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Browsing by Author "Martin, Darren"

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Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus

Author: Monjane, Aderito ; Pande, Daniel ; Lakay, Francisco ; Shepherd, Dionne ; van der Walt, Eric ; Lefeuvre, Pierre ; Lett, Jean-Michel ; Varsani, Arvind ; Rybicki, Edward ; Martin, Darren Date: 2012 BACKGROUND: Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA ... Read more c b
Characterization of HIV-1 gag and nef in Cameroon: further evidence of extreme diversity at the origin of the HIV-1 group M epidemic

Author: Tongo, Marcel ; Martin, Darren ; Zembe, Lycias ; Mpoudi-Ngole, Eitel ; Williamson, Carolyn ; Burgers, Wendy Date: 2013 BACKGROUND: Cameroon, in west central Africa, has an extraordinary degree of HIV diversity, presenting a major challenge for the development of an effective HIV vaccine. Given the continuing need to closely monitor the emergence of new HIV ... Read more c b
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection

Author: Bandawe, Gama ; Martin, Darren ; Treurnicht, Florette ; Mlisana, Koleka ; Karim, Salim ; Williamson, Carolyn Date: 2008 BACKGROUND:The high diversity of HIV variants driving the global AIDS epidemic has caused many to doubt whether an effective vaccine against the virus is possible. However, by identifying the selective forces that are driving the ongoing ... Read more c b
East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus

Author: De Bruyn, Alexandre ; Villemot, Julie ; Lefeuvre, Pierre ; Villar, Emilie ; Hoareau, Murielle ; Harimalala, Mireille ; Abdoul-Karime, Anli ; Abdou-Chakour, Chadhouliati ; Reynaud, Bernard ; Harkins, Gordon ; Varsani, Arvind ; Martin, Darren ; Lett, Jean-Michel Date: 2012 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 ... Read more c b
Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts

Author: Harkins, Gordon ; Delport, Wayne ; Duffy, Siobain ; Wood, Natasha ; Monjane, Aderito ; Owor, Betty ; Donaldson, Lara ; Saumtally, Salem ; Triton, Guy ; Briddon, Rob ; Shepherd, Dionne ; Rybicki, Edward ; Martin, Darren ; Varsani, Arvind Date: 2009 BACKGROUND:Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus ... Read more c b
Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias

Author: van der Walt, Eric ; Martin, Darren ; Varsani, Arvind ; Polston, Jane ; Rybicki, Edward Date: 2008 BACKGROUND: Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). These ... Read more c b
Exploring the phylodynamics, genetic reassortment and RNA secondary structure formation patterns of orthomyxoviruses by comparative sequence analysis

Author: Nindo, Fredrick Nzabanyi Date: 2019 RNA viruses are among the most virulent microorganisms that threaten the health of humans and livestock. Among the most socio-economically important of the known RNA viruses are those found in the family Orthomyxovirus. In this era of rapid ... Read more
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

Author: Ngandu, Nobubelo ; Scheffler, Konrad ; Moore, Penny ; Woodman, Zenda ; Martin, Darren ; Seoighe, Cathal Date: 2008 BACKGROUND: Positive selection pressure acting on protein-coding sequences is usually inferred when the rate of nonsynonymous substitution is greater than the synonymous rate. However, purifying selection acting directly on the nucleotide ... Read more c b
Genetic variation and recombination of RdRp and HSP 70h genes of Citrus tristeza virus isolates from orange trees showing symptoms of citrus sudden death disease

Author: Gomes, Clarissa ; Nagata, Tatsuya ; de Jesus, Waldir ; Neto, Carlos ; Pappas, Georgios ; Martin, Darren Date: 2008 BACKGROUND: Citrus sudden death (CSD), a disease that rapidly kills orange trees, is an emerging threat to the Brazilian citrus industry. Although the causal agent of CSD has not been definitively determined, based on the disease's distribution ... Read more c b
A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family

Author: Varsani, Arvind ; Shepherd, Dionne ; Dent, Kyle ; Monjane, Aderito ; Rybicki, Edward ; Martin, Darren Date: 2009 BACKGROUND:We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a ... Read more c b
Human Immunodeficiency Virus? One of nature's greatest evolutionary machines

Author: Martin, Darren ; Williamson, Carolyn Date: 2004 Transmission of an HIV-like virus from chimpanzees to humans approximately 80 years ago triggered the worldwide AIDS pandemic. Possessing very high mutation and recombination rates, the descendants of this ancestral virus have evolved greatly. ... Read more
Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes

Author: Golden, Michael Thomas Date: 2013 Large single-stranded nucleotide sequences such as certain DNA and RNA virus genomes form complex secondary structures through Watson-Crick base-pairing interactions between bases on the same DNA or RNA strand. Both computational and experimental ... Read more
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

Author: Lemey, Philippe ; Lott, Martin ; Martin, Darren ; Moulton, Vincent Date: 2009 BACKGROUND:Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying ... Read more c b
Immunology and virology of HIV-1 infection in Cameroon

Author: Tongo Passo, Aime Marcel Simon Date: 2014 This study confirms the widespread existence of highly divergent HIV lineages in Cameroon. While the genetic complexity of the Cameroonian HIV-1 epidemic has potentially serious implications for the design of biomedical interventions, detailed ... Read more
In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health

Author: Happel, Anna-Ursula ; Kullin, Brian R ; Gamieldien, Hoyam ; Jaspan, Heather B ; Varsani, Arvind ; Martin, Darren ; Passmore, Jo-Ann S ; Froissart, Rémy Date: 20 Jan 2022 While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of ... Read more c b
The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates

Author: Cloete, Leendert ; Tanov, Emil ; Muhire, Brejnev ; Martin, Darren ; Harkins, Gordon Date: 2014 BACKGROUND: Annually, rubella virus (RV) still causes severe congenital defects in around 100 000 children globally. An attempt to eradicate RV is currently underway and analytical tools to monitor the global decline of the last remaining RV ... Read more c b
Leveraging big data resources and data integration in biology: applying computational systems analyses and machine learning to gain insights into the biology of cancers

Author: Sinkala, Musalula Date: 2020 Recently, many "molecular profiling" projects have yielded vast amounts of genetic, epigenetic, transcription, protein expression, metabolic and drug response data for cancerous tumours, healthy tissues, and cell lines. We aim to facilitate ... Read more
The population genomics of begomoviruses: global scale population structure and gene flow

Author: Prasanna, HC ; Sinha, D ; Verma, Ajay ; Singh, Major ; Singh, Bijendra ; Rai, Mathura ; Martin, Darren Date: 2010 BACKGROUND: The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, ... Read more c b
Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

Author: Monjane, Aderito ; van der Walt, Eric ; Varsani, Arvind ; Rybicki, Edward ; Martin, Darren Date: 2011 BACKGROUND:Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous ... Read more c b
Viable chimaeric viruses confirm the biological importance of sequence specific maize streak virus movement protein and coat protein interactions

Author: van der Walt, Eric ; Palmer, Kenneth ; Martin, Darren ; Rybicki, Edward Date: 2008 BACKGROUND: A variety of interactions between up to three different movement proteins (MPs), the coat protein (CP) and genomic DNA mediate the inter- and intra-cellular movement of geminiviruses in the genus Begomovirus. Although movement of ... Read more c b

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