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B.W. Neuman
CASE, Department of Biology, Texas A&M University-Texarkana, 7100 University Avenue, Texarkana, TX, 75503, USA

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Journal article
Published: 10 November 2020 in Viruses
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Bacterial diseases of the edible white button mushroom Agaricus bisporus caused by Pseudomonas species cause a reduction in crop yield, resulting in considerable economic loss. We examined bacterial pathogens of mushrooms and bacteriophages that target them to understand the disease and opportunities for control. The Pseudomonastolaasii genome encoded a single type III protein secretion system (T3SS), but contained the largest number of non-ribosomal peptide synthase (NRPS) genes, multimodular enzymes that can play a role in pathogenicity, including a putative tolaasin-producing gene cluster, a toxin causing blotch disease symptom. However, Pseudomonasagarici encoded the lowest number of NRPS and three putative T3SS while non-pathogenic Pseudomonas sp. NS1 had intermediate numbers. Potential bacteriophage resistance mechanisms were identified in all three strains, but only P. agarici NCPPB 2472 was observed to have a single Type I-F CRISPR/Cas system predicted to be involved in phage resistance. Three novel bacteriophages, NV1, ϕNV3, and NV6, were isolated from environmental samples. Bacteriophage NV1 and ϕNV3 had a narrow host range for specific mushroom pathogens, whereas phage NV6 was able to infect both mushroom pathogens. ϕNV3 and NV6 genomes were almost identical and differentiated within their T7-like tail fiber protein, indicating this is likely the major host specificity determinant. Our findings provide the foundations for future comparative analyses to study mushroom disease and phage resistance.

ACS Style

Nathaniel Storey; Mojgan Rabiey; Benjamin W. Neuman; Robert W. Jackson; Geraldine Mulley. Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages. Viruses 2020, 12, 1286 .

AMA Style

Nathaniel Storey, Mojgan Rabiey, Benjamin W. Neuman, Robert W. Jackson, Geraldine Mulley. Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages. Viruses. 2020; 12 (11):1286.

Chicago/Turabian Style

Nathaniel Storey; Mojgan Rabiey; Benjamin W. Neuman; Robert W. Jackson; Geraldine Mulley. 2020. "Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages." Viruses 12, no. 11: 1286.

Journal article
Published: 22 September 2020 in Viruses
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Coronaviruses (CoVs) are enveloped, positive sense, single strand RNA viruses that cause respiratory, intestinal and neurological diseases in mammals and birds. Following replication, CoVs assemble on intracellular membranes including the endoplasmic reticulum Golgi intermediate compartment (ERGIC) where the envelope protein (E) functions in virus assembly and release. In consequence, E potentially contains membrane-modifying peptides. To search for such peptides, the E coding sequence of Mouse Hepatitis Virus (MHV) was inspected for its amino acid conservation, proximity to the membrane and/or predicted amphipathic helices. Peptides identified in silico were synthesized and tested for membrane-modifying activity in the presence of giant unilamellar vesicles (GUVs) consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), sphingomyelin and cholesterol. To confirm the presence of membrane binding peptides identified in the context of a full-length E protein, the wild type and a number of mutants in the putative membrane binding peptide were expressed in Lenti-X-293T mammalian and insect cells, and the distribution of E antigen within the expressing cell was assessed. Our data identify a role for the post-transmembrane region of MHV E in membrane binding.

ACS Style

Entedar A. J. Alsaadi; Benjamin W. Neuman; Ian M. Jones. Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus. Viruses 2020, 12, 1054 .

AMA Style

Entedar A. J. Alsaadi, Benjamin W. Neuman, Ian M. Jones. Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus. Viruses. 2020; 12 (9):1054.

Chicago/Turabian Style

Entedar A. J. Alsaadi; Benjamin W. Neuman; Ian M. Jones. 2020. "Identification of a Membrane Binding Peptide in the Envelope Protein of MHV Coronavirus." Viruses 12, no. 9: 1054.

Journal article
Published: 21 September 2020 in Applied Physics Letters
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Lateral flow assay (LFA) has long been used as a biomarker detection technique. It has advantages such as low cost, rapid readout, portability, and ease of use. However, its qualitative readout process and lack of sensitivity are limiting factors. We report a photon-counting approach to accurately quantify LFAs while enhancing sensitivity. In particular, we demonstrate that the density of SARS-CoV-2 antibodies can be quantified and measured with an enhanced sensitivity using this simple laser optical analysis.

ACS Style

Tao Peng; Xiangpei Liu; L. Garry Adams; Girish Agarwal; Bruce Akey; Jeffrey Cirillo; Volker Deckert; Sahar Delfan; Edward Fry; Zehua Han; Philip Hemmer; George Kattawar; Moochan Kim; Ming-Che Lee; Chaoyang Lu; Jon Mogford; Reed Nessler; Ben Neuman; Xiaoyu Nie; Jianwei Pan; Jane Pryor; Navid Rajil; Yanhua Shih; Alexei Sokolov; Anatoly Svidzinsky; Dawei Wang; Zhenhuan Yi; Aleksei Zheltikov; Marlan Scully. Enhancing sensitivity of lateral flow assay with application to SARS-CoV-2. Applied Physics Letters 2020, 117, 120601 .

AMA Style

Tao Peng, Xiangpei Liu, L. Garry Adams, Girish Agarwal, Bruce Akey, Jeffrey Cirillo, Volker Deckert, Sahar Delfan, Edward Fry, Zehua Han, Philip Hemmer, George Kattawar, Moochan Kim, Ming-Che Lee, Chaoyang Lu, Jon Mogford, Reed Nessler, Ben Neuman, Xiaoyu Nie, Jianwei Pan, Jane Pryor, Navid Rajil, Yanhua Shih, Alexei Sokolov, Anatoly Svidzinsky, Dawei Wang, Zhenhuan Yi, Aleksei Zheltikov, Marlan Scully. Enhancing sensitivity of lateral flow assay with application to SARS-CoV-2. Applied Physics Letters. 2020; 117 (12):120601.

Chicago/Turabian Style

Tao Peng; Xiangpei Liu; L. Garry Adams; Girish Agarwal; Bruce Akey; Jeffrey Cirillo; Volker Deckert; Sahar Delfan; Edward Fry; Zehua Han; Philip Hemmer; George Kattawar; Moochan Kim; Ming-Che Lee; Chaoyang Lu; Jon Mogford; Reed Nessler; Ben Neuman; Xiaoyu Nie; Jianwei Pan; Jane Pryor; Navid Rajil; Yanhua Shih; Alexei Sokolov; Anatoly Svidzinsky; Dawei Wang; Zhenhuan Yi; Aleksei Zheltikov; Marlan Scully. 2020. "Enhancing sensitivity of lateral flow assay with application to SARS-CoV-2." Applied Physics Letters 117, no. 12: 120601.

Journal article
Published: 24 February 2020 in Biological Control
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“Moko disease”, caused by the bacterium Ralstonia solanacearum, is one of the most devastating diseases of banana and plantain. Its management is difficult, given the aggressiveness and easy dispersion of R. solanacearum, and the lack of products for its control. Environmental and human health concerns limit the use of antibiotics in the field, and, in addition, the effectiveness of those that are used is quite low. Bacteriophages (phages) have emerged as an alternative for the control of bacterial plant diseases, but their potential for the control of moko is yet to be tested. Thus, in this study, phages isolated from soils cultivated with banana and plantain were selected and evaluated for their capacity to control R. solanacearum both in vitro and on banana plants under greenhouse. For this, eight lytic phages were isolated from plantations of Colombia and tested against 65 native strains of R. solanacearum. The two most effective phages were further evaluated for their capacity to inhibit the growth in vitro and in soil microcosm of a highly pathogenic strain, R. solanacearum UA1591. Here, both phages reduced the growth of the pathogen in liquid media and soil microcosm to levels that were below the threshold of detection in 24 h. Lastly, in a greenhouse experiment, plants treated with the two-phage cocktail were 100% protected from moko, even though in most plants of the individual treatments there were symptoms of moko disease. These results support that two-phage cocktail are promising biological control agents against moko disease.

ACS Style

María Ramírez; Benjamin W. Neuman; Camilo A. Ramírez. Bacteriophages as promising agents for the biological control of Moko disease (Ralstonia solanacearum) of banana. Biological Control 2020, 149, 104238 .

AMA Style

María Ramírez, Benjamin W. Neuman, Camilo A. Ramírez. Bacteriophages as promising agents for the biological control of Moko disease (Ralstonia solanacearum) of banana. Biological Control. 2020; 149 ():104238.

Chicago/Turabian Style

María Ramírez; Benjamin W. Neuman; Camilo A. Ramírez. 2020. "Bacteriophages as promising agents for the biological control of Moko disease (Ralstonia solanacearum) of banana." Biological Control 149, no. : 104238.

Brief report
Published: 05 September 2019 in Viruses
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Coronaviruses represent current and emerging threats for many species, including humans. Middle East respiratory syndrome-related coronavirus (MERS-CoV) is responsible for sporadic infections in mostly Middle Eastern countries, with occasional transfer elsewhere. A key step in the MERS-CoV replication cycle is the fusion of the virus and host cell membranes mediated by the virus spike protein, S. The location of the fusion peptide within the MERS S protein has not been precisely mapped. We used isolated peptides and giant unilamellar vesicles (GUV) to demonstrate membrane binding for a peptide located near the N-terminus of the S2 domain. Key residues required for activity were mapped by amino acid replacement and their relevance in vitro tested by their introduction into recombinant MERS S protein expressed in mammalian cells. Mutations preventing membrane binding in vitro also abolished S-mediated syncytium formation consistent with the identified peptide acting as the fusion peptide for the S protein of MERS-CoV.

ACS Style

Entedar A. J. Alsaadi; Benjamin W. Neuman; Ian M. Jones. A Fusion Peptide in the Spike Protein of MERS Coronavirus. Viruses 2019, 11, 825 .

AMA Style

Entedar A. J. Alsaadi, Benjamin W. Neuman, Ian M. Jones. A Fusion Peptide in the Spike Protein of MERS Coronavirus. Viruses. 2019; 11 (9):825.

Chicago/Turabian Style

Entedar A. J. Alsaadi; Benjamin W. Neuman; Ian M. Jones. 2019. "A Fusion Peptide in the Spike Protein of MERS Coronavirus." Viruses 11, no. 9: 825.

Journal article
Published: 07 September 2018 in Virology
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Transcriptomics has the potential to discover new RNA virus genomes by sequencing total intracellular RNA pools. In this study, we have searched publicly available transcriptomes for sequences similar to viruses of the Nidovirales order. We report two potential nidovirus genomes, a highly divergent 35.9 kb likely complete genome from the California sea hare Aplysia californica, which we assign to a nidovirus named Aplysia abyssovirus 1 (AAbV), and a coronavirus-like 22.3 kb partial genome from the ornamented pygmy frog Microhyla fissipes, which we assign to a nidovirus named Microhyla alphaletovirus 1 (MLeV). AAbV was shown to encode a functional main proteinase, and a translational readthrough signal. Phylogenetic analysis suggested that AAbV represents a new family, proposed here as Abyssoviridae. MLeV represents a sister group to the other known coronaviruses. The importance of MLeV and AAbV for understanding nidovirus evolution, and the origin of terrestrial nidoviruses are discussed.

ACS Style

Khulud Bukhari; Geraldine Mulley; Anastasia A. Gulyaeva; Lanying Zhao; Guocheng Shu; Jianping Jiang; Benjamin W. Neuman. Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus. Virology 2018, 524, 160 -171.

AMA Style

Khulud Bukhari, Geraldine Mulley, Anastasia A. Gulyaeva, Lanying Zhao, Guocheng Shu, Jianping Jiang, Benjamin W. Neuman. Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus. Virology. 2018; 524 ():160-171.

Chicago/Turabian Style

Khulud Bukhari; Geraldine Mulley; Anastasia A. Gulyaeva; Lanying Zhao; Guocheng Shu; Jianping Jiang; Benjamin W. Neuman. 2018. "Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus." Virology 524, no. : 160-171.

Journal article
Published: 06 September 2018 in Viruses
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Positive-strand RNA viruses, such as coronaviruses, induce cellular membrane rearrangements during replication to form replication organelles allowing for efficient viral RNA synthesis. Infectious bronchitis virus (IBV), a pathogenic avian Gammacoronavirus of significant importance to the global poultry industry, has been shown to induce the formation of double membrane vesicles (DMVs), zippered endoplasmic reticulum (zER) and tethered vesicles, known as spherules. These membrane rearrangements are virally induced; however, it remains unclear which viral proteins are responsible. In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. Three non-structural transmembrane proteins, nsp3, nsp4, and nsp6, were expressed in cells singularly or in combination and the effects on cellular membranes investigated using electron microscopy and electron tomography. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. This study highlights further differences in the mechanism of membrane rearrangements between members of the coronavirus family.

ACS Style

Nicole Doyle; Benjamin W. Neuman; Jennifer Simpson; Philippa C. Hawes; Judith Mantell; Paul Verkade; Hasan Alrashedi; Helena J. Maier. Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing. Viruses 2018, 10, 477 .

AMA Style

Nicole Doyle, Benjamin W. Neuman, Jennifer Simpson, Philippa C. Hawes, Judith Mantell, Paul Verkade, Hasan Alrashedi, Helena J. Maier. Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing. Viruses. 2018; 10 (9):477.

Chicago/Turabian Style

Nicole Doyle; Benjamin W. Neuman; Jennifer Simpson; Philippa C. Hawes; Judith Mantell; Paul Verkade; Hasan Alrashedi; Helena J. Maier. 2018. "Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing." Viruses 10, no. 9: 477.

Other
Published: 18 August 2017
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Many pathogenic viruses can transmit between humans and animals as zoonotic infectious often to cause dangerous disease with obvious clinical signs, sometimes globally. However, these outbreaks are generally only dealt with seriously when the viruses concerned have been confirmed and classified as zoonotic. Arenavirus haemorrhagic fever viruses can cause epidemics in some areas of the world. To assess the potential of similar viruses to become zoonotic in the future, bioinformatics of relatively conserved virus proteins, such as the L polymerase of arenaviruses, can be used to identify homology with viruses that might give future outbreaks. In this paper, new and archival metazoan transcriptome sequence data was used as a resource to identify similar sequences to known arenavirus sequences for the purpose of risk prediction. In essence, bioinformatics was utilized to provide a better understanding of the potential evolution and natural history of uncharacterized virus sequences in the GenBank database. Several matches were identified which, along with a reasoned approach to their phyla, was used to provide a likelihood score of their zoonotic potential.

ACS Style

Hasan Salam Alrashedi; Ian Jones; Geraldine Mulley; Benjamin W Neuman. Bioinformatics analysis for L polymerase homology of arenaviruses. 2017, 178012 .

AMA Style

Hasan Salam Alrashedi, Ian Jones, Geraldine Mulley, Benjamin W Neuman. Bioinformatics analysis for L polymerase homology of arenaviruses. . 2017; ():178012.

Chicago/Turabian Style

Hasan Salam Alrashedi; Ian Jones; Geraldine Mulley; Benjamin W Neuman. 2017. "Bioinformatics analysis for L polymerase homology of arenaviruses." , no. : 178012.

Review article
Published: 13 October 2016 in Antiviral Research
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Replication of eukaryotic positive-stranded RNA viruses is usually linked to the presence of membrane-associated replicative organelles. The purpose of this review is to discuss the function of proteins responsible for formation of the coronavirus replicative organelle. This will be done by identifying domains that are conserved across the order Nidovirales, and by summarizing what is known about function and structure at the level of protein domains.

ACS Style

Benjamin W. Neuman. Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles. Antiviral Research 2016, 135, 97 -107.

AMA Style

Benjamin W. Neuman. Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles. Antiviral Research. 2016; 135 ():97-107.

Chicago/Turabian Style

Benjamin W. Neuman. 2016. "Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles." Antiviral Research 135, no. : 97-107.

Book chapter
Published: 15 September 2016 in Advances in Applied Microbiology
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Coronavirus particles serve three fundamentally important functions in infection. The virion provides the means to deliver the viral genome across the plasma membrane of a host cell. The virion is also a means of escape for newly synthesized genomes. Lastly, the virion is a durable vessel that protects the genome on its journey between cells. This review summarizes the available X-ray crystallography, NMR, and cryoelectron microscopy structural data for coronavirus structural proteins, and looks at the role of each of the major structural proteins in virus entry and assembly. The potential wider conservation of the nucleoprotein fold identified in the Arteriviridae and Coronaviridae families and a speculative model for the evolution of corona-like virus architecture are discussed.

ACS Style

B.W. Neuman; M.J. Buchmeier. Supramolecular Architecture of the Coronavirus Particle. Advances in Applied Microbiology 2016, 96, 1 -27.

AMA Style

B.W. Neuman, M.J. Buchmeier. Supramolecular Architecture of the Coronavirus Particle. Advances in Applied Microbiology. 2016; 96 ():1-27.

Chicago/Turabian Style

B.W. Neuman; M.J. Buchmeier. 2016. "Supramolecular Architecture of the Coronavirus Particle." Advances in Applied Microbiology 96, no. : 1-27.

Journal article
Published: 01 August 2016 in Journal of Virology
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The order Nidovirales currently comprises four virus families: Arteriviridae , Coronaviridae (divided into the subfamilies Coronavirinae and Torovirinae ), Roniviridae , and the recently recognized Mesoniviridae . RNA cap formation and methylation have been best studied for coronaviruses, with emphasis on the identification and characterization of two virus-encoded methyltransferases (MTases) involved in RNA capping, a guanine-N7-MTase and a ribose-2′- O -MTase. Although bioinformatics analyses suggest that these MTases may also be encoded by other nidoviruses with large genomes, such as toroviruses and roniviruses, no experimental evidence has been reported thus far. In this study, we show that a ronivirus, gill-associated virus (GAV), encodes the 2′- O -MTase activity, although we could not detect 2′- O -MTase activity for the homologous protein of a torovirus, equine torovirus, which is more closely related to coronaviruses. Like the coronavirus 2′- O -MTase, the roniviral 2′- O -MTase harbors a catalytic K-D-K-E tetrad that is conserved among 2′- O -MTases and can target only the N7-methylated cap structure of adenylate-primed RNA substrates. However, in contrast with the coronavirus protein, roniviral 2′- O -MTase does not require a protein cofactor for stimulation of its activity and differs in its preference for several biochemical parameters, such as reaction temperature and pH. Furthermore, the ronivirus 2′- O -MTase can be targeted by MTase inhibitors. These results extend our current understanding of nidovirus RNA cap formation and methylation beyond the coronavirus family. IMPORTANCE Methylation of the 5′-cap structure of viral RNAs plays important roles in genome replication and evasion of innate recognition of viral RNAs by cellular sensors. It is known that coronavirus nsp14 acts as an N7-(guanine)-methyltransferase (MTase) and nsp16 as a 2′- O -MTase, which are involved in the modification of RNA cap structure. However, these enzymatic activities have not been shown for any other nidoviruses beyond coronaviruses in the order Nidovirales . In this study, we identified a 2′- O -methyltransferase encoded by ronivirus that shows common and unique features in comparison with that of coronaviruses. Ronivirus 2′- O -MTase does not need a protein cofactor for MTase activity, whereas coronavirus nsp16 needs the stimulating factor nsp10 for its full activity. The conserved K-D-K-E catalytic tetrad is identified in ronivirus 2′- O -MTase. These results extend our understanding of nidovirus RNA capping and methylation beyond coronaviruses and also strengthen the evolutionary and functional links between roniviruses and coronaviruses.

ACS Style

Cong Zeng; Andong Wu; Yi Wang; Shan Xu; Yingke Tang; Xu Jin; Shilei Wang; Lei Qin; Ying Sun; Chengpeng Fan; Eric J. Snijder; Benjamin Neuman; Yu Chen; Tero Ahola; Deyin Guo. Identification and Characterization of a Ribose 2′- O -Methyltransferase Encoded by the Ronivirus Branch of Nidovirales. Journal of Virology 2016, 90, 6675 -6685.

AMA Style

Cong Zeng, Andong Wu, Yi Wang, Shan Xu, Yingke Tang, Xu Jin, Shilei Wang, Lei Qin, Ying Sun, Chengpeng Fan, Eric J. Snijder, Benjamin Neuman, Yu Chen, Tero Ahola, Deyin Guo. Identification and Characterization of a Ribose 2′- O -Methyltransferase Encoded by the Ronivirus Branch of Nidovirales. Journal of Virology. 2016; 90 (15):6675-6685.

Chicago/Turabian Style

Cong Zeng; Andong Wu; Yi Wang; Shan Xu; Yingke Tang; Xu Jin; Shilei Wang; Lei Qin; Ying Sun; Chengpeng Fan; Eric J. Snijder; Benjamin Neuman; Yu Chen; Tero Ahola; Deyin Guo. 2016. "Identification and Characterization of a Ribose 2′- O -Methyltransferase Encoded by the Ronivirus Branch of Nidovirales." Journal of Virology 90, no. 15: 6675-6685.

Comparative study
Published: 03 June 2016 in Scientific Reports
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Positive-strand RNA (+RNA) viruses rearrange cellular membranes during replication, possibly in order to concentrate and arrange viral replication machinery for efficient viral RNA synthesis. Our previous work showed that in addition to the conserved coronavirus double membrane vesicles (DMVs), Beau-R, an apathogenic strain of avian Gammacoronavirus infectious bronchitis virus (IBV), induces regions of ER that are zippered together and tethered open-necked double membrane spherules that resemble replication organelles induced by other +RNA viruses. Here we compared structures induced by Beau-R with the pathogenic lab strain M41 to determine whether membrane rearrangements are strain dependent. Interestingly, M41 was found to have a low spherule phenotype. We then compared a panel of pathogenic, mild and attenuated IBV strains in ex vivo tracheal organ culture (TOC). Although the low spherule phenotype of M41 was conserved in TOCs, each of the other tested IBV strains produced DMVs, zippered ER and spherules. Furthermore, there was a significant correlation for the presence of DMVs with spherules, suggesting that these structures are spatially and temporally linked. Our data indicate that virus induced membrane rearrangements are fundamentally linked to the viral replicative machinery. However, coronavirus replicative apparatus clearly has the plasticity to function in different structural contexts.

ACS Style

Helena J. Maier; Benjamin Neuman; Erica Bickerton; Sarah M. Keep; Hasan Alrashedi; Ross Hall; Paul Britton. Extensive coronavirus-induced membrane rearrangements are not a determinant of pathogenicity. Scientific Reports 2016, 6, 27126 .

AMA Style

Helena J. Maier, Benjamin Neuman, Erica Bickerton, Sarah M. Keep, Hasan Alrashedi, Ross Hall, Paul Britton. Extensive coronavirus-induced membrane rearrangements are not a determinant of pathogenicity. Scientific Reports. 2016; 6 (1):27126.

Chicago/Turabian Style

Helena J. Maier; Benjamin Neuman; Erica Bickerton; Sarah M. Keep; Hasan Alrashedi; Ross Hall; Paul Britton. 2016. "Extensive coronavirus-induced membrane rearrangements are not a determinant of pathogenicity." Scientific Reports 6, no. 1: 27126.

Journal article
Published: 01 December 2015 in Journal of General Virology
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Infectious bronchitis is a highly contagious respiratory disease of poultry caused by the coronavirus infectious bronchitis virus (IBV). It was thought that coronavirus virions were composed of three major viral structural proteins until investigations of other coronaviruses showed that the virions also include viral non-structural and genus-specific accessory proteins as well as host-cell proteins. To study the proteome of IBV virions, virus was grown in embryonated chicken eggs, purified by sucrose-gradient ultracentrifugation and analysed by mass spectrometry. Analysis of three preparations of purified IBV yielded the three expected structural proteins plus 35 additional virion-associated host proteins. The virion-associated host proteins had a diverse range of functional attributions, being involved in cytoskeleton formation, RNA binding and protein folding pathways. Some of these proteins were unique to this study, while others were found to be orthologous to proteins identified in severe acute respiratory syndrome coronavirus virions and also virions from a number of other RNA and DNA viruses.

ACS Style

Stuart D. Dent; Dong Xia; Jonathan M. Wastling; Benjamin W. Neuman; Paul Britton; Helena J. Maier. The proteome of the infectious bronchitis virus Beau-R virion. Journal of General Virology 2015, 96, 3499 -3506.

AMA Style

Stuart D. Dent, Dong Xia, Jonathan M. Wastling, Benjamin W. Neuman, Paul Britton, Helena J. Maier. The proteome of the infectious bronchitis virus Beau-R virion. Journal of General Virology. 2015; 96 (12):3499-3506.

Chicago/Turabian Style

Stuart D. Dent; Dong Xia; Jonathan M. Wastling; Benjamin W. Neuman; Paul Britton; Helena J. Maier. 2015. "The proteome of the infectious bronchitis virus Beau-R virion." Journal of General Virology 96, no. 12: 3499-3506.

Journal article
Published: 19 February 2015 in ChemInform
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A synthetic route to the title compound class is presented, including a 1,3‐dipolar cycloaddition as the key‐step.

ACS Style

Antonio Dell'isola; Matthew M. W. McLachlan; Benjamin W. Neuman; Hawaa M. N. Al-Mullah; Alexander W. D. Binks; Warren Elvidge; Kenneth Shankland; Alexander J. A. Cobb. ChemInform Abstract: Synthesis and Antiviral Properties of Spirocyclic [1,2,3]-Triazolooxazine Nucleosides. ChemInform 2015, 46, 1 .

AMA Style

Antonio Dell'isola, Matthew M. W. McLachlan, Benjamin W. Neuman, Hawaa M. N. Al-Mullah, Alexander W. D. Binks, Warren Elvidge, Kenneth Shankland, Alexander J. A. Cobb. ChemInform Abstract: Synthesis and Antiviral Properties of Spirocyclic [1,2,3]-Triazolooxazine Nucleosides. ChemInform. 2015; 46 (10):1.

Chicago/Turabian Style

Antonio Dell'isola; Matthew M. W. McLachlan; Benjamin W. Neuman; Hawaa M. N. Al-Mullah; Alexander W. D. Binks; Warren Elvidge; Kenneth Shankland; Alexander J. A. Cobb. 2015. "ChemInform Abstract: Synthesis and Antiviral Properties of Spirocyclic [1,2,3]-Triazolooxazine Nucleosides." ChemInform 46, no. 10: 1.

Book chapter
Published: 12 February 2015 in Methods in Molecular Biology
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Purification of intact enveloped virus particles can be useful as a first step in understanding the structure and function of both viral and host proteins that are incorporated into the virion. Purified preparations of virions can be used to address these questions using techniques such as mass spectrometry proteomics. Recent studies on the proteome of coronavirus virions have shown that in addition to the structural proteins, accessory and non-structural virus proteins and a wide variety of host cell proteins associate with virus particles. To further study the presence of virion proteins, high-quality sample preparation is crucial to ensure reproducible analysis by the wide variety of methods available for proteomic analysis.

ACS Style

Stuart Dent; Benjamin W. Neuman. Purification of Coronavirus Virions for Cryo-EM and Proteomic Analysis. Methods in Molecular Biology 2015, 1282, 99 -108.

AMA Style

Stuart Dent, Benjamin W. Neuman. Purification of Coronavirus Virions for Cryo-EM and Proteomic Analysis. Methods in Molecular Biology. 2015; 1282 ():99-108.

Chicago/Turabian Style

Stuart Dent; Benjamin W. Neuman. 2015. "Purification of Coronavirus Virions for Cryo-EM and Proteomic Analysis." Methods in Molecular Biology 1282, no. : 99-108.

Journal article
Published: 27 December 2014 in Virus Research
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The replication of coronaviruses, as in other positive-strand RNA viruses, is closely tied to the formation of membrane-bound replicative organelles inside infected cells. The proteins responsible for rearranging cellular membranes to form the organelles are conserved not just among the Coronaviridae family members, but across the order Nidovirales. Taken together, these observations suggest that the coronavirus replicative organelle plays an important role in viral replication, perhaps facilitating the production or protection of viral RNA. However, the exact nature of this role, and the specific contexts under which it is important have not been fully elucidated. Here, we collect and interpret the recent experimental evidence about the role and importance of membrane-bound organelles in coronavirus replication.

ACS Style

Philip V’Kovski; Hawaa Al-Mulla; Volker Thiel; Benjamin W. Neuman. New insights on the role of paired membrane structures in coronavirus replication. Virus Research 2014, 202, 33 -40.

AMA Style

Philip V’Kovski, Hawaa Al-Mulla, Volker Thiel, Benjamin W. Neuman. New insights on the role of paired membrane structures in coronavirus replication. Virus Research. 2014; 202 ():33-40.

Chicago/Turabian Style

Philip V’Kovski; Hawaa Al-Mulla; Volker Thiel; Benjamin W. Neuman. 2014. "New insights on the role of paired membrane structures in coronavirus replication." Virus Research 202, no. : 33-40.

Journal article
Published: 31 July 2014 in Chemistry – A European Journal
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An efficient synthesis of spirocyclic triazolooxazine nucleosides is described. This was achieved by the conversion of β-D-psicofuranose to the corresponding azido-derivative, followed by alkylation of the primary alcohol with a range of propargyl bromides, obtained by Sonogashira chemistry. The products of these reactions underwent 1,3-dipolar addition smoothly to generate the protected spirocyclic adducts. These were easily deprotected to give the corresponding ribose nucleosides. The library of compounds obtained was investigated for its antiviral activity using MHV (mouse hepatitis virus) as a model wherein derivative 3 f showed the most promising activity and tolerability.

ACS Style

Antonio Dell'isola; Matthew M. W. McLachlan; Benjamin W. Neuman; Hawaa M. N. Al-Mullah; Alexander W. D. Binks; Warren Elvidge; Kenneth Shankland; Alexander J. A. Cobb. Synthesis and Antiviral Properties of Spirocyclic [1,2,3]-Triazolooxazine Nucleosides. Chemistry – A European Journal 2014, 20, 11685 -11689.

AMA Style

Antonio Dell'isola, Matthew M. W. McLachlan, Benjamin W. Neuman, Hawaa M. N. Al-Mullah, Alexander W. D. Binks, Warren Elvidge, Kenneth Shankland, Alexander J. A. Cobb. Synthesis and Antiviral Properties of Spirocyclic [1,2,3]-Triazolooxazine Nucleosides. Chemistry – A European Journal. 2014; 20 (37):11685-11689.

Chicago/Turabian Style

Antonio Dell'isola; Matthew M. W. McLachlan; Benjamin W. Neuman; Hawaa M. N. Al-Mullah; Alexander W. D. Binks; Warren Elvidge; Kenneth Shankland; Alexander J. A. Cobb. 2014. "Synthesis and Antiviral Properties of Spirocyclic [1,2,3]-Triazolooxazine Nucleosides." Chemistry – A European Journal 20, no. 37: 11685-11689.

Review
Published: 15 July 2014 in Trends in Microbiology
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If we use the analogy of a virus as a living entity, then the replicative organelle is the part of the body where its metabolic and reproductive activities are concentrated. Recent studies have illuminated the intricately complex replicative organelles of coronaviruses, a group that includes the largest known RNA virus genomes. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle.

ACS Style

Benjamin W. Neuman; Megan M. Angelini; Michael J. Buchmeier. Does form meet function in the coronavirus replicative organelle? Trends in Microbiology 2014, 22, 642 -647.

AMA Style

Benjamin W. Neuman, Megan M. Angelini, Michael J. Buchmeier. Does form meet function in the coronavirus replicative organelle? Trends in Microbiology. 2014; 22 (11):642-647.

Chicago/Turabian Style

Benjamin W. Neuman; Megan M. Angelini; Michael J. Buchmeier. 2014. "Does form meet function in the coronavirus replicative organelle?" Trends in Microbiology 22, no. 11: 642-647.

Journal article
Published: 01 May 2014 in mBio
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Positive-stranded viruses synthesize their RNA in membrane-bound organelles, but it is not clear how this benefits the virus or the host. For coronaviruses, these organelles take the form of double-membrane vesicles (DMVs) interconnected by a convoluted membrane network. We used electron microscopy to identify murine coronaviruses with mutations in nsp3 and nsp14 that replicated normally while producing only half the normal amount of DMVs under low-temperature growth conditions. Viruses with mutations in nsp5 and nsp16 produced small DMVs but also replicated normally. Quantitative reverse transcriptase PCR (RT-PCR) confirmed that the most strongly affected of these, the nsp3 mutant, produced more viral RNA than wild-type virus. Competitive growth assays were carried out in both continuous and primary cells to better understand the contribution of DMVs to viral fitness. Surprisingly, several viruses that produced fewer or smaller DMVs showed a higher fitness than wild-type virus at the reduced temperature, suggesting that larger and more numerous DMVs do not necessarily confer a competitive advantage in primary or continuous cell culture. For the first time, this directly demonstrates that replication and organelle formation may be, at least in part, studied separately during infection with positive-stranded RNA virus. IMPORTANCE The viruses that cause severe acute respiratory syndrome (SARS), poliomyelitis, and hepatitis C all replicate in double-membrane vesicles (DMVs). The big question about DMVs is why they exist in the first place. In this study, we looked at thousands of infected cells and identified two coronavirus mutants that made half as many organelles as normal and two others that made typical numbers but smaller organelles. Despite differences in DMV size and number, all four mutants replicated as efficiently as wild-type virus. To better understand the relative importance of replicative organelles, we carried out competitive fitness experiments. None of these viruses was found to be significantly less fit than wild-type, and two were actually fitter in tests in two kinds of cells. This suggests that viruses have evolved to have tremendous plasticity in the ability to form membrane-associated replication complexes and that large and numerous DMVs are not exclusively associated with efficient coronavirus replication.

ACS Style

Hawaa M. N. Al-Mulla; Lauren Turrell; Nicola M. Smith; Luke Payne; Surendranath Baliji; Roland Züst; Volker Thiel; Susan C. Baker; Stuart Siddell; Benjamin W. Neuman. Competitive Fitness in Coronaviruses Is Not Correlated with Size or Number of Double-Membrane Vesicles under Reduced-Temperature Growth Conditions. mBio 2014, 5, e01017-14 -13.

AMA Style

Hawaa M. N. Al-Mulla, Lauren Turrell, Nicola M. Smith, Luke Payne, Surendranath Baliji, Roland Züst, Volker Thiel, Susan C. Baker, Stuart Siddell, Benjamin W. Neuman. Competitive Fitness in Coronaviruses Is Not Correlated with Size or Number of Double-Membrane Vesicles under Reduced-Temperature Growth Conditions. mBio. 2014; 5 (2):e01017-14-13.

Chicago/Turabian Style

Hawaa M. N. Al-Mulla; Lauren Turrell; Nicola M. Smith; Luke Payne; Surendranath Baliji; Roland Züst; Volker Thiel; Susan C. Baker; Stuart Siddell; Benjamin W. Neuman. 2014. "Competitive Fitness in Coronaviruses Is Not Correlated with Size or Number of Double-Membrane Vesicles under Reduced-Temperature Growth Conditions." mBio 5, no. 2: e01017-14-13.

Journal article
Published: 01 March 2014 in DNA and Cell Biology
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All known positive sense single-stranded RNA viruses induce host cell membrane rearrangement for purposes of aiding viral genome replication and transcription. Members of the Nidovirales order are no exception, inducing intricate regions of double membrane vesicles and convoluted membranes crucial for the production of viral progeny. Although these structures have been well studied for some members of this order, much remains unclear regarding the biogenesis of these rearranged membranes. Here, we discuss what is known about these structures and their formation, compare some of the driving viral proteins behind this process across the nidovirus order, and examine possible routes of mechanism by which membrane rearrangement may occur.

ACS Style

Megan Mary Angelini; Benjamin Neuman; Michael J. Buchmeier. Untangling Membrane Rearrangement in theNidovirales. DNA and Cell Biology 2014, 33, 122 -127.

AMA Style

Megan Mary Angelini, Benjamin Neuman, Michael J. Buchmeier. Untangling Membrane Rearrangement in theNidovirales. DNA and Cell Biology. 2014; 33 (3):122-127.

Chicago/Turabian Style

Megan Mary Angelini; Benjamin Neuman; Michael J. Buchmeier. 2014. "Untangling Membrane Rearrangement in theNidovirales." DNA and Cell Biology 33, no. 3: 122-127.