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Abstract The protection of the replication fork structure under stress conditions is essential for genome maintenance and cancer prevention. A key signaling pathway for fork protection involves TRPV2-mediated Ca2+ release from the ER, which is triggered after the generation of cytosolic DNA and the activation of cGAS/STING. This results in CaMKK2/AMPK activation and subsequent Exo1 phosphorylation, which prevent aberrant fork processing, thereby ensuring genome stability. However, it remains poorly understood how the TRPV2 channel is activated by the presence of cytosolic DNA. Here, through a genome-wide CRISPR-based screen, we identify TRPM8 channel-associated factor 1 (TCAF1) as a key factor promoting TRPV2-mediated Ca2+ release under replication stress or other conditions that activate cGAS/STING. Mechanistically, TCAF1 assists Ca2+ release by facilitating the dissociation of STING from TRPV2, thereby relieving TRPV2 repression. Consistent with this function, TCAF1 is required for fork protection, chromosomal stability, and cell survival after replication stress.

The escalating public debt in African nations has sparked global discussions regarding the sustainability within the region. This concern primarily stems from China's increasing role as a significant financier of African infrastructure projects, raising fears that China might be using debt to gain geopolitical leverage by ensnaring impoverished nations in unmanageable loan agreements. To address this issue, we employ three distinct approaches: a descriptive trend analysis, an examination of the debt-to-GDP ratio, and a modelling approach.For the modelling, we utilize a panel Autoregressive Distributed Lag model to assess the short and long-term relationships between economic growth and specified independent variables, including loans. We choose this model because it allows for panel data analysis encompassing the African countries over a span of 20 years and accounts for potential autocorrelation through the inclusion of lagged terms.Our key findings indicate that, based on the debt-to-GDP ratio, some African countries have sustainable debt levels, while others are at risk of facing financial distress. Furthermore, the results of the Autoregressive Distributed Lag model suggest that Chinese loans contribute to long-term economic growth in the region. Therefore, our study recommends that African governments implement robust debt management strategies to avoid default. Additionally, they should recognize that debt can stimulate economic growth when utilized to enhance infrastructure and production capacity.

Single nucleotide polymorphisms (SNPs) in the Plasmodium falciparum multi-drug resistance protein 1 (Pfmrp1) gene have previously been reported to confer resistance to Artemisinin-based Combination Therapies (ACTs) in Southeast Asia. A total of 300 samples collected from six sites between 2008 and 2019 under an ongoing malaria drug sensitivity patterns in Kenya study were evaluated for the presence of SNPs at Pfmrp1 gene codons: H191Y, S437A, I876V, and F1390I using the Agena MassARRAY® platform. Each isolate was further tested against artemisinin (ART), lumefantrine (LU), amodiaquine (AQ), mefloquine (MQ), quinine (QN), and chloroquine (CQ) using malaria the SYBR Green I-based method to determine their in vitro drug sensitivity. Of the samples genotyped, polymorphism at Pfmrp1 codon I876V was the most frequent, with 59.3% (163/275) mutants, followed by F1390I, 7.2% (20/278), H191Y, 4.0% (6/151), and S437A, 3.3% (9/274). A significant decrease in median 50% inhibition concentrations (IC50s) and interquartile range (IQR) was noted; AQ from 2.996 ng/ml [IQR = 2.604-4.747, n = 51] in 2008 to 1.495 ng/ml [IQR = 0.7134-3.318, n = 40] (P

Background There are limited data on the immunogenicity of coronavirus disease 2019 (COVID-19) vaccines in African populations. Here we report the immunogenicity and safety of the ChAdOx1 nCoV-19 (AZD1222) vaccine from a phase 1/2 single-blind, randomised, controlled trial among adults in Kenya conducted as part of the early studies assessing vaccine performance in different geographical settings to inform Emergency Use Authorisation. Methods We recruited and randomly assigned (1:1) 400 healthy adults aged ≥18 years in Kenya to receive ChAdOx1 nCoV-19 or control rabies vaccine, each as a two-dose schedule with a 3-month interval. The co-primary outcomes were safety, and immunogenicity assessed using total IgG enzyme-linked immunosorbent assay (ELISA) against SARS-CoV-2 spike protein 28 days after the second vaccination. Results Between 28th October 2020 and 19th August 2021, 400 participants were enrolled and assigned to receive ChAdOx1 nCoV-19 (n=200) or rabies vaccine (n=200). Local and systemic adverse events were self-limiting and mild or moderate in nature. Three serious adverse events were reported but these were deemed unrelated to vaccination. The geometric mean anti-spike IgG titres 28 days after second dose vaccination were higher in the ChAdOx1 group (2773 ELISA units [EU], 95% CI 2447, 3142) than in the rabies vaccine group (61 EU, 95% CI 45, 81) and persisted over the 12 months follow-up. We did not identify any symptomatic infections or hospital admissions with respiratory illness and so vaccine efficacy against clinically apparent infection could not be measured. Vaccine efficacy against asymptomatic SARS-CoV-2 infection was 38.4% (95% CI -26.8%, 70.1%; p=0.188). Conclusions The safety, immunogenicity and efficacy against asymptomatic infection of ChAdOx1 nCoV-19 among Kenyan adults was similar to that observed elsewhere in the world, but efficacy against symptomatic infection or severe disease could not be measured in this cohort. Pan-African Clinical Trials Registration PACTR202005681895696 (11/05/2020)

Abstract This study presents the real-time energy consumption of a container ship’s generator engine on two round-trips from the West Coast of the US to the East Asian ports and analyzes the ship’s PM10, PM2.5, NOx, SOx, CO, and HC emissions, shore power usage, and factors affecting energy consumption. The average total energy consumption and air emissions for the two round trips were 1.72 GWh and 42.1 tons, respectively. The transpacific crossing segment had the highest average energy consumption (2848 ± 361 kWh) and pollutant emission rate (78.9 ± 10.0 kg h−1). On the other hand, the West Coast of the US had the least energy consumption due to shore power adoption. Furthermore, switching from heavy fuel oil (HFO) to ultra-low-sulfur fuel oil (ULSFO) greatly reduced the emissions of PM and SOx by > 96% and NOx by 17.0%. However, CO and HC increased by 16.9% and 36.1%, respectively, implying incomplete combustion. In addition, the energy consumption was influenced by the number of reefers and wind. Therefore, this study recommends further research on energy-efficient reefers, generator engine optimization, and shore power adoption to reduce emissions from container ships.

Background: The COVID-19 pandemic relies on real-time polymerase chain reaction (qRT-PCR) for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to facilitate roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers’ recommendations to sustain the testing capability in a resource-limited setting. Methods: We used a SARS-CoV-2 positive control RNA sample to generate several 10-fold dilution series that were used for optimization and comparison of the performance of the four qRT-PCR assays: i) Charité Berlin primer-probe set, ii) European Virus Archive – GLOBAL (EVAg) primer-probe set, iii) DAAN premixed commercial kit and iv) Beijing Genomics Institute (BGI) premixed commercial kit. We adjusted the manufacturer- and protocol-recommended reaction component volumes for these assays and assessed the impact on cycle threshold (Ct) values. Results: The Berlin and EVAg E gene and RdRp assays reported mean Ct values within range of each other across the different titrations and with less than 5% difference. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit improved in performance following a reduction of the reaction components. Conclusion: We achieved a 2.6-fold and 4-fold increase in the number of tests per kit for the commercial kits and the primer-probe sets, respectively. All the assays had optimal performance when the primers and probes were used at 0.375X, except for the Berlin N gene assay. The DAAN kit was a reliable assay for primary screening of SARS-CoV-2 whereas the BGI kit’s performance was dependent on the volumes and concentrations of both the reaction buffer and enzyme mix. Our recommendation for SARS-CoV-2 diagnostic testing in resource-limited settings is to optimize the assays available to establish the lowest volume and suitable concentration of reagents required to produce valid results.

Laboratory diagnosis plays a critical role in the containment of a pandemic. Strong laboratory quality management systems (QMS) are essential for laboratory diagnostic services. However, low laboratory capacities in resource-limited countries has made the maintenance of laboratory quality assurance, especially during a pandemic, a daunting task. In this paper, we describe our experience of how we went about providing diagnostic testing services for SARS-CoV-2 through laboratory reorganization, redefining of the laboratory workflow, and training and development of COVID-19 documented procedures, all while maintaining the quality assurance processes during the COVID-19 pandemic at the Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme (KWTRP) laboratory. The KWTRP laboratory managed to respond to the COVID-19 outbreak in Kenya by providing diagnostic testing for the coastal region of the country, while maintaining its research standard quality assurance processes. A COVID-19 team comprising of seven sub-teams with assigned specific responsibilities and an organizational chart with established reporting lines were developed. Additionally, a total of four training sessions were conducted for county Rapid Response Teams (RRTs) and laboratory personnel. A total of 11 documented procedures were developed to support the COVID-19 testing processes, with three for the pre-analytical phases, seven for the analytical phase, and one for the post-analytical phase. With the workflow re-organization, the development of appropriate standard operating procedures, and training, research laboratories can effectively respond to pandemic outbreaks while maintaining research standard QMS procedures.

Abstract While understanding the genetic basis of heat tolerance is crucial in the context of global warming’s effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual’s heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature–humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand–receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.

Provision of the bed net in Sub-Saharan Africa has substantially resulted in the decrease in malaria incidences in the region. However, malaria still ravages these regions causing significant deaths. This situation has been attributed to socio-economic inequalities that reduce access to the net, failure to seek treatment, and poor antimalarial drug use. Information about these factors in malaria control in Western Kenya highlands is not clearly documented. This study sought to find out bed net availability and use, treatment-seeking, and antimalarial drug use behavior in two rural communities. The study was a qualitative-quantitative baseline cross-sectional survey carried out in two rural villages in Western Kenya highlands in November – December 2018. Focus group discussion, a semi-structured questionnaire, and in-depth interviews were conducted in 736 households to determine: socio-demographic characteristics; bed net availability and use; action taken when sick with malaria, and antimalarial drug usage. Socio-demographic characteristics and the responses of the participants were expressed as percentages. Dependent and independent variables were cross-tabulated for calculation of OR and association was tested using Pearson Chi-square at 95% CI and a p ≤ 0.05 was considered significant. Ninety-three percent of the respondents had used the net the previous night, females (56.50%) constituted the majority of respondents, going to health facility (84.26%) was the preferred action taken when a person had malaria, Artemether Lumefantrine (90.19%), and a pain killer was the most cited drug, 22.96% of the responders reported to have failed to complete antimalarial dose saying that they had recovered from the malaria bout and 9.80% reported to re-use the remaining part of the dosage. This was the first study in mining and sugarcane growing communities in Western Kenya Highlands that has shown that there was no association between socio-demographic parameters and bed net use, action taken when having malaria, and adherence to drug use. The two rural communities have the bed net and know its use. They have good knowledge of malaria and seek treatment whenever they saw malaria signs. The study also reported that the action the sick person took when they had a malaria bout, the drug they got from the health facility, or failure to complete an AL dosage regimen was not associated with socio-demographic characteristics of the responder. These findings raise the need for further qualitative studies in other settings to accept or deny that there was no association between socio-demographics and action taken when hit with malaria bout, the drug used, and failure to complete drug dosage.

Background: The emergence of artemisinin resistance in South East Asia calls for urgent discovery of new drug compounds that have antiplasmodial activity. Unlike the classical compound screening drug discovery methods, the rational approach involving targeted drug discovery is less cumbersome and therefore key for innovation of new antiplasmodial compounds. Plasmodium falciparum (Pf) utilizes the process of host erythrocyte remodeling using Plasmodium-helical interspersed sub-telomeric domain (PHIST) containing proteins, which are amenable drug targets. The aim of this study is to identify inhibitors of PHIST from sulfated polysaccharides as new antimalarials. Methods: 251 samples from an ongoing study of epidemiology of malaria and drug resistance sensitivity patterns in Kenya were sequenced for PHISTb/RLP1 gene using Sanger sequencing. The sequenced reads were mapped to the reference Pf3D7 protein sequence of PHISTb/RLP1 using CLC Main Workbench. Homology modeling of both reference and mutant protein structures was achieved using the LOMETs tool. The models were refined using ModRefiner for energy minimization. Ramachandran plot was generated by ProCheck to assess the conformation of amino acids in the protein model. Protein binding sites predictions were assessed using FT SITE software. We searched for prospective antimalarials from PubChem. Docking experiments were achieved using AutoDock Vina and analysis results visualized in PyMOL. Results: Sanger sequencing generated 86 complete sequences. Upon mapping of the sequences to the reference, 12 non-synonymous single nucleotide polymorphisms were considered for mutant protein structure analysis. Eleven drug compounds with antiplasmodial activity were identified. Both modeled PHISTb/RLP1 reference and mutant structures had a Ramachandran score of >90% of the amino acids in the favored region. Ten of the drug compounds interacted with amino acid residues in PHISTb and RESA domains, showing potential activity against these proteins. Conclusion: This research identifies inhibitors of exported proteins that can be used in in vitro tests against the Plasmodium parasite.

Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: allele frequency differentials, minor allele frequency profiles, and Wright's Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis, and discriminant analysis of principal components. The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.

Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: allele frequency differentials, minor allele frequency profiles, and Wright’s Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis, and discriminant analysis of principal components. The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.

Accumulating data suggest an important role of growth factors in autoimmune diseases and parasitic nematode infections. Nematodes are used in clinical studies of autoimmune diseases and parasite-derived molecules are widely studied for their therapeutic potential in various types of disorders. However, the effect of nematode infection on growth factors in autoimmune disorders has not been studied. The objective of this study was to evaluate the influence of infection with the intestinal nematode Heligmosomoides polygyrus in murine autoimmune models on the production of growth factors. Here, the level of a variety of growth factors related mainly to angiogenesis was evaluated by protein array in the intestinal mucosa of C57BL/6 dextran sodium sulfate-induced colitic mice and in cerebral spinal fluid of experimental autoimmune encephalomyelitis (EAE) mice infected with nematodes. In addition, vessel formation was evaluated in the brains of EAE mice infected with H. polygyrus. A significant influence of nematode infection on the level of angiogenic factors was observed. Parasitic infection of colitic mice resulted in upregulation of mucosal AREG, EGF, FGF-2, and IGFBP-3 in the intestine of the host and better adaptation (infectivity). In EAE mice, infection increased the level of FGF-2 and FGF-7 in CSF. In addition, remodeling of brain vessels was observed, with a higher density of long vessels. Nematode-derived factors are promising tools to fight autoimmune diseases and to study angiogenesis.

Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.

Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.

Abstract Yield-phenology relation is a critical issue affecting rainfed maize field productivity in semiarid east African Plateau (EAP). We first introduced Chinese ridge-furrow mulching (RFM) system to EAP, using three maize cultivars with early-, mid- and late-maturing traits as test materials. A two-year field experiment was conducted in a semiarid farm of Kenya from 2012 to 2013. Three treatments were designed: alternative ridge and furrow with transparent plastic mulching (FT), with black plastic mulching (FB) and without mulching (CK). We found that FT and FB significantly increased soil moisture and accelerated crop maturity across two growing seasons. Leaf area and shoot biomass were increased by 30.2% and 67.5% in FT, 35.2% and 73.5% in FB, respectively, compared with CK. Grain yield, water use efficiency and economic output were increased by 55.6%, 57.5% and 26.7% in FT, and 50.8%, 53.3% and 19.8% in FB, respectively. Optimal yield and economic benefit were observed in late-maturing cultivar due to increased topsoil temperature in FT in 2012 (cool), and in early-maturing cultivar owing to cooling effect in FB in 2013 (warm). Our study suggested RFM system, combined with crop phenology selection, be a promising strategy to boost maize productivity and profitability in semiarid EAP.

Crystal violet (CV) dye is a water-soluble, toxic, recalcitrant organic dye that causes severe health problems and environment pollution. The current study assesses the potential of Waste Coffee Husks (WCH) in adsorption of crystal violet (CV) dye. Batch experiments were designed to determine the effect of pH, dye concentration, adsorbent dose, and contact time in dye removal. Result revealed that removal of CV was highly favored by lower temperatures and acidic medium. Dye removal per unit mass of WCH increased with increase in contact time, dye concentration and surface area. At ambient temperature, the maximum adsorption efficiency of up to 94% was achieved within 10 min at pH 3. Adsorption capacity of Waste Coffee Husks was found to be 12.0360 mg/l for initial dye concentration of 12.2394 mg/l at 25 °C. The experimental data followed pseudo-second-order kinetic models indicating that dye adsorption was controlled by chemical process involving valence forces through sharing or exchange of electrons between CV dye and WCH. Adsorption equilibrium data followed Freundlich and Langmuir isotherm models. Gibbs free energy (∆G°) of the system showed increasing spontaneity with temperatures while positive entropy value (∆S°) implied random disorder of molecules featured at solution/solid interface. Negative enthalpy value (∆H°) confirmed exothermic nature of this adsorption process. These results demonstrate that Waste Coffee Husk are cost-effective, eco-friendly and low-cost bio renewable material for dye removal in industrial effluents. Keywords: Adsorption, Crystal violet dye, Waste coffee husk, Isotherms, Kinetics, Equilibrium

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a "local indigenous' composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.

The nonsense mediated RNA decay (NMD) pathway safeguards the integrity of the transcriptome by targeting mRNAs with premature translation termination codons (PTCs) for degradation. It also regulates gene expression by degrading a large number of non-mutant RNAs (including mRNAs and noncoding RNAs) that bear NMD-inducing features. Consequently, NMD has been shown to influence development, cellular response to stress, and clinical outcome of many genetic diseases. Small molecules that can modulate NMD activity provide critical tools for understanding the mechanism and physiological functions of NMD, and they also offer potential means for treating certain genetic diseases and cancer. Therefore, there is an intense interest in identifying small-molecule NMD inhibitors or enhancers. It was previously reported that both inhibition of NMD and treatment with the AMPK-selective inhibitor Compound C (CC) induce autophagy in human cells, raising the possibility that CC may be capable of inhibiting NMD. Here we show that CC indeed has a NMD-inhibitory activity. Inhibition of NMD by CC is, however, independent of AMPK activity. As a competitive ATP analog, CC does not affect the kinase activity of SMG1, an essential NMD factor and the only known kinase in the NMD pathway. However, CC treatment down-regulates the protein levels of several NMD factors. The induction of autophagy by CC treatment is independent of ATF4, a NMD target that has been shown to promote autophagy in response to NMD inhibition. Our results reveal a new activity of CC as a NMD inhibitor, which has implications for its use in basic research and drug development.

The Plasmodium falciparum in vitro culture system is critical for genotypic and phenotypic analyses of the parasites. For genotypic analysis, the genomic DNA can be obtained directly from the patient blood sample or from culture adapted parasites whereas for phenotypic analysis, immediate ex vivo or in vitro culture adapted parasites are used. However, parasite biology studies have not investigated whether culture adaptation process affects genotypic and/or phenotypic characteristics of the parasites in short- or long-term cultures. Here, we set out to study the dynamics and stability of parasite genetic and phenotypic profiles as field isolate parasites were adapted in continuous cultures. Parasites collected from three different patients presenting with uncomplicated malaria were adapted and maintained in drug-free continuous cultures. Aliquots from the continuous cultures were collected every 24-48 hours for analyses. Each aliquot was treated as a separate parasite sample. For genetic analysis, microsatellite (MS) typing and single nucleotide polymorphism (SNP) analyses of 23 drug resistance markers were done. The 50% inhibitory concentrations (IC50) for some of the samples were also established for four antimalarial drugs. Samples from each patient (parasite-line) were compared as they were passed through the continuous culture. Data revealed genotypic and phenotypic profiles for the three parasite-lines fluctuated from one generation to the next with no specific pattern or periodicity. With few exceptions, multilocus analysis revealed samples from each parasite-line had high genetic diversity with unique haplotypes. Interestingly, changes in MS and SNP profiles occurred simultaneously. The difference in the IC50s of samples in each parasite-line reached statistical significance. However, phenotypic changes did not correspond or correlate to genotypic changes. Our study revealed parasite genetic and phenotypic characteristics fluctuates in short- and long-term cultures, which indicates parasite genetic information obtained even in short cultures is likely to be different from the natural infection parasites.

Malaria causes about half a million deaths annually, with Plasmodium falciparum being responsible for 90% of all the cases. Recent reports on artemisinin resistance in Southeast Asia warrant urgent discovery of novel drugs for the treatment of malaria. However, most bioactive compounds fail to progress to treatments due to safety concerns. Drug repositioning offers an alternative strategy where drugs that have already been approved as safe for other diseases could be used to treat malaria. This study screened approved drugs for antimalarial activity using an in silico chemogenomics approach prior to in vitro verification. All the P. falciparum proteins sequences available in NCBI RefSeq were mined and used to perform a similarity search against DrugBank, TTD and STITCH databases to identify similar putative drug targets. Druggability indices of the potential P. falciparum drug targets were obtained from TDR targets database. Functional amino acid residues of the drug targets were determined using ConSurf server which was used to fine tune the similarity search. This study predicted 133 approved drugs that could target 34 P. falciparum proteins. A literature search done at PubMed and Google Scholar showed 105 out of the 133 drugs to have been previously tested against malaria, with most showing activity. For further validation, drug susceptibility assays using SYBR Green I method were done on a representative group of 10 predicted drugs, eight of which did show activity against P. falciparum 3D7 clone. Seven had IC50 values ranging from 1 μM to 50 μM. This study also suggests drug-target association and hence possible mechanisms of action of drugs that did show antiplasmodial activity. The study results validate the use of proteome-wide target similarity approach in identifying approved drugs with activity against P. falciparum and could be adapted for other pathogens.

To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work) with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV), are associated with increased prevalence of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied.A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19) and women engaged in sex work (female sex workers, FSW, N = 48), using Illumina sequencing (16S rRNA, V3 region).Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002) and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001). Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota.High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour.

Harvesting stage of sweet sorghum (Sorghum bicolor L. Moench) cane is an important aspect in the content of sugar for production of industrial alcohol. Four sweet sorghum genotypes were evaluated for harvesting stage in a randomized complete block design. In order to determine sorghum harvest growth stage for bioethanol production, sorghum canes were harvested at intervals of seven days after anthesis. The genotypes were evaluated at different stages of development for maximum production of bioethanol from flowering to physiological maturity. The canes were crushed and juice fermented to produce ethanol. Measurements of chlorophyll were taken at various stages as well as panicles from the harvested canes. Dried kernels at 14% moisture content were also weighed at various stages. Chlorophyll, grain weight, absolute ethanol volume, juice volume, cane yield, and brix showed significant (p=0.05) differences for genotypes as well as the stages of harvesting. Results from this study showed that harvesting sweet sorghum at stages IV and V (104 to 117 days after planting) would be appropriate for production of kernels and ethanol. EUSS10 has the highest ethanol potential (1062.78 l ha−1) due to excellent juice volume (22976.9 l ha−1) and EUSS11 (985.26 l ha−1) due to its high brix (16.21).

Delineation of aquatic plants and estimation of its surface extent are crucial to the efficient control of its proliferation, and this information can be derived accurately with fine resolution remote sensing products. However, small swath and low observation frequency associated with them may be prohibitive for application to large water bodies with rapid proliferation and dynamic floating aquatic plants. The information can be derived from products with large swath and high observation frequency, but with coarse resolution; and the quality of so derived information must be eventually assessed using finer resolution data. In this study, we evaluate two methods: Normalized Difference Vegetation Index (NDVI) slicing and maximum likelihood in terms of delineation; and two methods: Gutman and Ignatov’s NDVI-based fractional cover retrieval and linear spectral unmixing in terms of area estimation of aquatic plants from 300 m Medium Resolution Imaging Spectrometer (MERIS) data, using as reference results obtained with 30 m Landsat-7 ETM+. Our results show for delineation, that maximum likelihood with an average classification accuracy of 80% is better than NDVI slicing at 75%, both methods showing larger errors over sparse vegetation. In area estimation, we found that Gutman and Ignatov’s method and spectral unmixing produce almost the same root mean square (RMS) error of about 0.10, but the former shows larger errors of about 0.15 over sparse vegetation while the latter remains invariant. Where an endmember spectral library is available, we recommend the spectral unmixing approach to estimate extent of vegetation with coarse resolution data, as its performance is relatively invariant to the fragmentation of aquatic vegetation cover.

The appraisal of crop water requirements (CWR) is crucial for the management of water resources, especially in arid and semi-arid regions where irrigation represents the largest consumer of water, such as the Doukkala area, western Morocco. Simple and (semi) empirical approaches have been applied to estimate CWR: the first one is called Kc-NDVI method, based on the correlation between the Normalized Difference Vegetation Index (NDVI) and the crop coefficient (Kc); the second one is the analytical approach based on the direct application of the Penman-Monteith equation with reflectance-based estimates of canopy biophysical variables, such as surface albedo (r), leaf area index (LAI) and crop height (hc). A time series of high spatial resolution RapidEye (REIS), SPOT4 (HRVIR1) and Landsat 8 (OLI) images acquired during the 2012/2013 agricultural season has been used to assess the spatial and temporal variability of crop evapotranspiration ETc and biophysical variables. The validation using the dual crop coefficient approach (Kcb) showed that the satellite-based estimates of daily ETc were in good agreement with ground-based ETc, i.e., R2 = 0.75 and RMSE = 0.79 versus R2 = 0.73 and RMSE = 0.89 for the Kc-NDVI, respective of the analytical approach. The assessment of irrigation performance in terms of adequacy between water requirements and allocations showed that CWR were much larger than allocated surface water for the entire area, with this difference being small at the beginning of the growing season. Even smaller differences were observed between surface water allocations and Irrigation Water Requirements (IWR) throughout the irrigation season. Finally, surface water allocations were rather close to Net Irrigation Water Requirements (NIWR).

Temporal variability analysis of rainfall and river discharges is useful in determining the likelihood of the occurrence of extreme events such as drought or flooding for the purposes of developing policies to mitigate their effects. This study investigated the temporal variability of rainfall and discharges into Lake Nakuru, Kenya using meteorological drought indicators and hydrological drought indicators from 1981 to 2018. The standardized precipitation index (SPI) and standardized precipitation evaporation index (SPEI) were used to characterize meteorological drought, while the streamflow drought index (SDI) was used to characterize hydrological drought. A SWAT model was applied for the prediction of streamflow on five tributaries of Lake Nakuru (Njoro, Ngosur, Nderit, Larmudiac, and Makalia Rivers). The model was successfully calibrated on Njoro River at the upstream of river gauging station 2FCO5 from 1984 to 1996, and the parameters were validated from 1997 to 2007. The SUFI-2 algorithm was applied in SWATCup to perform the calibration of the model. The model performance was considered satisfactory in daily time step (NSE = 0.58, R2 = 0.58 during calibration and NSE = 0.52, R2 = 0.68 during validation). The average annual water balance revealed that out of 823 mm received annual precipitation, 154 mm was surface runoff and 178 mm was the annual average water yield. The average annual actual evapotranspiration (ET) was 607 mm. The results for the temporal variation of the SPI and SDI for the five subcatchments indicated that the drought events identified by the 12-month SPI/SPEI were almost all identified by the 12-month SDI. At the catchment scale, SPI showed an equal distribution of wet and dry periods, with 50.00% of positive anomalies and 50.00% of negative anomalies being observed from 1981 to 2018, while SDI observes a high frequency of dry periods (52.63%) and a lower frequency of wet periods (47.37%). There is a higher frequency of wet periods compared to dry periods for both indices from 2009 to 2010 at 60.00% and 40.00% for SPI and 90.00% and 10.00% for SDI, respectively. Both indices observed that 1984 and 2000 were severely dry years (SPI/SPEI < −2.00), while 2018 was severely wet (SPI/SPEI > 2.00). The results for the variability in rainfall and streamflow indices revealed that the last 10 years (2009−2018) were wetter than the period from 1981 to 2008.

Genetically determined artemisinin resistance in Plasmodium falciparum has been described in Southeast Asia. The relevance of recently described Kelch 13-propeller mutations for artemisinin resistance in Sub-Saharan Africa parasites is still unknown. Southeast Asia parasites have low genetic diversity compared to Sub-Saharan Africa, where parasites are highly genetically diverse. This study attempted to elucidate whether genetics provides a basis for discovering molecular markers in response to artemisinin drug treatment in P. falciparum in Kenya. The genetic diversity of parasites collected pre- and post- introduction of artemisinin combination therapy (ACT) in western Kenya was determined. A panel of 12 microsatellites and 91 single nucleotide polymorphisms (SNPs) distributed across the P. falciparum genome were genotyped. Parasite clearance rates were obtained for the post-ACT parasites. The 12 microsatellites were highly polymorphic with post-ACT parasites being significantly more diverse compared to pre-ACT (p < 0.0001). The median clearance half-life was 2.55 hours for the post-ACT parasites. Based on SNP analysis, 15 of 90 post-ACT parasites were single-clone infections. Analysis revealed 3 SNPs that might have some causal association with parasite clearance rates. Further, genetic analysis using Bayesian tree revealed parasites with similar clearance phenotypes were more closely genetically related. With further studies, SNPs described here and genetically determined response to artemisinin treatment might be useful in tracking artemisinin resistance in Kenya.

The genotype and environment interaction influences the selection criteria of sorghum (Sorghum bicolor) genotypes. Eight sweet sorghum genotypes were evaluated at five different locations in two growing seasons of 2014. The aim was to determine the interaction between genotype and environment on cane, juice, and ethanol yield and to identify best genotypes for bioethanol production in Kenya. The experiments were conducted in a randomized complete block design replicated three times. Sorghum canes were harvested at hard dough stage of grain development and passed through rollers to obtain juice that was then fermented to obtain ethanol. Cane, juice, and ethanol yield was analyzed using the additive main effect and multiplication interaction model (AMMI) and genotype plus genotype by environment (GGE) biplot. The combined analysis of variance of cane and juice yield of sorghum genotypes showed that sweet sorghum genotypes were significantly (P

Single Nucleotide Polymorphisms (SNPs) in the Pfmdr1, and Pfcrt, genes of Plasmodium falciparum may confer resistance to a number of anti-malaria drugs. Pfmdr1 86Y and haplotypes at Pfcrt 72-76 have been linked to chloroquine (CQ) as well as amodiaquine (AQ) resistance. mefloquine (MQ) and lumefantrine (LU) sensitivities are linked to Pfmdr1 86Y. Additionally, Pfcrt K76 allele carrying parasites have shown tolerance to LU. We investigated the association between Pfmdr1 86/Pfcrt 72-76 and P. falciparum resistance to CQ, AQ, MQ and LU using field samples collected during 2008-2011 from malaria endemic sites in western Kenya. Genomic DNA from these samples was genotyped to examine SNPs and haplotypes in Pfmdr1 and Pfcrt respectively. Additionally, immediate ex vivo and in vitro drug sensitivity profiles were assessed using the malaria SYBR Green I fluorescence-based assay. We observed a rapid but steady percent increase in wild-type parasites with regard to both Pfmdr1 and Pfcrt between 2008 and 2011 (p

There is an urgent need to improve our understanding of the mucosal immuno-pathogenesis of HIV acquisition in the female genital tract, particularly in high-risk women such as female sex workers (FSWs). Cervical biopsy samples offer technical advantages over cytobrush sampling, but there are concerns that this might increase HIV acquisition, particularly if healing is slow and/or women do not abstain from sex during healing.Cervical biopsy samples and cervico-vaginal swabs for co-infection diagnostics, prostate specific antigen (PSA) and immune studies were collected from 59 women, including HIV seropositive and HIV-exposed seronegative (HESN) FSWs as well as lower risk women from Nairobi, Kenya. A clinical-demographic questionnaire was administered and women were instructed to avoid sexual intercourse, douching and the insertion of tampons for 14 days. All participants underwent a repeat exam to assess healing within the 14 days, and had HIV diagnostics at six months. Cervical sampling was well tolerated, and 82% of participants had healed macroscopically by 5 days. Both self-report and PSA screening suggested high levels of compliance with pre- and post-procedure abstinence. Delayed healing was associated with vulvovaginal candidiasis (VVC) and HESN status. At six-month follow up all low-risk and HESN participants remained HIV seronegative.Cervical biopsy sampling is a safe and well-tolerated method to obtain cervical biopsies in this context, particularly if participants with VVC are excluded. As healing could be delayed up to 11 days, it is important to support (both financially and with rigorous counseling) a period of post-procedure abstinence to minimize HIV risk.