Leucine residues in conserved region of 33K protein of bovine adenovirus – 3 are important for binding to major late promoter and activation of late gene expression

AbstractThe L6 region of bovine adenovirus 3 (BAdV-3) encode 33K (spliced) and 22K (unspliced) proteins. Earlier, anti-33K serum detected five major and three minor proteins in BAdV-3 infected cells. Here, we demonstrate that anti-sera raised against L6-22K protein detected two proteins of 42 and 37kDa in BAdV-3 infected cells and one protein of 42kDa in transfected cells expressing splice-site variant 22K protein (pC.22K containing substituted splice acceptor/donor sequence). Unlike 22K, 33K stimulated the transcription from the major late promoter (MLP) by binding to the downstream sequence elements (DE). Analysis of the variant proteins demonstrated that amino acids 201–240 of the conserved C-terminus of 33K containing the potential leucine zipper and RS repeat are required for the activation of MLP. Furthermore, amino acid substitution analysis demonstrated that unlike arginine residues of RS repeat, the leucine residues (217, 224, 232 and 240) of the conserved leucine zipper appear required for the binding of 33K to the MLP

Evaluation of bio-physiological and yield responses of stay green QTL introgression sorghum lines to post-flowering drought stress

Drought is the most drastic abiotic stress that limits crop production in sub-Sahara Africa. Sorghum ( Sorghum bicolor (L.) Moench) is among the most climate resilient cereals of the future due to its tolerance to drought and heat. Thus, identification of tolerant genotypes and plant characteristics that contribute to drought adaptation is timely. The objective of this study was to evaluate the response of 12 genotypes, including seven Stay-green (Stg) QTL introgression sorghum lines and their two donor; and three recurrent parents, to induced post-flowering drought stress. The recurrent parents were varieties released for drought prone lowlands of the country, and the donor parents were lines known to have stay-green properties. The study was conducted at Werer, in the Great Rift-valley of Ethiopia, during the off-season of 2014 under well-watered and water limited conditions. Significant differences (P<0.05) were observed among genotypes under water deficit regimes, for all measured physiological, biochemical (proline content), yield and yield related traits. Three Stg QTL introgression lines showed better tolerance to drought than their recurrent parents, as reflected by yield and maintenance of green leaf area. Three Stg QTL introgression lines, Teshale/E36-1, Gambella/B35-5 and Meko/B35-12, gave the highest grain yield under post-flowering drought stress, and B35 and Teshale/B35 gave the poorest yield under similar conditions. Therefore, these improved lines bear potential for use as alternatives in breeding programmes and for possible release in parts of the country where post-flowering drought stress is frequent. Proline content, weight of hundred seeds (HSW) and CO2 assimilation are effective screening tools for Stg property due to their high correlation with other parameters.La s\ue8cheresse est le stress abiotique le plus drastique qui limite la production agricole en Afrique Sub-saharienne. Le sorgho ( Sorghum bicolor (L.) Moench) est parmi les c\ue9r\ue9ales les plus r\ue9silientes au climat pour le futur d\ufb \ue0 sa tol\ue9rance \ue0 la s\ue9cheresse et \ue0 la chaleur. Donc, l\u2019identification des g\ue9notypes tol\ue9rants et les caract\ue9ristiques des plants qui contribuent \ue0 l\u2019adaptation \ue0 la s\ue9cheresse est opportune. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer la r\ue9ponse de 12 g\ue9notypes, comportant sept lign\ue9es de sorgho conf\ue9rant l\u2019introgression des QTL des attributs verts (Stg), leurs deux donneurs\ua0; et les trois parents r\ue9currents, au stress de la s\ue9cheresse post floraison induite. Les parents r\ue9currents ont \ue9t\ue9 les vari\ue9t\ue9s lib\ue9r\ue9es sensibles \ue0 la s\ue9cheresse dans les plaines du pays, et les donneurs ont \ue9t\ue9 les lign\ue9es connues pour leurs propri\ue9t\ue9s relatives aux attributs verts. L\u2019\ue9tude a \ue9t\ue9 conduite \ue0 Werer, dans la grande vall\ue9e du Rift d\u2019Ethiopie, pendant la contre saison de 2014 dans des conditions d\u2019irrigation abondante et d\u2019irrigation limit\ue9e. De diff\ue9rences significatives (P<0.05) ont \ue9t\ue9 observ\ue9es entre les g\ue9notypes sous des r\ue9gimes de d\ue9ficit hydriques, pour tous les traits physiologiques, biochimiques (teneur en proline), le rendement et les composantes de rendement. Trois lign\ue9es d\u2019introgression de Stg QTL ont montr\ue9 de meilleure tol\ue9rance \ue0 la s\ue9cheresse que leurs parents r\ue9currents, comme refl\ue9t\ue9 par le rendement et la maintenance de la surface verte de la feuille. Trois lign\ue9es d\u2019introgression de Stg QTL, Teshale/E36-1, Gambella/B35-5 et Meko/B35-12, ont donn\ue9 le plus haut rendement sous le stress de s\ue9cheresse de post floraison, et B35 et Teshale/B35 ont donn\ue9 le plus faible rendement dans des conditions similaires. En cons\ue9quence, ces lign\ue9es am\ue9lior\ue9es d\ue9tiennent tout le potentiel pour leur usage comme alternatives dans des programmes d\u2019am\ue9lioration g\ue9n\ue9tiques et pour une lib\ue9ration possible dans les r\ue9gions du pays o\uf9 le stress de la s\ue9cheresse post floraison est fr\ue9quent. La teneur en proline, le poids de 100 graines (HSW) et l\u2019assimilation du CO2 sont des outils effectifs de criblage pour la propri\ue9t\ue9 de Stg due \ue0 leur forte corr\ue9lation avec les autres param\ue8tres

HIV care coverage among HIV-positive adolescent girls and young women in South Africa: Results from the HERStory Study

Background. Health service coverage cascades measure the proportion of a population in need of a service that experienced a positive health outcome from the service, and enable tracking of progress in achieving universal health coverage and inequities in care coverage.Objectives. To investigate HIV care coverage among HIV-positive adolescent girls and young women (AGYW) living in six South African districts, compare coverage by age and socioeconomic status (SES), and investigate other associated factors including participation in a combination HIV prevention intervention.Methods. The HERStory Study was an evaluation of the combination intervention, comprising a representative household survey of AGYW aged 15 - 24 years living in six intervention districts. From September 2017 to November 2018, biological, sociodemographic and behavioural data were collected. HIV-positive status, initiation of antiretroviral therapy (ART) and viral suppression were determined through laboratory tests (enzyme-linked immunosorbent assay for HIV antibodies, antiretroviral (ARV) metabolites and viral load (VL) testing). Viral suppression was defined as a VL <1 000 copies/mL. Knowledge of HIV-positive status was self-reported, and participants testing positive for ARV metabolites were assumed to have known their HIV-positive status. Unconditional HIV care cascades were created, stratified by age and SES. We used Pearson’s χ2 tests corrected for survey-based analysis to describe factors associated with knowledge of HIV status, and being on ART.Results. Of the 4 399 participants, 568 were HIV-positive (12.4%), of whom 60.8% (95% confidence interval (CI) 57.1 - 64.5) knew their status, 50.6% (95% CI 46.6 - 54.0) were on ART, and 62.1% (95% CI 58.4 - 65.9) were virally suppressed. Most participants (84.9%) were in the lower SES group, and they had better coverage than the higher SES group: 61.9% (95% CI 58.3 - 65.4) knew their status, 52.1% (95% CI 48.4 - 55.9) were on ART, and 64.9% (95% CI 61.3 - 68.4) were virally suppressed, compared with 55.0% (95% CI 42.1 - 68.0), 40.0% (95% CI 29.2 - 50.8), and 46.6% (95% CI 34.5 - 58.7), respectively. Participants aged 15 - 19 years had slightly inferior coverage to the 20 - 24-year-old group: 57.5% knew their status, 46.1% were on ART and 59.5% were virally suppressed, compared with 62.3%, 52.2% and 63.3%.Conclusions. These findings emphasise the need to close the gaps in HIV care coverage among AGYW, of whom only 61% knew their HIV-positive status and only 62% were virally suppressed. There is pro-poor inequality in HIV care coverage, with those in lower socioeconomic groups more likely to be virally suppressed

Study of growth and physiological characters in stay-green QTL introgression Sorghum bicolor (L.) lines under post-flowering drought stress

This experiment was carried out to evaluate the growth, physiological and yield traits of stay-green (Stg) QTL introgression sorghum lines, which were developed by the Ethiopian Institute of Agricultural Research in collaboration with ICRISAT between 2006 and 2008, under induced post-flowering drought stress. It involved a total of 12 genotypes including seven Stg QTL introgression lines, two Stg donor parents and three senescent recurrent parents. It was organized in a split plot design with three replications under well-watered and induced drought stress growing conditions at Melka Werer, Ethiopia during the post-rainy season of 2014. Analysis of variance revealed that the effect of moisture regimes on all measured traits was significant (P > 0.05). Differences among the genotypes and genotypeby- water regime interaction were also significant (P > 0.05) for all the traits considered. Postflowering drought stress was observed to significantly reduce most of the growth, physiological and yield related traits. The Stg introgression lines Meko/B35-selection 120, Teshale/B35-selection 2 and Teshale/E36-1 showed better drought stress tolerance properties than the rest of the genotypes based on the measured growth and physiological traits. These introgression lines also showed better grain yield than their recurrent parents under post-flowering drought stress and can be used as new versions of the existing varieties (served as recurrent parents) and for future breeding programs. Furthermore, leaf chlorophyll content, assimilation rate, transpiration rate, water use efficiency, root length and root dry weight were found to have strong correlation and can be used to screen genotypes for post-flowering drought tolerance

Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia

BACKGROUND: Previous work has shown differential predominance of certain Mycobacterium tuberculosis (M. tb) lineages and sub-lineages among different human populations in diverse geographic regions of Ethiopia. Nevertheless, how strain diversity is evolving under the ongoing rapid socio-economic and environmental changes is poorly understood. The present study investigated factors associated with M. tb lineage predominance and rate of strain clustering within urban and peri-urban settings in Ethiopia. METHODS: Pulmonary Tuberculosis (PTB) and Cervical tuberculous lymphadenitis (TBLN) patients who visited selected health facilities were recruited in the years of 2016 and 2017. A total of 258 M. tb isolates identified from 163 sputa and 95 fine-needle aspirates (FNA) were characterized by spoligotyping and compared with international M.tb spoligotyping patterns registered at the SITVIT2 databases. The molecular data were linked with clinical and demographic data of the patients for further statistical analysis. RESULTS: From a total of 258 M. tb isolates, 84 distinct spoligotype patterns that included 58 known Shared International Type (SIT) patterns and 26 new or orphan patterns were identified. The majority of strains belonged to two major M. tb lineages, L3 (35.7%) and L4 (61.6%). The observed high percentage of isolates with shared patterns (n = 200/258) suggested a substantial rate of overall clustering (77.5%). After adjusting for the effect of geographical variations, clustering rate was significantly lower among individuals co-infected with HIV and other concomitant chronic disease. Compared to L4, the adjusted odds ratio and 95% confidence interval (AOR; 95% CI) indicated that infections with L3 M. tb strains were more likely to be associated with TBLN [3.47 (1.45, 8.29)] and TB-HIV co-infection [2.84 (1.61, 5.55)]. CONCLUSION: Despite the observed difference in strain diversity and geographical distribution of M. tb lineages, compared to earlier studies in Ethiopia, the overall rate of strain clustering suggests higher transmission and warrant more detailed investigations into the molecular epidemiology of TB and related factors

Sulfur degassing at Erta Ale (Ethiopia) and Masaya (Nicaragua) volcanoes: Implications for degassing processes and oxygen fugacities of basaltic systems

We investigate the relationship between sulfur and oxygen fugacity at Erta Ale and Masaya volcanoes. Oxygen fugacity was assessed utilizing Fe3+/∑Fe and major element compositions measured in olivine‐hosted melt inclusions and matrix glasses. Erta Ale melts have Fe3+/∑Fe of 0.15–0.16, reflecting fO2 of ΔQFM 0.0 ± 0.3, which is indistinguishable from fO2 calculated from CO2/CO ratios in high‐temperature gases. Masaya is more oxidized at ΔQFM +1.7 ± 0.4, typical of arc settings. Sulfur isotope compositions of gases and scoria at Erta Ale (δ34Sgas − 0.5‰; δ34Sscoria + 0.9‰) and Masaya (δ34Sgas + 4.8‰; δ34Sscoria + 7.4‰) reflect distinct sulfur sources, as well as isotopic fractionation during degassing (equilibrium and kinetic fractionation effects). Sulfur speciation in melts plays an important role in isotope fractionation during degassing and S6+/∑S is 0.67 in Masaya melt inclusions. No change is observed in Fe3+/∑Fe or S6+/∑S with extent of S degassing at Erta Ale, indicating negligible effect on fO2, and further suggesting that H2S is the dominant gas species exsolved from the S2−‐rich melt (i.e., no redistribution of electrons). High SO2/H2S observed in Erta Ale gas emissions is due to gas re‐equilibration at low pressure and fixed fO2. Sulfur budget considerations indicate that the majority of S injected into the systems is emitted as gas, which is therefore representative of the magmatic S isotope composition. The composition of the Masaya gas plume (+4.8‰) cannot be explained by fractionation effects but rather reflects recycling of high δ34S oxidized sulfur through the subduction zone

Survey of Viruses Affecting Legume Crops in the Amhara and Oromia Regions of Ethiopia

Field surveys were undertaken to identify the viral diseases affecting lentil, faba bean, chickpea, pea, fenugreek and grass pea in two regions of Ethiopia. The surveys were conducted in the regions of Amhara (Gonder and Gojam administrative zones) and Oromia (Bale administrative zone) during the 2003/2004 and 2004/2005 growing seasons, respectively. The survey covered 138 randomly selected fields (48 faba bean, 10 pea, 38 grass pea, 34 chickpea, 8 lentil) in the Amhara region, and 51 legume fields (29 faba bean, 12 pea, 3 lentil, 5 fenugreek, 2 chickpea) in the Oromia region. Virus disease incidence was determined by laboratory testing of 100–200 randomly-collected samples from each field against the antisera of 12 legume viruses. Of the 189 fields surveyed, 121 and 7 had, at the time of the survey, a virus disease incidence of 1% or less and more than 6%, respectively, based on visual inspection in the field; later laboratory testing showed that the number of fields in these two categories was in fact 99 and 56, respectively. Serological tests indicated that the most important viruses in the Amhara region were Faba bean necrotic yellows virus (FBNYV), Bean yellow mosaic virus (BYMV), Pea seed-borne mosaic virus (PSbMV) and the luteoviruses [e.g. Beet western yellows virus (BWYV), Bean leaf roll virus (BLRV), Soybean dwarf virus (SbDV)]. By contrast, only FBNYV and the luteoviruses were detected in the Oromia region. Other viruses, such as Broad bean mottle virus (BBMV) and Alfalfa mosaic virus (AMV), were rarely detected in the Amhara region. This is the first report in Ethiopia of natural infection of faba bean, pea and fenugreek with SbDV, of fenugreek with BWYV, and of grass pea with BYMV, PSbMV and BWYV, and it is also the first recorded instance of BBMV infecting legume crops in Ethiopia

HIV care coverage among HIV-positive adolescent girls and young women in South Africa: Results from the HERStory Study

BACKGROUND. Health service coverage cascades measure the proportion of a population in need of a service that experienced a positive health outcome from the service, and enable tracking of progress in achieving universal health coverage and inequities in care coverage. OBJECTIVES. To investigate HIV care coverage among HIV-positive adolescent girls and young women (AGYW) living in six South African districts, compare coverage by age and socioeconomic status (SES), and investigate other associated factors including participation in a combination HIV prevention intervention. METHODS. The HERStory Study was an evaluation of the combination intervention, comprising a representative household survey of AGYW aged 15 - 24 years living in six intervention districts. From September 2017 to November 2018, biological, sociodemographic and behavioural data were collected. HIV-positive status, initiation of antiretroviral therapy (ART) and viral suppression were determined through laboratory tests (enzyme-linked immunosorbent assay for HIV antibodies, antiretroviral (ARV) metabolites and viral load (VL) testing). Viral suppression was defined as a VL <1 000 copies/mL. Knowledge of HIV-positive status was self-reported, and participants testing positive for ARV metabolites were assumed to have known their HIV-positive status. Unconditional HIV care cascades were created, stratified by age and SES. We used Pearson’s χ2 tests corrected for survey-based analysis to describe factors associated with knowledge of HIV status, and being on ART. RESULTS. Of the 4 399 participants, 568 were HIV-positive (12.4%), of whom 60.8% (95% confidence interval (CI) 57.1 - 64.5) knew their status, 50.6% (95% CI 46.6 - 54.0) were on ART, and 62.1% (95% CI 58.4 - 65.9) were virally suppressed. Most participants (84.9%) were in the lower SES group, and they had better coverage than the higher SES group: 61.9% (95% CI 58.3 - 65.4) knew their status, 52.1% (95% CI 48.4 - 55.9) were on ART, and 64.9% (95% CI 61.3 - 68.4) were virally suppressed, compared with 55.0% (95% CI 42.1 - 68.0), 40.0% (95% CI 29.2 - 50.8), and 46.6% (95% CI 34.5 - 58.7), respectively. Participants aged 15 - 19 years had slightly inferior coverage to the 20 - 24-year-old group: 57.5% knew their status, 46.1% were on ART and 59.5% were virally suppressed, compared with 62.3%, 52.2% and 63.3%. CONCLUSIONS. These findings emphasise the need to close the gaps in HIV care coverage among AGYW, of whom only 61% knew their HIVpositive status and only 62% were virally suppressed. There is pro-poor inequality in HIV care coverage, with those in lower socioeconomic groups more likely to be virally suppressed.The South African Medical Research Council (SAMRC), the Global Fund, the South African National Treasury and a CIPHER Growing the Leaders of Tomorrow grant from the International AIDS Society.http://www.samj.org.zadm2022Internal Medicin

Statistical tools for transgene copy number estimation based on real-time PCR

Background As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination. Results Three experimental designs and four data quality control integrated statistical models are presented. For the first method, external calibration curves are established for the transgene based on serially-diluted templates. The Ct number from a control transgenic event and putative transgenic event are compared to derive the transgene copy number or zygosity estimation. Simple linear regression and two group T-test procedures were combined to model the data from this design. For the second experimental design, standard curves were generated for both an internal reference gene and the transgene, and the copy number of transgene was compared with that of internal reference gene. Multiple regression models and ANOVA models can be employed to analyze the data and perform quality control for this approach. In the third experimental design, transgene copy number is compared with reference gene without a standard curve, but rather, is based directly on fluorescence data. Two different multiple regression models were proposed to analyze the data based on two different approaches of amplification efficiency integration. Our results highlight the importance of proper statistical treatment and quality control integration in real-time PCR-based transgene copy number determination. Conclusion These statistical methods allow the real-time PCR-based transgene copy number estimation to be more reliable and precise with a proper statistical estimation. Proper confidence intervals are necessary for unambiguous prediction of trangene copy number. The four different statistical methods are compared for their advantages and disadvantages. Moreover, the statistical methods can also be applied for other real-time PCR-based quantification assays including transfection efficiency analysis and pathogen quantification