Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing

Abstract: Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity

Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing

Abstract: Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity

Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations.

Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of maize chlorotic mottle virus with Potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa

Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

Background: Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Results: Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi virus (RhPV), and a novel Big Sioux River virus (BSRV)-like dicistrovirus in aphid and maize samples was confirmed using reverse transcription-polymerase chain reactions and sequencing of amplified DNA products. Phylogenetic, nucleotide and protein sequence analyses of eight ALPV genomes revealed evidence of intra-species recombination, with the data suggesting there may be two ALPV lineages. Analysis of BSRV-like virus genomic RNA sequences revealed features that are consistent with other dicistroviruses and that it is phylogenetically closely related to dicistroviruses of the genus Cripavirus.Work was funded by a grant from the Sustainable Crop Production Research for International Development programme funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) with co-funding from the UK Department for International Development, the Bill & Melinda Gates Foundation, the Department of Biotechnology of India’s Ministry of Science and Technology, and the Indian Council of Agricultural Research (BB/J011762/1) and a Global Challenges Research Fund Foundation Award (BB/P023223/1). LAB was funded by a Cambridge BBSRC doctoral training programme studentship

Comparison of the accuracy of digital models obtained from scans of impressions versus direct intra-oral scans

Magister Chirurgiae Dentium - MChDMeasurements and a variety of analyses of dental casts are essential for precise diagnosis of an orthodontic case. Study models have long been an essential part of orthodontic diagnosis and treatment planning. Currently virtual computerized models are available to clinicians, supplemented by dedicated software for performing needed measurements (Zilberman et al, 2003). Digital impression methods are now available and intraoral digital scanning techniques make it possible to generate study models directly from the scanning of the dentition. The aim of this study was to compare measurements taken after scanning the dental impressions to the measurements obtained from using direct intraoral scanning of the dentition. Alginate impressions of the maxillary and mandibular dentitions were taken on 20 patients and these impressions were scanned using a 3 Shape R 700 TM scanner. Direct intraoral scans of both dentitions were then performed for the same patient. Ortho analyzer TM software was used to measure the mesiodistal widths of individual teeth, and the intercanine and intermolar on digital models of the scanned impressions and digital models obtained from direct intraoral scans of the maxillary and the mandibular dentitions. The results indicated that there were no statistically significant differences between mesiodistal widths, and intercanine and intermolar distances between the two techniques (p > 0.05). Because of the high level of accuracy of the virtual measurements compared to those of the scanned impressions, it can be concluded that direct intraoral scanning of the dentition can be used with confidence in the clinical situation to measure tooth sizes and inter-arch distances for orthodontic purposes. Orthodontists commonly use models for various areas in the practice, clinical research and medico-legal documentation (Marcel, 2001

Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing.

Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity

A first global phylogeny of<i>Maize chlorotic mottle virus</i>

ABSTRACT Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of Maize chlorotic mottle virus with potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained Maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa

Corporate Ownership Structure and the Cash Flow Sensitivity of Cash

This article examines the effects of excess control rights of the controlling shareholder and the presence of multiple large shareholders on financial constraints, proxied by cash flow sensitivity of cash. Using a unique data set of 745 French listed firms during 1998—2013, the results show that firms have high cash flow sensitivity of cash when the controlling shareholder’s control rights exceed its cash-flow ownership. This sensitivity decreases, however, with the contestability of the controlling owner’s power. Taken together, these findings provide empirical support to the argument that firms experiencing excess control rights face considerable financial constraints that are lowered in the presence of high control contestability