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Lagan Tregaskis P, Staines A, Gordon A, Sheridan P, McMenamy M, Duffy C, Collins PJ, Mooney MH, Lemon K. Co-infection status of novel parvovirus's (PPV2 to 4) with porcine circovirus 2 in porcine respiratory disease complex and porcine circovirus-associated disease from 1997 to 2012. Transbound Emerg Dis 2020; 68:1979-1994. [PMID: 32969579 DOI: 10.1111/tbed.13846] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/27/2019] [Revised: 09/07/2020] [Accepted: 09/12/2020] [Indexed: 12/19/2022]
Abstract
As global pig health diseases, porcine respiratory disease complex (PRDC) and porcine circovirus-associated disease (PCVAD) generate substantial economic losses despite pigs been vaccinated against the primary causative virus, highlighting the importance of understanding virome interactions and specifically co-factor infections. Established primary endemic pathogens for PRDC include porcine circovirus 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSv) and swine influenza virus (SIV), and PCV2 aetiology in interaction with other co-infecting viruses can result in PCVAD. Porcine parvovirus (PPV) 1 is a well-characterized virus with an available vaccine preventing reproductive failure in sows. However, whilst novel PPV 2 to 7 viruses have been identified since 2001, their viral pathogenic potential in clinical and subclinical disease remains to be determined. Therefore, this study has sought to develop a better understanding of their potential role as associated co-infections in PRDC and PCVAD by examining archival samples for the presence of PCV2 and the novel parvoviruses PPV2-4 from clinically diseased pigs across production age stages. Epidemiologically, the novel PPV2 was found to be the most prevalent within the fattener age group with PPV2-4 statistically associated with pig respiratory disease and enteric ulcers. Additionally, statistical modelling by latent class analysis (LCA) on veterinary pathology scored pigs found a clustering co-factor association between PPV2 and PCV2, suggesting the novel PPV may be involved in PRDC and PCVAD. Phylogenetic analysis of novel PPVs revealed the PPV2 capsid evolution to be diverged from the original strains with a low nucleotide homology of 88%-96% between two distinct clades. These findings determine that novel PPV 2-4 viruses are statistically associated as co-infectors in a diseased pig population, and significantly detected PPV2 clustering co-infection frequency with PCV2 in PRDC and PCVAD diseased pigs through LCA analysis.
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Affiliation(s)
- Paula Lagan Tregaskis
- Department of Virology, Veterinary Science Division, Agri-food and Biosciences Institute, Belfast, UK.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Anthony Staines
- Department of Nursing and Human Sciences, Dublin City University, Dublin, Ireland
| | - Alan Gordon
- Statistical Services Branch, Veterinary Science Division, Agri-food and Biosciences Institute, Belfast, UK
| | - Pauline Sheridan
- Department of Virology, Veterinary Science Division, Agri-food and Biosciences Institute, Belfast, UK
| | - Michael McMenamy
- Department of Virology, Veterinary Science Division, Agri-food and Biosciences Institute, Belfast, UK
| | - Catherine Duffy
- Department of Virology, Veterinary Science Division, Agri-food and Biosciences Institute, Belfast, UK
| | - P J Collins
- Department of Virology, Veterinary Science Division, Agri-food and Biosciences Institute, Belfast, UK
| | - Mark H Mooney
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Ken Lemon
- Department of Virology, Veterinary Science Division, Agri-food and Biosciences Institute, Belfast, UK
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2
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Fitzgerald RM, Collins PJ, McMenamey MJ, Leonard FC, McGlynn H, O'Shea H. Porcine reproductive and respiratory syndrome virus: phylogenetic analysis of circulating strains in the Republic of Ireland from 2016 to 2017. Arch Virol 2020; 165:2057-2063. [PMID: 32594320 DOI: 10.1007/s00705-020-04710-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/22/2020] [Indexed: 10/24/2022]
Abstract
In order to investigate the genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) strains currently circulating in the Republic of Ireland (ROI), the ORF5 gene from 17 field strains originating from four vaccinating commercial herds was sequenced and phylogenetically analysed. High genetic variability was observed between farms at the nucleotide (86.3-95.2%) and amino acid (85.5-96%) levels. Phylogenetic analysis confirmed that all field strains belonged to the European species (type 1) and clustered into three separate groups within the subtype 1 subgroup. This variation may pose challenges for diagnosis and prophylactic control of PRRSV through vaccination in the ROI.
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Affiliation(s)
- Rose M Fitzgerald
- Bio-Explore, Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, T12 P928, Republic of Ireland.
| | - Patrick J Collins
- Veterinary Science Division, Agri-Food and Biosciences Institute, Stormont, Belfast, BT4 3SD, Northern Ireland
| | - Michael J McMenamey
- Veterinary Science Division, Agri-Food and Biosciences Institute, Stormont, Belfast, BT4 3SD, Northern Ireland
| | - Finola C Leonard
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, D04 W6F6, Republic of Ireland
| | - Hugh McGlynn
- Bio-Explore, Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, T12 P928, Republic of Ireland
| | - Helen O'Shea
- Bio-Explore, Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, T12 P928, Republic of Ireland
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Meisen WH, Nejad ZB, Hardy M, Zhao H, Oliverio O, Wang S, Hale C, Ollmann MM, Collins PJ. Pooled Screens Identify GPR108 and TM9SF2 as Host Cell Factors Critical for AAV Transduction. Mol Ther Methods Clin Dev 2020; 17:601-611. [PMID: 32280726 PMCID: PMC7139131 DOI: 10.1016/j.omtm.2020.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022]
Abstract
Adeno-associated virus (AAV) has been used extensively as a vector for gene therapy. Despite its widespread use, the mechanisms by which AAV enters the cell and is trafficked to the nucleus are poorly understood. In this study, we performed two pooled, genome-wide screens to identify positive and negative factors modulating AAV2 transduction. Genome-wide libraries directed against all human genes with four designs per gene or eight designs per gene were transduced into U-2 OS cells. These pools were transduced with AAV2 encoding EGFP and sorted based on the intensity of EGFP expression. Analysis of enriched and depleted barcodes in the sorted samples identified several genes that putatively decreased AAV2 transduction. A subset of screen hits was validated in flow cytometry and imaging studies. In addition to KIAA0319L (AAVR), we confirmed the role of two genes, GPR108 and TM9SF2, in mediating viral transduction in eight different AAV serotypes. Interestingly, GPR108 displayed serotype selectivity and was not required for AAV5 transduction. Follow-up studies suggested that GPR108 localized primarily to the Golgi, where it may interact with AAV and play a critical role in mediating virus escape or trafficking. Cumulatively, these results expand our understanding of the process of AAV transduction in different cell types and serotypes.
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Affiliation(s)
- W. Hans Meisen
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | | | - Miki Hardy
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Huiren Zhao
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Oliver Oliverio
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Songli Wang
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
| | - Christopher Hale
- Genome Analysis Unit, Amgen Research, South San Francisco, CA, USA
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4
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Hwaidi MI, Sissons M, Pleming D, Collins PJ. Does Fumigation of Durum Wheat and Semolina with Sulfuryl Fluoride Affect Quality of the Grain, Semolina, and Derived Spaghetti and Bread? Cereal Chem 2016. [DOI: 10.1094/cchem-12-15-0244-r] [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: 11/03/2022]
Affiliation(s)
- Mudhir I. Hwaidi
- NSW Department of Primary Industries, Tamworth Agricultural Institute, 4 Marsden Park Road, Calala, NSW 2340, Australia
- Department of Field Crops, College of Agriculture, University of Tikrit, Tikrit, Salahuddin, Iraq
| | - Mike Sissons
- NSW Department of Primary Industries, Tamworth Agricultural Institute, 4 Marsden Park Road, Calala, NSW 2340, Australia
| | - Denise Pleming
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW 2650, Australia
| | - Patrick J. Collins
- Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
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5
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Kallewaard NL, Corti D, Collins PJ, Neu U, McAuliffe JM, Benjamin E, Wachter-Rosati L, Palmer-Hill FJ, Yuan AQ, Walker PA, Vorlaender MK, Bianchi S, Guarino B, De Marco A, Vanzetta F, Agatic G, Foglierini M, Pinna D, Fernandez-Rodriguez B, Fruehwirth A, Silacci C, Ogrodowicz RW, Martin SR, Sallusto F, Suzich JA, Lanzavecchia A, Zhu Q, Gamblin SJ, Skehel JJ. Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes. Cell 2016; 166:596-608. [PMID: 27453466 PMCID: PMC4967455 DOI: 10.1016/j.cell.2016.05.073] [Citation(s) in RCA: 268] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/04/2016] [Accepted: 05/25/2016] [Indexed: 01/12/2023]
Abstract
Influenza virus remains a threat because of its ability to evade vaccine-induced immune responses due to antigenic drift. Here, we describe the isolation, evolution, and structure of a broad-spectrum human monoclonal antibody (mAb), MEDI8852, effectively reacting with all influenza A hemagglutinin (HA) subtypes. MEDI8852 uses the heavy-chain VH6-1 gene and has higher potency and breadth when compared to other anti-stem antibodies. MEDI8852 is effective in mice and ferrets with a therapeutic window superior to that of oseltamivir. Crystallographic analysis of Fab alone or in complex with H5 or H7 HA proteins reveals that MEDI8852 binds through a coordinated movement of CDRs to a highly conserved epitope encompassing a hydrophobic groove in the fusion domain and a large portion of the fusion peptide, distinguishing it from other structurally characterized cross-reactive antibodies. The unprecedented breadth and potency of neutralization by MEDI8852 support its development as immunotherapy for influenza virus-infected humans.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/isolation & purification
- Antibodies, Monoclonal, Humanized
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Antibody Specificity
- Binding Sites, Antibody
- Crystallography, X-Ray
- Epitopes/immunology
- Ferrets
- Humans
- Influenza Vaccines
- Alphainfluenzavirus/immunology
- Mice
- Orthomyxoviridae Infections/prevention & control
- Protein Conformation
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Affiliation(s)
- Nicole L Kallewaard
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Davide Corti
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Patrick J Collins
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK
| | - Ursula Neu
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK
| | - Josephine M McAuliffe
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Ebony Benjamin
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Leslie Wachter-Rosati
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Frances J Palmer-Hill
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Andy Q Yuan
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Philip A Walker
- Structural Biology Science Technology Platform, Mill Hill Laboratory, Francis Crick Institute, London NW7 1AA, UK
| | | | - Siro Bianchi
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | | | - Gloria Agatic
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Debora Pinna
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | - Alexander Fruehwirth
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Chiara Silacci
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Roksana W Ogrodowicz
- Structural Biology Science Technology Platform, Mill Hill Laboratory, Francis Crick Institute, London NW7 1AA, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, Mill Hill Laboratory, Francis Crick Institute, London NW7 1AA, UK
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - JoAnn A Suzich
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland; Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Qing Zhu
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA.
| | - Steven J Gamblin
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK
| | - John J Skehel
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK.
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Jagadeesan R, Collins PJ, Nayak MK, Schlipalius DI, Ebert PR. Genetic characterization of field-evolved resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Laemophloeidae: Coleoptera). Pestic Biochem Physiol 2016; 127:67-75. [PMID: 26821660 DOI: 10.1016/j.pestbp.2015.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 06/05/2023]
Abstract
Inheritance of resistance to phosphine fumigant was investigated in three field-collected strains of rusty grain beetle, Cryptolestes ferrugineus, Susceptible (S-strain), Weakly Resistant (Weak-R) and Strongly Resistant (Strong-R). The strains were purified for susceptibility, weak resistance and strong resistance to phosphine, respectively, to ensure homozygosity of resistance genotype. Crosses were established between S-strain×Weak-R, S-strain×Strong-R and Weak-R×Strong-R, and the dose mortality responses to phosphine of these strains and their F1, F2 and F1-backcross progeny were obtained. The fumigations were undertaken at 25°C and 55% RH for 72h. Weak-R and Strong-R showed resistance factors of 6.3× and 505× compared with S-strain at the LC50. Both weak and strong resistances were expressed as incompletely recessive with degrees of dominance of -0.48 and -0.43 at the LC50, respectively. Responses of F2 and F1-backcross progeny indicated the existence of one major gene in Weak-R, and at least two major genes in Strong-R, one of which was allelic with the major factor in Weak-R. Phenotypic variance analyses also estimated that the number of independently segregating genes conferring weak resistance was 1 (nE=0.89) whereas there were two genes controlling strong resistance (nE=1.2). The second gene, unique to Strong-R, interacted synergistically with the first gene to confer a very high level of resistance (~80×). Neither of the two major resistance genes was sex linked. Despite the similarity of the genetics of resistance to that previously observed in other pest species, a significant proportion (~15 to 30%) of F1 individuals survived at phosphine concentrations higher than predicted. Thus it is likely that additional dominant heritable factors, present in some individuals in the population, also influenced the resistance phenotype. Our results will help in understanding the process of selection for phosphine resistance in the field which will inform resistance management strategies. In addition, this information will provide a basis for the identification of the resistance genes.
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Affiliation(s)
- Rajeswaran Jagadeesan
- Department of Agriculture and Fisheries, Ecosciences Precinct, Level 3C West, GPO Box 267, Brisbane, Queensland 4001, Australia.
| | - Patrick J Collins
- Department of Agriculture and Fisheries, Ecosciences Precinct, Level 3C West, GPO Box 267, Brisbane, Queensland 4001, Australia
| | - Manoj K Nayak
- Department of Agriculture and Fisheries, Ecosciences Precinct, Level 3C West, GPO Box 267, Brisbane, Queensland 4001, Australia
| | - David I Schlipalius
- Department of Agriculture and Fisheries, Ecosciences Precinct, Level 3C West, GPO Box 267, Brisbane, Queensland 4001, Australia
| | - Paul R Ebert
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
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7
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Nguyen TT, Collins PJ, Duong TM, Schlipalius DI, Ebert PR. Genetic Conservation of Phosphine Resistance in the Rice Weevil Sitophilus oryzae (L.). J Hered 2016; 107:228-37. [PMID: 26774057 DOI: 10.1093/jhered/esw001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 10/22/2015] [Accepted: 12/30/2015] [Indexed: 11/14/2022] Open
Abstract
High levels of resistance to phosphine in the rice weevil Sitophilus oryzae have been detected in Asian countries including China and Vietnam, however there is limited knowledge of the genetic mechanism of resistance in these strains. We find that the genetic basis of strong phosphine resistance is conserved between strains of S. oryzae from China, Vietnam, and Australia. Each of 4 strongly resistant strains has an identical amino acid variant in the encoded dihydrolipoamide dehydrogenase (DLD) enzyme that was previously identified as a resistance factor in Rhyzopertha dominica and Tribolium castaneum. The unique amino acid substitution, Asparagine > Threonine (N505T) of all strongly resistant S. oryzae corresponds to the position of an Asparagine > Histidine variant (N506H) that was previously reported in strongly resistant R. dominica. Progeny (F16 and F18) from 2 independent crosses showed absolute linkage of N505T to the strong resistance phenotype, indicating that if N505T was not itself the resistance variant that it resided within 1 or 2 genes of the resistance factor. Non-complementation between the strains confirmed the shared genetic basis of strong resistance, which was supported by the very similar level of resistance between the strains, with LC50 values ranging from 0.20 to 0.36 mg L(-1) for a 48-h exposure at 25 °C. Thus, the mechanism of high-level resistance to phosphine is strongly conserved between R. dominica, T. castaneum and S. oryzae. A fitness cost associated with strongly resistant allele was observed in segregating populations in the absence of selection.
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Affiliation(s)
- Tam T Nguyen
- From the School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia (Nguyen and Ebert); Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam (Nguyen); Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, Queensland, Australia (Collins and Schlipalius); and Plant Protection Department, Ministry of Agriculture and Rural Development, Hanoi, Vietnam (Duong)
| | - Patrick J Collins
- From the School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia (Nguyen and Ebert); Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam (Nguyen); Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, Queensland, Australia (Collins and Schlipalius); and Plant Protection Department, Ministry of Agriculture and Rural Development, Hanoi, Vietnam (Duong)
| | - Tu M Duong
- From the School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia (Nguyen and Ebert); Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam (Nguyen); Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, Queensland, Australia (Collins and Schlipalius); and Plant Protection Department, Ministry of Agriculture and Rural Development, Hanoi, Vietnam (Duong)
| | - David I Schlipalius
- From the School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia (Nguyen and Ebert); Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam (Nguyen); Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, Queensland, Australia (Collins and Schlipalius); and Plant Protection Department, Ministry of Agriculture and Rural Development, Hanoi, Vietnam (Duong)
| | - Paul R Ebert
- From the School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia (Nguyen and Ebert); Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam (Nguyen); Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, Queensland, Australia (Collins and Schlipalius); and Plant Protection Department, Ministry of Agriculture and Rural Development, Hanoi, Vietnam (Duong).
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8
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Gunn L, Collins PJ, O'Connell MJ, O'Shea H. Phylogenetic investigation of enteric bovine coronavirus in Ireland reveals partitioning between European and global strains. Ir Vet J 2015; 68:31. [PMID: 26719792 PMCID: PMC4696222 DOI: 10.1186/s13620-015-0060-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 12/16/2015] [Indexed: 11/13/2022] Open
Abstract
Background Bovine coronavirus is a primary cause of neonatal calf diarrhea worldwide, and is also associated with acute diarrhea in adult cattle during the winter season. There are no reports on molecular characterization of bovine coronavirus in Ireland, and little data exists apart from serological studies. Findings In this study, 11 neonatal (mean age 9 days) calf BCoV strains from the south of Ireland were collected over a one year period and characterized using molecular methods. The spike gene which encodes a protein involved in viral entry, infectivity and immune response shows the most variability amongst the isolates and was subsequently selected for in depth analysis. Phylogenetic analysis of the spike gene revealed that the Irish strains clustered with novel BCoV strains from Europe in a unique clade, possibly indicating lineage partitioning. Direct analysis of alignments identified amino acid changes in the spike protein unique to the Irish clade. Conclusion Thus, monitoring of bovine coronavirus in Ireland is important as the current isolates in circulation in the south of Ireland may be diverging from the available vaccine strain, which may have implications regarding future BCoV vaccine efficacy.
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Affiliation(s)
- L Gunn
- Department of Biological Sciences, Cork Institute of Technology, Rossa Ave, Bishopstown, Cork Ireland
| | - P J Collins
- Department of Biological Sciences, Cork Institute of Technology, Rossa Ave, Bishopstown, Cork Ireland
| | - M J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9 Ireland
| | - H O'Shea
- Department of Biological Sciences, Cork Institute of Technology, Rossa Ave, Bishopstown, Cork Ireland
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9
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Jagadeesan R, Nayak MK, Pavic H, Chandra K, Collins PJ. Susceptibility to sulfuryl fluoride and lack of cross-resistance to phosphine in developmental stages of the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae). Pest Manag Sci 2015; 71:1379-1386. [PMID: 25382378 DOI: 10.1002/ps.3940] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/12/2014] [Accepted: 11/05/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND Our aim was to ascertain the potential of sulfuryl fluoride (SF) as an alternative fumigant to manage phosphine-resistant pests. We tested the susceptibility of all life stages of red flour beetle, Tribolium castaneum (Herbst), to SF and assessed the presence of cross-resistance to this fumigant in phosphine-resistant strains of this species. RESULTS Analysis of dose-response data indicated that the egg was the stage most tolerant to SF under a 48 h exposure period. At LC50 , eggs were 29 times more tolerant than other immature stages and adults, and required a relatively high concentration of 48.2 mg L(-1) for complete mortality. No significant differences in tolerance to SF were observed among the three larval instars, pupae and adults, and all of these stages were controlled at a low concentration of 1.32 mg L(-1) . Phosphine-resistant strains did not show cross-resistance to SF. CONCLUSION Our research concluded that the current maximum registered rate of SF, 1500 gh m(-3) , is adequate to control all the post-embryonic life stages of T. castaneum over a 48 h fumigation period, but it will fail to achieve complete mortality of eggs, indicating the risk of some survival of eggs under this short exposure period. As there is no cross-resistance to SF in phosphine-resistant insects, it will play a key role in managing phosphine resistance in stored-grain insect pests.
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Affiliation(s)
- Rajeswaran Jagadeesan
- Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT, Australia
| | - Manoj K Nayak
- Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT, Australia
| | - Hervoika Pavic
- Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT, Australia
| | - Kerri Chandra
- Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
| | - Patrick J Collins
- Department of Agriculture, Fisheries and Forestry, Brisbane, Qld, Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT, Australia
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10
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Nguyen TT, Collins PJ, Ebert PR. Inheritance and characterization of strong resistance to phosphine in Sitophilus oryzae (L.). PLoS One 2015; 10:e0124335. [PMID: 25886629 PMCID: PMC4401577 DOI: 10.1371/journal.pone.0124335] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 03/06/2015] [Indexed: 11/19/2022] Open
Abstract
Sitophilus oryzae (Linnaeus) is a major pest of stored grain across Southeast Asia and is of increasing concern in other regions due to the advent of strong resistance to phosphine, the fumigant used to protect stored grain from pest insects. We investigated the inheritance of genes controlling resistance to phosphine in a strongly resistant S. oryzae strain (NNSO7525) collected in Australia and find that the trait is autosomally inherited and incompletely recessive with a degree of dominance of -0.66. The strongly resistant strain has an LC50 52 times greater than a susceptible reference strain (LS2) and 9 times greater than a weakly resistant strain (QSO335). Analysis of F2 and backcross progeny indicates that two or more genes are responsible for strong resistance, and that one of these genes, designated So_rph1, not only contributes to strong resistance, but is also responsible for the weak resistance phenotype of strain QSO335. These results demonstrate that the genetic mechanism of phosphine resistance in S. oryzae is similar to that of other stored product insect pests. A unique observation is that a subset of the progeny of an F1 backcross generation are more strongly resistant to phosphine than the parental strongly resistant strain, which may be caused by multiple alleles of one of the resistance genes.
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Affiliation(s)
- Tam T. Nguyen
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Patrick J. Collins
- Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, Queensland, Australia
| | - Paul R. Ebert
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
- * E-mail:
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Vachieri SG, Xiong X, Collins PJ, Walker PA, Martin SR, Haire LF, Zhang Y, McCauley JW, Gamblin SJ, Skehel JJ. Receptor binding by H10 influenza viruses. Nature 2014; 511:475-7. [PMID: 24870229 DOI: 10.1038/nature13443] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/07/2014] [Indexed: 01/18/2023]
Abstract
H10N8 follows H7N9 and H5N1 as the latest in a line of avian influenza viruses that cause serious disease in humans and have become a threat to public health. Since December 2013, three human cases of H10N8 infection have been reported, two of whom are known to have died. To gather evidence relating to the epidemic potential of H10 we have determined the structure of the haemagglutinin of a previously isolated avian H10 virus and we present here results relating especially to its receptor-binding properties, as these are likely to be major determinants of virus transmissibility. Our results show, first, that the H10 virus possesses high avidity for human receptors and second, from the crystal structure of the complex formed by avian H10 haemagglutinin with human receptor, it is clear that the conformation of the bound receptor has characteristics of both the 1918 H1N1 pandemic virus and the human H7 viruses isolated from patients in 2013 (ref. 3). We conclude that avian H10N8 virus has sufficient avidity for human receptors to account for its infection of humans but that its preference for avian receptors should make avian-receptor-rich human airway mucins an effective block to widespread infection. In terms of surveillance, particular attention will be paid to the detection of mutations in the receptor-binding site of the H10 haemagglutinin that decrease its avidity for avian receptor, and could enable it to be more readily transmitted between humans.
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Affiliation(s)
- Sebastien G Vachieri
- 1] MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK [2]
| | - Xiaoli Xiong
- 1] MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK [2]
| | - Patrick J Collins
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Philip A Walker
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stephen R Martin
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Lesley F Haire
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Ying Zhang
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - John W McCauley
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Steven J Gamblin
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - John J Skehel
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Collins PJ, Mulherin E, Cashman O, Lennon G, Gunn L, O'Shea H, Fanning S. Detection and characterisation of bovine rotavirus in Ireland from 2006-2008. Ir Vet J 2014; 67:13. [PMID: 24987518 PMCID: PMC4076433 DOI: 10.1186/2046-0481-67-13] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/05/2014] [Indexed: 12/23/2022] Open
Abstract
Background Worldwide, Group A bovine rotavirus (RVA boRV) is one of the main causes of neonatal calf diarrhoea. Currently, limited epidemiological and sequence data exists on the RVA disease in bovines in Southern Ireland only. The aim of the study was to generate epidemiological and sequence data of RVA boRV distributed over a wide geographical area in Ireland. Findings 272 stool samples were obtained from symptomatic calves and analysed to identify the prevalent G and P genotypes. Viral type combinations including G6P[5], G6P[11] and G10P[11] genotype were the most frequently identified. The G6P[5] combination was predominant throughtout the study, accounting for 70% (n = 191). Sequence analysis of the VP7 gene revealed that Irish G6 strains fell within Lineage IV, similiar to previous reports in Ireland. Conclusion The detection of unusual G and P combinations may have an impact on rotavirus control programmes and current vaccines may need to incorporate new strains, as the current vaccine available may not offer protection against all of these circulating types.
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Affiliation(s)
- P J Collins
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Emily Mulherin
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Olivia Cashman
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Grainne Lennon
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Lynda Gunn
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Helen O'Shea
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin 4, Ireland.,Herd and Veterinary Public Health Unit, School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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13
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Escuret V, Collins PJ, Casalegno JS, Vachieri SG, Cattle N, Ferraris O, Sabatier M, Frobert E, Caro V, Skehel JJ, Gamblin S, Valla F, Valette M, Ottmann M, McCauley JW, Daniels RS, Lina B. A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. J Infect Dis 2014; 210:1260-9. [PMID: 24795482 PMCID: PMC4176448 DOI: 10.1093/infdis/jiu244] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Influenza B viruses with a novel I221L substitution in neuraminidase (NA) conferring high-level resistance to oseltamivir were isolated from an immunocompromised patient after prolonged oseltamivir treatment. METHODS Enzymatic characterization of the NAs (Km, Ki) and the in vitro fitness of viruses carrying wild-type or mutated (I221L) NA genes were evaluated. Proportions of wild-type and mutated NA genes were directly quantified in the patient samples. Structural characterizations by X-ray crystallography of a wild-type and I221L variant NA were performed. RESULTS The Km and Ki revealed that the I221L variant NA had approximately 84 and 51 times lower affinity for oseltamivir carboxylate and zanamivir, respectively, compared with wild-type NA. Viruses with a wild-type or I221L variant NA had similar growth kinetics in Madin-Darby canine kidney (MDCK) cells, and 5 passages in MDCK cells revealed no reversion of the I221L substitution. The crystal structure of the I221L NA and oseltamivir complex showed that the leucine side chain protrudes into the hydrophobic pocket of the active site that accommodates the pentyloxy substituent of oseltamivir. CONCLUSIONS Enzyme kinetic and NA structural analyses provide an explanation for the high level of resistance to oseltamivir while retaining good fitness of viruses carrying I221L variant NA.
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Affiliation(s)
- Vanessa Escuret
- Laboratoire de Virologie et Centre National de Référence virus influenzae Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and
| | | | - Jean-Sébastien Casalegno
- Laboratoire de Virologie et Centre National de Référence virus influenzae Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and
| | | | - Nicholas Cattle
- WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Olivier Ferraris
- Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and
| | - Murielle Sabatier
- Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and
| | - Emilie Frobert
- Laboratoire de Virologie et Centre National de Référence virus influenzae Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and
| | - Valérie Caro
- Genotyping of Pathogens and Public Health Platform, Institut Pasteur, Paris, France
| | | | | | - Frédéric Valla
- Service de Réanimation Pédiatrique, Hôpital Femme Mère Enfant, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron
| | - Martine Valette
- Laboratoire de Virologie et Centre National de Référence virus influenzae
| | - Michèle Ottmann
- Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and
| | - John W McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Rodney S Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Bruno Lina
- Laboratoire de Virologie et Centre National de Référence virus influenzae Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and
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14
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Xiong X, Xiao H, Martin SR, Coombs PJ, Liu J, Collins PJ, Vachieri SG, Walker PA, Lin YP, McCauley JW, Gamblin SJ, Skehel JJ. Enhanced human receptor binding by H5 haemagglutinins. Virology 2014; 456-457:179-87. [PMID: 24889237 PMCID: PMC4053833 DOI: 10.1016/j.virol.2014.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/10/2014] [Accepted: 03/07/2014] [Indexed: 11/24/2022]
Abstract
Mutant H5N1 influenza viruses have been isolated from humans that have increased human receptor avidity. We have compared the receptor binding properties of these mutants with those of wild-type viruses, and determined the structures of their haemagglutinins in complex with receptor analogues. Mutants from Vietnam bind tighter to human receptor by acquiring basic residues near the receptor binding site. They bind more weakly to avian receptor because they lack specific interactions between Asn-186 and Gln-226. In contrast, a double mutant, Δ133/Ile155Thr, isolated in Egypt has greater avidity for human receptor while retaining wild-type avidity for avian receptor. Despite these increases in human receptor binding, none of the mutants prefers human receptor, unlike aerosol transmissible H5N1 viruses. Nevertheless, mutants with high avidity for both human and avian receptors may be intermediates in the evolution of H5N1 viruses that could infect both humans and poultry. H5N1 influenza virus binding. Haemagglutinin receptor specificity using biolayer interferometry. Haemagglutinin receptor complex crystal structure determination.
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Affiliation(s)
- Xiaoli Xiong
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Haixia Xiao
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stephen R Martin
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Peter J Coombs
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Junfeng Liu
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Patrick J Collins
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Sebastien G Vachieri
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Philip A Walker
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Yi Pu Lin
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - John W McCauley
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Steven J Gamblin
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - John J Skehel
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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15
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Lennon G, Reidy N, Collins PJ, Gunn L, Coyle PV, Cryan B, Fanning S, O'Shea H. A comparison of the efficiency of ELISA and selected primer sets to detect Norovirus isolates in southern Ireland over a four-year period (2002-2006): variation in detection rates and evidence for continuing predominance of NoV GII.4 genotype. Arch Virol 2014; 159:1697-705. [PMID: 24473708 DOI: 10.1007/s00705-014-1987-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/11/2014] [Indexed: 11/26/2022]
Abstract
Norovirus (NoV) gastroenteritis occurs in all age groups and is the most common cause of gastroenteritis in the community. However, detection methods and rates vary widely, and few data are available to compare these, particularly in Ireland. Detection of noroviruses through antigen and molecular-based strategies was carried out on 135 suspected NoV-positive samples, collected over the course of three NoV outbreaks, from 2002 to 2006, in the southern region of Ireland. A commercially available ELISA and a panel of six primer sets were evaluated to determine their suitability for NoV detection in Irish clinical samples. The key findings of this study were the detection of both GGI and GGII noroviruses by ELISA, but the detection of only GGII noroviruses by RT-PCR. In addition to this, a variation in the levels of detection from 9.4 % to 17.3 % was observed for conventional PCR assays, while a detection rate of 46.3 % was observed for the real-time PCR assay. A proportion (17.8 %) of samples were found to be negative by all detection strategies, suggesting the possibility of reporting false positives for these samples or low-copy positives that do not often repeat. Sequencing information from selected samples also revealed nucleotide polymorphisms, compromising efficient primer binding in the case of one primer pairing. Phylogenetic analysis of the partial polymerase gene identified NoV GII.4 as the dominant genotype, in accordance with previous NoV studies in Ireland. Investigating the NoV diversity of the circulating strains and the dynamics of strain replacement is important to better assess the efficacy of future NoV vaccines and to facilitate the early detection of changes in circulating NoV strains.
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Affiliation(s)
- G Lennon
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
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Abstract
Previously regarded as minor nuisance pests, psocids belonging to the genus Liposcelis now pose a major problem for the effective protection of stored products worldwide. Here we examine the apparent biological and operational reasons behind this phenomenon and why conventional pest management seems to be failing. We investigate what is known about the biology, behavior, and population dynamics of major pest species to ascertain their strengths, and perhaps find weaknesses, as a basis for a rational pest management strategy. We outline the contribution of molecular techniques to clarifying species identification and understanding genetic diversity. We discuss progress in sampling and trapping and our comprehension of spatial distribution of these pests as a foundation for developing management strategies. The effectiveness of various chemical treatments and the availability and potential of nonchemical control methods are critically examined. Finally, we identify research gaps and suggest future directions for research.
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Affiliation(s)
- Manoj K Nayak
- Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Brisbane, QLD 4001, Australia; ,
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17
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Shi M, Collins PJ, Ridsdill-Smith TJ, Emery RN, Renton M. Dosage consistency is the key factor in avoiding evolution of resistance to phosphine and population increase in stored-grain pests. Pest Manag Sci 2013; 69:1049-1060. [PMID: 23292953 DOI: 10.1002/ps.3457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 09/14/2012] [Accepted: 11/01/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Control of pests in stored grain and the evolution of resistance to pesticides are serious problems worldwide. A stochastic individual-based two-locus model was used to investigate the impact of two important issues, the consistency of pesticide dosage through the storage facility and the immigration rate of the adult pest, on overall population control and avoidance of evolution of resistance to the fumigant phosphine in an important pest of stored grain, the lesser grain borer. RESULTS A very consistent dosage maintained good control for all immigration rates, while an inconsistent dosage failed to maintain control in all cases. At intermediate dosage consistency, immigration rate became a critical factor in whether control was maintained or resistance emerged. CONCLUSION Achieving a consistent fumigant dosage is a key factor in avoiding evolution of resistance to phosphine and maintaining control of populations of stored-grain pests; when the dosage achieved is very inconsistent, there is likely to be a problem regardless of immigration rate.
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Affiliation(s)
- Mingren Shi
- School of Plant Biology, FNAS, The University of Western Australia, Crawley, WA, Australia.
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18
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Xiong X, Martin SR, Haire LF, Wharton SA, Daniels RS, Bennett MS, McCauley JW, Collins PJ, Walker PA, Skehel JJ, Gamblin SJ. Receptor binding by an H7N9 influenza virus from humans. Nature 2013; 499:496-9. [PMID: 23787694 DOI: 10.1038/nature12372] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/13/2013] [Indexed: 12/18/2022]
Abstract
Of the 132 people known to have been infected with H7N9 influenza viruses in China, 37 died, and many were severely ill. Infection seems to have involved contact with infected poultry. We have examined the receptor-binding properties of this H7N9 virus and compared them with those of an avian H7N3 virus. We find that the human H7 virus has significantly higher affinity for α-2,6-linked sialic acid analogues ('human receptor') than avian H7 while retaining the strong binding to α-2,3-linked sialic acid analogues ('avian receptor') characteristic of avian viruses. The human H7 virus does not, therefore, have the preference for human versus avian receptors characteristic of pandemic viruses. X-ray crystallography of the receptor-binding protein, haemagglutinin (HA), in complex with receptor analogues indicates that both human and avian receptors adopt different conformations when bound to human H7 HA than they do when bound to avian H7 HA. Human receptor bound to human H7 HA exits the binding site in a different direction to that seen in complexes formed by HAs from pandemic viruses and from an aerosol-transmissible H5 mutant. The human-receptor-binding properties of human H7 probably arise from the introduction of two bulky hydrophobic residues by the substitutions Gln226Leu and Gly186Val. The former is shared with the 1957 H2 and 1968 H3 pandemic viruses and with the aerosol-transmissible H5 mutant. We conclude that the human H7 virus has acquired some of the receptor-binding characteristics that are typical of pandemic viruses, but its retained preference for avian receptor may restrict its further evolution towards a virus that could transmit efficiently between humans, perhaps by binding to avian-receptor-rich mucins in the human respiratory tract rather than to cellular receptors.
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Affiliation(s)
- Xiaoli Xiong
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW71AA, UK
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19
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Xiong X, Coombs PJ, Martin SR, Liu J, Xiao H, McCauley JW, Locher K, Walker PA, Collins PJ, Kawaoka Y, Skehel JJ, Gamblin SJ. Receptor binding by a ferret-transmissible H5 avian influenza virus. Nature 2013; 497:392-6. [PMID: 23615615 DOI: 10.1038/nature12144] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/05/2013] [Indexed: 01/17/2023]
Abstract
Cell-surface-receptor binding by influenza viruses is a key determinant of their transmissibility, both from avian and animal species to humans as well as from human to human. Highly pathogenic avian H5N1 viruses that are a threat to public health have been observed to acquire affinity for human receptors, and transmissible-mutant-selection experiments have identified a virus that is transmissible in ferrets, the generally accepted experimental model for influenza in humans. Here, our quantitative biophysical measurements of the receptor-binding properties of haemagglutinin (HA) from the transmissible mutant indicate a small increase in affinity for human receptor and a marked decrease in affinity for avian receptor. From analysis of virus and HA binding data we have derived an algorithm that predicts virus avidity from the affinity of individual HA-receptor interactions. It reveals that the transmissible-mutant virus has a 200-fold preference for binding human over avian receptors. The crystal structure of the transmissible-mutant HA in complex with receptor analogues shows that it has acquired the ability to bind human receptor in the same folded-back conformation as seen for HA from the 1918, 1957 (ref. 4), 1968 (ref. 5) and 2009 (ref. 6) pandemic viruses. This binding mode is substantially different from that by which non-transmissible wild-type H5 virus HA binds human receptor. The structure of the complex also explains how the change in preference from avian to human receptors arises from the Gln226Leu substitution, which facilitates binding to human receptor but restricts binding to avian receptor. Both features probably contribute to the acquisition of transmissibility by this mutant virus.
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Affiliation(s)
- Xiaoli Xiong
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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20
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Gunn L, Feeney SA, Cashman O, Collins PJ, Coyle PV, O'Shea H. Molecular characterization of group A rotavirus found in elderly patients in Ireland; predominance of G1P[8], continued presence of G9P[8], and emergence of G2P[4]. J Med Virol 2013; 84:2008-17. [PMID: 23080510 DOI: 10.1002/jmv.23416] [Citation(s) in RCA: 12] [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: 11/06/2022]
Abstract
Rotavirus is a major cause of gastroenteritis in young children worldwide. There have been several recent reports concerning rotavirus isolation from adults, particularly in the elderly, presenting with gastroenteritis. In this study, the authors report on rotavirus outbreaks in five separate elderly care facilities between April, and June 2011 in Ireland. The following genotypes were detected; G1P[8] (n = 5/11), G2P[4] (n = 2/11), and G9P[8] (n = 2/11). Thus, similarities to previous reports were found in that G1P[8] predominated, G9P[8] was still detected but G2P[4] was detected for the first time in a geriatric population in Ireland. Here also described is the detection of Group 2 lineage IIC rotavirus in Ireland for the first time.
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Affiliation(s)
- L Gunn
- Department of Biological Sciences, Cork Institute of Technology, Rossa Ave, Bishopstown, Cork, Ireland
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21
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Nayak MK, Holloway JC, Emery RN, Pavic H, Bartlet J, Collins PJ. Strong resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae): its characterisation, a rapid assay for diagnosis and its distribution in Australia. Pest Manag Sci 2013; 69:48-53. [PMID: 22807213 DOI: 10.1002/ps.3360] [Citation(s) in RCA: 17] [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] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 04/26/2012] [Accepted: 05/23/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND The recent development of very high resistance to phosphine in rusty grain beetle, Cryptolestes ferrugineus (Stephens), seriously threatens stored-grain biosecurity. The aim was to characterise this resistance, to develop a rapid bioassay for its diagnosis to support pest management and to document the distribution of resistance in Australia in 2007-2011. RESULTS Bioassays of purified laboratory reference strains and field-collected samples revealed three phenotypes: susceptible, weakly resistant and strongly resistant. With resistance factors of > 1000 × , resistance to phosphine expressed by the strong resistance phenotype was higher than reported for any stored-product insect species. The new time-to-knockdown assay rapidly and accurately diagnosed each resistance phenotype within 6 h. Although less frequent in western Australia, weak resistance was detected throughout all grain production regions. Strong resistance occurred predominantly in central storages in eastern Australia. CONCLUSION Resistance to phosphine in the rusty grain beetle is expressed through two identifiable phenotypes: weak and strong. Strong resistance requires urgent changes to current fumigation dosages. The development of a rapid assay for diagnosis of resistance enables the provision of same-day advice to expedite resistance management decisions.
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Affiliation(s)
- Manoj K Nayak
- Department of Employment, Economic Development and Innovation, Brisbane, Queensland, Australia.
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Ridley AW, Magabe S, Schlipalius DI, Rafter MA, Collins PJ. Sublethal exposure to phosphine decreases offspring production in strongly phosphine resistant female red flour beetles, Tribolium castaneum (Herbst). PLoS One 2012; 7:e53356. [PMID: 23300916 PMCID: PMC3534025 DOI: 10.1371/journal.pone.0053356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/27/2012] [Indexed: 11/18/2022] Open
Abstract
The red flour beetle is a cosmopolitan pest of stored grain and stored grain products. The pest has developed resistance to phosphine, the primary chemical used for its control. The reproductive output of survivors from a phosphine treatment is an important element of resistance development but experimental data are lacking. We exposed mated resistant female beetles to 0.135 mg/L of phosphine for 48 h at 25°C. Following one week of recovery we provided two non-exposed males to half of the phosphine exposed females and to half of the non-exposed control females. Females that had been exposed produced significantly fewer offspring than non-exposed females. Females that remained isolated produced significantly fewer offspring than both exposed females with access to males and non-exposed controls (P<0.05). Some females were permanently damaged from exposure to phosphine and did not reproduce even when given access to males. We also examined the additional effects of starvation prior to phosphine exposure on offspring production. Non-exposed starved females experienced a small reduction in mean offspring production in the week following starvation, followed by a recovery in the second week. Females that were starved and exposed to phosphine demonstrated a very significant reduction in offspring production in the first week following exposure which remained significantly lower than that of starved non-exposed females (P<0.05). These results demonstrate a clear sublethal effect of phosphine acting on the female reproductive system and in some individuals this can lead to permanent reproductive damage. Pest population rebound after a fumigation may be slower than expected which may reduce the rate of phosphine resistance development. The results presented strongly suggest that phosphine resistance models should include sublethal effects.
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Affiliation(s)
- Andrew W Ridley
- Agri-Science Queensland, Department of Agriculture, Fisheries and Forestry, EcoSciences Precinct, Brisbane, Queensland, Australia.
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Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng Z. Functional analysis of transcription factor binding sites in human promoters. Genome Biol 2012; 13:R50. [PMID: 22951020 PMCID: PMC3491394 DOI: 10.1186/gb-2012-13-9-r50] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 04/19/2012] [Accepted: 06/18/2012] [Indexed: 12/19/2022] Open
Abstract
Background The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1. Results In each cell line, between 36% and 49% of binding sites made a functional contribution to the promoter activity; the overall rate for observing function in any of the cell lines was 70%. Transcription factor binding resulted in transcriptional repression in more than a third of functional sites. When compared with predicted binding sites whose function was not experimentally verified, the functional binding sites had higher conservation and were located closer to transcriptional start sites (TSSs). Among functional sites, repressive sites tended to be located further from TSSs than were activating sites. Our data provide significant insight into the functional characteristics of YY1 binding sites, most notably the detection of distinct activating and repressing classes of YY1 binding sites. Repressing sites were located closer to, and often overlapped with, translational start sites and presented a distinctive variation on the canonical YY1 binding motif. Conclusions The genomic properties that we found to associate with functional TF binding sites on promoters -- conservation, TSS proximity, motifs and their variations -- point the way to improved accuracy in future TFBS predictions.
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Affiliation(s)
- Troy W Whitfield
- Program in Bioinformatics and Integrative Biology and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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van der Vries E, Collins PJ, Vachieri SG, Xiong X, Liu J, Walker PA, Haire LF, Hay AJ, Schutten M, Osterhaus ADME, Martin SR, Boucher CAB, Skehel JJ, Gamblin SJ. H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. PLoS Pathog 2012; 8:e1002914. [PMID: 23028314 PMCID: PMC3447749 DOI: 10.1371/journal.ppat.1002914] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 08/05/2012] [Indexed: 12/16/2022] Open
Abstract
Two classes of antiviral drugs, neuraminidase inhibitors and adamantanes, are approved for prophylaxis and therapy against influenza virus infections. A major concern is that antiviral resistant viruses emerge and spread in the human population. The 2009 pandemic H1N1 virus is already resistant to adamantanes. Recently, a novel neuraminidase inhibitor resistance mutation I223R was identified in the neuraminidase of this subtype. To understand the resistance mechanism of this mutation, the enzymatic properties of the I223R mutant, together with the most frequently observed resistance mutation, H275Y, and the double mutant I223R/H275Y were compared. Relative to wild type, K(M) values for MUNANA increased only 2-fold for the single I223R mutant and up to 8-fold for the double mutant. Oseltamivir inhibition constants (K(I)) increased 48-fold in the single I223R mutant and 7500-fold in the double mutant. In both cases the change was largely accounted for by an increased dissociation rate constant for oseltamivir, but the inhibition constants for zanamivir were less increased. We have used X-ray crystallography to better understand the effect of mutation I223R on drug binding. We find that there is shrinkage of a hydrophobic pocket in the active site as a result of the I223R change. Furthermore, R223 interacts with S247 which changes the rotamer it adopts and, consequently, binding of the pentoxyl substituent of oseltamivir is not as favorable as in the wild type. However, the polar glycerol substituent present in zanamivir, which mimics the natural substrate, is accommodated in the I223R mutant structure in a similar way to wild type, thus explaining the kinetic data. Our structural data also show that, in contrast to a recently reported structure, the active site of 2009 pandemic neuraminidase can adopt an open conformation.
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Affiliation(s)
| | - Patrick J. Collins
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Sebastien G. Vachieri
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Xiaoli Xiong
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Junfeng Liu
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing, People's Republic of China
| | - Philip A. Walker
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Lesley F. Haire
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Alan J. Hay
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Martin Schutten
- Erasmus Medical Centre, Department of Virology, Rotterdam, The Netherlands
| | | | - Steve R. Martin
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | | | - John J. Skehel
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
- * E-mail:
| | - Steve J. Gamblin
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
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Mau YS, Collins PJ, Daglish GJ, Nayak MK, Ebert PR. The rph2 gene is responsible for high level resistance to phosphine in independent field strains of Rhyzopertha dominica. PLoS One 2012; 7:e34027. [PMID: 22461899 PMCID: PMC3312893 DOI: 10.1371/journal.pone.0034027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/20/2012] [Indexed: 11/19/2022] Open
Abstract
The lesser grain borer Rhyzopertha dominica (F.) is one of the most destructive insect pests of stored grain. This pest has been controlled successfully by fumigation with phosphine for the last several decades, though strong resistance to phosphine in many countries has raised concern about the long term usefulness of this control method. Previous genetic analysis of strongly resistant (SR) R. dominica from three widely geographically dispersed regions of Australia, Queensland (SRQLD), New South Wales (SRNSW) and South Australia (SRSA), revealed a resistance allele in the rph1 gene in all three strains. The present study confirms that the rph1 gene contributes to resistance in a fourth strongly resistant strain, SR2QLD, also from Queensland. The previously described rph2 gene, which interacts synergistically with rph1 gene, confers strong resistance on SRQLD and SRNSW. We now provide strong circumstantial evidence that weak alleles of rph2, together with rph1, contribute to the strong resistance phenotypes of SRSA and SR2QLD. To test the notion that rph1 and rph2 are solely responsible for the strong resistance phenotype of all resistant R. dominica, we created a strain derived by hybridising the four strongly resistant lines. Following repeated selection for survival at extreme rates of phosphine exposure, we found only slightly enhanced resistance. This suggests that a single sequence of genetic changes was responsible for the development of resistance in these insects.
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Affiliation(s)
- Yosep S. Mau
- School of Integrative Biology, The University of Queensland, Saint Lucia, Queensland, Australia
- Faculty of Agriculture, The University of Nusa Cendana, Kupang, Nusa Tenggara Timur, Indonesia
| | - Patrick J. Collins
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Brisbane, Queensland, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia
| | - Gregory J. Daglish
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Brisbane, Queensland, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia
| | - Manoj K. Nayak
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Brisbane, Queensland, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia
| | - Paul R. Ebert
- School of Integrative Biology, The University of Queensland, Saint Lucia, Queensland, Australia
- * E-mail:
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Jagadeesan R, Collins PJ, Daglish GJ, Ebert PR, Schlipalius DI. Phosphine resistance in the rust red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae): inheritance, gene interactions and fitness costs. PLoS One 2012; 7:e31582. [PMID: 22363681 PMCID: PMC3283673 DOI: 10.1371/journal.pone.0031582] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 01/09/2012] [Indexed: 11/19/2022] Open
Abstract
The recent emergence of heritable high level resistance to phosphine in stored grain pests is a serious concern among major grain growing countries around the world. Here we describe the genetics of phosphine resistance in the rust red flour beetle Tribolium castaneum (Herbst), a pest of stored grain as well as a genetic model organism. We investigated three field collected strains of T. castaneum viz., susceptible (QTC4), weakly resistant (QTC1012) and strongly resistant (QTC931) to phosphine. The dose-mortality responses of their test- and inter-cross progeny revealed that most resistance was conferred by a single major resistance gene in the weakly (3.2×) resistant strain. This gene was also found in the strongly resistant (431×) strain, together with a second major resistance gene and additional minor factors. The second major gene by itself confers only 12-20× resistance, suggesting that a strong synergistic epistatic interaction between the genes is responsible for the high level of resistance (431×) observed in the strongly resistant strain. Phosphine resistance is not sex linked and is inherited as an incompletely recessive, autosomal trait. The analysis of the phenotypic fitness response of a population derived from a single pair inter-strain cross between the susceptible and strongly resistant strains indicated the changes in the level of response in the strong resistance phenotype; however this effect was not consistent and apparently masked by the genetic background of the weakly resistant strain. The results from this work will inform phosphine resistance management strategies and provide a basis for the identification of the resistance genes.
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Affiliation(s)
- Rajeswaran Jagadeesan
- School of Biological Sciences, University of Queensland, St. Lucia, Australia
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Agri-Science Queensland, Brisbane, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australia
| | - Patrick J. Collins
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Agri-Science Queensland, Brisbane, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australia
| | - Gregory J. Daglish
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Agri-Science Queensland, Brisbane, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australia
| | - Paul R. Ebert
- School of Biological Sciences, University of Queensland, St. Lucia, Australia
| | - David I. Schlipalius
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Agri-Science Queensland, Brisbane, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australia
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Mau YS, Collins PJ, Daglish GJ, Nayak MK, Pavic H, Ebert PR. The rph1 gene is a common contributor to the evolution of phosphine resistance in independent field isolates of Rhyzopertha dominica. PLoS One 2012; 7:e31541. [PMID: 22363668 PMCID: PMC3282749 DOI: 10.1371/journal.pone.0031541] [Citation(s) in RCA: 18] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 01/12/2012] [Indexed: 12/04/2022] Open
Abstract
Phosphine is the only economically viable fumigant for routine control of insect pests of stored food products, but its continued use is now threatened by the world-wide emergence of high-level resistance in key pest species. Phosphine has a unique mode of action relative to well-characterised contact pesticides. Similarly, the selective pressures that lead to resistance against field sprays differ dramatically from those encountered during fumigation. The consequences of these differences have not been investigated adequately. We determine the genetic basis of phosphine resistance in Rhyzopertha dominica strains collected from New South Wales and South Australia and compare this with resistance in a previously characterised strain from Queensland. The resistance levels range from 225 and 100 times the baseline response of a sensitive reference strain. Moreover, molecular and phenotypic data indicate that high-level resistance was derived independently in each of the three widely separated geographical regions. Despite the independent origins, resistance was due to two interacting genes in each instance. Furthermore, complementation analysis reveals that all three strains contain an incompletely recessive resistance allele of the autosomal rph1 resistance gene. This is particularly noteworthy as a resistance allele at rph1 was previously proposed to be a necessary first step in the evolution of high-level resistance. Despite the capacity of phosphine to disrupt a wide range of enzymes and biological processes, it is remarkable that the initial step in the selection of resistance is so similar in isolated outbreaks.
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Affiliation(s)
- Yosep S. Mau
- School of Integrative Biology, The University of Queensland, Saint Lucia, Queensland, Australia
- Faculty of Agriculture, the University of Nusa Cendana, Kupang, Nusa Tenggara Timur, Indonesia
| | - Patrick J. Collins
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Brisbane, Queensland, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia
| | - Gregory J. Daglish
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Brisbane, Queensland, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia
| | - Manoj K. Nayak
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Brisbane, Queensland, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia
| | - Hervoika Pavic
- Department of Employment, Economic Development and Innovation, Ecosciences Precinct, Brisbane, Queensland, Australia
- Cooperative Research Centre for National Plant Biosecurity, Bruce, Australian Capital Territory, Australia
| | - Paul R. Ebert
- School of Integrative Biology, The University of Queensland, Saint Lucia, Queensland, Australia
- * E-mail:
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D. Kurkuri M, Saunders C, J. Collins P, Pavic H, Losic D. Combining Micro and Nanoscale Structures: Emerging Applications of Diatoms. ACTA ACUST UNITED AC 2011. [DOI: 10.2174/1876402911103040277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Boutz DR, Collins PJ, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, Abreu RDS, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein ND, Marcotte EM, Penalva LOF. Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. J Biol Chem 2011; 286:18066-78. [PMID: 21402708 DOI: 10.1074/jbc.m110.196451] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs function as important regulators of gene expression and are commonly linked to development, differentiation, and diseases such as cancer. To better understand their roles in various biological processes, identification of genes targeted by microRNAs is necessary. Although prediction tools have significantly helped with this task, experimental approaches are ultimately required for extensive target search and validation. We employed two independent yet complementary high throughput approaches to map a large set of mRNAs regulated by miR-122, a liver-specific microRNA implicated in regulation of fatty acid and cholesterol metabolism, hepatitis C infection, and hepatocellular carcinoma. The combination of luciferase reporter-based screening and shotgun proteomics resulted in the identification of 260 proteins significantly down-regulated in response to miR-122 in at least one method, 113 of which contain predicted miR-122 target sites. These proteins are enriched for functions associated with the cell cycle, differentiation, proliferation, and apoptosis. Among these miR-122-sensitive proteins, we identified a large group with strong connections to liver metabolism, diseases, and hepatocellular carcinoma. Additional analyses, including examination of consensus binding motifs for both miR-122 and target sequences, provide further insight into miR-122 function.
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Affiliation(s)
- Daniel R Boutz
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
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Ridley AW, Hereward JP, Daglish GJ, Raghu S, Collins PJ, Walter GH. The spatiotemporal dynamics of Tribolium castaneum (Herbst): adult flight and gene flow. Mol Ecol 2011; 20:1635-46. [PMID: 21375637 DOI: 10.1111/j.1365-294x.2011.05049.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [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]
Abstract
Tribolium castaneum (Herbst) has been used as a model organism to develop and test important ecological and evolutionary concepts and is also a major pest of grain and grain products globally. This beetle species is assumed to be a good colonizer of grain storages through anthropogenic movement of grain, and active dispersal by flight is considered unlikely. Studies using T. castaneum have therefore used confined or walking insects. We combine an ecological study of dispersal with an analysis of gene flow using microsatellites to investigate the spatiotemporal dynamics and adult flight of T. castaneum in an ecological landscape in eastern Australia. Flying beetles were caught in traps at grain storages and in fields at least 1 km from the nearest stored grain at regular intervals for an entire year. Significantly more beetles were trapped at storages than in fields, and almost no beetles were caught in native vegetation reserves many kilometres from the nearest stored grain. Genetic differentiation between beetles caught at storages and in fields was low, indicating that although T. castaneum is predominantly aggregated around grain storages, active dispersal takes place to the extent that significant gene flow occurs between them, mitigating founder effects and genetic drift. By combining ecological and molecular techniques, we reveal much higher levels of active dispersal through adult flight in T. castaneum than previously thought. We conclude that the implications of adult flight to previous and future studies on this model organism warrant consideration.
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Affiliation(s)
- A W Ridley
- Agri-Science Queensland, Department of Employment, Economic Development and Innovation, EcoSciences Precinct, GPO Box 46, Brisbane, Qld 4001, Australia.
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Collins PJ, Martella V, Buonavoglia C, O'Shea H. Identification of a G2-like porcine rotavirus bearing a novel VP4 type, P[32]. Vet Res 2010; 41:73. [PMID: 20663474 PMCID: PMC2939698 DOI: 10.1051/vetres/2010045] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 07/23/2010] [Indexed: 01/22/2023] Open
Abstract
A porcine group A rotavirus (GARV) strain, 61/07/Ire, was isolated from a 4–5 week asymptomatic piglet, during an epidemiological survey of porcine herds in Southern Ireland, in 2007. The nucleotide (nt) and amino acid (aa) sequence of the full-length VP4 protein of the PoRV strain 61/07/Ire was determined. Based on the entire VP4 open reading frame (nt), strain 61/07/Ire displayed ≤ 76.5% identity to representatives of the established 31 P-types, a value far lower than the percentage identity cutoff value (80%) established by the Rotavirus Classification Working Group (RCWG) to define a novel P genotype. Strain 61/07/Ire revealed low aa identity, ranging from 57.1% to 83.6%, to the cognate sequences of representatives of the various P genotypes. The aa identity was lower in the VP8* trypsin-cleavage fragment of the VP4, which encompasses the VP4 hypervariable region, ranging from 36.9% to 75.3%. Sequence analyses of the VP7, VP6, and NSP4 genes revealed that the GARV strain 61/07/Ire possessed a G2-like VP7, an E9 NSP4 genotype and an I5 VP6 genotype. Altogether, these results indicate that the GARV strain 61/07/Ire should be considered as a prototype of a new VP4 genotype, P[32], and provide further evidence for the vast heterogeneity of group A rotaviruses.
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Affiliation(s)
- Patrick J Collins
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
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Chen Z, Zheng YH, Lin Y, Collins PJ, Hay AJ. [Impact of avian influenza virus H5N1 neuraminidase mutations on the activity of neuraminidase and the sensibility to neuraminidase inhibitors]. Zhonghua Yi Xue Za Zhi 2010; 90:1924-1928. [PMID: 20979914] [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] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To study the impact of avian influenza virus H5N1 neuraminidase mutations I117V, I314V and I117V + I314V on the sensibility of neuraminidase inhibitors (NAIs) and the activity of neuraminidase (NA). METHODS The mutations were introduced into NA genes of virus strain A/Vietnam/1203/04 (H5N1) by site-directed mutagenesis. With the A/WSN/33 (H1N1) background, recombinant influenza viruses containing NA mutations were rescued by reverse genetics. After viral propagation in chicken embryos, fluorimetric assays were conducted to assess the sensibility to NAIs and NA activity (IC(50), Km & Ki). RESULTS Compared to the wild-type virus VN1203, the mutation I117V decreased the susceptibility to oseltamivir (17-fold increment of IC(50) value, 20-fold increment of Ki value) and the NA activity (23-fold increment of Km value) while there was little impact on zanamivir sensitivity (2-fold increment of IC(50) value, 3-fold increment of Ki value). The mutation I314V had no marked influence on either the NA activity or the NAIs susceptibility. CONCLUSION It appears that the NA mutations of I117V and I314V can not cause NAIs resistance. Oseltamivir or zanamivir may still be prescribed for anti-viral treatment.
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Affiliation(s)
- Zi Chen
- Department of Infectious Diseases, Second Xiangya Hospital, Central South University, Changsha 410011, China
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Collins PJ, Martella V, Sleator RD, Fanning S, O'Shea H. Detection and characterisation of group A rotavirus in asymptomatic piglets in southern Ireland. Arch Virol 2010; 155:1247-59. [PMID: 20526785 DOI: 10.1007/s00705-010-0713-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 05/25/2010] [Indexed: 01/16/2023]
Abstract
Porcine group A rotaviruses (GARV) are causative agents of enteritis in piglets and are a large reservoir of genetic material for the diversification of human GARVs. Accumulation of information on the genetic heterogeneity of porcine viruses is pivotal for readily characterising unusual human strains. Screening of 292 fecal samples, collected from 4-5- to 8-9-week-old asymptomatic pigs from four herds in Ireland between 2005 and 2007 resulted in 19 (6.5%) samples testing positive by reverse-transcription PCR (RT-PCR) for GARV. The strains were molecularly characterized to collate data on the VP7 and partial VP4 outer capsid genes. By sequence analysis of the VP7 gene, the Irish strains were identified as G2, G4, G5, G9 and G11 viruses. The G11 strains were closely related to other human and porcine G11 strains, while the G2 strains resembled porcine G2 viruses detected recently in Europe and southern Asia. The G4 strains were distantly related to other G4 human and animal strains, constituting a separate G4 VP7 lineage. Analysis of the G5 strains revealed that they were similar to a selection of G5 human and porcine strains, while the G9 strains resembled other porcine G9 viruses. By sequence analysis of the VP8* fragment of the VP4, the Irish viruses were characterised as P[6], P[7], P[13], P[13]/[22], P[26] and P[32].
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Affiliation(s)
- P J Collins
- Department of Biological Sciences, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
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Carbain B, Collins PJ, Callum L, Martin SR, Hay AJ, McCauley J, Streicher H. Efficient synthesis of highly active phospha-isosteres of the influenza neuraminidase inhibitor oseltamivir. ChemMedChem 2009; 4:335-7. [PMID: 19156651 DOI: 10.1002/cmdc.200800379] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
With a Hunsdiecker-Barton iododecarboxylation strategy, we converted the carboxylate group of the oseltamivir precursor into exemplary phosphonate monoesters. In all cases, K(i) values towards influenza virus sialidase remained in the sub-nanomolar range. We have thus made valuable structural space available for the design of novel oseltamivir-based tools for influenza virus research.
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Affiliation(s)
- Benoit Carbain
- Department of Chemistry and Biochemistry, University of Sussex, Brighton, BN1 9QG, UK
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Carbain B, Martin SR, Collins PJ, Hitchcock PB, Streicher H. Galactose-conjugates of the oseltamivir pharmacophore—new tools for the characterization of influenza virus neuraminidases. Org Biomol Chem 2009; 7:2570-5. [DOI: 10.1039/b903394g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 2008; 40:1253-60. [PMID: 18776909 DOI: 10.1038/ng.237] [Citation(s) in RCA: 608] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 08/18/2008] [Indexed: 11/09/2022]
Abstract
Accurate and complete measurement of single nucleotide (SNP) and copy number (CNV) variants, both common and rare, will be required to understand the role of genetic variation in disease. We present Birdsuite, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus (for example, including genotypes such as A-null, AAB and BBB in addition to AA, AB and BB calls). Such genotypes more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies. The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype.
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Affiliation(s)
- Joshua M Korn
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA.
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McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PIW, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 2008; 40:1166-74. [PMID: 18776908 DOI: 10.1038/ng.238] [Citation(s) in RCA: 702] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 08/18/2008] [Indexed: 11/10/2022]
Abstract
Dissecting the genetic basis of disease risk requires measuring all forms of genetic variation, including SNPs and copy number variants (CNVs), and is enabled by accurate maps of their locations, frequencies and population-genetic properties. We designed a hybrid genotyping array (Affymetrix SNP 6.0) to simultaneously measure 906,600 SNPs and copy number at 1.8 million genomic locations. By characterizing 270 HapMap samples, we developed a map of human CNV (at 2-kb breakpoint resolution) informed by integer genotypes for 1,320 copy number polymorphisms (CNPs) that segregate at an allele frequency >1%. More than 80% of the sequence in previously reported CNV regions fell outside our estimated CNV boundaries, indicating that large (>100 kb) CNVs affect much less of the genome than initially reported. Approximately 80% of observed copy number differences between pairs of individuals were due to common CNPs with an allele frequency >5%, and more than 99% derived from inheritance rather than new mutation. Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes.
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Affiliation(s)
- Steven A McCarroll
- Program in Medical and Population Genetics and Genetic Analysis Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Nayak MK, Collins PJ. Influence of concentration, temperature and humidity on the toxicity of phosphine to the strongly phosphine-resistant psocid Liposcelis bostrychophila Badonnel (Psocoptera: Liposcelididae). Pest Manag Sci 2008; 64:971-976. [PMID: 18416433 DOI: 10.1002/ps.1586] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND The psocid Liposcelis bostrychophila Badonnel, is a widespread, significant pest of stored commodities, has developed strong resistance to phosphine, the major grain disinfestant. The aim was to develop effective fumigation protocols to control this resistant pest. RESULTS Time to population extinction of all life stages (TPE) in days was evaluated at a series of phosphine concentrations and temperatures at two relative humidities. Regression analysis showed that temperature, concentration and relative humidity all contributed significantly to describing TPE (P<0.001, R(2)=0.95), with temperature being the dominant variable, accounting for 74.4% of the variation. Irrespective of phosphine concentration, TPE was longer at lower temperatures and high humidity (70% RH) and shorter at higher temperatures and low humidity (55% RH). At any concentration of phosphine, a combination of higher temperature and lower humidity provides the shortest fumigation period to control resistant L. bostrychophila. For example, 19 and 11 days of fumigation are required at 15 degrees C and 70% RH at 0.1 and 1.0 mg L(-1) of phosphine respectively, whereas only 4 and 2 days are required at 35 degrees C and 55% RH for the same respective concentrations. CONCLUSIONS The developed fumigation protocols will provide industry with flexibility in application of phosphine.
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Affiliation(s)
- Manoj K Nayak
- Department of Primary Industries and Fisheries, 80 Meiers Road, Indooroopilly, Queensland 4068, Australia.
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Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics 2008; 9 Suppl 9:S10. [PMID: 18793455 PMCID: PMC2537561 DOI: 10.1186/1471-2105-9-s9-s10] [Citation(s) in RCA: 182] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists. RESULTS Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan - the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations. CONCLUSION We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.
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Affiliation(s)
- Leming Shi
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Wendell D Jones
- Expression Analysis Inc., 2605 Meridian Parkway, Durham, NC 27713, USA
| | - Roderick V Jensen
- University of Massachusetts Boston, Department of Physics, 100 Morrissey Boulevard, Boston, MA 02125, USA
| | - Stephen C Harris
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Roger G Perkins
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Federico M Goodsaid
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Lei Guo
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Lisa J Croner
- Biogen Idec Inc., 5200 Research Place, San Diego, CA 92122, USA
| | - Cecilie Boysen
- ViaLogy Inc., 2400 Lincoln Avenue, Altadena, CA 91001, USA
| | - Hong Fang
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Feng Qian
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Shashi Amur
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Wenjun Bao
- SAS Institute Inc., SAS Campus Drive, Cary, NC 27513, USA
| | | | - Vincent Bertholet
- Eppendorf Array Technologies, rue du Séminaire 20a, 5000 Namur, Belgium
| | - Xiaoxi Megan Cao
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Tzu-Ming Chu
- SAS Institute Inc., SAS Campus Drive, Cary, NC 27513, USA
| | - Patrick J Collins
- Agilent Technologies Inc., 5301 Stevens Creek Boulevard, Santa Clara, CA 95051, USA
| | - Xiao-hui Fan
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
- Pharmaceutical Informatics Institute, Zhejiang University, Hangzhou 310027, China
| | - Felix W Frueh
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - James C Fuscoe
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Xu Guo
- Affymetrix Inc., 3420 Central Expressway, Santa Clara, CA 95051, USA
| | - Jing Han
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
| | - Damir Herman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Huixiao Hong
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Ernest S Kawasaki
- National Cancer Institute Advanced Technology Center, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA
| | - Quan-Zhen Li
- University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yuling Luo
- Panomics Inc., 6519 Dumbarton Circle, Fremont, CA 94555, USA
| | - Yunqing Ma
- Panomics Inc., 6519 Dumbarton Circle, Fremont, CA 94555, USA
| | - Nan Mei
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Ron L Peterson
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Raj K Puri
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard Shippy
- GE Healthcare, 7700 S River Parkway, Tempe, AZ 85284, USA
| | - Zhenqiang Su
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | | | - Hongmei Sun
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Brett Thorn
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Yaron Turpaz
- Pharmaceutical Informatics Institute, Zhejiang University, Hangzhou 310027, China
| | - Charles Wang
- UCLA David Geffen School of Medicine, Transcriptional Genomics Core, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Sue Jane Wang
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | | | - James C Willey
- Ohio Medical University, 3000 Arlington Avenue, Toledo, OH 43614, USA
| | - Jie Wu
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Qian Xie
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Liang Zhang
- CapitalBio Corporation, 18 Life Science Parkway, Changping District, Beijing 102206, China
| | - Lu Zhang
- Solexa Inc., 25861 Industrial Boulevard, Hayward, CA 94545, USA
| | - Sheng Zhong
- University of Illinois at Urbana-Champaign, Department of Bioengineering, 1304 W. Springfield Avenue, Urbana, IL 61801, USA
| | | | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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Collins PJ, Kobayashi Y, Nguyen L, Trinklein ND, Myers RM. The ets-related transcription factor GABP directs bidirectional transcription. PLoS Genet 2008; 3:e208. [PMID: 18020712 PMCID: PMC2077898 DOI: 10.1371/journal.pgen.0030208] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [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: 07/10/2007] [Accepted: 10/05/2007] [Indexed: 11/18/2022] Open
Abstract
Approximately 10% of genes in the human genome are distributed such that their transcription start sites are located less than 1 kb apart on opposite strands. These divergent gene pairs have a single intergenic segment of DNA, which in some cases appears to share regulatory elements, but it is unclear whether these regions represent functional bidirectional promoters or two overlapping promoters. A recent study showed that divergent promoters are enriched for consensus binding sequences of a small group of transcription factors, including the ubiquitous ets-family transcription factor GA-binding protein (GABP). Here we show that GABP binds to more than 80% of divergent promoters in at least one cell type. Furthermore, we demonstrate that GABP binding is correlated and associated with bidirectional transcriptional activity in a luciferase transfection assay. In addition, we find that the addition of a strict consensus GABP site into a set of promoters that normally function in only one direction significantly increases activity in the opposite direction in 67% of cases. Our findings demonstrate that GABP regulates the majority of divergent promoters and suggest that bidirectional transcriptional activity is mediated through GABP binding and transactivation at both divergent and nondivergent promoters. Surveys of the locations of genes in the human genome have revealed that a surprising number of genes, greater than 10%, have transcription start sites within 1 kb of one another on opposite strands. These divergent gene pairs, sometimes referred to as bidirectional genes, are common in organisms such as bacteria and yeast, but it is unknown why such an arrangement exists in large, mammalian genomes. Recently, it has become apparent that the promoters of these divergent genes are regulated by a subset of transcription factors, and we have focused on one of these, GA-binding protein (GABP). We find that it regulates a large number of human genes, including the majority of divergent genes, and that its binding is associated with, correlated with, and sufficient for bidirectional transcriptional activity. Although clearly GABP is a major regulator of divergent genes, which carry out a variety of roles critical for the function and survival of the cell, these data also propose novel roles for GABP as a transcription factor. For example, the ability of GABP to promote bidirectional transcription may prove to be biologically relevant in generating many of the transcripts that have been observed outside of protein coding genes.
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Affiliation(s)
- Patrick J Collins
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yuya Kobayashi
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Loan Nguyen
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nathan D Trinklein
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Richard M Myers
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Schlipalius DI, Chen W, Collins PJ, Nguyen T, Reilly PEB, Ebert PR. Gene interactions constrain the course of evolution of phosphine resistance in the lesser grain borer, Rhyzopertha dominica. Heredity (Edinb) 2008; 100:506-16. [DOI: 10.1038/hdy.2008.4] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res 2007; 17:720-31. [PMID: 17567992 PMCID: PMC1891333 DOI: 10.1101/gr.5716607] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [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] [Indexed: 11/24/2022]
Abstract
The regulation of transcriptional initiation in the human genome is a critical component of global gene regulation, but a complete catalog of human promoters currently does not exist. In order to identify regulatory regions, we developed four computational methods to integrate 129 sets of ENCODE-wide chromatin immunoprecipitation data. They collectively predicted 1393 regions. Roughly 47% of the regions were unique to one method, as each method makes different assumptions about the data. Overall, predicted regions tend to localize to highly conserved, DNase I hypersensitive, and actively transcribed regions in the genome. Interestingly, a significant portion of the regions overlaps with annotated 3'-UTRs, suggesting that some of them might regulate anti-sense transcription. The majority of the predicted regions are >2 kb away from the 5'-ends of previously annotated human cDNAs and hence are novel. These novel regions may regulate unannotated transcripts or may represent new alternative transcription start sites of known genes. We tested 163 such regions for promoter activity in four cell lines using transient transfection assays, and 25% of them showed transcriptional activity above background in at least one cell line. We also performed 5'-RACE experiments on 62 novel regions, and 76% of the regions were associated with the 5'-ends of at least two RACE products. Our results suggest that there are at least 35% more functional promoters in the human genome than currently annotated.
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Affiliation(s)
- Nathan D. Trinklein
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ulaş Karaöz
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | - Jiaqian Wu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Anason Halees
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | - Shelley Force Aldred
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Patrick J. Collins
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Deyou Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zhengdong D. Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Michael Snyder
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Richard M. Myers
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Corresponding authors.E-mail ; fax (617) 353-6766.E-mail ; fax (650) 725-9689
| | - Zhiping Weng
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
- Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, USA
- Corresponding authors.E-mail ; fax (617) 353-6766.E-mail ; fax (650) 725-9689
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Abstract
Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcription factors, and modified histones as overrepresented, shared, or underrepresented in bidirectional promoters with respect to unidirectional promoters. We found that a small set of motifs, including GABPA, MYC, E2F1, E2F4, NRF-1, CCAAT, YY1, and ACTACAnnTCC are overrepresented in bidirectional promoters, while the majority (73%) of known vertebrate motifs are underrepresented. We performed chromatin-immunoprecipitation (ChIP), followed by quantitative PCR for GABPA, on 118 regions in the human genome and showed that it binds to bidirectional promoters more frequently than unidirectional promoters, and its position-specific scoring matrix is highly predictive of binding. Signatures of active transcription, such as occupancy of RNA polymerase II and the modified histones H3K4me2, H3K4me3, and H3ac, are overrepresented in regions around bidirectional promoters, suggesting that a higher fraction of divergent genes are transcribed in a given cell than the fraction of other genes. Accordingly, analysis of whole-genome microarray data indicates that 68% of divergent genes are transcribed compared with 44% of all human genes. By combining the analysis of publicly available ENCODE data and a detailed study of GABPA, we survey bidirectional promoters with breadth and depth, leading to biological insights concerning their motif composition and bidirectional regulatory mode.
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Affiliation(s)
- Jane M. Lin
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA
| | - Patrick J. Collins
- Department of Genetics, Stanford University, School of Medicine, Stanford, California 94305-5120, USA
| | - Nathan D. Trinklein
- Department of Genetics, Stanford University, School of Medicine, Stanford, California 94305-5120, USA
| | - Yutao Fu
- Program in Bioinformatics and Systems Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Hualin Xi
- Program in Bioinformatics and Systems Biology, Boston University, Boston, Massachusetts, 02215, USA
| | - Richard M. Myers
- Department of Genetics, Stanford University, School of Medicine, Stanford, California 94305-5120, USA
| | - Zhiping Weng
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, USA
- Program in Bioinformatics and Systems Biology, Boston University, Boston, Massachusetts, 02215, USA
- Corresponding author.E-mail ; fax (617) 353-6766
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Lorini I, Collins PJ, Daglish GJ, Nayak MK, Pavic H. Detection and characterisation of strong resistance to phosphine in Brazilian Rhyzopertha dominica (F.) (Coleoptera: Bostrychidae). Pest Manag Sci 2007; 63:358-64. [PMID: 17315137 DOI: 10.1002/ps.1344] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
As failure to control Rhyzopertha dominica (F.) with phosphine is a common problem in the grain-growing regions of Brazil, a study was undertaken to investigate the frequency, distribution and strength of phosphine resistance in R. dominica in Brazil. Nineteen samples of R. dominica were collected between 1991 and 2003 from central storages where phosphine fumigation had failed to control this species. Insects were cultured without selection until testing in 2005. Each sample was tested for resistance to phosphine on the basis of the response of adults to discriminating concentrations of phosphine (20 and 48 h exposures) and full dose-response assays (48 h exposure). Responses of the Brazilian R. dominica samples were compared with reference susceptible, weak-resistance and strong-resistance strains from Australia in parallel assays. All Brazilian population samples showed resistance to phosphine: five were diagnosed with weak resistance and 14 with strong resistance. Five samples showed levels of resistance similar to the reference strong-resistance strain. A representative highly resistant sample was characterised by exposing mixed-age cultures to a range of constant concentrations of phosphine for various exposure periods. Time to population extinction (TPE) and time to 99.9% suppression of population (LT(99.9)) values of this sample were generally similar to those of the reference strong-resistance strain. For example, at 0.1, 0.5 and 1.0 mg L(-1), LT(99.9) values for BR33 and the reference strong-resistance strain were respectively 21, 6.4 and 3.7 days and 17, 6.2 and 3.8 days. With both strains, doubling phosphine concentrations to 2 mg L(-1) resulted in increased LT(99.9) and TPE. High level and frequency of resistance in all population samples, some of which had been cultured without selection for up to 12 years, suggest little or no fitness deficit associated with phosphine resistance. The present research indicates that widespread phosphine resistance may be developing in Brazil. Fumigation practices should be monitored and resistance management plans implemented to alleviate further resistance development.
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Affiliation(s)
- Irineu Lorini
- Brazilian Agricultural Research Corporation (Embrapa), National Wheat Research Centre (Embrapa Wheat), Rodovia BR 285, km 294, Caixa Postal 451, CEP 99001-970 Passo Fundo, RS, Brazil
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Cha'on U, Valmas N, Collins PJ, Reilly PEB, Hammock BD, Ebert PR. Disruption of Iron Homeostasis Increases Phosphine Toxicity in Caenorhabditis elegans. Toxicol Sci 2006; 96:194-201. [PMID: 17175555 DOI: 10.1093/toxsci/kfl187] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [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: 11/12/2022] Open
Abstract
The aim of this study is to identify the biochemical mechanism of phosphine toxicity and resistance, using Caenorhabditis elegans as a model organism. To date, the precise mode of phosphine action is unclear. In this report, we demonstrate the following dose-dependent actions of phosphine, in vitro: (1) reduction of ferric iron (Fe3+) to ferrous iron (Fe2+), (2) release of iron from horse ferritin, (3) and the peroxidation of lipid as a result of iron release from ferritin. Using in situ hybridization, we show that the ferritin genes of C. elegans, both ferritin-1 and ferritin-2, are expressed along the digestive tract with greatest expression at the proximal and distal ends. Basal expression of the ferritin-2 gene, as determined by quantitative PCR, is approximately 80 times that of ferritin-1. However, transcript levels of ferritin-1 are induced at least 20-fold in response to phosphine, whereas there is no change in the level of ferritin-2. This resembles the reported pattern of ferritin gene regulation by iron, suggesting that phosphine toxicity may be related to an increase in the level of free iron. Indeed, iron overload increases phosphine toxicity in C. elegans at least threefold. Moreover, we demonstrate that suppression of ferritin-2 gene expression by RNAi, significantly increases sensitivity to phosphine. This study identifies similarities between phosphine toxicity and iron overload and demonstrates that phosphine can trigger iron release from storage proteins, increasing lipid peroxidation, leading to cell injury and/or cell death.
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Affiliation(s)
- Ubon Cha'on
- School of Molecular and Microbial Sciences, The University of Queensland, St Lucia, QLD 4072 Australia
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Tong W, Lucas AB, Shippy R, Fan X, Fang H, Hong H, Orr MS, Chu TM, Guo X, Collins PJ, Sun YA, Wang SJ, Bao W, Wolfinger RD, Shchegrova S, Guo L, Warrington JA, Shi L. Evaluation of external RNA controls for the assessment of microarray performance. Nat Biotechnol 2006; 24:1132-9. [PMID: 16964227 DOI: 10.1038/nbt1237] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [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: 11/09/2022]
Abstract
External RNA controls (ERCs), although important for microarray assay performance assessment, have yet to be fully implemented in the research community. As part of the MicroArray Quality Control (MAQC) study, two types of ERCs were implemented and evaluated; one was added to the total RNA in the samples before amplification and labeling; the other was added to the copyRNAs (cRNAs) before hybridization. ERC concentration-response curves were used across multiple commercial microarray platforms to identify problematic assays and potential sources of variation in the analytical process. In addition, the behavior of different ERC types was investigated, resulting in several important observations, such as the sample-dependent attributes of performance and the potential of using these control RNAs in a combinatorial fashion. This multiplatform investigation of the behavior and utility of ERCs provides a basis for articulating specific recommendations for their future use in evaluating assay performance across multiple platforms.
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Affiliation(s)
- Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA.
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48
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Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ, Zhang L, Hurban P, de Longueville F, Fuscoe JC, Tong W, Shi L, Wolfinger RD. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 2006; 24:1140-50. [PMID: 16964228 DOI: 10.1038/nbt1242] [Citation(s) in RCA: 352] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microarray-based expression profiling experiments typically use either a one-color or a two-color design to measure mRNA abundance. The validity of each approach has been amply demonstrated. Here we provide a simultaneous comparison of results from one- and two-color labeling designs, using two independent RNA samples from the Microarray Quality Control (MAQC) project, tested on each of three different microarray platforms. The data were evaluated in terms of reproducibility, specificity, sensitivity and accuracy to determine if the two approaches provide comparable results. For each of the three microarray platforms tested, the results show good agreement with high correlation coefficients and high concordance of differentially expressed gene lists within each platform. Cumulatively, these comparisons indicate that data quality is essentially equivalent between the one- and two-color approaches and strongly suggest that this variable need not be a primary factor in decisions regarding experimental microarray design.
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Affiliation(s)
- Tucker A Patterson
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA.
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49
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Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006; 24:1151-61. [PMID: 16964229 PMCID: PMC3272078 DOI: 10.1038/nbt1239] [Citation(s) in RCA: 1497] [Impact Index Per Article: 83.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Accepted: 07/31/2006] [Indexed: 11/08/2022]
Abstract
Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.
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Russell RJ, Haire LF, Stevens DJ, Collins PJ, Lin YP, Blackburn GM, Hay AJ, Gamblin SJ, Skehel JJ. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 2006; 443:45-9. [PMID: 16915235 DOI: 10.1038/nature05114] [Citation(s) in RCA: 612] [Impact Index Per Article: 34.0] [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: 06/06/2006] [Accepted: 07/25/2006] [Indexed: 02/07/2023]
Abstract
The worldwide spread of H5N1 avian influenza has raised concerns that this virus might acquire the ability to pass readily among humans and cause a pandemic. Two anti-influenza drugs currently being used to treat infected patients are oseltamivir (Tamiflu) and zanamivir (Relenza), both of which target the neuraminidase enzyme of the virus. Reports of the emergence of drug resistance make the development of new anti-influenza molecules a priority. Neuraminidases from influenza type A viruses form two genetically distinct groups: group-1 contains the N1 neuraminidase of the H5N1 avian virus and group-2 contains the N2 and N9 enzymes used for the structure-based design of current drugs. Here we show by X-ray crystallography that these two groups are structurally distinct. Group-1 neuraminidases contain a cavity adjacent to their active sites that closes on ligand binding. Our analysis suggests that it may be possible to exploit the size and location of the group-1 cavity to develop new anti-influenza drugs.
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Affiliation(s)
- Rupert J Russell
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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