Browsing by Author "Beyene, Dereje (PhD)"

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    DNA Methylation Changes, Prevalence and Risk Factors Associated With HPV Genotypes Among Ethiopian Women Diagnosed for Cervical Cancer
    (Addis Ababa University, 2020-07-07) Kumbi, Birhanu; Beyene, Dereje (PhD); Gebrehiwot, Yirgu (Msc); Seifu, Daniel (PhD); Lorincz, Attila T. (PhD)
    Cervical cancer is the second most common among cancers in Ethiopia with an incidence of more than 6000 cases and around 5000 deaths per year. Infection by high risk human papillomavirus (hrHPV) is the major risk factor for cervical cancer with almost all cases being infected. HPV infection is a very common sexually transmitted infection that majority of sexually active women acquire. Most of the infected women however clear the infection spontaneously in short time while it persists and causes cervical cancer in only small portion of the infected women. Various factors are known to determine the outcome of the infection but with scarce information on the mechanisms. DNA methylation changes in both human genes and HPV genes are among the biological events associated with cervical cancer progression. This study was aimed at determining prevalence of hrHPV, socio-demographic risk factors for cervical cancer and epigenetic changes associated with cervical cancer and evaluate their potential as diagnostic markers. The study was conducted as an observational case-control study by taking records of various risk factors and clinical information along with cervical cell samples for hrHPV testing and DNA methylation analysis. The human EPB41L3 gene promoter region and HPV L1 and L2 regions were PCR amplified from bisulphite converted DNA. The PCR amplicons were then pyrosequenced and proportion of converted cytosine is measured and means of the targeted CpG sites methylation were recorded. Prevalence of both hrHPV and demographic risk factors were compared among women with cervical lesions (cases) and women with normal cytology (controls) to determine associations with various stages of cervical cancer. The DNA methylation assays were evaluated and compared for their performance using Reciever Operating Characteristics (ROC) curve analysis. From a total of 135 women, 96 had cervical cell lesions ranging from CIN1 to invasive cancer (cases) and 39 had no lesion (controls). Parity was higher in cases 5.44(±3.01) than in controls 2.03(±2.04). Cases started sexual intercourse earlier, at mean age of 16.57(±4.04) years, than the controls 20.18(±4.24) years. Hormonal contraceptive use showed no significant difference among cases and controls. HPV DNA was detected in 79(82.3%) of cases and 7(17.9%) of controls from which 77(80.2%) of cases and 6(15.4%) of controls were hrHPV. HPV16 was the most prevalent virus constituting 84% of all hrHPV positive cases and 33.3% of hrHPV positive controls. HPV45, HPV18 and HPV31 were detected in 17.7%, 5.2% and 3.8% respectively of the hrHPV positive cases. Level of methylation in both human and hrHPV DNA was found to be higher in higher grade lesions than in low grade lesions (CIN1) and normal cervical cells. Methylation assays, both EPB41L3 promoter methylation and S5 score discriminated normal and CIN1 from CIN3 or worse lesions with sensitivity and specificity of greater than 95%. In conclusion, higher parity and earlier age at first sexual intercourse are among the factors that put women at higher risk of cervical cancer in addition to hrHPV infection. HPV16 is the most prevalent (69.8%) hrHPV type followed by HPV45 (14.6%) in Ethiopian women with cervical lesions. Methylation levels of the human EPB41L3 promoter region and HPV L1 and L2 regions are potential biomarker to improve precision of diagnosing the cancer and targeting for therapy. EBP41L3 methylation alone discriminated normal and CIN1 cells from CIN3 or worse lesions with 95% sensitivity and 96% specificity while S5 detected with 96% sensitivity and 95% specifi
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    Inheritance Variation in some Human Morphogenetic Traits Among School Age Children of Kale Primary School Kolfea Keraniyo Subcity Addis Ababa
    (Addis Ababa University, 2021-11-03) Mulugeta, Tseganeh; Beyene, Dereje (PhD)
    Morphogenetic characters are physical characters of an individual which are inherited and expressed in different ways. Therefore, this makes it ideal to know the extent of variation among population. However, few studies have been conducted in Ethiopia to know the extent of variation that exist in different races. The study was focused on six morphogenetic characteristics such as tongue rolling, ear lobe attachment, hair line distribution, bent little finger, hitchhiker’s thumb, and palmaris longus muscle (PLM) among the students of kale primary school Addis Ababa Ethiopia. The aim of this study was to find out the inheritance variation of some morphogenetic traits among children of kale primary school having age between 13-18 years. A cross-sectional study was carried out on 325(170 males and 155 females) volunteer students to explore the extent of variation in some morphogenetic traits and to give awareness about the application of morphological variation of the human external ear and that could be translatable for forensic recording of fugitives. The investigator collected the required information by observing the subject and the result was analyzed and association study of traits were conducted by using chi-square test of independence with alpha value of 5% level of significance to identify which trait has association with gender. The study presented distribution of traits in the following order, widow’s peak 116(35.7%) where most males 63(37.1%) exhibit this trait, tongue rolling 242(74.5%) and it was dominated by males 128(75.3%), free ear lobe 217(66.8%) it was also found more in males 115(67.6%), straight thumb 188(57.8%) the difference between gender was found marginal, bent little finger 59(18.2%) which was dominated by females 42(27.1%) and PLM presence 313(96.3%) and absence of this muscle was frequently observed in females 10(6.5%) and as we understand from this study, 96% were found to have PLM muscle, which indicates that there is a sufficient tendon that is essential for various medical procedures. Association evaluation showed no significant association was found between all morphogenetic traits and ages, however, it was found that there is significant association between gender and bent little finger(Χ 2=15.950, p<0.001) and between gender and absence of PLM(Χ 2=6.345, p<0.005). Since the study was conducted in heterogeneous population it is suitable for biomedical, anthropological and forensic studies.
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    Knowledge, Attitude and Practice Regarding Mycobacterium Tuberculosis Among Abiotkirs Preparatory School Students, Addis Ababa
    (Addis Ababa University, 2019-10-10) Wogari, Sewinet; Beyene, Dereje (PhD)
    Tuberculosis (TB) is still among the top ten tropical diseases in the world and affects millions of people in the developing world including Ethiopia. This study aimed to assess the knowledge, attitude and practice (KAP) about TB in Abiotkirs Preparatory School students from September 2019 to October 2019. Qualitative data were collected through well-structured questionnaire and the data analyzed by descriptive statistics. The findings showed that from the total of 76 respondents 64(84.2%) of the students have information about TB and 12(15.8 %) of them have no information. Only 5(6.6%) of participant students gate an information about TB through the activity of co-curricular activity or TB&HIV clubs. Students who got information through TV and radio were 18(23.7%). The participants who indicated that discussion and drama scenes of passing information about TB were 34.2% and18.4% respectively. On the other hand, 14 (14.5%) respondents believed that TB is transmitted by Mosquito bite, 15(19.7%) unsterile sharp instruments, 44 (57.9%) and 17 (22.4%) didn't know the route of transmission of the disease. From the total of 76 respondents only 10(13%)of them had greater than 5000 Birr monthly income while 54(71%) of the respondents had less than 1000 Birr. It was also recorded that 28.9% of the students were feeling ashamed of having TB as a disease and 46.1% of them did not feel ashamed if they have TB or not and on the other hand 25% of them didn't know their feelings. In conclusion the KAP study showed that there is a need to raise the knowledge, attitude and practice of the students about TB as a public health problem and need att4enction by concerned bodies.
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    Molecular Characterization of Drug-Resistant Mycobacterium Tuberculosis and Evaluation of the Performance of Genexpert Mtb/Rif® Assay Using Urine Specimen to Diagnose Pulmonary Tuberculosis in Sputum-Scarce Patients in Addis Ababa, Ethiopia
    (Addis Ababa University, 2018-06-03) Abera, Eyob; Beyene, Dereje (PhD); Tessema, Belay (PhD); Tesfaye, Abraham (PhD)
    Multidrug drug-resistant tuberculosis (MDR-TB) is a major health problem and seriously threatens TB control globally. Ethiopia is among the 30th highest TB burden countries. MDR-TB is a result of unsuccessful TB control programs and associated with mutations in drug target genes. Another challenge of TB is that about one-third of TB/HIV co-infected patients fail to produce a sputum specimen for diagnosis. Understanding of the pattern of resistance and genotyping of strains, and identify alternative specimen for diagnosis are important for TB/MDR-TB control. Thus, the aim of this study was to determine the pattern of mutations associated with resistance, genotype, and performance of GeneXpert MTB/RIF using urine specimens. A cross-sectional study was conducted in Addis Ababa from June 2015 to December 2016. Sputum specimens and socio-demographic data were collected from 358 MDR-TB suspected cases, and 150 urine specimens from sputum scarce cases and cases capable of giving sputum suspected of pulmonary TB. Specimens were analyzed using Ziehl-Neelsen, GeneXpert MTB/RIF assay, and cultures. All culture-positive specimens were analyzed for drug susceptibility tests. Sequence analysis for rpoB, katG, fabG1-inhA, embB, pncA, rrs and rpsL genes, and genotyping was performed using 24 MIRU-VNTR and spoligotype. Data were analyzed using SPSS version 23. Of 358 MDR-TB suspected cases, 226 were culture positive for Mycobacterium tuberculosis, of these, 162 (71.7%) had been previously treated for tuberculosis, while 128 (56.6%) were TB/HIV co-infected. An analysis of drug resistance indicated that 110 (48.7%) strains were resistant to isoniazid, 94 (41.6%) to streptomycin, 89 (39.4%) to rifampicin, 72 (31.9%) to ethambutol, and 70 (30.9%) to pyrazinamide. Among the 226 study participants, 89 (39.4%) were determined to be MDR-TB with TB/HIV co-infection, cigarette smoking, alcohol drinking, and admissions and/or visits to hospitals significantly (p<0.044) associated with the observed MDR-TB prevalence. Among the 209 isolates submitted for drug target gene sequencing, 101 (48.3%) isolates had the mutations in a katG gene, of these, 98 (98.0%) mutations were found at codon S315T, and other XIII mutations were found 90 (43.1%) isolates in rpoB gene. Out of these, 61 (67.8%) and 15 (16.7%) mutations occurred at codons S531L/W and H526Y/S/D/L respectively. Moreover, 73 (34.9%) isolates had a mutation in embB gene, and majority 48 (65.8%) of the mutations were found at codon M306I/V/L. In another finding, 68 (30.1%) isolates had a mutation in pncA gene with high mutation at codon 65 in 19 (27.9%) isolates. Likewise, mutations in rrs and rpsl genes were found in 56 (26.8%) isolates and the highest 50 (89.3%) proportion of mutation was found in rpsL gene at codon K88R/T and K43R. Furthermore, the least frequency of mutation was observed in fabG1-inhA promoter region in 7 (3.3%) isolates. A total of 167 isolates had a valid genotyping results, of thse 157 (94.0%) were classified as known lineages; Dehli/CAS 50 (29.9%), TUR 44 (26.3%), H37Rv like 25 (15.0%), TUR_Ethiopia_3 17 (10.2%), Haarlem 14 (8.4%), Ural 4 (2.4%), LAM 1 (0.6%), X-type 1 (0.6%), and EIA 1 (0.6%). The remaining 10 (6.0%) isolates were undefined. Among MDR-TB, the highest predominant genotype was TUR with 35 (46.1%). Cluster analysis showed that a total of 103 (61.7%) strains shared a genotyping pattern, and a recent transmission index was 50.3%. In another finding, of the 150 urine specimens tested, 5 (3.3%) were positive by GeneXpert MTB/RIF and culture. The sensitivity and specificity of GeneXpert MTB/RIF were 100% and 99.3% (95%CI: 97.4-100%) respectively, and overall performance agreement was 99.3% (95% CI: 97.4-100%). In conclusion, a highly diverse M. tuberculosis population structure was found, with a predominance of the Dehli/CAS genotype. The prevalence of MDR-TB in the study population was significantly high and the predominant lineage among MDR-TB strains was TUR, and there was a high rate of recent transmission among MDR-TB strains. A substantial number of mutations were observed at codons 531, 315, 306, 65, and 88 in rpoB, katG, embB, pncA, and rpsl genes respectively. TB/HIV co-infection, smoking of a cigarette, alcohol drinking, admission and visit of health facility were identified as risk factors for developing MDR-TB. A good sensitivity and specificity of GeneXpert MTB/RIF were observed using urine specimen, thus, urine can be used XIV as an alternative specimen for diagnosis of PTB from sputum scare patients. In general, our findings support us to conclude that there is weak health system for prevention and control of MDR-TB/TB in Ethiopia. Therefore, effective strategies should be designed considering the identified risk factors for control of MDR-TB.
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    RNA-Seq Transcriptome Profiling of Ethiopian Lowland Bamboo (Oxytenanthera Abyssinica (A.Rich) Munro Under Drought and Salt Stresses and SSR Based Genetic Diversity Analysis o f Ethiopian Highland Bamboo (Arundinaria Alpina K. Schum).
    (Addis Ababa University, 2019-07-02) Adem, Muhamed; Beyene, Dereje (PhD); Feyissa, Tileye (PhD); Tingbo, Jiang (Professor)
    Bamboos are perennial grasses classified under family Poaceae and subfamily Bambusoideae and are among the fastest growing plants on earth. Although bamboos have ecological and economic importance in Ethiopia, scientific inquiry particularly on genomics, transcriptomics and genetic diversity and structure is lacking. Ethiopian lowland bamboo (O. abyssinica) adapted in hot areas of Ethiopia hence inquiry on global transcriptome profiling is very important to elucidate the most important genes, transcript factors and metabolic pathways associated to abiotic stress. To do so, plastic pot germinated seedlings of lowland bamboo were subjected to 200 mM NaCl and 25% PEG-6000 (Poly Ethylene glycol) to induce salt and drought stress, respectively. Using the Illumina sequencing platform, fifteen cDNA libraries were constructed and sequenced to generate the first drought and salt stress global transcriptome profiling of the species. Following quality control, 754,444,646 clean paired-ends reads were generated, and then de novo assembled into 406,181 unigenes. Functional annotation against the public databases presented annotation of 217,067 (53.4%) unigenes, where NCBI-Nr 203,777, Swissport 115,741, COG 81,632 and KEGG 80,587. Prediction of Transcripts Factors (TFs) has generated 4,332 TFs organized into 64 TF families. Analysis of Differentially Expressed Genes (DEGs) provided 65,471 genes where 569 genes belongs to all stresses. Transcript factors (TFs) with a higher number of differentially expressed genes include bZIP (49), WRKY (43), MYB (38), AP2/ERF (30), HD-ZIP (25) and MYB related (21). Such 569 genes could serve for engineering plants for multiple abiotic tolerances. Despite the important role of bZIPs in plants, particularly in abiotic tolerances, bZIP family members and their corresponding functions remain elusive in the lowland bamboo. Through genome-wide analysis, a total of 162 bZIP lowland bamboo TFs having the bZIP binding domain (PF00170) were identified. For the identified bZIPs, functional annotation, phylogenetic relationship and their expression under drought and salt stress were investigated. The expression profile of the bZIP TFs revealed that majority of the bZIPs were highly responsive to drought and salt stress as 99 of the 162 TFs were up-regulated. Metabolic pathway analysis revealed that environmental information processing and genetic information processing categories were the only represented pathway which implies that the bZIPs are associated to drought and salt stress. Understanding on the genetic diversity and structure of highland bamboo is important particularly for conservation. For genetic diversity analysis 150 samples, representing 15 populations, 10 samples from each population were collected. The sources of SSR primers were; first, primers developed through reduced-representation genome sequencing of lowland bamboo were checked for their polymorphism and transferability, then 7 primers were selected and used for highland bamboo. Second, primers were directly taken from literature from Chinese Moso bamboo, after checking their transferability 9 primers were used. The genetic diversity indices (H= 0.398 and I= 0.639) for the 16 SSR markers used were moderate in capturing genetic variability. Both individual phylogeny and population structure merged the 15 populations in to nine clusters, with less geographic origin or collection based pattern. UPGMA clustered the 15 populations in 2, while NJ clustered in to 3, however pattern of their grouping is not in line with their pattern of origin of collection. The principal component analysis revealed that individuals are highly dispersed and did not group the populations into stridently distinct clusters which tells the presences of high genetic admixture possibly attributed to gene flow or the reproductive biology of the species. In conclusion, the RNA-Seq based global transcriptome profiling has generated transcriptomics resources for lowland bamboo which can be employed for itself and related species for further research. Most importantly the study uncovered key stress responsive genes, transcription factors, metabolic pathways and even genes differentially expressed to all stress groups which could be used as the basis for further studies aiming to confer plants for multiple abiotic stress tolerances. The study on bZIPs genome wide analysis also provided valuable information on how bZIPs are highly associated to abiotic stress tolerance since only pathways related to stress tolerances were represented in metabolic pathway analysis. The genetic diversity and population structure analysis of highland bamboo uncovered the presences of moderate genetic variability with high genetic admixture. The information could be used as a basis particularly for conservation interventions and for further investigations.
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    Some Monogenic Morphogenetics Traits Frequency Among Students of Dagmawi Berhan Primary School Addis Ketema Sub City Addis Ababa Ethiopia
    (Addis Ababa University, 2022-03-28) Demsew, Alemshet; Beyene, Dereje (PhD)
    Morphological traits are a structural characteristic of an organism that is determined genetically and transmitted from parent to offspring. Some of these characteristics, such as tongue rolling, widow's peak hairline, bent little finger, and ear lobe attachment, are thought to be exact epitome of simple dominant and recessive patterns of transmission; as a demonstration of how Mendelian genetics works, they are clear, and easy to follow epitomes. Thus, these traits were little to No study conducted and documented in Ethiopian population. So, this study has its own contribution to asses and documents the data for next studies as reference. The general objective of this study was to investigate the distribution and frequencies of the morphological traits of tongue rolling, earlobe attachment, widow’s peak, Hitch-hiker’s thumb, Bent little finger and long palmar muscles pattern among Students of Dagmawi Berhan primary school in 2020/2021 academic year. Morphological traits of grade 7 and 8 students of both sexes who volunteered were taken from each participant after agreement or consent was obtained from the students and their respective parents, indicating their readiness to participate. Data collection for morphological traits was done utilizing an observation and recording technique. Figures, tables, and words were used to present the findings. In this study the frequency distribution of the curved widow’s peak was lower than straight hairlines among the population. There were also the more frequency distribution present long Palmaris muscle was found to be male 106 (36%) and lower distribution in female 83 (29%). The study showed that among the morphogenetic traits assessed with the selected population, a significant association was observed in morphogenetic traits of Widow’s peak; tongue rolling, Earlobe attachment and Palmaris longues muscle with sex in the selected population. Other morphogenetic traits which were bent little finger and hitchhiker thumbs did not show association with either of the sex in the study.