Breeding groundnut for rust resistance: A review

Sustainable groundnut production can be realised through development and adoption of high yielding cultivars possessing durable rust resistance. Integrating conventional breeding with genomic tools in identifying candidate rust resistance genes, and introgressing the genes into adapted elite germplasm, with the aid of molecular makers, could enhance breeding for rust resistance. This review highlights breeding approaches for groundnut rust resistance, with emphasis on integrating conventional breeding with marker-assisted selection. The life cycle, symptoms and epidemiology of the pathogen are also discussed to understand the host-pathogen interaction and guide groundnut rust resistance breeding

INDIGO : better geomagnetic observatories where we need them

The INDIGO project aims to improve the global coverage of digital observatories by deploying digital magnetometer systems in: i) Observatories where existing analog recording equipment is in need of upgrading. ii) Newly established digital observatories. iii) Existing digital observatories for the purpose of quality control and redundancy. In implementing the project and selecting suitable sites, special attention is paid to parts of the Earth devoid of magnetic observatories, increasing the reliability and long-term operation of existing observatories and cost-effective use of local resources. The Poster reviews the current status of the project. We examine the different steps and initiatives taken since the initiation of INDIGO in 2004 and assess their effectiveness in achieving progress towards our aims of improving global coverage and enhanced data quality

Primacy of effective communication and its influence on adherence to artemether-lumefantrine treatment for children under five years of age: a qualitative study.

BACKGROUND\ud \ud Prompt access to artemesinin-combination therapy (ACT) is not adequate unless the drug is taken according to treatment guidelines. Adherence to the treatment schedule is important to preserve efficacy of the drug. Although some community based studies have reported fairly high levels of adherence, data on factors influencing adherence to artemether-lumefantrine (AL) treatment schedule remain inadequate. This study was carried-out to explore the provider's instructions to caretakers, caretakers' understanding of the instructions and how that understanding was likely to influence their practice with regard to adhering to AL treatment schedule.\ud \ud METHODS\ud \ud A qualitative study was conducted in five villages in Kilosa district, Tanzania. In-depth interviews were held with providers that included prescribers and dispensers; and caretakers whose children had just received AL treatment. Information was collected on providers' instructions to caretakers regarding dose timing and how to administer AL; and caretakers' understanding of providers' instructions.\ud \ud RESULTS\ud \ud Mismatch was found on providers' instructions as regards to dose timing. Some providers' (dogmatists) instructions were based on strict hourly schedule (conventional) which was likely to lead to administering some doses in awkward hours and completing treatment several hours before the scheduled time. Other providers (pragmatists) based their instruction on the existing circumstances (contextual) which was likely to lead to delays in administering the initial dose with serious treatment outcomes. Findings suggest that, the national treatment guidelines do not provide explicit information on how to address the various scenarios found in the field. A communication gap was also noted in which some important instructions on how to administer the doses were sometimes not provided or were given with false reasons.\ud \ud CONCLUSIONS\ud \ud There is need for a review of the national malaria treatment guidelines to address local context. In the review, emphasis should be put on on-the-job training to address practical problems faced by providers in the course of their work. Further research is needed to determine the implication of completing AL treatment prior to scheduled time

Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania

Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30-36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21-24 nt) to contiguous sequences and searches for homologous viral sequences in data-bases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9-99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.Peer reviewe

Transcriptional activity, chromosomal distribution and expression effects of transposable elements in Coffea genomes

Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences. (Résumé d'auteur

QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

SUMMARY: Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the tools for analyzing HIV-1 drug resistance (HIVDR) testing data are mostly web-based which requires uploading data to webservers. This is a challenge for laboratories with internet connectivity issues and instances with restricted data transfer across networks. We present QuasiFlow, a pipeline for reproducible analysis of NGS-based HIVDR testing data across different computing environments. Since QuasiFlow entirely depends on command-line tools and a local copy of the reference database, it eliminates challenges associated with uploading HIV-1 NGS data onto webservers. The pipeline takes raw sequence reads in FASTQ format as input and generates a user-friendly report in PDF/HTML format. The drug resistance scores obtained using QuasiFlow were 100% and 99.12% identical to those obtained using web-based HIVdb program and HyDRA web respectively at a mutation detection threshold of 20%. AVAILABILITY AND IMPLEMENTATION: QuasiFlow and corresponding documentation are publicly available at https://github.com/AlfredUg/QuasiFlow. The pipeline is implemented in Nextflow and requires regular updating of the Stanford HIV drug resistance interpretation algorithm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online

Finite element, analytical, artificial neural network models for carbon fibre reinforced polymer confined concrete filled steel columns with elliptical cross sections

In the present era of architecture, different cross-sectional shapes of structural concrete elements have been utilized. However, this change in shape has a significant effect on load-carrying capacity. To restore this, the use of column confinements with elliptical sections has gained attention. This paper aim to investigate the effect of elliptical shape sections of confined concrete reinforced with Carbon Fiber Reinforced Polymer (CFRP) and steel tube on axial load-carrying capacity. This study is achieved using following tools Finite Element (FE) in Abaqus and Artificial Neural Networks (ANN) modeling. The study involved a 500-mm-high column with three sets of aspect ratios: 1.0, 1.5, and 2.0. In each aspect ratio, three different layers of CFRP were used, i.e., .167, .334, and .501-mm. Analytical results showed that with the increase in aspect ratio from 1 to 2, there is a decrease in ultimate axial load of about 23.2% on average. In addition, the combined confining pressure of steel tube and CFRP increases with a decrease in dilation angle as the number of CFRP layers increases. The failure mode for the column with a large aspect ratio is local buckling at its mid-height along the minor axis. The result showed a good correlation between FE and experimental results of ultimate stress and strains, with a mean squared error of 2.27 and .001, respectively. Moreover, ANN and analytical models showed a delightful correlation of R2 of .97 for stress models and .88 for strain models, respectively. The elliptical concrete section of the column confined with steel tubes can be adopted for a new architectural type of construction; however, with more than three aspect ratios, the wrapping of the section with CFRP jackets is highly recommended

Invasive Disease Caused by Nontuberculous Mycobacteria, Tanzania

Data on nontuberculous mycobacterial (NTM) disease in sub-Saharan Africa are limited. During 2006–2008, we identified 3 HIV-infected patients in northern Tanzania who had invasive NTM; 2 were infected with “Mycobacterium sherrisii” and 1 with M. avium complex sequevar MAC-D. Invasive NTM disease is present in HIV-infected patients in sub-Saharan Africa

Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses

Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components

Building a sustainable sweetpotato seed system in Malawi: Experiences from the "Rooting out hunger in Malawi" project.

The project “Rooting out Hunger in Malawi with Nutritious Orange-Fleshed Sweetpotato (OFSP)” was launched in October 2009 for the benefit of women and children in the country. This 4.5-year effort targets 115,000 households to improve vitamin A and energy intake using improved sweetpotato varieties. It also seeks to boost yields by 50% and improve incomes by 20%. The project aligns with the Agriculture Sector Wide Approach to food and nutrition security and crop diversification. With Irish Aid support, CIP initially worked in partnership with government agencies and three NGOs as implementing partners (IPs) and targeted 4 districts. The project established a “1-2-3” seed multiplication system, with clean planting material produced at a primary multiplication site, and decentralized vine multiplication sites (DVMs) doing multiplication at the community level. DVMs run by individuals or groups of farmers with access to irrigation were established by the IPs and supervised by district Extension staff. Mutiplication at the DVMs was termed secondary (vine production using rapid multiplication) or tertiary (production of both roots and vines, particularly during the hungry season). A subsidized voucher system was used by partners to allow at-risk households to purchase sweetpotato planting material from DVMs. Promotion and awareness campaigns were conducted in each district to stimulate demand for OFSP. By February 2012, the project had reached 36,403 households in 5 districts with subsidized vouchers, and an additional 19,331 beneficiaries through non-voucher sales. Seven IPs in 14 districts partnered in the effort. Lessons learned and sustainability of the system will be discussed