Transcriptome-wide identification and expression analysis of the NAC gene family in lowland bamboo [Oxytenanthera abyssinica (A.Rich) Munro] under abiotic stresses

NAC (NAM, no apical meristem, ATAF and CUC) is one of the largest gene families of the plant-specific transcription factors (TF). NAC TFs have immense involvement in plant growth and developmental processes and have particular importance in enhancing plant resistance to multiple abiotic stresses. NAC members have unique structural makeup and a range of biological activities. Despite their enormous roles in plants, comprehensive study on identification, characterization and expression profiling of NACs under abiotic stress is lacking in Lowland bamboo [Oxytenanthera abyssinica (A.Rich) Munro]. Thus, this study aimed to identify NAC members, characterize their protein properties, construct their phylogenetic relationships and more importantly, establish their expression profiling under abiotic stress. From this abiotic stress-induced transcriptome, 220 lowland bamboo TFs with intact and complete NAC DNA binding domains (PF01849) were identified. Following their identification, analysis of functional annotation, protein characterization, phylogenetic relationships and expression profiling were conducted. The analysis presented up-regulation of 142 unigenes in response to abiotic stress, the association of 26 unigenes directly to stress response and the involvement of 92 unigenes in genetic information processing and 29 in environmental information processing according to KEGG analysis. These results suggest the most likely involvement of NACs in lowland bamboo stress response and adaptation. As a species best survived in a moisture-stressed environment, this study has provided valuable information that could shed light on further functional analysis research efforts aiming to exploit NACs in developing stress-resilient bamboo and related plants

Evaluation of direct colorimetric MTT assay for rapid detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis

With the spread of multidrug-resistant tuberculosis (MDR-TB) strains there is an increasing need for new accurate and cost-effective methods for a rapid diagnostic and drug susceptibility testing (DST), particularly in low-income countries where tuberculosis is hyperendemic. A colorimetric assay using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) has been suggested as a promising method for DST, especially to rifampicin. In this study, we standardized and evaluated the MTT assay for a rapid direct detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis strains from sputum specimens using Lowenstein-Jensen (LJ) culture medium as a gold standard. The MTT assay sensitivity, specificity, positive and negative predictive values for rifampicin were 100%, 86%, 100%, 99%, respectively. For isoniazid, the MTT assay had a 100% sensitivity, specificity, positive and negative predictive values. Interestingly, the MTT assay gave interpretable results within two weeks for 94% of the samples compared to 7-14 weeks for LJ media. Overall, an excellent agreement was observed between MTT assay and LJ proportion method (Kappa, 0.91 for rifampicin and 1.00 for isoniazid). In conclusion, the direct colorimetric MTT assay simultaneously detects susceptible and resistant strains of M. tuberculosis within three weeks. It significantly shortens the time required to obtain a DST result and could be a reliable alternative method for rapid detection of drug-resistant TB strains in high-TB-burden resource-limited settings

Genetic Diversity of Hepatitis B and Hepatitis C Viruses in Ethiopia

Hepatitis B and C viruses are a major cause of mortality and morbidity worldwide. In 2015 alone, viral hepatitis caused 1.34 million deaths, a number comparable to annual deaths caused by tuberculosis but higher than those caused by either HIV or malaria. However, in contrast to these three infectious diseases, viral hepatitis has received relatively little attention. Worldwide, only 9% of HBV-infected and 20% of HCV-infected persons have access to affordable hepatitis testing. Even more worrisome is the fact that only 8% of those diagnosed with HBV and 7.4% of those diagnosed with HCV had started treatment. This is even more problematic in low-income countries like Ethiopia where more than 80% of the population are living in rural areas with a very limited access to healthcare and where viral hepatitis has never been considered a major health priority. Most importantly, the clinical and treatment outcomes of HBV and HCV infections are largely influenced by the high genetic diversity (genotype, subgenotype, recombinants and quasispecies variants) of these viruses that also display distinct geographical distribution worldwide. In this thesis, therefore, we studied the seroepidemiology of HBV and HCV infection and determined the molecular epidemiology and genetic diversity of HBV and HCV in different geographic regions of Ethiopia. We identified that genotype A (A1) and genotype D (D2 and novel D10) of HBV and genotype 4 ( 4d and 4r ) of HCV are the most prevalent in Ethiopia. We further analyzed HBV and HCV quasispecies variants and their association with patients’ clinical characteristics using ultra-deep sequencing approach and found some important variants

The shape of the iceberg: quantification of submicroscopic Plasmodium falciparum and Plasmodium vivax parasitaemia and gametocytaemia in five low endemic settings in Ethiopia.

BACKGROUND: The widespread presence of low-density asymptomatic infections with concurrent gametocytes may be a stumbling block for malaria elimination. This study investigated the asymptomatic reservoir of Plasmodium falciparum and Plasmodium vivax infections in schoolchildren from five settings in northwest Ethiopia. METHODS: Two cross-sectional surveys were conducted in June and November 2015, enrolling 551 students from five schools and 294 students from three schools, respectively. Finger prick whole blood and plasma samples were collected. The prevalence and density of P. falciparum and P. vivax parasitaemia and gametocytaemia were determined by 18S rRNA quantitative PCR (qPCR) and pfs25 and pvs25 reverse transcriptase qPCR. Antibodies against blood stage antigens apical membrane antigen-1 (AMA-1) and merozoite surface protein-1 (MSP-119) were measured for both species. RESULTS: Whilst only 6 infections were detected by microscopy in 881 slides (0.7%), 107 of 845 blood samples (12.7%) were parasite positive by (DNA-based) qPCR. qPCR parasite prevalence between sites and surveys ranged from 3.8 to 19.0% for P. falciparum and 0.0 to 9.0% for P. vivax. The median density of P. falciparum infections (n = 85) was 24.4 parasites/µL (IQR 18.0-34.0) and the median density of P. vivax infections (n = 28) was 16.4 parasites/µL (IQR 8.8-55.1). Gametocyte densities by (mRNA-based) qRT-PCR were strongly associated with total parasite densities for both P. falciparum (correlation coefficient = 0.83, p = 0.010) and P. vivax (correlation coefficient = 0.58, p = 0.010). Antibody titers against P. falciparum AMA-1 and MSP-119 were higher in individuals who were P. falciparum parasite positive in both surveys (p < 0.001 for both comparisons). DISCUSSION: This study adds to the available evidence on the wide-scale presence of submicroscopic parasitaemia by quantifying submicroscopic parasite densities and concurrent gametocyte densities. There was considerable heterogeneity in the occurrence of P. falciparum and P. vivax infections and serological markers of parasite exposure between the examined low endemic settings in Ethiopia