Evidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.Department of HE and Training approved lis

Equity for health delivery: Opportunity costs and benefits among Community Health Workers in Rwanda.

Community Health Workers (CHWs) play a vital role delivering health services to vulnerable populations in low resource settings. In Rwanda, CHWs provide village-level care focused on maternal/child health, control of infectious diseases, and health education, but do not receive salaries for these services. CHWs make up the largest single group involved in health delivery in the country; however, limited information is available regarding the socio-economic circumstances and satisfaction levels of this workforce. Such information can support governments aiming to control infectious diseases and alleviate poverty through enhanced healthcare delivery. The objectives of this study were to (1) evaluate CHW opportunity costs, (2) identify drivers for CHW motivation, job satisfaction and care provision, and (3) report CHW ideas for improving retention and service delivery. In this mixed-methods study, our team conducted in-depth interviews with 145 CHWs from three districts (Kirehe, Kayonza, Burera) to collect information on household economics and experiences in delivering healthcare. Across the three districts, CHWs contributed approximately four hours of volunteer work per day (range: 0-12 hrs/day), which translated to 127 684 RWF per year (range: 2 359-2 247 807 RWF/yr) in lost personal income. CHW out-of-pocket expenditures (e.g. patient transportation) were estimated at 36 228 RWF per year (range: 3 600-364 800 RWF/yr). Participants identified many benefits to being CHWs, including free healthcare training, improved social status, and the satisfaction of helping others. They also identified challenges, such as aging equipment, discrepancies in financial reimbursements, poverty, and lack of formal workspaces or working hours. Lastly, CHWs provided perspectives on reasonable and feasible improvements to village-level health programming that could improve conditions and equity for those providing and using the CHW system

Analysis of Climate and Topography Impacts on the Spatial Distribution of Vegetation in the Virunga Volcanoes Massif of East-Central Africa

This paper aimed to investigate the influence of climatic and topographic factors on the distribution of vegetation in the Virunga Volcanoes Massif using GIS and remote sensing techniques. The climatic variables considered were precipitation, Land Surface Temperature (LST), and evapotranspiration (ET), whereas the topographic factors considered were elevation and aspect. The dataset consisted of MODIS NDVI data, satellite-delivered precipitation, ET, and the LST. A 2014 Landsat 8 OLI image was used to produce a vegetation map of the study area, while DEM was used to derive the elevation attributes and to calculate the aspect angles. Moran’s I and Geographically Weighted Regression (GWR) Model was used to analyze the relationships between the climatic factors and NDVI changes over elevation and aspect. The results indicated that among the nine vegetation types inventoried in the area, the Mean NDVI varied from 0.33 to 0.59 and the optimal vegetation growth was found at an elevation between 2000 and 3900 m, with mean NDVI values larger than 0.50. The peak mean NDVI value of 0.59 was found at the elevation from 2100 to 2800 m. Vegetation growth was found to be more sensitive to elevation, as NDVI values were more varied at a lower elevation (<4000 m) than at a higher elevation (>4000 m). Considering the aspect, the greater vegetation growth was found in SE (132°, 148°), SW (182°, 186°), and NW (309.5°–337.5°), with mean NDVI values larger than 0.56. This indicated that vegetation was susceptible to better growth conditions in the lower elevation ranges and in shady areas. The vegetation NDVI in this study area was mostly uncorrelated with precipitation (R2 = 0.34), but was strongly correlated with LST (R2 = 0.99) and ET (R2 = 98). LST (≥18 °C) and ET (1286 mm/year−1) were found to provide optimal conditions for vegetation growth in the Virunga Volcanoes Massif. Empirically, the results concluded that elevation, aspect, LST, and ET are the main factors controlling the spatial distribution and vegetation growth in this area. This information is significantly helpful for biodiversity conservation and constitutes a valuable input to environmental and ecological research

Can Cold Plasma Be Used for Boosting Plant Growth and Plant Protection in Sustainable Plant Production?

Sustainable agriculture with low inputs of chemicals and fertilizers has been recently attracting more attention from producers and researchers in the EU. The main reason for such attention is The European Green Deal—the EU’s latest growth strategy concerning environmental degradation and climate change. One of its main components is the Farm to Fork strategy, which especially features the reduction in pesticide and mineral fertilizer application and also supports the development of organic farming. At the same time, food demand is rising. These ambitious challenges require extensive research, development and innovation. Therefore, new non-chemical techniques for improving plant growth and resistance to biotic and abiotic stresses must be explored for their potential in this field. One of the most promising is the use of non-thermal plasma for such purposes. As this physical factor is a complex mixture of ions, atoms, electrons, radicals and molecules, its effect on plants and pathogens is also complex. This review presents different aspects of the effect of non-thermal plasma on seed germination, development of seedlings, plants and pathogens. The literature was explored to provide evidence for the possible use of non-thermal plasma for boosting plant growth and plant protection

Can Cold Plasma Be Used for Boosting Plant Growth and Plant Protection in Sustainable Plant Production?

Sustainable agriculture with low inputs of chemicals and fertilizers has been recently attracting more attention from producers and researchers in the EU. The main reason for such attention is The European Green Deal—the EU’s latest growth strategy concerning environmental degradation and climate change. One of its main components is the Farm to Fork strategy, which especially features the reduction in pesticide and mineral fertilizer application and also supports the development of organic farming. At the same time, food demand is rising. These ambitious challenges require extensive research, development and innovation. Therefore, new non-chemical techniques for improving plant growth and resistance to biotic and abiotic stresses must be explored for their potential in this field. One of the most promising is the use of non-thermal plasma for such purposes. As this physical factor is a complex mixture of ions, atoms, electrons, radicals and molecules, its effect on plants and pathogens is also complex. This review presents different aspects of the effect of non-thermal plasma on seed germination, development of seedlings, plants and pathogens. The literature was explored to provide evidence for the possible use of non-thermal plasma for boosting plant growth and plant protection

Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context

Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share >91% genome-wide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations

Partnerships for Health - Jeff Health and the Rwanda Village Concept Project – A model of interdisciplinary health professions student global education

Background The Rwanda Health and Healing Project (RHHP) • Started in 2006: Barefoot Artists and TJU Department of Family and Community Medicine – Global health immersion experience – Interdisciplinary – Focus: team-based, sustainable public health programming, economic development, community empowerment • Public-Health Programming: Akarambi, Rugerero – Hygiene and Sanitation – Childhood Nutrition – Helminth Prevention – HIV Education – Income Generation: chicken coop, rabbit rearing, mushroom farming, bee keeping, pig farmin