Search

Your search keyword '"Biomolecular Interaction Center"' showing total 14 results
Start Over Author "Biomolecular Interaction Center"
14 results on '"Biomolecular Interaction Center"'

1. Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus

Author

Joaquim Segalés, Karyna Rosario, Mya Breitbart, Eric Delwart, Balázs Harrach, Philippe Biagini, Arvind Varsani, College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Blood Systems Research Institute, University of California [San Francisco] (UCSF), University of California-University of California, Department of Laboratory Medicine [San Francisco], Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, University of California [San Francisco] (UC San Francisco), and University of California (UC)-University of California (UC)

Subjects
0301 basic medicine, food.ingredient, viruses, [SDV]Life Sciences [q-bio], 030106 microbiology, Genome, Viral, Genome, 03 medical and health sciences, food, Gyrovirus, Genus, Virology, Animals, Anelloviridae, Circoviridae Infections, Genetics, biology, Base Sequence, General Medicine, Animal virus, biology.organism_classification, 3. Good health, 030104 developmental biology, Cyclovirus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, DNA, Viral, Circoviridae, Circovirus
Abstract

International audience; The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae. Notably, these methods have uncovered a distinct group of viruses that are closely related to members of the genus Circovirus and comprise a new genus, Cyclovirus. The discovery of new viruses and a re-evaluation of genomic features that characterize members of the Circoviridae prompted a revision of the classification criteria used for this family of animal viruses. Here we provide details on an updated Circoviridae taxonomy ratified by the International Committee on the Taxonomy of Viruses in 2016, which establishes the genus Cyclovirus and reassigns the genus Gyrovirus to the family Anelloviridae, a separate lineage of animal viruses that also contains circular ssDNA genomes. In addition, we provide a new species demarcation threshold of 80% genome-wide pairwise identity for members of the family Circoviridae, based on pairwise identity distribution analysis, and list guidelines to distinguish between members of this family and other eukaryotic viruses with circular, ssDNA genomes.

Published
2016
Full Text
View/download PDF

2. Cassava mosaic disease in Madagascar: complex epidemiology and evolutionary dynamics of cassava mosaic geminiviruses

Author

Mireille Aurélie Harimalala, Alexandre de Bruyn, Frédéric Chiroleu, Murielle Hoareau, Innocent Zinga, Sahondramalala Ranomenjanahary, Virginie Ravigné, Bernard Reynaud, Arvind Varsani, Gordon William Harkins, Darren Patrick Martin, Pierre Lefeuvre, Jean-Michel LETT, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Université de Bangui, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Institut National de la Recherche Agronomique (INRA), Univ, Réunion, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], parasitic diseases, Sciences du vivant, U30 - Méthodes de recherche, Biologie végétale, H20 - Maladies des plantes
Abstract

International audience; BACKGROUND and OBJECTIVES Cassava is the staple food for hundreds of millions of people in Africa but its cultivation is seriously constrained by cassava mosaic disease (CMD) in Madagascar and in Africa in general. We have undertaken (1) to identify the cassava mosaic geminiviruses (CMGs) involved in CMD in Madagascar and their epidemiological characteristics from country-wide surveys, and (2) to study the genetic and spatial structure of Malagasy CMGs populations. MATERIAL and METHODS Altogether 708 cassava leaf samples were collected with and without CMD symptoms from the main cassavagrowing areas of Madagascar during 2009 to 2011. Prevalence and symptom severity of CMD, origin of infection (whitefly or cutting), and abundance of whiteflies were assessed. RESULTS Molecular diagnosis of CMGs in Madagascar revealed an unprecedented diversity and co-occurrence of six CMGs. Distinct geographical distributions were observed for the six viruses. While EACMCV and SACMV were widespread, ACMV was more prevalent in the central highlands, and EACMV and EACMKV were prevalent in lowlands and coastal regions. PCR diagnosis revealed that mixed infection (up to four co-infected viruses) occurred in 21% of the samples and were associated with higher symptom severity scores. Pairwise comparisons of virus associations showed that EACMCV was found in mixed infections more often than expected while ACMV and SACMV were mostly found in single infections. Even if the whitefly vector Bemisia tabaci was more abundant in lowland and coastal areas, infected cuttings remain the primary source of CMD propagation (95%) in Madagascar. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (EACMV, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. CONCLUSIONS Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. (Résumé d'auteur)

Published
2016

3. Alfalfa Leaf Curl Virus: an Aphid-Transmitted Geminivirus

Author

Philippe Roumagnac, Romain Ferdinand, Pauline Bernardo, Michel Peterschmitt, Stéphane Blanc, Isabelle Abt, Charlotte Julian, Maëlle Deshoux, François Mesléard, Denis Filloux, Serge Galzi, Martine Granier, Emmanuel Fernandez, Arvind Varsani, Darren P. Martin, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Centre de recherche de la Tour du Valat, Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, NRA, Departement Sante des Plantes et Environnement : AAP SPE 2015, National Research Foundation of South Africa, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
0106 biological sciences, Immunology, Index Medicus, 01 natural sciences, Microbiology, Genome, DNA sequencing, 03 medical and health sciences, Genus, Virology, Botany, Animals, Alfalfa leaf curl virus, H20 - Maladies des plantes, 030304 developmental biology, Genomic organization, Plant Diseases, 0303 health sciences, Aphid, biology, fungi, food and beverages, biology.organism_classification, 3. Good health, Geminiviridae, Genetic Diversity and Evolution, Insect Science, Vector (epidemiology), Aphids, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Aphis craccivora, 010606 plant biology & botany
Abstract

The family Geminiviridae comprises seven genera differentiated by genome organization, sequence similarity, and insect vector. Capulavirus, an eighth genus, has been proposed to accommodate two newly discovered highly divergent geminiviruses that presently have no known vector. Alfalfa leaf curl virus, identified here as a third capulavirus, is shown to be transmitted by Aphis craccivora. This is the first report of an aphid-transmitted geminivirus.

Published
2015
Full Text
View/download PDF

4. Identification of novel Bromus- and Trifolium-associated circular DNA viruses

Author

Darren P. Martin, Pauline Bernardo, Philippe Roumagnac, François Mesléard, Arvind Varsani, Cameron Booker, Simona Kraberger, Kata Farkas, Gerardo R. Argüello-Astorga, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Centre de recherche de la Tour du Valat, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
Sequence analysis, Bromus, trifolium resupinatum, viruses, Molecular Sequence Data, Sequence Homology, Genome, Plant Viruses, chemistry.chemical_compound, Open Reading Frames, Phylogenetics, Virology, Plant virus, Cluster Analysis, bromus hordeaceus, Geminiviridae, Amino Acid Sequence, gemycircularvirus, Phylogeny, H20 - Maladies des plantes, Genetics, biology, Bromus hordeaceus, DNA Helicases, DNA Viruses, General Medicine, Sequence Analysis, DNA, biology.organism_classification, Trifolium resupinatum, chemistry, DNA, Viral, Capsid Proteins, Trifolium, France, DNA, Circular, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sequence Alignment, DNA, New Zealand, circular DNA virus
Abstract

BGPI : équipe 7; International audience; The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share \textgreater 99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand.

Published
2015
Full Text
View/download PDF

5. Cassava mosaic disease in Madagascar: complex epidemiology and evolutionary dynamics of cassava mosaic geminiviruses

Author

De Bruyn, Alexandre, Harimalala, Mireille Aurélie, Chiroleu, Frédéric, Hoareau, Murielle, Ranomenjanahary, Sahondramalala, Ravigné, Virginie, Reynaud, Bernard, Varsani, Arvind, Martin, Darren Patrick, Lefeuvre, Pierre, Lett, Jean-Michel, Univ, Réunion, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Institut National de la Recherche Agronomique (INRA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], parasitic diseases, Sciences du vivant, Biologie végétale
Abstract

International audience; Cassava is the staple food for hundreds of millions of people in Africa but its cultivation is seriously constrained by cassava mosaic disease (CMD) in Madagascar and in Africa in general. In this study, we first identified the cassava mosaic geminiviruses (CMGs) involved in CMD in Madagascar and their associated epidemiological characteristics from countrywide surveys. Molecular diagnosis of CMGs in Madagascar revealed an unprecedented diversity and co-occurrence of six CMGs. Distinct geographical distributions were observed for the six viruses. While EACMCV and SACMV were widespread, ACMV was more prevalent in the central highlands, and EACMV and EACMKV were prevalent in lowlands and coastal regions. PCR diagnosis revealed that mixed infection (up to four co-infected viruses) occurred in 21% of the samples and were associated with higher symptom severity scores. Pairwise comparisons of virus associations showed that EACMCV was found in mixed infections more often than expected while ACMV and SACMV were mostly found in single infections. Even if the whitefly vector Bemisia tabaci was more abundant in lowland and coastal areas, infected cuttings remain the primary source of CMD propagation (95%) in Madagascar. Secondly, the genetic and spatial structure of CMGs populations was studied and we applied Bayesian phylogeographic modelling to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean islands. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (EACMV, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Our study highlights both the complexity of CMD on Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. (Résumé d'auteur)

Published
2015

6. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains

Author

Murray Sharman, Simona Kraberger, Bruno Gronenborn, Arvind Varsani, John E. Thomas, Brejnev M. Muhire, Abdelmagid A. Hamed, Gordon William Harkins, Safaa G. Kumari, Darren P. Martin, Biomolecular Interaction Center, University of Canterburry, Virology Laboratory, International Centre for Agricultural Research in the Dry Areas [Tunisie] (ICARDA), Plant Pathology Research Program, Agricultural Research Corporation, P.O. Box 126, Wadmedani, Sudan., Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland [Brisbane], South African National Bioinformatics Institute (SANBI), University of the Western Cape, Computational Biology Group, Dept Clinical Laboratory Sciences, University of Cape Town, Electron Microscopy Unit, School of Biological Sciences, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis, Maturation des proteines, destinée cellulaire et thérapeutique ( PROMTI ), Département Biologie des Génomes ( DBG ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), South African National Bioinformatics Institute ( SANBI ), Computational BiologyGroup,DeptClinicalLaboratorySciences, Cape Town University, and University of the Western Cape (UWC)

Subjects
Microbiology (medical), [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, Microbiology, Genome, Sudan, Mastrevirus, Chickpea, Botany, Genetics, Selection, Genetic, Molecular Biology, Phylogeny, Ecology, Evolution, Behavior and Systematics, Plant Diseases, Recombination, Genetic, High rate, Natural selection, [ SDV ] Life Sciences [q-bio], Strain (biology), Genetic Variation, Chickpea chlorotic dwarf virus, Sequence Analysis, DNA, Cicer, Recombination, Indian subcontinent, Geminiviridae, Infectious Diseases, DNA, Viral, Geminivirus
Abstract

International audience; In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.

Published
2015
Full Text
View/download PDF

7. East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus

Author

Bernard Reynaud, Gordon William Harkins, Arvind Varsani, Emilie Villar, Pierre Lefeuvre, Jean-Michel Lett, Julie Villemot, Anli Liachouroutu Abdoul-Karime, Chadhouliati Abdou-Chakour, Murielle Hoareau, Mireille Aurélie Harimalala, Alexandre De Bruyn, Darren P. Martin, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Institut National de la Recherche Agronomique (INRA), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), and Univ, Réunion

Subjects
sub-Saharan Africa, Entomology, Manihot, [SDV]Life Sciences [q-bio], Dissemination, Comoros, Cluster Analysis, Phylogeny, 2. Zero hunger, 0303 health sciences, geography.geographical_feature_category, biology, Geography, Ecology, food and beverages, [SDV] Life Sciences [q-bio], Phylogeography, Begomoviruses, Begomovirus, Archipelago, Sciences du vivant, Mainland, Research Article, Evolution, Molecular Sequence Data, Genome, Viral, Seychelles, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Indian Ocean Islands, Plant virus, QH359-425, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, H20 - Maladies des plantes, Plant Diseases, geography, Cassava, CMG complex, 030306 microbiology, cassava mosaic disease (CMD), Cassava (Manihot esculenta), Genetic Variation, Bayes Theorem, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, Recombination, Africa, DNA, Viral, Biologie végétale
Abstract

Background Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands. Results The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG’s presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components. Conclusions Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthropic factors in CMGs spread as the principal axes of viral migration correspond with major routes of human movement and commercial trade. Finer-scale temporal analyses of CMGs to precisely scale the relative contributions of human and insect transmission to their movement dynamics will require further extensive sampling in the SWIO region.

Published
2012

8. Development of phoH as a novel signature gene for assessing marine phage diversity

Author

Giuseppe Crosti, Arvind Varsani, Dawn B. Goldsmith, Mya Breitbart, Lauren D. McDaniel, Bhakti Dwivedi, Curtis A. Suttle, Ruth-Anne Sandaa, Markus G. Weinbauer, Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, Department of Earth, Ocean and Atmospheric Sciences [Vancouver] (UBC EOAS), University of British Columbia (UBC), Canadian Institute for Advanced Research (CIFAR), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Bergen (UiB), College of Marine Science [St Petersburg, FL], University of South Florida [Tampa] (USF), Observatoire océanologique de Villefranche-sur-mer (OOVM), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Sequence analysis, viruses, Molecular Sequence Data, Applied Microbiology and Biotechnology, Genome, Bacteriophage, 03 medical and health sciences, Viral Proteins, Phylogenetics, Virology, Environmental Microbiology, Cluster Analysis, Bacteriophages, Seawater, 14. Life underwater, Gene, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Phylogeny, 030304 developmental biology, Genetics, 0303 health sciences, Ecology, biology, Phylogenetic tree, 030306 microbiology, Biodiversity, Sequence Analysis, DNA, biology.organism_classification, Phosphoric Monoester Hydrolases, Regulon, GenBank, DNA, Viral, Food Science, Biotechnology
Abstract

Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified, phoH was the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phage phoH sequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of the phoH gene were used to determine the diversity of phage phoH sequences throughout a depth profile in the Sargasso Sea and at six locations worldwide. phoH was present at all sites examined, and a high diversity of phoH sequences was recovered. Most phoH sequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinct phoH composition, although most phoH clusters were recovered from multiple sites. Overall, phoH is an effective signature gene for examining phage diversity in the marine environment.

Published
2011
Full Text
View/download PDF

9. Recombination in eukaryotic single stranded DNA viruses

Author

Arvind Varsani, Pierre Lefeuvre, Darren P. Martin, Philippe Biagini, Philippe Roumagnac, Michael Golden, Institute of Infectious Diseases and Moleculare MedicineComputational Biolohy Group, University of Cape Town, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Electron Microscopy Unit, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, UMR 6578 : Adaptabilité Biologique et Culturelle (UAABC), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)

Subjects
Virologie, Biological anthropology, viruses, Reassortment, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, lcsh:QR1-502, Review, L73 - Maladies des animaux, Genetic recombination, lcsh:Microbiology, Parvoviridae, ssDNA viruses [EN], parvovirus, geminivirus, anellovirus, circovirus, nanovirus, chemistry.chemical_compound, Anthropologie biologique, Recombination, Genetic, Genetics, Circoviridae, 0303 health sciences, Eukaryota, Plants, Infectious Diseases, Viral evolution, S50 - Santé humaine, Recombination, DNA, Single-Stranded, Genome, Viral, Biology, Virus, Evolution, Molecular, 03 medical and health sciences, Virology, Animals, Humans, Selection, Genetic, Virus classification, Géminivirus, 030304 developmental biology, H20 - Maladies des plantes, 030306 microbiology, DNA Viruses, Genetic Variation, Recombinaison, chemistry, DNA, Viral, Homologous recombination, DNA
Abstract

Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

Published
2011
Full Text
View/download PDF

10. Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

Author

Darren P. Martin, Virginie Ravigné, Innocent Zinga, Jean-Michel Lett, Arvind Varsani, Mireille Aurélie Harimalala, Matthew Walters, Pierre Lefeuvre, Murielle Hoareau, Alexandre De Bruyn, Bernard Reynaud, Gordon William Harkins, Batsirai Mabvakure, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Université de Bangui, University of the Western Cape (UWC), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Canterbury [Christchurch], Electron Microscopy Unit, University of Cape Town, Biomolecular Interaction Center, University of Canterburry, School of Biological Sciences, UMR Peuplement Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT - INRA), Institut National de la Recherche Agronomique (INRA), University of the Western Cape, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute of Infectious Disease and Molecular Medicine, and Faculty of Health Sciences

Subjects
0106 biological sciences, 0301 basic medicine, Entomology, Phylogénie, Manihot, Manihot esculenta, Epidemiology, Évolution, phylogeography, 01 natural sciences, African cassava mosaic virus, Génétique des populations, Recombination, Genetic, biology, Virus mosaïque manioc, Biological Evolution, Épidémiologie, Begomoviruses, Begomovirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Sciences du vivant, geographic locations, Research Article, Distribution géographique, Zoology, Context (language use), 03 medical and health sciences, Plant virus, Genetic variation, parasitic diseases, Madagascar, Géminivirus, Ecology, Evolution, Behavior and Systematics, Plant Diseases, H20 - Maladies des plantes, Genetic diversity, Cassava, Genetic Variation, Bayes Theorem, Virus des végétaux, biology.organism_classification, Recombination, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Recombinaison, Phylogeography, 030104 developmental biology, Evolutionary biology, DNA, Viral, Biologie végétale, 010606 plant biology & botany
Abstract

Background Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands. Results The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. Conclusions Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0749-2) contains supplementary material, which is available to authorized users.

Full Text
View/download PDF

11. Examination of embolisms in maple and birch saplings utilising microCT.

Author

Robinson JA, Rennie M, Clearwater M, Holland DJ, van den Berg AK, and Watson M

Subjects
Betula chemistry, X-Ray Microtomography, Acer chemistry, Embolism
Abstract

We demonstrate the application of synchrotron x-ray microtomography (microCT) to non-invasively examine the internal structure of a maple and birch sapling. We show that, through the use of standard image analysis techniques, embolised vessels can be extracted from reconstructed slices of the stem. By combining these thresholded images with connectivity analysis, we map out the embolisms within the sapling in three dimensions and evaluate the size distribution, showing that large embolisms over 0.005 mm 3 in volume compose the majority of the saplings' total embolised volume. Finally we evaluate the radial distribution of embolisms, showing that in maple fewer embolisms are present towards the cambium, while birch has a more uniform distribution., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Published
2023
Full Text
View/download PDF

12. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.

Author

Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, and Gardner PP

Subjects
Computational Biology, Codon, Initiator genetics, Codon, Terminator genetics, Recombinant Proteins chemistry, Recombinant Proteins genetics, Silent Mutation genetics
Abstract

Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression., Competing Interests: The authors have declared that no competing interests exist.

Published
2021
Full Text
View/download PDF

13. Direct Synthesis of para -Nitrophenyl Glycosides from Reducing Sugars in Water.

Author

Qiu X and Fairbanks AJ

Abstract

Reducing sugars may be directly converted into the corresponding para -nitrophenyl ( p NP) glycosides using 2-chloro-1,3-dimethylimidazolinium chloride (DMC), para -nitrophenol, and a suitable base in aqueous solution. The reaction is stereoselective for sugars with either a hydroxyl or an acetamido group at position 2, yielding the 1,2- trans p NP glycosides. A judicious choice of base allows extension to di- and oligosaccharide substrates, including a complex N-glycan oligosaccharide isolated from natural sources, without the requirement of any protecting group manipulations.

Published
2020
Full Text
View/download PDF

14. Aggregation and fibrillogenesis of proteins not associated with disease: a few case studies.

Author

Lassé M, Gerrard JA, and Pearce FG

Subjects
Amyloidogenic Proteins genetics, Amyloidogenic Proteins metabolism, Animals, Crystallins chemistry, Crystallins genetics, Crystallins metabolism, Humans, Insulin chemistry, Insulin genetics, Insulin metabolism, Lactoglobulins chemistry, Lactoglobulins genetics, Lactoglobulins metabolism, Multiprotein Complexes genetics, Multiprotein Complexes metabolism, Muramidase chemistry, Muramidase genetics, Muramidase metabolism, Ovalbumin chemistry, Ovalbumin genetics, Ovalbumin metabolism, Proteostasis Deficiencies metabolism, Proteostasis Deficiencies pathology, Amyloidogenic Proteins chemistry, Multiprotein Complexes chemistry
Abstract

While amyloid structures have been well characterised in a medical context, there is increasing interest in studying amyloid-like aggregates in other areas, such as food science and nanomaterials. Several proteins relevant to food processing, including serum albumen, lactoglobulin, lysozyme, ovalbumin, casein, and soy protein isolate have been shown to form fibrillar structures under both physiological and non-physiological conditions. These structures are likely to contribute to the structural characteristics of the final food product. In a biotechnological context, proteins such as insulin and eye lens crystallins can be induced to form amyloid structures which can subsequently be used in biotechnology. One example of this is the use of amyloid fibrils as a scaffold for the immobilisation of enzymes. Another current interest in amyloid fibrils is as a storage form for peptide hormones, including insulin, glucagon and calcitonin. Here, we give an overview of a selection of well characterised proteins that have been studied outside the context of disease.

Published
2012
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results