College, Eugene F. Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, USA.
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14
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Abstract
Medullary thyroid cancer is a rare type of neuroendocrine tumour that arises from the parafollicular cells (C cells) of the thyroid gland. It accounts for 3%-5% of thyroid cancer cases. Close to 25% of cases are familial, and 75% are considered sporadic. Familial cases are associated with a germline RET mutation; 43%-65% of sporadic cases harbour a somatic event in the gene. Germline RET mutations are associated with the autosomal-dominant inherited multiple endocrine neoplasia (men) 2a and 2b syndromes and the isolated familial medullary thyroid cancer syndrome. More than 100 RET codon mutations have been reported to date, with genotype-phenotype correlations that include the extent and aggressiveness of the medullary thyroid cancer and the presence of other features of the men2 syndromes. The latter include pheochromocytoma-paraganglioma, hyperparathyroidism, cutaneous lichen amyloidosis, and Hirschsprung disease. In this narrative review, we focus on RET proto-oncogene physiology and pathogenesis induced by germline and somatic RET mutations, the genotype-phenotype correlation, and the management and follow-up of patients with germline-mutated medullary thyroid cancer.
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Affiliation(s)
- V Larouche
- Endocrine Oncology Site Group, Princess Margaret Cancer Centre, Toronto, ON.,Division of Endocrinology and Metabolism, Department of Medicine, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montreal, QC
| | - A Akirov
- Endocrine Oncology Site Group, Princess Margaret Cancer Centre, Toronto, ON.,Institute of Endocrinology, Beilinson Hospital, Petach Tikva.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C M Thomas
- Endocrine Oncology Site Group, Princess Margaret Cancer Centre, Toronto, ON.,Department of Otolaryngology-Head and Neck Surgery, Princess Margaret Cancer Centre, University Health Network, Toronto, ON
| | - M K Krzyzanowska
- Endocrine Oncology Site Group, Princess Margaret Cancer Centre, Toronto, ON
| | - S Ezzat
- Endocrine Oncology Site Group, Princess Margaret Cancer Centre, Toronto, ON
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15
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Pike LC, Thomas CM, Guerrero-Urbano T, Michaelidou A, Greener T, Miles E, Eaton D, Barrington SF. Guidance on the use of PET for treatment planning in radiotherapy clinical trials. Br J Radiol 2019; 92:20190180. [PMID: 31437023 PMCID: PMC6849663 DOI: 10.1259/bjr.20190180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 02/15/2019] [Revised: 07/16/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
The aim of this article is to propose meaningful guidance covering the practical and technical issues involved when planning or conducting clinical trials involving positron emission tomography (PET)-guided radiotherapy. The complexity of imaging requirements will depend on the study aims, design and PET methods used. Where PET is used to adapt radiotherapy, a high level of accuracy and reproducibility is required to ensure effective and safe treatment delivery. The guidance in this document is intended to assist researchers designing clinical trials involving PET-guided radiotherapy to provide sufficient information about the appropriate methods to complete PET-CT imaging to a consistent standard at participating centres. The guidance is divided into six categories: application of PET in radiotherapy, resource requirements, quality assurance, imaging protocol design, data management and image processing. Each section provides an overview of the recent literature to support the specific recommendations. This guidance builds on previous recommendations from the National Cancer Research Institute PET Research Network and has been produced in collaboration with the National Radiotherapy Trials Quality Assurance Group.
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Affiliation(s)
- Lucy C Pike
- King’s College London and Guy’s and St Thomas’ PET Centre, School of Biomedical Engineering and Imaging Sciences, King’s College London, King’s Health Partners, London, UK
| | | | | | | | - Tony Greener
- Radiotherapy Physics, Guy's & St Thomas’ NHS Foundation Trust, London, UK
| | - Elizabeth Miles
- National Radiotherapy Trials QA Group, Mount Vernon Hospital, Northwood, UK
| | | | - Sally F Barrington
- King’s College London and Guy’s and St Thomas’ PET Centre, School of Biomedical Engineering and Imaging Sciences, King’s College London, King’s Health Partners, London, UK
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16
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Thomas CM, Asa SL, Ezzat S, Sawka AM, Goldstein D. Diagnosis and pathologic characteristics of medullary thyroid carcinoma-review of current guidelines. Curr Oncol 2019; 26:338-344. [PMID: 31708652 PMCID: PMC6821118 DOI: 10.3747/co.26.5539] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Medullary thyroid carcinoma (mtc) is a rare malignancy of the thyroid gland, and raising awareness of the recommended diagnostic workup and pathologic characteristics of this malignancy is therefore important. Methods We reviewed the current clinical practice guidelines and recent literature on mtc, and here, we summarize the recommendations for its diagnosis and workup. We also provide an overview of the pathology of mtc. Results A neuroendocrine tumour, mtc arises from parafollicular cells ("C cells"), which secrete calcitonin. As part of the multiple endocrine neoplasia (men) type 2 syndromes, mtc can occur sporadically or in a hereditary form. This usually poorly delineated and infiltrative tumour is composed of solid nests of discohesive cells within a fibrous stroma that might also contain amyloid. Suspicious nodules on thyroid ultrasonography should be assessed with fine-needle aspiration (fna). If a diagnosis of mtc is made on fna, patients require baseline measurements of serum calcitonin and carcinoembryonic antigen. Calcitonin levels greater than 500 pg/mL or clinical suspicion for metastatic disease dictate the need for further imaging studies. All patients should undergo dna analysis for RET mutations to diagnose men type 2 syndromes, and if positive, they should be assessed for possible pheochromocytoma and hyperparathyroidism. Summary Although the initial diagnosis of a suspicious thyroid nodule is the same for differentiated thyroid carcinoma and mtc, the remainder of the workup and diagnosis for mtc is distinct.
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Affiliation(s)
- C M Thomas
- Department of Otolaryngology-Head and Neck Surgery, University Health Network, Toronto, ON
- Department of Surgical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON
| | - S L Asa
- Department of Pathology, Case Western Reserve University, Cleveland, OH, U.S.A
- Department of Pathology, University Health Network, Toronto, ON
| | - S Ezzat
- Department of Medicine and Oncology, University of Toronto, Toronto, ON
| | - A M Sawka
- Department of Medicine, Division of Endocrinology, University of Toronto, Toronto, ON
| | - D Goldstein
- Department of Otolaryngology-Head and Neck Surgery, University Health Network, Toronto, ON
- Department of Surgical Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON
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17
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Giles M, Cawthraw SA, AbuOun M, Thomas CM, Munera D, Waldor MK, La Ragione RM, Ritchie JM. Host-specific differences in the contribution of an ESBL IncI1 plasmid to intestinal colonization by Escherichia coli O104:H4. J Antimicrob Chemother 2019; 73:1579-1585. [PMID: 29506073 DOI: 10.1093/jac/dky037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/18/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives To assess stability and contribution of a large ESBL-encoding IncI1 plasmid to intestinal colonization by Escherichia coli O104:H4 in two different mammalian hosts. Methods Specific-pathogen-free 3-4-day-old New Zealand White rabbits and conventionally reared 6-week-old weaned lambs were orally infected with WT E. coli O104:H4 or the ESBL-plasmid-cured derivative, and the recovery of bacteria in intestinal homogenates and faeces monitored over time. Results Carriage of the ESBL plasmid had differing impacts on E. coli O104:H4 colonization of the two experimental hosts. The plasmid-cured strain was recovered at significantly higher levels than WT during late-stage colonization of rabbits, but at lower levels than WT in sheep. Regardless of the animal host, the ESBL plasmid was stably maintained in virtually all in vivo passaged bacteria that were examined. Conclusions These findings suggest that carriage of ESBL plasmids has distinct effects on the host bacterium depending upon the animal species it encounters and demonstrates that, as for E. coli O157:H7, ruminants could represent a potential transmission reservoir.
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Affiliation(s)
- M Giles
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - S A Cawthraw
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - M AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, UK
| | - C M Thomas
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - D Munera
- Division of Infectious Diseases, Brigham and Women's Hospital/Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - M K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital/Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - R M La Ragione
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - J M Ritchie
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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18
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Connolly JA, Wilson A, Macioszek M, Song Z, Wang L, Mohammad HH, Yadav M, di Martino M, Miller CE, Hothersall J, Haines AS, Stephens ER, Crump MP, Willis CL, Simpson TJ, Winn PJ, Thomas CM. Defining the genes for the final steps in biosynthesis of the complex polyketide antibiotic mupirocin by Pseudomonas fluorescens NCIMB10586. Sci Rep 2019; 9:1542. [PMID: 30733464 PMCID: PMC6367315 DOI: 10.1038/s41598-018-38038-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/17/2018] [Indexed: 11/09/2022] Open
Abstract
The mupirocin trans-AT polyketide synthase pathway, provides a model system for manipulation of antibiotic biosynthesis. Its final phase involves removal of the tertiary hydroxyl group from pseudomonic acid B, PA-B, producing the fully active PA-A in a complex series of steps. To further clarify requirements for this conversion, we fed extracts containing PA-B to mutants of the producer strain singly deficient in each mup gene. This additionally identified mupM and mupN as required plus the sequence but not enzymic activity of mupL and ruled out need for other mup genes. A plasmid expressing mupLMNOPVCFU + macpE together with a derivative of the producer P. fluorescens strain NCIMB10586 lacking the mup cluster allowed conversion of PA-B to PA-A. MupN converts apo-mAcpE to holo-form while MupM is a mupirocin-resistant isoleucyl tRNA synthase, preventing self-poisoning. Surprisingly, the expression plasmid failed to allow the closely related P. fluorescens strain SBW25 to convert PA-B to PA-A.
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Affiliation(s)
- Jack A Connolly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,School of Chemistry, University of St Andrews, BMS Building, North Haugh, St Andrews, KY16 9ST, UK
| | - Amber Wilson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Malgorzata Macioszek
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Dr M. Macioszek, DOCS International Poland, ul. Grojecka 5, 02-019, Warszawa, Poland
| | - Zhongshu Song
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Luoyi Wang
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Hadi H Mohammad
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,College of Medicine, Kirkuk University, Kirkuk, Iraq
| | - Mukul Yadav
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Maura di Martino
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Ms M. di Martino, Dept Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Claire E Miller
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Dr C. E. Miller, The BioHub Birmingham, Birmingham Research Park, 97 Vincent Drive, Edgbaston, Birmingham, B15 2SQ, UK
| | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Peter J Winn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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19
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Mohammad HH, Connolly JA, Song Z, Hothersall J, Race PR, Willis CL, Simpson TJ, Winn PJ, Thomas CM. Fine Tuning of Antibiotic Activity by a Tailoring Hydroxylase in a Trans-AT Polyketide Synthase Pathway. Chembiochem 2018; 19:836-841. [PMID: 29363252 DOI: 10.1002/cbic.201800036] [Citation(s) in RCA: 2] [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: 01/18/2018] [Indexed: 11/06/2022]
Abstract
The addition or removal of hydroxy groups modulates the activity of many pharmacologically active biomolecules. It can be integral to the basic biosynthetic factory or result from associated tailoring steps. For the anti-MRSA antibiotic mupirocin, removal of a C8-hydroxy group late in the biosynthetic pathway gives the active pseudomonic acid A. An extra hydroxylation, at C4, occurs in the related but more potent antibiotic thiomarinol A. We report here in vivo and in vitro studies that show that the putative non-haem-iron(II)/α-ketoglutaratedependent dioxygenase TmuB, from the thiomarinol cluster, 4-hydroxylates various pseudomonic acids whereas C8-OH, and other substituents around the tetrahydropyran ring, block enzyme action but not substrate binding. Molecular modelling suggested a basis for selectivity, but mutation studies had a limited ability to rationally modify TmuB substrate specificity. 4-Hydroxylation had opposite effects on the potency of mupirocin and thiomarinol. Thus, TmuB can be added to the toolbox of polyketide tailoring technologies for the in vivo generation of new antibiotics in the future.
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Affiliation(s)
- Hadi H Mohammad
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,College of Medicine, Kirkuk University, Kirkuk, Iraq
| | - Jack A Connolly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Zhongshu Song
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Peter J Winn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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20
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Peeters CF, Thomas CM, Sweep FC, Span PN, Wobbes T, Ruers TM. Elevated Serum Endothelin-1 Levels in Patients with Colorectal Cancer; Relevance for Prognosis. Int J Biol Markers 2018; 15:288-93. [PMID: 11192823 DOI: 10.1177/172460080001500402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 11/16/2022]
Abstract
Background It has been demonstrated that the Doppler Perfusion Index (DPI) is increased in patients who are at risk of developing liver metastases from colorectal cancer. It has been postulated that a circulating hormonal factor is involved in the relative vasoconstriction throughout the splanchnic bed. Endothelin-1 (ET-1), a potent vasoconstrictor which has been associated with tumor growth and is produced by colorectal tumors, may play an important role in this phenomenon. In this paper the prognostic value of serum ET-1 in colorectal cancer is discussed. Methods Preoperative serum levels of ET-1 were assessed in three groups of patients: group A underwent resection of the colorectal tumor and remained free of recurrence (n=20); group B developed metachronous liver metastases at least six months after colorectal resection (n=14); and group C presented with colorectal cancer and synchronous liver metastases (n=22). Results The mean (SD) serum ET-1 levels in groups A, B and C were 1.59 (0.41) pmol/L, 1.70 (0.32) pmol/L and 1.85 (0.47) pmol/L, respectively. These values were significantly different from those of healthy controls (1.22 (0.31), p<0.05). Kaplan-Meier analyses revealed no prognostic value of preoperative serum ET-1 levels. Conclusions These preliminary results demonstrate that serum ET-1 levels are raised in patients with colorectal cancer. Serum ET-1 levels do not seem to be of prognostic value for survival.
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Affiliation(s)
- C F Peeters
- Department of Surgery, University Medical Centre, Nijmegen, The Netherlands
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21
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Hyde EI, Callow P, Rajasekar KV, Timmins P, Patel TR, Siligardi G, Hussain R, White SA, Thomas CM, Scott DJ. Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA. Biochem J 2017; 474:3121-3135. [PMID: 28760886 PMCID: PMC5577506 DOI: 10.1042/bcj20170281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022]
Abstract
The ParB protein, KorB, from the RK2 plasmid is required for DNA partitioning and transcriptional repression. It acts co-operatively with other proteins, including the repressor KorA. Like many multifunctional proteins, KorB contains regions of intrinsically disordered structure, existing in a large ensemble of interconverting conformations. Using NMR spectroscopy, circular dichroism and small-angle neutron scattering, we studied KorB selectively within its binary complexes with KorA and DNA, and within the ternary KorA/KorB/DNA complex. The bound KorB protein remains disordered with a mobile C-terminal domain and no changes in the secondary structure, but increases in the radius of gyration on complex formation. Comparison of wild-type KorB with an N-terminal deletion mutant allows a model of the ensemble average distances between the domains when bound to DNA. We propose that the positive co-operativity between KorB, KorA and DNA results from conformational restriction of KorB on binding each partner, while maintaining disorder.
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Affiliation(s)
- Eva I Hyde
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K.
| | - Philip Callow
- Institut Laue Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | | | - Peter Timmins
- Institut Laue Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Trushar R Patel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Rohanah Hussain
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Scott A White
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | | | - David J Scott
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, U.K.
- ISIS Neutron and Muon Spallation Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, U.K
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22
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Abstract
Good annotation of plasmid genomes is essential to maximise the value of the rapidly increasing volume of plasmid sequences. This short review highlights some of the current issues and suggests some ways forward. Where a well-studied related plasmid system exists we recommend that new annotation adheres to the convention already established for that system, so long as it is based on sound principles and solid experimental evidence, even if some of the new genes are more similar to homologues in different systems. Where a well-established model does not exist we provide generic gene names that reflect likely biochemical activity rather than overall purpose particularly, for example, where genes clearly belong to a type IV secretion system but it is not known whether they function in conjugative transfer or virulence. We also recommend that annotators use a whole system naming approach to avoid ending up with an illogical mixture of names from other systems based on the highest scoring match from a BLAST search. In addition, where function has not been experimentally established we recommend using just the locus tag, rather than a function-related gene name, while recording possible functions as notes rather than in a provisional name.
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Affiliation(s)
- Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | | | | | - Celeste J Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, United States
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, United States
| | - Laura S Frost
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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23
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Gao SS, Wang L, Song Z, Hothersall J, Stevens ER, Connolly J, Winn PJ, Cox RJ, Crump MP, Race PR, Thomas CM, Simpson TJ, Willis CL. Back Cover: Selected Mutations Reveal New Intermediates in the Biosynthesis of Mupirocin and the Thiomarinol Antibiotics (Angew. Chem. Int. Ed. 14/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201702123] [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: 11/10/2022]
Affiliation(s)
- Shu-Shan Gao
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Luoyi Wang
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Zhongshu Song
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Joanne Hothersall
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Elton R. Stevens
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Jack Connolly
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Peter J. Winn
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Russell J. Cox
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BMWZ; Leibniz-Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | | | - Paul R. Race
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
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24
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Gao SS, Wang L, Song Z, Hothersall J, Stevens ER, Connolly J, Winn PJ, Cox RJ, Crump MP, Race PR, Thomas CM, Simpson TJ, Willis CL. Rücktitelbild: Selected Mutations Reveal New Intermediates in the Biosynthesis of Mupirocin and the Thiomarinol Antibiotics (Angew. Chem. 14/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702123] [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: 11/10/2022]
Affiliation(s)
- Shu-Shan Gao
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Luoyi Wang
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Zhongshu Song
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Joanne Hothersall
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Elton R. Stevens
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Jack Connolly
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Peter J. Winn
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Russell J. Cox
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BMWZ; Leibniz-Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | | | - Paul R. Race
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
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25
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Kamruzzaman M, Shoma S, Thomas CM, Partridge SR, Iredell JR. Plasmid interference for curing antibiotic resistance plasmids in vivo. PLoS One 2017; 12:e0172913. [PMID: 28245276 PMCID: PMC5330492 DOI: 10.1371/journal.pone.0172913] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 11/22/2016] [Accepted: 02/10/2017] [Indexed: 11/21/2022] Open
Abstract
Antibiotic resistance increases the likelihood of death from infection by common pathogens such as Escherichia coli and Klebsiella pneumoniae in developed and developing countries alike. Most important modern antibiotic resistance genes spread between such species on self-transmissible (conjugative) plasmids. These plasmids are traditionally grouped on the basis of replicon incompatibility (Inc), which prevents coexistence of related plasmids in the same cell. These plasmids also use post-segregational killing (‘addiction’) systems, which poison any bacterial cells that lose the addictive plasmid, to guarantee their own survival. This study demonstrates that plasmid incompatibilities and addiction systems can be exploited to achieve the safe and complete eradication of antibiotic resistance from bacteria in vitro and in the mouse gut. Conjugative ‘interference plasmids’ were constructed by specifically deleting toxin and antibiotic resistance genes from target plasmids. These interference plasmids efficiently cured the corresponding antibiotic resistant target plasmid from different Enterobacteriaceae in vitro and restored antibiotic susceptibility in vivo to all bacterial populations into which plasmid-mediated resistance had spread. This approach might allow eradication of emergent or established populations of resistance plasmids in individuals at risk of severe sepsis, enabling subsequent use of less toxic and/or more effective antibiotics than would otherwise be possible, if sepsis develops. The generalisability of this approach and its potential applications in bioremediation of animal and environmental microbiomes should now be systematically explored.
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Affiliation(s)
- Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Shereen Shoma
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Christopher M. Thomas
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Sally R. Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
- * E-mail:
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Gao SS, Wang L, Song Z, Hothersall J, Stevens ER, Connolly J, Winn PJ, Cox RJ, Crump MP, Race PR, Thomas CM, Simpson TJ, Willis CL. Selected Mutations Reveal New Intermediates in the Biosynthesis of Mupirocin and the Thiomarinol Antibiotics. Angew Chem Int Ed Engl 2017; 56:3930-3934. [PMID: 28181382 DOI: 10.1002/anie.201611590] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 11/28/2016] [Indexed: 11/08/2022]
Abstract
Thiomarinol and mupirocin are assembled on similar polyketide/fatty acid backbones and exhibit potent antibiotic activity against methicillin-resistant Staphylococcus aureus (MRSA). They both contain a tetrasubstituted tetrahydropyran (THP) ring that is essential for biological activity. Mupirocin is a mixture of pseudomonic acids (PAs). Isolation of the novel compound mupirocin P, which contains a 7-hydroxy-6-keto-substituted THP, from a ΔmupP strain and chemical complementation experiments confirm that the first step in the conversion of PA-B into the major product PA-A is oxidation at the C6 position. In addition, nine novel thiomarinol (TM) derivatives with different oxidation patterns decorating the central THP core were isolated after gene deletion (tmlF). These metabolites are in accord with the THP ring formation and elaboration in thiomarinol following a similar order to that found in mupirocin biosynthesis, despite the lack of some of the equivalent genes. Novel mupirocin-thiomarinol hybrids were also synthesized by mutasynthesis.
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Affiliation(s)
- Shu-Shan Gao
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Luoyi Wang
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Zhongshu Song
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Elton R Stevens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jack Connolly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Peter J Winn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Russell J Cox
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,BMWZ, Leibniz-Universität Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
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27
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Gao SS, Wang L, Song Z, Hothersall J, Stevens ER, Connolly J, Winn PJ, Cox RJ, Crump MP, Race PR, Thomas CM, Simpson TJ, Willis CL. Selected Mutations Reveal New Intermediates in the Biosynthesis of Mupirocin and the Thiomarinol Antibiotics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shu-Shan Gao
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Luoyi Wang
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Zhongshu Song
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
| | - Joanne Hothersall
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Elton R. Stevens
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Jack Connolly
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Peter J. Winn
- School of Biosciences; University of Birmingham, Edgbaston; Birmingham B15 2TT UK
| | - Russell J. Cox
- School of Chemistry; University of Bristol; Bristol BS8 1TS UK
- BMWZ; Leibniz-Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | | | - Paul R. Race
- School of Biochemistry; University of Bristol; Bristol BS8 1TD UK
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Jones AS, Kwasnicka L, Thomas CM, Griffiths A. Understanding the Principles of Electrosurgery During Laparoscopic Surgery: A Survey Amongst Trainees and Consultants in Obstetrics and Gynaecology. J Minim Invasive Gynecol 2016. [DOI: 10.1016/j.jmig.2016.08.595] [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: 10/20/2022]
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Jones AS, Thomas CM, Griffiths A, Nargund A. Accurate Identification of Anatomical Structures in a Normal Female Pelvis During Laparoscopic Surgery: A Survey Amongst Trainees and Consultants in Obstetrics and Gynaecology. J Minim Invasive Gynecol 2016; 22:S158. [PMID: 27678895 DOI: 10.1016/j.jmig.2015.08.595] [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: 10/22/2022]
Affiliation(s)
- A S Jones
- Women's Health, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - C M Thomas
- Women's Health, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - A Griffiths
- Women's Health, University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - A Nargund
- Women's Health, University Hospital of Wales, Cardiff, Wales, United Kingdom
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31
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Kingsbury SR, Dube B, Thomas CM, Conaghan PG, Stone MH. Is a questionnaire and radiograph-based follow-up model for patients with primary hip and knee arthroplasty a viable alternative to traditional regular outpatient follow-up clinic? Bone Joint J 2016; 98-B:201-8. [PMID: 26850425 DOI: 10.1302/0301-620x.98b2.36424] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIMS Increasing demand for total hip and knee arthroplasty (THA/TKA) and associated follow-up has placed huge demands on orthopaedic services. Feasible follow-up mechanisms are therefore essential. METHODS We conducted an audit of clinical follow-up decision-making for THA/TKA based on questionnaire/radiograph review compared with local practice of Arthroplasty Care Practitioner (ACP)-led outpatient follow-up. In all 599 patients attending an ACP-led THA/TKA follow-up clinic had a pelvic/knee radiograph, completed a pain/function questionnaire and were reviewed by an ACP. An experienced orthopaedic surgeon reviewed the same radiographs and questionnaires, without patient contact or knowledge of the ACP's decision. Each pathway classified patients into: urgent review, annual monitoring, routine follow-up or discharge. RESULTS In total, 401 hip and 198 knee patients were included. There was substantial agreement between the ACP and surgeon for both hip (kappa = 0.69, 95% confidence interval (CI) 0.62 to 0.76) and knee (kappa = 0.81, 95% CI 0.74 to 0.88). Positive agreement was very high for discharge and routine follow-up; however the ACP was more likely to select annual monitoring and the surgeon urgent review. DISCUSSION Review of the questionnaire/radiograph together identified all patients in need of increased surveillance, with good agreement for on-going patient management. However, review of the radiograph or questionnaire alone missed some patients with potential problems. A radiograph in conjunction with a questionnaire as a review may represent a cost effective THA/TKA follow-up mechanism. TAKE HOME MESSAGE A questionnaire and radiograph-based remote review may represent a cost-effective total joint arthroplasty follow-up mechanism; thereby reducing the considerable burden that follow-up currently places on the NHS.
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Affiliation(s)
- S R Kingsbury
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Chapeltown Road, Leeds LS7 4SA, UK
| | - B Dube
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Chapeltown Road, Leeds LS7 4SA, UK
| | - C M Thomas
- NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Chapeltown Road, Leeds, LS7 4SA, UK
| | - P G Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds and NIHR Leeds Musculoskeletal Biomedical Research Unit, Chapel Allerton Hospital, Chapeltown Road, Leeds LS7 4SA, UK
| | - M H Stone
- NIHR Leeds Musculoskeletal Biomedical Research Unit, and Leeds Teaching Hospitals NHS Trust, Chapeltown Road, Leeds, LS7 4SA, UK
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Rajasekar KV, Lovering AL, Dancea F, Scott DJ, Harris SA, Bingle LEH, Roessle M, Thomas CM, Hyde EI, White SA. Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator. Nucleic Acids Res 2016; 44:4947-56. [PMID: 27016739 PMCID: PMC4889941 DOI: 10.1093/nar/gkw191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 07/29/2015] [Revised: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/03/2022] Open
Abstract
The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53.
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Affiliation(s)
- Karthik V Rajasekar
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew L Lovering
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Felician Dancea
- School of Cancer Studies, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David J Scott
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Nottingham LE12 5RD, UK
| | - Sarah A Harris
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Lewis E H Bingle
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Christopher M Thomas
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Scott A White
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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33
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Freire Martín I, Thomas CM, Laing E, AbuOun M, La Ragione RM, Woodward MJ. Curing vector for IncI1 plasmids and its use to provide evidence for a metabolic burden of IncI1 CTX-M-1 plasmid pIFM3791 on Klebsiella pneumoniae. J Med Microbiol 2016; 65:611-618. [PMID: 27166141 DOI: 10.1099/jmm.0.000271] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using a sequence-based approach we previously identified an IncI1 CTX-M-1 plasmid, pIFM3791, on a single pig farm in the UK that was harboured by Klebsiella pneumoniae, Escherichia coli and Salmonella enterica serotype 4,5,12:i:-. To test the hypothesis that the plasmid had spread rapidly into these differing host bacteria we wished to assess whether the plasmid conferred a fitness advantage. To do this an IncI1 curing vector was constructed and used to displace the IncI1 CTX-M-1 plasmids from K. pneumoniae strain B3791 and several other unrelated IncI1-harbouring strains indicating the potential wider application of the curing vector. The IncI1 CTX-M-1 plasmid was reintroduced by conjugation into the cured K. pneumoniae strain and also a naturally IncI1 plasmid free S. enterica serotype 4,5,12:i:-, S348/11. Original, cured and complemented strains were tested for metabolic competence using Biolog technology and in competitive growth, association to mammalian cells and biofilm formation experiments. The plasmid-cured K. pneumoniae strain grew more rapidly than either the original plasmid-carrying strain or plasmid-complemented strains in competition experiments. Additionally, the plasmid-cured strain was significantly better at respiring with l-sorbose as a carbon source and putrescine, γ-amino-n-butyric acid, l-alanine and l-proline as nitrogen sources. By contrast, no differences in phenotype were found when comparing plasmid-harbouring and plasmid-free S. enterica S348/11. In conclusion, the IncI1 curing vector successfully displaced multiple IncI plasmids. The IncI1 CTX-M1 plasmid conferred a growth disadvantage upon K. pneumoniae, possibly by imposing a metabolic burden, the mechanism of which remains to be determined.
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Affiliation(s)
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Emma Laing
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Roberto M La Ragione
- Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7AL, UK
| | - Martin J Woodward
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights Park, Reading RG6 5AP, UK
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Czaplewski L, Bax R, Clokie M, Dawson M, Fairhead H, Fischetti VA, Foster S, Gilmore BF, Hancock REW, Harper D, Henderson IR, Hilpert K, Jones BV, Kadioglu A, Knowles D, Ólafsdóttir S, Payne D, Projan S, Shaunak S, Silverman J, Thomas CM, Trust TJ, Warn P, Rex JH. Alternatives to antibiotics-a pipeline portfolio review. Lancet Infect Dis 2016; 16:239-51. [PMID: 26795692 DOI: 10.1016/s1473-3099(15)00466-1] [Citation(s) in RCA: 524] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 11/06/2015] [Accepted: 11/10/2015] [Indexed: 01/21/2023]
Abstract
Antibiotics have saved countless lives and enabled the development of modern medicine over the past 70 years. However, it is clear that the success of antibiotics might only have been temporary and we now expect a long-term and perhaps never-ending challenge to find new therapies to combat antibiotic-resistant bacteria. A broader approach to address bacterial infection is needed. In this Review, we discuss alternatives to antibiotics, which we defined as non-compound approaches (products other than classic antibacterial agents) that target bacteria or any approaches that target the host. The most advanced approaches are antibodies, probiotics, and vaccines in phase 2 and phase 3 trials. This first wave of alternatives to antibiotics will probably best serve as adjunctive or preventive therapies, which suggests that conventional antibiotics are still needed. Funding of more than £1·5 billion is needed over 10 years to test and develop these alternatives to antibiotics. Investment needs to be partnered with translational expertise and targeted to support the validation of these approaches in phase 2 trials, which would be a catalyst for active engagement and investment by the pharmaceutical and biotechnology industry. Only a sustained, concerted, and coordinated international effort will provide the solutions needed for the future.
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Affiliation(s)
- Lloyd Czaplewski
- Chemical Biology Ventures, Abingdon, Oxfordshire, UK; Abgentis, Edgbaston, Birmingham, UK; Persica Pharmaceuticals, Canterbury, Kent, UK.
| | | | - Martha Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Mike Dawson
- Novacta Biosystems, Welwyn Garden City, Hertfordshire, UK; Cantab Anti-infectives, Welwyn Garden City, Hertfordshire, UK
| | | | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA
| | - Simon Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK; Absynth Biologics, Liverpool, UK
| | | | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - David Harper
- Evolution Biotechnologies, Ampthill, Bedfordshire, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK
| | - Kai Hilpert
- Institute of Infection and Immunity, St George's, University of London, London, UK; TiKa Diagnostics, London, UK
| | - Brian V Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK; Queen Victoria Hospital NHS Foundation Trust, East Grinstead, West Sussex, UK
| | - Aras Kadioglu
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - David Knowles
- Absynth Biologics, Liverpool, UK; Procarta Biosystems, Norwich, UK
| | | | - David Payne
- GlaxoSmithKline, Collegeville, Pennsylvania, PA, USA
| | | | - Sunil Shaunak
- Department of Medicine, Imperial College London, London, UK
| | | | - Christopher M Thomas
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK; Plasgene, Edgbaston, Birmingham, UK
| | - Trevor J Trust
- Pan-Provincial Vaccine Enterprise, Saskatoon, SK, Canada
| | | | - John H Rex
- AstraZeneca, Boston, MA, USA; F2G, Manchester, UK
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35
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Jones AS, Nargund A, Thomas CM, Griffiths A. Unusual Presentation of an Ovarian Cyst: Successful Laparoscopic Excision. J Minim Invasive Gynecol 2015; 22:S145. [DOI: 10.1016/j.jmig.2015.08.513] [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: 11/28/2022]
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Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJN, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJM, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O’Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol 2015; 11:625-31. [PMID: 26284661 PMCID: PMC5714517 DOI: 10.1038/nchembio.1890] [Citation(s) in RCA: 544] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marnix H Medema
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Renzo Kottmann
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Matthew Cummings
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Kai Blin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Irene de Bruijn
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands
| | - Yit Heng Chooi
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California, USA,Departmentof Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA,School of Chemistry and Biochemistry, University of Western Australia, Perth, Western Australia, Australia
| | - Jan Claesen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - R Cameron Coates
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Srikanth Duddela
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Stephanie Düsterhus
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Daniel J Edwards
- Department of Chemistry and Biochemistry, California State University, Chico, California, USA
| | - David P Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Neha Garg
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Christoph Geiger
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | | | - Anja Greule
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Michalis Hadjithomas
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | | | - Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Matthew L Hillwig
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, California, USA
| | - Carla S Jones
- Sustainable Studies Program, Roosevelt University Chicago, Illinois, USA
| | - Katrin Jungmann
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Carsten Kegler
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany
| | - Hyun Uk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark,BioInformatics Research Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Joleen Masschelein
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium,Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Alexey V Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Simone M Mantovani
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Emily A Monroe
- Department of Biology, William Paterson University, Wayne, New Jersey, USA
| | - Marcus Moore
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Nathan Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Guohui Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Amrita Pati
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork–National University of Ireland, Cork, Ireland
| | - Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, IBCE, Montevideo, Uruguay
| | - Zhe Rui
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California, USA,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, USA
| | - Zhenhua Tian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Nicholas J Tobias
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany
| | - Yuta Tsunematsu
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany,Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Elizabeth Wyckoff
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA,Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
| | - Grace Yim
- Department of Biochemistry and Biomedical Sciences, The M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yunchang Xie
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, Université de Lorraine and Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1128, Vandoeuvre-lès-Nancy, France
| | - Alexander K Apel
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Carl J Balibar
- Infectious Disease Research, Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekular Biotechnologie, Goethe Universität Frankfurt, Fachbereich Biowissenschaften, Frankfurt, Germany,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt, Germany
| | - Rainer Borriss
- Fachbereich Phytomedizin, Albrecht Thaer Institut, Humboldt Universität Berlin, Berlin, Germany
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Axel A Brakhage
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Patrick Caffrey
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Russell J Cox
- Institut für Organische Chemie, Leibniz Universität Hannover, Hannover, Germany,School of Chemistry, University of Bristol, Bristol, UK
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, University of Leuven, Heverlee, Belgium
| | | | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA,Howard Hughes Medical Institute, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA,Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, California, USA
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Monika Ehling-Schulz
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Michael A Fischbach
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - William H Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Bertolt Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany,Friedrich Schiller University, Jena, Germany
| | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Susan E Jensen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jianhua Ju
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Leonard Katz
- Synthetic Biology Engineering Research Center (SynBERC), University of California Emeryville, Emeryville, California, USA
| | - Leonard Kaysser
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany,German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, USA,Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Nikos C Kyrpides
- Department of Energy (DOE) Joint Genome Institute, Walnut Creek, California, USA,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hyung-Jin Kwon
- Division of Bioscience and Bioinformatics, Myongji University, Yongin-si, Gyeonggi-Do, South Korea
| | - Sylvie Lautru
- Institute of Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Orsay, France
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium
| | - Chia Y Lee
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Bai Linquan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China,School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Yvonne Mast
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Carmen Méndez
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain,Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
| | | | | | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois, USA
| | - Bradley S Moore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leonilde M Moreira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark,Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fergal O’Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork–National University of Ireland, Cork, Ireland,Curtin University, School of Biomedical Sciences, Perth, Western Australia, Australia
| | - Hideaki Oikawa
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcia S Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Shelley M Payne
- Department of Molecular Biosciences, The University of Texas, Austin, Texas, USA,Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas, USA
| | - Jean-Luc Pernodet
- Institute of Integrative Biology of the Cell (I2BC), Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud, Orsay, France
| | - Miroslav Petricek
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czech Republic
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Olivier Ploux
- Laboratoire Interdisciplinaire des Energies de Demain (LIED), UMR 8236 CNRS, Université Paris Diderot, Paris, France
| | - Jos M Raaijmakers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands
| | - José A Salas
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - Esther K Schmitt
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Barry Scott
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA,Molecular Therapeutics and Natural Products Library Initiative, The Scripps Research Institute, Jupiter, Florida, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA,Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Michael J Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota–Twin Cities, Saint Paul, Minnesota, USA,BioTechnology Institute, University of Minnesota–Twin Cities, Saint Paul, Minnesota, USA
| | | | - Evi Stegmann
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | | | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | | | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California, USA,Departmentof Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Muriel Viaud
- Unité BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA), Grignon, France
| | - Jonathan D Walton
- Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Christopher T Walsh
- Chemistry, Engineering & Medicine for Human Health (ChEM-H) Institute, Stanford University, Stanford, California, USA
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Joanne M Willey
- Hofstra North Shore–Long Island Jewish School of Medicine, Hempstead, New York, USA
| | - Wolfgang Wohlleben
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, The M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany,Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Faculty of Science, University of Tübingen, Tübingen, Germany
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Sergey B Zotchev
- Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Eriko Takano
- Manchester Centre for Synthetic Biology ofFine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Frank Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany,Jacobs University Bremen gGmbH, Bremen, Germany
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Thomas CM, Pike LC, Hartill CE, Baker S, Woods E, Convery DJ, Greener AG. Specific recommendations for accurate and direct use of PET-CT in PET guided radiotherapy for head and neck sites. Med Phys 2014; 41:041710. [PMID: 24694130 DOI: 10.1118/1.4867856] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE To provide specific experience-based guidance and recommendations for centers wishing to develop, validate, and implement an accurate and efficient process for directly using positron emission tomography-computed tomography (PET-CT) for the radiotherapy planning of head and neck cancer patients. METHODS A PET-CT system was modified with hard-top couch, external lasers and radiotherapy immobilization and indexing devices and was subject to a commissioning and quality assurance program. PET-CT imaging protocols were developed specifically for radiotherapy planning and the image quality and pathway tested using phantoms and five patients recruited into an in-house study. Security and accuracy of data transfer was tested throughout the whole data pathway. The patient pathway was fully established and tested ready for implementation in a PET-guided dose-escalation trial for head and neck cancer patients. RESULTS Couch deflection was greater than for departmental CT simulator machines. An area of high attenuation in the couch generated image artifacts and adjustments were made accordingly. Using newly developed protocols CT image quality was suitable to maintain delineation and treatment accuracy. Upon transfer of data to the treatment planning system a half pixel offset between PET and CT was observed and corrected. By taking this into account, PET to CT alignment accuracy was maintained below 1 mm in all systems in the data pathway. Transfer of structures delineated in the PET fusion software to the radiotherapy treatment planning system was validated. CONCLUSIONS A method to perform direct PET-guided radiotherapy planning was successfully validated and specific recommendations were developed to assist other centers. Of major concern is ensuring that the quality of PET and CT data is appropriate for radiotherapy treatment planning and on-treatment verification. Couch movements can be compromised, bore-size can be a limitation for certain immobilization techniques, laser positioning may affect setup accuracy and couch deflection may be greater than scanners dedicated to radiotherapy. The full set of departmental commissioning and routine quality assurance tests applied to radiotherapy CT simulators must be carried out on the PET-CT scanner. CT image quality must be optimized for radiotherapy planning whilst understanding that the appearance will differ between scanners and may affect delineation. PET-CT quality assurance schedules will need to be added to and modified to incorporate radiotherapy quality assurance. Methods of working for radiotherapy and PET staff will change to take into account considerations of both parties. PET to CT alignment must be subject to quality control on a loaded and unloaded couch preferably using a suitable emission phantom, and tested throughout the whole data pathway. Data integrity must be tested throughout the whole pathway and a system included to verify that delineated structures are transferred correctly. Excellent multidisciplinary team communication and working is vital, and key staff members on both sides should be specifically dedicated to the project. Patient pathway should be clearly devised to optimize patient care and the resources of all departments. Recruitment of a cohort of patients into a methodology study is valuable to test the quality assurance methods and pathway.
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Affiliation(s)
- C M Thomas
- Guy's and St. Thomas' NHS Foundation Trust, Medical Physics Department, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - L C Pike
- Division of Imaging Sciences and Biomedical Engineering, King's College London, King's Health Partners, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - C E Hartill
- Guy's and St. Thomas' NHS Foundation Trust, Radiotherapy, Clinical Outpatients Clinic, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - S Baker
- Division of Imaging Sciences and Biomedical Engineering, King's College London, King's Health Partners, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - E Woods
- Division of Imaging Sciences and Biomedical Engineering, King's College London, King's Health Partners, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - D J Convery
- Guy's and St. Thomas' NHS Foundation Trust, Medical Physics Department, St. Thomas' Hospital, London SE1 7EH, United Kingdom
| | - A G Greener
- Guy's and St. Thomas' NHS Foundation Trust, Medical Physics Department, St. Thomas' Hospital, London SE1 7EH, United Kingdom
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38
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Matthijs S, Vander Wauven C, Cornu B, Ye L, Cornelis P, Thomas CM, Ongena M. Antimicrobial properties of Pseudomonas strains producing the antibiotic mupirocin. Res Microbiol 2014; 165:695-704. [PMID: 25303834 DOI: 10.1016/j.resmic.2014.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/17/2014] [Accepted: 09/29/2014] [Indexed: 11/19/2022]
Abstract
Mupirocin is a polyketide antibiotic with broad antibacterial activity. It was isolated and characterized about 40 years ago from Pseudomonas fluorescens NCIMB 10586. To study the phylogenetic distribution of mupirocin producing strains in the genus Pseudomonas a large collection of Pseudomonas strains of worldwide origin, consisting of 117 Pseudomonas type strains and 461 strains isolated from different biological origins, was screened by PCR for the mmpD gene of the mupirocin gene cluster. Five mmpD(+) strains from different geographic and biological origin were identified. They all produced mupirocin and were strongly antagonistic against Staphylococcus aureus. Phylogenetic analysis showed that mupirocin production is limited to a single species. Inactivation of mupirocin production leads to complete loss of in vitro antagonism against S. aureus, except on certain iron-reduced media where the siderophore pyoverdine is responsible for the in vitro antagonism of a mupirocin-negative mutant. In addition to mupirocin some of the strains produced lipopeptides of the massetolide group. These lipopeptides do not play a role in the observed in vitro antagonism of the mupirocin producing strains against S. aureus.
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Affiliation(s)
- Sandra Matthijs
- Institut de Recherches Microbiologiques - Wiame, Campus du CERIA, 1 avenue Emile Gryson, bât 4B, B-1070 Bruxelles, Belgium.
| | - Corinne Vander Wauven
- Institut de Recherches Microbiologiques - Wiame, Campus du CERIA, 1 avenue Emile Gryson, bât 4B, B-1070 Bruxelles, Belgium.
| | - Bertrand Cornu
- Institut de Recherches Microbiologiques - Wiame, Campus du CERIA, 1 avenue Emile Gryson, bât 4B, B-1070 Bruxelles, Belgium.
| | - Lumeng Ye
- Department of Bioengineering Sciences, Research Group of Microbiology and Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Pierre Cornelis
- Department of Bioengineering Sciences, Research Group of Microbiology and Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Marc Ongena
- Walloon Center for Industrial Biology, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium.
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39
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Bartosik AA, Glabski K, Jecz P, Lasocki K, Mikosa M, Plochocka D, Thomas CM, Jagura-Burdzy G. Dissection of the region of Pseudomonas aeruginosa ParA that is important for dimerization and interactions with its partner ParB. Microbiology (Reading) 2014; 160:2406-2420. [PMID: 25139949 PMCID: PMC4219104 DOI: 10.1099/mic.0.081216-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas aeruginosa ParA belongs to a large subfamily of Walker-type ATPases acting as partitioning proteins in bacteria. ParA has the ability to both self-associate and interact with its partner ParB. Analysis of the deletion mutants defined the part of the protein involved in dimerization and interactions with ParB. Here, a set of ParA alanine substitution mutants in the region between E67 and L85 was created and analysed in vivo and in vitro. All mutants impaired in dimerization (substitutions at positions M74, H79, Y82 and L84) were also defective in interactions with ParB, suggesting that ParA-ParB interactions depend on the ability of ParA to dimerize. Mutants with alanine substitutions at positions E67, C68, L70, E72, F76, Q83 and L85 were not impaired in dimerization, but were defective in interactions with ParB. The dimerization interface partly overlapped the pseudo-hairpin, involved in interactions with ParB. ParA mutant derivatives tested in vitro showed no defects in ATPase activity. Two parA alleles (parA84, whose product can neither self-interact nor interact with ParB, and parA67, whose product is impaired in interactions with ParB, but not in dimerization) were introduced into the P. aeruginosa chromosome by homologous gene exchange. Both mutants showed defective separation of ParB foci, but to different extents. Only PAO1161 parA84 was visibly impaired in terms of chromosome segregation, growth rate and motility, similar to a parA-null mutant.
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Affiliation(s)
- Aneta A. Bartosik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Krzysztof Glabski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Paulina Jecz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Krzysztof Lasocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Malgorzata Mikosa
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Danuta Plochocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | | | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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40
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Gao SS, Hothersall J, Wu J, Murphy AC, Song Z, Stephens ER, Thomas CM, Crump MP, Cox RJ, Simpson TJ, Willis CL. Biosynthesis of Mupirocin by Pseudomonas fluorescens NCIMB 10586 Involves Parallel Pathways. J Am Chem Soc 2014; 136:5501-7. [DOI: 10.1021/ja501731p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shu-Shan Gao
- School of
Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Joanne Hothersall
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Ji’en Wu
- School of
Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | | | - Zhongshu Song
- School of
Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Elton R. Stephens
- School
of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | | | - Matthew P. Crump
- School of
Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Russell J. Cox
- School of
Chemistry, University of Bristol, Bristol BS8 1TS, U.K
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Murphy AC, Gao SS, Han LC, Carobene S, Fukuda D, Song Z, Hothersall J, Cox RJ, Crosby J, Crump MP, Thomas CM, Willis CL, Simpson TJ. Biosynthesis of thiomarinol A and related metabolites of Pseudoalteromonas sp. SANK 73390. Chem Sci 2014. [DOI: 10.1039/c3sc52281d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Thomas CM, Clyde J. Game as Book: Selecting Video Games for Academic Libraries based on Discipline Specific Knowledge. The Journal of Academic Librarianship 2013. [DOI: 10.1016/j.acalib.2013.07.002] [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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Haines AS, Dong X, Song Z, Farmer R, Williams C, Hothersall J, Płoskoń E, Wattana-Amorn P, Stephens ER, Yamada E, Gurney R, Takebayashi Y, Masschelein J, Cox RJ, Lavigne R, Willis CL, Simpson TJ, Crosby J, Winn PJ, Thomas CM, Crump MP. A conserved motif flags acyl carrier proteins for β-branching in polyketide synthesis. Nat Chem Biol 2013; 9:685-692. [PMID: 24056399 PMCID: PMC4658705 DOI: 10.1038/nchembio.1342] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/22/2013] [Indexed: 11/14/2022]
Abstract
Type I PKSs often utilise programmed β-branching, via enzymes of an “HMG-CoA synthase (HCS) cassette”, to incorporate various side chains at the second carbon from the terminal carboxylic acid of growing polyketide backbones. We identified a strong sequence motif in Acyl Carrier Proteins (ACPs) where β-branching is known. Substituting ACPs confirmed a correlation of ACP type with β-branching specificity. While these ACPs often occur in tandem, NMR analysis of tandem β-branching ACPs indicated no ACP-ACP synergistic effects and revealed that the conserved sequence motif forms an internal core rather than an exposed patch. Modelling and mutagenesis identified ACP Helix III as a probable anchor point of the ACP-HCS complex whose position is determined by the core. Mutating the core affects ACP functionality while ACP-HCS interface substitutions modulate system specificity. Our method for predicting β-carbon branching expands the potential for engineering novel polyketides and lays a basis for determining specificity rules.
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Affiliation(s)
- Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Xu Dong
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Zhongshu Song
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Rohit Farmer
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Eliza Płoskoń
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | | | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erika Yamada
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Rachel Gurney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Yuiko Takebayashi
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Joleen Masschelein
- Division of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 - box 2462, 3001 Heverlee, Belgium
| | - Russell J Cox
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Rob Lavigne
- Division of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 - box 2462, 3001 Heverlee, Belgium
| | | | - Thomas J Simpson
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - John Crosby
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
| | - Peter J Winn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Matthew P Crump
- School of Chemistry, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
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Wellington EMH, Boxall AB, Cross P, Feil EJ, Gaze WH, Hawkey PM, Johnson-Rollings AS, Jones DL, Lee NM, Otten W, Thomas CM, Williams AP. The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect Dis 2013; 13:155-65. [PMID: 23347633 DOI: 10.1016/s1473-3099(12)70317-1] [Citation(s) in RCA: 606] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
During the past 10 years, multidrug-resistant Gram-negative Enterobacteriaceae have become a substantial challenge to infection control. It has been suggested by clinicians that the effectiveness of antibiotics is in such rapid decline that, depending on the pathogen concerned, their future utility can be measured in decades or even years. Unless the rise in antibiotic resistance can be reversed, we can expect to see a substantial rise in incurable infection and fatality in both developed and developing regions. Antibiotic resistance develops through complex interactions, with resistance arising by de-novo mutation under clinical antibiotic selection or frequently by acquisition of mobile genes that have evolved over time in bacteria in the environment. The reservoir of resistance genes in the environment is due to a mix of naturally occurring resistance and those present in animal and human waste and the selective effects of pollutants, which can co-select for mobile genetic elements carrying multiple resistant genes. Less attention has been given to how anthropogenic activity might be causing evolution of antibiotic resistance in the environment. Although the economics of the pharmaceutical industry continue to restrict investment in novel biomedical responses, action must be taken to avoid the conjunction of factors that promote evolution and spread of antibiotic resistance.
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Abstract
The korAB operon in RK2 plasmids is a beautiful natural example of a negatively and cooperatively self-regulating operon. It has been particularly well characterized both experimentally and with mathematical models. We have carried out a detailed investigation of the role of the regulatory mechanism using a biologically grounded mechanistic multi-scale stochastic model that includes plasmid gene regulation and replication in the context of host growth and cell division. We use the model to compare four hypotheses for the action of the regulatory mechanism: increased robustness to extrinsic factors, decreased protein fluctuations, faster response-time of the operon and reduced host burden through improved efficiency of protein production. We find that the strongest impact of all elements of the regulatory architecture is on improving the efficiency of protein synthesis by reduction in the number of mRNA molecules needed to be produced, leading to a greater than ten-fold reduction in host energy required to express these plasmid proteins. A smaller but still significant role is seen for speeding response times, but this is not materially improved by the cooperativity. The self-regulating mechanisms have the least impact on protein fluctuations and robustness. While reduction of host burden is evident in a plasmid context, negative self-regulation is a widely seen motif for chromosomal genes. We propose that an important evolutionary driver for negatively self-regulated genes is to improve the efficiency of protein synthesis.
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Affiliation(s)
- Dorota Herman
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
- Department of Plant Systems Biology, VIB – Ghent University, Ghent, Belgium
| | | | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, United Kingdom
- * E-mail:
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Krasowiak R, Smalla K, Sokolov S, Kosheleva I, Sevastyanovich Y, Titok M, Thomas CM. PCR primers for detection and characterisation of IncP-9 plasmids. FEMS Microbiol Ecol 2012; 42:217-25. [PMID: 19709281 DOI: 10.1111/j.1574-6941.2002.tb01011.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
IncP-9 plasmids are best known as the vehicles for spreading biodegradation functions among Pseudomonas species but can also carry resistance determinants. New PCR primer systems targeting different replicon-specific regions were designed to allow detection of IncP-9 plasmids. Their specificity was checked against a range of IncP-9 plasmids as well as representatives of incompatibility groups IncFI, IncFII, IncN, IncQ, IncP-1alpha, IncP-1beta, IncP-2, IncP-7, IncP-13, IncW, IncU, IncX and IncZ. Products obtained for plasmids assigned to IncP-9 group by traditional incompatibility testing varied in size and restriction pattern suggesting diversity in the 'core' sequence among related replicons. Specific primer pairs were applied to community DNA extracted from a range of environments including those subject to strong selective pressure, caused by antibiotics, metals and organic pollutants. Abundant products were observed in manure and sewage, independently of the presence of antibiotics and metals, but could also be detected in coastal water and streptomycin-treated soil. Community DNA from faeces of piglets treated and non-treated with Zn gave particularly strong PCR product with IncP-9 rep primers. Therefore, an attempt was made to isolate bacteria carrying the IncP-9-like plasmids, but this was not successful. The results of application of these newly designed primer pairs to plasmid isolates as well as community DNA indicate that the IncP-9-related plasmids are a diverse family prevalent in various environments and widely distributed geographically.
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Mierzejewska J, Bartosik AA, Macioszek M, Płochocka D, Thomas CM, Jagura-Burdzy G. Identification of C-terminal hydrophobic residues important for dimerization and all known functions of ParB of Pseudomonas aeruginosa. Microbiology (Reading) 2012; 158:1183-1195. [PMID: 22322962 PMCID: PMC3542827 DOI: 10.1099/mic.0.056234-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ParB protein of Pseudomonas aeruginosa is important for growth, cell division, nucleoid segregation and different types of motility. To further understand its function we have demonstrated a vital role of the hydrophobic residues in the C terminus of ParB(P.a.). By in silico modelling of the C-terminal domain (amino acids 242-290) the hydrophobic residues L282, V285 and I289 (but not L286) are engaged in leucine-zipper-like structure formation, whereas the charged residues R290 and Q266 are implicated in forming a salt bridge involved in protein stabilization. Five parB mutant alleles were constructed and their functionality was defined in vivo and in vitro. In agreement with model predictions, the substitution L286A had no effect on mutant protein activities. Two ParBs with single substitutions L282A or V285A and deletions of two or seven C-terminal amino acids were impaired in both dimerization and DNA binding and were not able to silence genes adjacent to parS, suggesting that dimerization through the C terminus is a prerequisite for spreading on DNA. The defect in dimerization also correlated with loss of ability to interact with partner protein ParA. Reverse genetics demonstrated that a parB mutant producing ParB lacking the two C-terminal amino acids as well as mutants producing ParB with single substitution L282A or V285A had defects similar to those of a parB null mutant. Thus so far all the properties of ParB seem to depend on dimerization.
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Affiliation(s)
- J Mierzejewska
- The Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - A A Bartosik
- The Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - M Macioszek
- The Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - D Płochocka
- The Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - C M Thomas
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - G Jagura-Burdzy
- The Institute of Biochemistry and Biophysics, PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
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Herman D, Thomas CM, Stekel DJ. Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration. BMC Syst Biol 2011; 5:119. [PMID: 21801369 PMCID: PMC3199767 DOI: 10.1186/1752-0509-5-119] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 07/29/2011] [Indexed: 11/10/2022]
Abstract
Background IncP-1 plasmids are broad host range plasmids that have been found in clinical and environmental bacteria. They often carry genes for antibiotic resistance or catabolic pathways. The archetypal IncP-1 plasmid RK2 is a well-characterized biological system, with a fully sequenced and annotated genome and wide range of experimental measurements. Its central control operon, encoding two global regulators KorA and KorB, is a natural example of a negatively self-regulated operon. To increase our understanding of the regulation of this operon, we have constructed a dynamical mathematical model using Ordinary Differential Equations, and employed a Bayesian inference scheme, Markov Chain Monte Carlo (MCMC) using the Metropolis-Hastings algorithm, as a way of integrating experimental measurements and a priori knowledge. We also compared MCMC and Metabolic Control Analysis (MCA) as approaches for determining the sensitivity of model parameters. Results We identified two distinct sets of parameter values, with different biological interpretations, that fit and explain the experimental data. This allowed us to highlight the proportion of repressor protein as dimers as a key experimental measurement defining the dynamics of the system. Analysis of joint posterior distributions led to the identification of correlations between parameters for protein synthesis and partial repression by KorA or KorB dimers, indicating the necessary use of joint posteriors for correct parameter estimation. Using MCA, we demonstrated that the system is highly sensitive to the growth rate but insensitive to repressor monomerization rates in their selected value regions; the latter outcome was also confirmed by MCMC. Finally, by examining a series of different model refinements for partial repression by KorA or KorB dimers alone, we showed that a model including partial repression by KorA and KorB was most compatible with existing experimental data. Conclusions We have demonstrated that the combination of dynamical mathematical models with Bayesian inference is valuable in integrating diverse experimental data and identifying key determinants and parameters for the IncP-1 central control operon. Moreover, we have shown that Bayesian inference and MCA are complementary methods for identification of sensitive parameters. We propose that this demonstrates generic value in applying this combination of approaches to systems biology dynamical modelling.
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Affiliation(s)
- Dorota Herman
- Center for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Scott RW, Murphy AC, Wu J, Hothersall J, Cox RJ, Simpson TJ, Thomas CM, Willis CL. Mupirocin F: structure elucidation, synthesis and rearrangements. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Murphy AC, Fukuda D, Song Z, Hothersall J, Cox RJ, Willis CL, Thomas CM, Simpson TJ. Engineered thiomarinol antibiotics active against MRSA are generated by mutagenesis and mutasynthesis of Pseudoalteromonas SANK73390. Angew Chem Int Ed Engl 2011; 50:3271-4. [PMID: 21381163 DOI: 10.1002/anie.201007029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 01/17/2011] [Indexed: 11/06/2022]
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