منصة إيفاد العلمية

حازم عبده محمد أبوبكر

إرسال رسالة

التخصص: الطب البيطري

الجامعة: الخرطوم

النقاط:

معامل الإنتاج البحثي

الخبرات العلمية

Lecturer
Veterinary Clinician

الأبحاث المنشورة

Evidence of multiple point mutations in Theileria annulata cytochrome b gene incriminated in buparvaquone treatment failure

المجلة: Acta Tropica

سنة النشر: 2018

تاريخ النشر: 2018-12-30

Drug resistance is one of the emerging and re-emerging epidemics affecting both veterinary and public health sectors. Buparvaquone provides the most satisfactory means in the treatment of bovine tropical theileriosis. However, recently there has been widespread reports of development of resistance of Theileria annulata to buparvaquone. To investigate the situation in Sudan where bovine tropical theileriosis is endemic, fifty blood samples from T. annulata-positive cattle. were used for DNA extraction, PCR and cytochrome b gene nucleotide sequencing. Analysis of the two buparvaquone binding site regions Q01 (130–148) and Q02 (244–266), revealed three non- synonymous mutations at codon 146; alanine (GCT) to threonine (ACT) within the Q01 region across all 50 isolates and the other mutation at codon 129; serine (AGC) to glycine (GGC) in 18 isolates which is very close to the Q01 binding site. However, we documented another mutation at position 227; valine (GTG) to methionine (ATG) close to the close to the Q02 binding site, in three isolates with mutation at codon 129. We concluded that this study has provided evidence of point mutations in the cytochrome b gene of T. annulata that might be associated with buparvaquone treatment failure in Sudan.

Recent transmission of dengue virus and associated risk Facors among residents of Kassala state, eastern Sudan

المجلة: BMC Public Health

سنة النشر: 2020

تاريخ النشر: 2020-04-19

Background: Acute arboviral infections are distributed worldwide including Sudan, and dengue fever (DENV) is not an exception. The virus activity has recently been frequently reported in Kassala State, eastern Sudan. However, an appropriate epidemiological study would be necessary to provide accurate and precise estimates of the magnitude of recent DENV transmission in this area of endemicity. Methods: In the present investigation, a cross sectional study was conducted to advance beyond the current knowledge of the epidemiology of the disease in Kassala State. The prevalence of the disease was estimated and associated risk factors were determined. Sampled sera were collected and screened for recent dengue transmissionas as determined by DENV-IgM enzyme-linked immunosorbent assay (ELISA). The collection of data for risk assessment was supported by a well designed structured questionnaire. Results: The prevalence of recent DENV infection was estimated to be (11.42%). Potential risk factors to DENV seropsitivity include, age (OR = 3.24, CI = 1.81–5.77,p-value = 0.001); low income (OR = 3.75, CI = 1.57–8.93, p-value = 0.027); mosquito control (OR = 4.18, CI = 2.33–7.51, p-value = 0.004); and localities. Conclusion: The present study showed a high rate of circulating DENV IgM antibodies among the participants of the study (11.42%), suggesting recent transmission of DENV in Kassala State, eastern Sudan. The frequent occurrence of DENV infections necessitates the need for improved surveillance programs and prevention measures to combat this important arboviral disease in Sudan.

Association of genotype III of dengue virus serotype 3 with disease outbreak in Eastern Sudan, 2019

المجلة: Virology Journal

سنة النشر: 2020

تاريخ النشر: 2020-07-30

Background: Dengue fever (DF) is an arthropod-borne disease caused by dengue virus (DENV). DENV is a member of the genus Flavivirus in the family Flaviviridae. Recently, DENV has been reported as an important emerging infectious viral pathogen in Sudan. Multiple outbreaks and sporadic cases of DF have been frequently reported in the eastern region of Sudan. The present study was conducted to confirm DENV outbreak in Kassala State, eastern Sudan, 2019, and to provide some information on the molecular characterization of the DENV isolate associated with the disease outbreak. Methods: A hundred serum samples were collected during the outbreak from residents of Kassala State, Sudan, 2019. ELISA was used to detect DENV non structural protein NS1 (DENV-NS1) in acute phase sera sampled during the disease outbreak. RT-PCR assays were used to amplify a fragment of the capsid/pre-membrane region (CprM) of the viral polyprotein gene. The PCR products of the amplified CprM region of the viral polyprotein gene were purified and partial sequences were generated and used to confirm the specificity of DENV sequences and to identify the virus serotype. Phylogenetic tree was constructed to determine the genotype of DENV associated with the outbreak. Results: Using DENV-NS1 ELISA assay, DENV infection was confirmed in 23% sampled sera. The detection of DENV RNA was made possible using group-specific RT-PCR assay. The virus was serotyped as DENV serotype 3 (DENV-3) using DENV serotype-specific RT-PCR assay. Phylogenetic analysis of the partial CprM sequences of the viral polyprotein gene indicates that the virus belonged to genotype III of DENV-3. Conclusion: The scientific data presented in this investigation confirmed that genotype III of DENV-3 was associated with the disease outbreak in eastern Sudan, 2019. The study represents the first report on molecular characterization of DENV-3 in Sudan.

In Silico approach for identification, prediction of AMPD1 gene nsSNPs associated with Myoadenylate Deaminase deficiency

المجلة: Journal of Bioscience and Applied Research

سنة النشر: 2023

تاريخ النشر: 2023-03-01

Background: Myoadenylate deaminase deficiency is an autosomal recessive metabolic myopathy caused by mutations in the Adenosine monophosphate deaminase 1 gene. Adenosine monophosphate deaminase 1 gene deficiency is one of the most common causes of exercise-induced myopathy. In this study, non-synonymous single nucleotide polymorphism was analyzed for its functional and structural impact which is deleterious to Adenosine monophosphate deaminase 1 protein. Methods: The data on human Adenosine monophosphate deaminase 1gene was retrieved from the NCBI database on 9 JUNE 2021 and then analyzed using different bioinformatics prediction algorithms, namely: SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, SNPs and GO, PMut, and I-Mutant to detect the deleterious nsSNPs and its association with diseases. In addition, a Consurf web server was used to detect the functional SNPs in the conserved region. Chimera, Project Hope, and MutPred2 software were used to visualize and analyze the effect of nsSNPs on the functions and structure of the AMPD1 protein. Finally, both the STRING database and KEGG were used for the prediction of protein-protein interaction. Results: A total of 6178 SNPs were reported in the human AMPD1 gene. In this study 583 missense nsSNPs were selected for investigation and only 72 nsSNPs were shortlisted and computationally evaluated for their impact on AMPD1 protein. From all servers that were used collectively (K320I, R421W, R458C, R458H, R51C, R757L, R761H, and G246S) nsSNPs were predicted as deleterious, associated with disease, highly conserved, and decrease effective stability of AMPD1 protein. In addition, the AMPD1 protein was predicted to have strong interactions with ten proteins involved in various ranges of biological processes.

Computational Analysis of Deleterious Single Nucleotide Polymorphisms (SNPs) in Human CALR Gene

المجلة: American Journal of Bioinformatics Research

سنة النشر: 2018

تاريخ النشر: 2018-08-01

Background: The human Calreticulin (CRT) is a multifunctional protein encoded by CALR gene (CALR) located on chromosome 19. Calreticulin plays an important role in protein folding and calcium homeostasis. It’s also has been associated with cell proliferation, cell cycle progression and immunogenic cell death. High CRT serum levels were reported in various cancer like prostate cancer and breast carcinoma. Being observed as an important molecule in biological responses and its association with various diseases, we aimed to systematically explore the probable effects of CALR genetic variants on functions and structure of calreticulin using in silico prediction softwares. Methods: The data on human CALR gene was retrieved from dbSNP/NCBI. Eleven different prediction algorithms; SIFT, Polyphen, PROVEAN, SNAP2, Condel, Pmut, nsSNPs Analyzer, PhD-SNP, I-Mutant, Mutpred and Project Hope were used to analyzing the effect of nsSNPs on functions and structure of the CRT protein. STRING and KEGG database were used for CRT protein-protein interaction. Results: As per dbSNP database, the human CALR gene investigated in this work contained a total of 682SNPs:53 SNPs in 3′ UTR region, 25 SNPs in 5′ UTR region, 343 SNPs in intron region, 103 SNPs in coding synonymous regions and 154 non-synonymous SNPs (nsSNPs) which comprises of 150 missense mutations, 3 frameshift mutations and one nonsense mutation. We selected missense nsSNPs for our investigation. A total of 4 nsSNPs P216L, R73C, W261G and Y128C were predicted to have the most damaging effects on CRT protein's structure and function. STRING and KEGG revealed that CRT protein had strong interactions with proteins that involved in protein processing and presentation networks. Therefore, any structural alterations in the CRT protein that interfere or harm these networks interactions would probably increase susceptibility to diseases. Conclusion: Based on these analyses, the present study suggested that the reported functional SNPs may act as potential targets in genetic association studies.

High Risk Functional nsSNP in SARS-CoV-2 (2019-nCoV) Main Peptidase as Potential Targets to Structure-Based Drug Design: A Computational Approach

المجلة: International Journal of Virology and Molecular Biology

سنة النشر: 2020

تاريخ النشر: 2020-07-01

On January 2020, a new coronavirus (officially named SARS-CoV-2) was associated with alarming outbreak of a pneumonia-like illness, which was later named by the WHO as COVID-19, originating from Wuhan City, China. Although many clinical studies involving antiviral and immunomodulatory drug treatments for COVID-19, no approved drugs have been found to effectively inhibit the virus so far. A promising target for SARS-COV-2 drug design is a (Mpro), a main protease (Mpro), responsible for the replication and maturation of functional proteins in the life cycle of the SARS coronavirus. Here we employed missense SNP analysis to all amino acid identified as functional residues and showed potential binding activities to predict the high risk missense mutations that are highly damaging to the structure and the function of the SARS-COV-2 M pro aiming to detect potential drug targets for inhibition of SARS-COV-2 M pro . Our results demonstrated essential roles of HIS41, GLY143, CYS145, HIS163, GLU166 as binding residues, structural and functional residues, participating in different physicochemical interaction for keeping the proteolytic activity and enzymatic function of the SARS-COV-2 M pro . Upon subjecting these residues to single-nucleotide polymorphism (SNP) analysis, out of 152 nsSNP, 34 nsSNP recognized to alters the functionality and stability of SARS-COV-2 Mpro. Furthermore, most of these deleterious nsSNPs were predicted as ligand binding residues. We conclude that these residues can be target sites for the fresh generation inhibitors for of the SARS‐CoV Mpro and overcome the current drugs ineffectiveness.