Copy Number Variation of Fc Gamma Receptor Genes in HIV-Infected and HIV-Tuberculosis Co-Infected Individuals in Sub-Saharan Africa

AIDS, caused by the retrovirus HIV, remains the largest cause of morbidity in sub-Saharan Africa yet almost all genetic studies have focused on cohorts from Western countries. HIV shows high co-morbidity with tuberculosis (TB), as HIV stimulates the reactivation of latent tuberculosis (TB). Recent clinical trials suggest that an effective anti-HIV response correlates with non-neutralising antibodies. Given that Fcγ receptors are critical in mediating the non-neutralising effects of antibodies, analysis of the extensive variation at Fcγ receptor genes is important. Single nucleotide variation and copy number variation (CNV) of Fcγ receptor genes affects the expression profile, activatory/inhibitory balance, and IgG affinity of the Fcγ receptor repertoire of each individual. In this study we investigated whether CNV of FCGR2C, FCGR3A and FCGR3B as well as the HNA1 allotype of FCGR3B is associated with HIV load, response to highly-active antiretroviral therapy (HAART) and co-infection with TB. We confirmed an effect of TB-co-infection status on HIV load and response to HAART, but no conclusive effect of the genetic variants we tested. We observed a small effect, in Ethiopians, of FCGR3B copy number, where deletion was more frequent in HIV-TB co-infected patients than those infected with HIV alone.     

Effect of mustard green manure and dried plant residue on chickpea wilt (Fusarium oxysporum f.sp. ciceris)

Pot experiments were carried out in the green house at Amhara Regional Agriculture Research Institute (ARARI) Bahirdar, Ethiopia, to evaluate the potential of Brassica carinata cultivars, namely Holleta-l, S-67 and Yellow Dodola in 2007 and 2008. The effect of B. carinata (Ethiopian mustard) cultivars Holleta-1, S-67 and Yellow Dodola as green manure and Holleta-1 as dried plant residue on chickpea fusarium wilt (Fusarium oxysporum f.sp. ciceris) was studied. Six rates of green manure and dried plant residue (0, 20, 40, 60, 80 and 100 g) each per kg of pathogen-infested soil were used in the experiments. Infested soil without B. carinata cultivars amendment as a control and susceptible check variety JG-62 without amendment was used in the experiments. In the experiments, the treatments were arranged in randomised complete block design in three replications and repeated twice. Data on seedling emergence, wilt incidence, fresh weight and dry weight were collected. The amendments of infested soil with B. carinata cultivars green manure and dried plant residue reduced the incidence of chickpea fusarium wilt. The incorporation of the green manure Holleta-1, S-67 and Yellow Dodola at 20–100 g/kg of infested soil was effective in reducing wilt incidences on chickpea. However, the incorporation of Yellow Dodola at 80 and 100 g green manure per kg of infested soil were the best combination in reducing significantly wilt incidence. The application of the dried plant residue at 20–100 g/kg of infested soil was effective in reducing wilt incidences on chickpea. However when applied dried plant residue at 60, 80 and 100 g green manure per kg of infested soil were better in reducing wilt incidence as compared to 20 and 40 g/kg of infested soil. The three cultivars green manure incorporated at different level of doses affected the influence of fusarium wilt on the fresh and dry weight respectively. The use of Holleta-1 green manure at 20–100 g/kg of infested soil significantly reduced disease incidence in the range of 20.0–33.3%. Green manure amendment S-67 significantly reduced disease incidence in the range of 20.0–46.6%. Yellow Dodola reduce disease incidence with 26.7–60%. The dried plant residue incorporated at different level influence fusarium wilt. The application of Holleta-1 dried plant residue at 20–100 g/kg of infested soil reduced disease incidence in the range 20.0–26.7%. The results imply the potential of using B. carinata green manure and dried plant residue as cultural management components in chickpea fusarium wilt disease management.     

Distribution and association of factors influencing bean common bacterial blight (Xanthomonas axonopodis pv. phaseoli) epidemics in Southern Ethiopia

Abstract

Field surveys were conducted to determine the spatiotemporal distribution and the association of disease intensity with cropping systems and other environmental factors in Southern Ethiopia during 2016 and 2017. In both years, a total of 190 bean fields were surveyed in five districts, and common bacterial blight (CBB) was 100% prevalent. But disease incidence and severity varied among districts and between cropping years. Bean planting in Arbaminch suffered from 31% to 38%, 6–13%, 12–17% and 8–12% higher CBB severity than bean cultivation in Burjdi, Mihirab Abaya, Demba Gofa and Konso districts, respectively. The associations of disease parameters with independent factors were assessed using the logistic regression analyses. District, cropping year, altitude, land preparation, cropping system, fertiliser application, planting date, growth stage and weed infestation were associated with both disease incidence and severity with variable levels of significance. Common bean genotype was also significantly (P?<?.005) associated with disease severity in a multiple variable model. Concerning incidence, variable associations were demonstrated by the model. These results indicate that CBB is severe and highly prevalent in Southern Ethiopia. Therefore, efforts should be geared towards crop residue management, optimal tillage and fertiliser application, weeding, clean seed source and early planting approach to manage the disease.     

Optimization of selection for growth in Menz Sheep while minimizing inbreeding depression in fitness traits

The genetic trends in fitness (inbreeding, fertility and survival) of a closed nucleus flock of Menz sheep under selection during ten years for increased body weight were investigated to evaluate the consequences of selection for body weight on fitness. A mate selection tool was used to optimize in retrospect the actual selection and matings conducted over the project period to assess if the observed genetic gains in body weight could have been achieved with a reduced level of inbreeding. In the actual selection, the genetic trends for yearling weight, fertility of ewes and survival of lambs were 0.81 kg, –0.00026% and 0.016% per generation. The average inbreeding coefficient remained zero for the first few generations and then tended to increase over generations. The genetic gains achieved with the optimized retrospective selection and matings were highly comparable with the observed values, the correlation between the average breeding values of lambs born from the actual and optimized matings over the years being 0.99. However, the level of inbreeding with the optimized mate selections remained zero until late in the years of selection. Our results suggest that an optimal selection strategy that considers both genetic merits and coancestry of mates should be adopted to sustain the Menz sheep breeding program.     

Ecology and management of the woolly whitefly (Hemiptera: Aleyrodidae), a new invasive citrus pest in Ethiopia

Distribution and importance of woolly whitefly (Aleurothrixus floccosus) (Maskell) (Hemiptera: Aleyrodidae), was studied in Ethiopia with an evaluation of treatments against it. Results showed that the pest is distributed in most citrus-growing parts of the country equally infesting all types of citrus crops. Only one pupal parasitoid, Amitus sp., was recorded at Melkaoba. During 2006-2007, eight treatments gave better control of woolly whitefly compared with the control: endod (Phytolacca dodecandra L'Herit) berry extract, white oil 80%, neem oil, omo detergent soap, band application of gasoline, cyhalothrin (karate) 5% EC, selecron (profenofos) 500 EC, and rimon (novaluron) 10 EC. Treatments were applied on 6-8 yr-old orange trees at Melkaoba and Nazareth. At Melkaoba, application of cyhalothrin, selecron, white oil, and Neem gave better control of woolly whitefly compared with the control. All the treatments resulted in a lower number of ants than the control. Ants disrupt biocontrol agents of honeydew-secreting pests, including woolly whiteflies. Mean infestation score was higher in the control than the rest of the treatments. Similarly, at Nazareth, woolly whitefly numbers were lower recorded on cyhalothrin-treated plants. However, the numbers of eggs were significantly higher in endod extract-sprayed plants than the control. All treatments controlled ants better than the control except endod. Infestation scores were lower on endod- and cyhalothrin-treated plants than the control. Mean number of adult woolly whiteflies and eggs were significantly higher on newly grown leaves than older leaves. In general, the number of live adult woolly whiteflies showed a decreasing trend at both sites after treatment applications compared with the control.     

Pharmacogenetic & pharmacokinetic biomarker for efavirenz based ARV and rifampicin based anti-TB drug induced liver injury in TB-HIV infected patients

Background

Implication of pharmacogenetic variations and efavirenz pharmacokinetics in concomitant efavirenz based antiviral therapy and anti-tubercular drug induced liver injury (DILI) has not been yet studied. We performed a prospective case-control association study to identify the incidence, pharmacogenetic, pharmacokinetic and biochemical predictors for anti-tubercular and antiretroviral drugs induced liver injury (DILI) in HIV and tuberculosis (TB) co-infected patients.

Methods and Findings

Newly diagnosed treatment naïve TB-HIV co-infected patients (n = 353) were enrolled to receive efavirenz based ART and rifampicin based anti-TB therapy, and assessed clinically and biochemically for DILI up to 56 weeks. Quantification of plasma efavirenz and 8-hydroxyefaviernz levels and genotyping for NAT2, CYP2B6, CYP3A5, ABCB1, UGT2B7 and SLCO1B1 genes were done. The incidence of DILI and identification of predictors was evaluated using survival analysis and the Cox Proportional Hazards Model. The incidence of DILI was 30.0%, or 14.5 per 1000 person-week, and that of severe was 18.4%, or 7.49 per 1000 person-week. A statistically significant association of DILI with being of the female sex (p = 0.001), higher plasma efavirenz level (p = 0.009), efavirenz/8-hydroxyefavirenz ratio (p = 0.036), baseline AST (p = 0.022), ALT (p = 0.014), lower hemoglobin (p = 0.008), and serum albumin (p = 0.007), NAT2 slow-acetylator genotype (p = 0.039) and ABCB1 3435TT genotype (p = 0.001).

Conclusion

We report high incidence of anti-tubercular and antiretroviral DILI in Ethiopian patients. Between patient variability in systemic efavirenz exposure and pharmacogenetic variations in NAT2, CYP2B6 and ABCB1 genes determines susceptibility to DILI in TB-HIV co-infected patients. Close monitoring of plasma efavirenz level and liver enzymes during early therapy and/or genotyping practice in HIV clinics is recommended for early identification of patients at risk of DILI.     

Bacterial profile and drug susceptibility pattern of urinary tract infection in pregnant women at University of Gondar Teaching Hospital, Northwest Ethiopia

ABSTRACT: BACKGROUND: Urinary tract infection (UTI) is a common health problem among pregnant women. Proper investigation and prompt treatment are needed to prevent serious life threatening condition and morbidity due to urinary tract infection that can occur in pregnant women. Recent report in Addis Ababa, Ethiopia indicated the prevalence of UTI in pregnant women was 11.6 % and Gram negative bacteria was the predominant isolates and showed multi drug resistance. This study aimed to assess bacterial profile that causes urinary tract infection and their antimicrobial susceptibility pattern among pregnant women visiting antenatal clinic at University of Gondar Teaching Hospital, Northwest Ethiopia. METHODS: A cross-sectional study was conducted at University of Gondar Teaching Hospital from March 22 to April 30, 2011. Mid stream urine samples were collected and inoculated into Cystine Lactose Electrolyte Deficient medium (CLED). Colony counts yielding bacterial growth of 105/ml of urine or more of pure isolates were regarded as significant bacteriuria for infection. Colony from CLED was sub cultured onto MacConkey agar and blood agar plates. Identification was done using cultural characteristics and a series of biochemical tests. A standard method of agar disc diffusion susceptibility testing method was used to determine susceptibility patterns of the isolates. RESULTS: The overall prevalence of UTI in pregnant women was 10.4 %. The predominant bacterial pathogens were Escherichia coli 47.5 % followed by coagulase-negative staphylococci 22.5 %, Staphylococcus aureus 10 %, and Klebsiella pneumoniae 10 %. Gram negative isolates were resulted low susceptibility to co-trimoxazole (51.9 %) and tetracycline (40.7 %) whereas Gram positive showed susceptibility to ceftriaxon (84.6 %) and amoxicillin-clavulanic acid (92.3 %). Multiple drug resistance (resistance to two or more drugs) was observed in 95 % of the isolates. CONCLUSION: Significant bacteriuria was observed in asymptomatic pregnant women. Periodic studies are recommended to check the outcome of asymptomatic bacteriuria and also monitor any changes in the susceptibility patterns of urinary tract pathogens in pregnant women.     

Identification and characterization of annexin gene family in rice

Plant annexins are Ca²⁺-dependent phospholipid-binding proteins and are encoded by multigene families. They are implicated in the regulation of plant development as well as protection from drought and other stresses. They are well characterized in Arabidopsis, however no such characterization of rice annexin gene family has been reported thus far. With the availability of the rice genome sequence information, we have identified ten members of the rice annexin gene family. At the protein level, they share 16–64% identity with predicted molecular masses ranging from 32 to 40 kDa. Phylogenetic analysis of rice annexins together with annexins from other monocots led to their classification into five different orthologous groups and share similar motif patterns in their protein sequences. Expression analysis by real-time RT-PCR revealed differential temporal and spatial regulation of these genes. The rice annexin genes are also found to be regulated in seedling stage by various abiotic stressors including salinity, drought, heat and cold. Additionally, in silico analysis of the putative upstream sequences was analyzed for the presence of stress-responsive cis-elements. These results provide a basis for further functional characterization of specific rice annexin genes at the tissue/developmental level and in response to abiotic stresses.