Avifauna of Ishaqbini Community Conservancy in Ijara District, NE Kenya

Ishaqbini community conservancy, in the arid northern-eastern Kenya was established in 2006 by local pastoralists as a community initiative to safeguard their wildlife heritage especially the endemic Hirola Beatragus hunteri. Prior to this survey there were no known recent avifaunal surveys for the area despite the fact that the conservancy lies adjacent to the relatively well-known lower Tana River forests, an important bird area (Bennun & Njoroge 1999), as well as the East Africa coast forests endemic bird area (Stattersfield et al. 1998). In this paper we present the results of an avifaunal survey of the conservancy that includes a description of the bird assemblages in the conservancy, and an annotated account of some species of global and regional conservation concern occurring there

Similarities in functional attributes and nutritional effects of magadi soda and bean debris-ash used in cooking African traditional dishes

Magadi soda and bean debris-ash have been used as condiments for a long time by various ethnic groups in East and Central Africa in cooking traditional dishes. The aim of the study was to investigate whether magadi soda and bean debris-ash had similar effects and functional attributes when added to traditional dishes during cooking. Reason for the addition of the two condiments has not been revealed by researchers. Mineral content, in-vitro bioavailability studies and pH of non-ashed and ashed magadi soda and bean debris were evaluated. The results indicated that high concentrations of sodium ions (30.2%) and potassium ions (64.2%) were observed in magadi soda and bean debris-ash, respectively. In-vitro iron and zinc bioavailability decreased significantly with the addition of magadi soda and bean debris-ash in maize, beans and sorghum. Equally, the cooking time was significantly reduced. The mean pH for both magadi soda (9.66) and bean debris-ash (9.75) were not significantly different indicating that both aqueous solutions had alkaline properties. The similarity in properties especially in mineral profile, alkalinity, decreased cooking time and lowered mineral uptake by magadi soda and bean  debris-ash explain similar functionality in foods they are added to during cooking. Despite the similarities  observed, communities should be informed of the negative nutritional effects of these condiments so as to diversify their meal patterns accordingly.Key words: Magadi soda, bean ash, traditional dishes, minerals, in-vitro bioavailabilit

Cattle Identification Using Muzzle Images and Deep Learning Techniques

Traditional animal identification methods such as ear-tagging, ear notching, and branding have been effective but pose risks to the animal and have scalability issues. Electrical methods offer better tracking and monitoring but require specialized equipment and are susceptible to attacks. Biometric identification using time-immutable dermatoglyphic features such as muzzle prints and iris patterns is a promising solution. This project explores cattle identification using 4923 muzzle images collected from 268 beef cattle. Two deep learning classification models are implemented - wide ResNet50 and VGG16\_BN and image compression is done to lower the image quality and adapt the models to work for the African context. From the experiments run, a maximum accuracy of 99.5\% is achieved while using the wide ResNet50 model with a compression retaining 25\% of the original image. From the study, it is noted that the time required by the models to train and converge as well as recognition time are dependent on the machine used to run the model.Comment: 8 pages, 4 figures, 2 table

Natural out-crossing in dwarf pigeonpea

Natural out-crossing rate in pigeonpea was studied at 1CRISAT Center using plant stature (tall plants in dwarf progenies) as the genetic marker. The data indicated natural out-crossing rates of 9.7% to 24.1 % with a pooled value of 13.1% in the six populations studied. These data were comparable to earlier studies at the same site using stem colour and growth habit as genetic markers in tall pigeonpea cultivars thus suggesting that foraging of insect pollination vectors is not influenced by plant type. The implications of natural out-crossing on breeding and maintenance of genetic purity of cultivars is discussed

Controlled human malaria infection (CHMI) outcomes in Kenyan adults is associated with prior history of malaria exposure and anti-schizont antibody response

BACKGROUND: Individuals living in endemic areas acquire immunity to malaria following repeated parasite exposure. We sought to assess the controlled human malaria infection (CHMI) model as a means of studying naturally acquired immunity in Kenyan adults with varying malaria exposure. METHODS: We analysed data from 142 Kenyan adults from three locations representing distinct areas of malaria endemicity (Ahero, Kilifi North and Kilifi South) enrolled in a CHMI study with Plasmodium falciparum sporozoites NF54 strain (Sanaria® PfSPZ Challenge). To identify the in vivo outcomes that most closely reflected naturally acquired immunity, parameters based on qPCR measurements were compared with anti-schizont antibody levels and residence as proxy markers of naturally acquired immunity. RESULTS: Time to endpoint correlated more closely with anti-schizont antibodies and location of residence than other parasite parameters such as growth rate or mean parasite density. Compared to observational field-based studies in children where 0.8% of the variability in malaria outcome was observed to be explained by anti-schizont antibodies, in the CHMI model the dichotomized anti-schizont antibodies explained 17% of the variability. CONCLUSIONS: The CHMI model is highly effective in studying markers of naturally acquired immunity to malaria. Trial registration Clinicaltrials.gov number NCT02739763. Registered 15 April 2016

Multiple disease resistance in snap bean genotypes in Kenya

Snap bean ( Phaseolus vulgaris L.) is an important export vegetable crop, produced mainly by small to medium scale farmers under various disease constraints. Disease resistant varieties can reduce reliance on fungicides, and enhance the capacities of smallholder farmers to meet the stringent European export requirements for allowable fungicide residues. This study was carried out to identify snap bean lines with multiple disease resistance to angular leaf spot ( Phaeoisareopsis griseola ), anthracnose ( Collectotrichum lindemuthianum ) and rust ( Uromyces appendiculatus ). Seven groups of snap bean populations of different generations, and 45 bush snap bean lines, including local checks, were evaluated for resistance to the three diseases at two locations in Kenya. The disease with the highest severity was rust, followed by angular leaf spot. Among the advanced lines, two bush lines (KSB 10 W and KSB 10 BR), and one climbing line (HAV 130) had consistent multiple resistance to angular leaf spot, anthracnose and rust at both locations. Nine lines and 674 single plants were selected from populations showing multiple disease resistance. Resistance in selected lines reduced angular leaf spot, anthracnose and rust severity by 17, 16 and 36%, respectively. The multiple disease resistant lines were not the highest yielders but had the highest number of pods per plant. Climbing snap bean lines had thick pods that could reduce pod quality.Le haricot vert ( Phaseolus vulgaris L.) est une importante l\ue9gume d\u2019exportation, produite principalement par de petits fermiers sous diff\ue9rentes contraintes de maladies. Des vari\ue9t\ue9s r\ue9sistantes aux maladies peuvent r\ue9duire l\u2019utilisation de fongicides, et promouvoir la capacit\ue9 des petits fermiers \ue0 satisfaire les exigencies rigoureuses des exportations europ\ue9ennes en r\ue9sidus acceptables de fongicides. Cette \ue9tude \ue9tait m\ue9n\ue9e afin d\u2019identifier des lign\ue9es de haricots verts avec multiple r\ue9sistance \ue0 la t\ue2che angulaire des feuilles ( Phaeoisareopsis griseola ), \ue0 l\u2019anthracnose ( Collectotrichum lindemuthianum ) et \ue0 la rouille ( Uromyces appendiculatus ). Sept groupes de populations de diff\ue9rentes g\ue9n\ue9rations, et 45 lign\ue9es de haricots verts nains incluant les t\ue9moins locaux, \ue9taient \ue9valu\ue9s pour r\ue9sistance aux trois maladies dans deux localisations au Kenya. La maladie avec une s\ue9v\ue9rit\ue9 la plus \ue9lev\ue9e \ue9tait la roulle, suivie par la t\ue2che angulaire des feuilles. Parmi les lign\ue9es avanc\ue9es, deux lign\ue9es naines (KSB 10 W et KSB 10 BR), et une volubile (HAV 130) avaient une resistance multiple consistante \ue0 la t\ue2che angulaire des feuilles, \ue0 l\u2019anthracnose et \ue0 la rouille dans toutes les deux localisations. Neuf lign\ue9es et 674 plantes simples s\ue9lectionnn\ue9es des populations avaient montr\ue9 une r\ue9sistance multiple aux maladies. La r\ue9sistance dans les lign\ue9es s\ue9lectionn\ue9es avaient r\ue9duit la s\ue9verit\ue9 de la t\ue2che angulaire des feuilles, de l\u2019anthracnose et de la rouille de 17, 16 et 36%, respectivement. Les lign\ue9es de r\ue9sistance multiple n\u2019avaient pas des rendements plus \ue9lev\ue9s mais avaient un nombre plus \ue9lev\ue9 de gousses par plante. Les lign\ue9es de haricots verts volubiles avaient des gousses \ue9paisses susceptibles \ue0 r\ue9duire la qualit\ue9 de gousses

Subtype-Specific Differences in Gag- Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression

ABSTRACT There are marked differences in the spread and prevalence of HIV-1 subtypes worldwide, and differences in clinical progression have been reported. However, the biological reasons underlying these differences are unknown. Gag-protease is essential for HIV-1 replication, and Gag-protease-driven replication capacity has previously been correlated with disease progression. We show that Gag-protease replication capacity correlates significantly with that of whole isolates ( r = 0.51; P = 0.04), indicating that Gag-protease is a significant contributor to viral replication capacity. Furthermore, we investigated subtype-specific differences in Gag-protease-driven replication capacity using large well-characterized cohorts in Africa and the Americas. Patient-derived Gag-protease sequences were inserted into an HIV-1 NL4-3 backbone, and the replication capacities of the resulting recombinant viruses were measured in an HIV-1-inducible reporter T cell line by flow cytometry. Recombinant viruses expressing subtype C Gag-proteases exhibited substantially lower replication capacities than those expressing subtype B Gag-proteases ( P &lt; 0.0001); this observation remained consistent when representative Gag-protease sequences were engineered into an HIV-1 subtype C backbone. We identified Gag residues 483 and 484, located within the Alix-binding motif involved in virus budding, as major contributors to subtype-specific replicative differences. In East African cohorts, we observed a hierarchy of Gag-protease-driven replication capacities, i.e., subtypes A/C &lt; D &lt; intersubtype recombinants ( P &lt; 0.0029), which is consistent with reported intersubtype differences in disease progression. We thus hypothesize that the lower Gag-protease-driven replication capacity of subtypes A and C slows disease progression in individuals infected with these subtypes, which in turn leads to greater opportunity for transmission and thus increased prevalence of these subtypes. IMPORTANCE HIV-1 subtypes are unevenly distributed globally, and there are reported differences in their rates of disease progression and epidemic spread. The biological determinants underlying these differences have not been fully elucidated. Here, we show that HIV-1 Gag-protease-driven replication capacity correlates with the replication capacity of whole virus isolates. We further show that subtype B displays a significantly higher Gag-protease-mediated replication capacity than does subtype C, and we identify a major genetic determinant of these differences. Moreover, in two independent East African cohorts we demonstrate a reproducible hierarchy of Gag-protease-driven replicative capacity, whereby recombinants exhibit the greatest replication, followed by subtype D, followed by subtypes A and C. Our data identify Gag-protease as a major determinant of subtype differences in disease progression among HIV-1 subtypes; furthermore, we propose that the poorer viral replicative capacity of subtypes A and C may paradoxically contribute to their more efficient spread in sub-Saharan Africa. </jats:p

Modelling nitrogen mineralization from manures: representing quality aspects by varying C:N ratio of sub-pools

The mineralization/immobilization of nitrogen when organic sources are added to soil is represented in many simulation models as the outcome of decomposition of the added material and synthesis of soil organic matter. These models are able to capture the pattern of N release that is attributable to the N concentration of plant materials, or more generally the C:N ratio of the organic input. However, the models are unable to simulate the more complex pattern of N release that has been observed for some animal manures, notably materials that exhibit initial immobilization of N even when the C:N of the material suggests it should mineralize N. The APSIM SoilN module was modified so that the three pools that constitute added organic matter could be specified in terms of both the fraction of carbon in each pool and also their C:N ratios (previously it has been assumed that all pools have the same C:N ratio). It is shown that the revised model is better able to simulate the general patterns on N mineralized that has been reported for various organic sources. By associating the model parameters with measured properties (the pool that decomposes most rapidly equates with water-soluble C and N; the pool that decomposes slowest equates with lignin-C) the model performed better than the unmodified model in simulating the N mineralization from a range of feeds and faecal materials measured in an incubation experimen

Natural Products-Based Drug Design against SARS-CoV-2 Mpro 3CLpro

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has received global attention due to the serious threat it poses to public health. Since the outbreak in December 2019, millions of people have been affected and its rapid global spread has led to an upsurge in the search for treatment. To discover hit compounds that can be used alone or in combination with repositioned drugs, we first analyzed the pharmacokinetic and toxicological properties of natural products from Brazil’s semiarid region. After, we analyzed the site prediction and druggability of the SARS-CoV-2 main protease (Mpro), followed by docking and molecular dynamics simulation. The best SARS-CoV-2 Mpro complexes revealed that other sites were accessed, confirming that our approach could be employed as a suitable starting protocol for ligand prioritization, reinforcing the importance of catalytic cysteine-histidine residues and providing new structural data that could increase the antiviral development mainly against SARSCoV-2. Here, we selected 10 molecules that could be in vitro assayed in response to COVID-19. Two compounds (b01 and b02) suggest a better potential for interaction with SARS-CoV-2 Mpro and could be further studied.Research Dean and Graduate Studies of the Federal University of Pará (PROPESP/UFPA)Brazilian National Council for Scientific and Technological Development (CNPq)Brazilian Coordination for Improvement of Personnel Higher Education (CAPES)Bahia Research Foundation (FAPESB, grant numbers APP071/2011, JCB-0039/2013, and RED-008/2013

Including PrEP for key populations in combination HIV prevention: a mathematical modelling analysis of Nairobi as a case-study

Background: The role of PrEP in combination HIV prevention remains uncertain. We aimed to identify an optimal portfolio of interventions to reduce HIV incidence for a given budget, and to identify the circumstances in which PrEP could be used in Nairobi, Kenya. Methods: A mathematical model was developed to represent HIV transmission among specific key populations (female sex workers (FSW), male sex workers (MSW), and men who have sex with men (MSM)) and among the wider population of Nairobi. The scale-up of existing interventions (condom promotion, anti-retroviral therapy (ART) and male circumcision) for key populations and the wider population as have occurred in Nairobi is represented. The model includes a detailed representation of a Pre-Exposure Prophylaxis (PrEP) intervention and is calibrated to prevalence and incidence estimates specific to key populations and the wider population. Findings: In the context of a declining epidemic overall but with a large sub-epidemic among MSM and MSW, an optimal prevention portfolio for Nairobi should focus on condom promotion for MSW and MSM in particular, followed by improved ART retention, earlier ART, and male circumcision as the budget allows. PrEP for MSW could enter an optimal portfolio at similar levels of spending to when earlier ART is included, however PrEP for MSM and FSW would be included only at much higher budgets. If PrEP for MSW cost as much $500, average annual spending on the interventions modelled would need to be less than$3·27 million for PrEP for MSW to be excluded from an optimal portfolio. Estimated costs per infection averted when providing PrEP to all FSW regardless of their risk of infection, and to high risk FSW only, are $65,160 (95$43,520 - $90,250) and$10,920 (95% credible interval: $4,700 -$51,560) respectively. Interpretation: PrEP could be a useful contribution to combination prevention, especially for underserved key populations in Nairobi. An ongoing demonstration project will provide important information regarding practical aspects of implementing PrEP for key populations in this setting