Background Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis, a pote... more Background Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis, a potentially fatal disease in humans and dogs. The epidemiology and transmission dynamics of L. donovani in Sudan are poorly understood. Objective To determine the prevalence and characterization of L. donovani in human hospital cases and domestic dogs using different diagnostic methods in two localities in Gadarif State, Sudan. Material and method: A cross-sectional study was conducted from October 2019 to April 2020 Whole blood samples and lymph node aspirates were collected from 69 human and 32 dog participants for parasitological, immunological, and molecular tests. Results No parasites were detected in blood samples from either humans or dogs. Lymph node microscopy revealed 71.01% positivity in humans and 9.4% in dogs. The IT Leish test showed 82.6% positivity in humans and 43.75% in dogs. PCR confirmed L. donovani infection in all six selected samples (three from humans and three from d...
Aim: This study aimed to investigate the effect of non-synonymous SNPs
(nsSNPs) of the Glucago... more Aim: This study aimed to investigate the effect of non-synonymous SNPs
(nsSNPs) of the Glucagon-like peptide-1 Receptor (GLP-1R) gene in protein
function and structure using different computational software. Introduction:
The GLP1R gene provides the necessary instruction for the synthesis of the
insulin hormones which is needed for glucose catabolism. Polymorphisms in
this gene are associated with diabetes. The protein is an important drug target
for the treatment of type-2 diabetes and stroke. Material and Methods: Different
nsSNPs and protein-related sequences were obtained from NCBI and
ExPASY database. Gene associations and interactions were predicted using
GeneMANIA software. Deleterious and damaging effects of nsSNPs were analyzed
using SIFT, Provean, and Polyphen-2. The association of the nsSNPs
with the disease was predicted using SNPs & GO software. Protein stability
was investigated using I-Mutant and MUpro software. The structural and
functional impact of point mutations was predicted using Project Hope software.
Project Hope analyzes the mutations according to their size, charge,
hydrophobicity, and conservancy. Results: The GLP1R gene was found to
have an association with 20 other different genes. Among the most important
ones is the GCG (glucagon) gene which is also a trans membrane protein.
Overall 7229 variants were seen, and the missense variants or nsSNPs (146)
were selected for further analysis. The total number of nsSNPs obtained in
this study was 146. After being subjected to SIFT software (27 Deleterious
and 119 Tolerated) were predicted. Analysis with Provean showed that (20
deleterious and 7 neutral). Analysis using Polyphen-2 revealed 17 probably
damaging, 2 possibly damaging and 1 benign nsSNPs. Using two additional
software SNPs & GO and PHD-SNPs showed that 14 and 17 nsSNPs had a
A pathogenic strain of Macrococcus caseolyticus (M. caseolyticus) was isolated from wounds infect... more A pathogenic strain of Macrococcus caseolyticus (M. caseolyticus) was isolated from wounds infection during an investigation on donkeys in Khartoum State. (122) samples were collected from external wounds (head, abdomen, back and leg) during different seasons. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified 31 virulent genes of disease and defense, including methicillin-resistant genes, TatR family and ANT(4′)-Ib. Plasmid rep22 was identified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel M. caseolyticus strain (DaniaSudan). The MLST−tree−V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain DaniaSudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. Mice modeling showed bacteremia and many clinical signs (swelling, allergy, wounds, and hair loss). Enlargement, hyperemia, adhesions and abscesses wer...
Background: Hepatitis B Virus (HBV) is a viral infection that attacks the liver and can cause bot... more Background: Hepatitis B Virus (HBV) is a viral infection that attacks the liver and can cause both acute and chronic disease. The virus is most commonly transmitted from mother to child during birth and delivery. Also, by contact with patient blood or other fluids during sex with an infected partner. The virus enters the cell body by sodium taurocholate cotransporting polypeptide receptor (NTCP), then it replicate and invade other healthy cells. Aim: the aim of this study is to design a drug that can block sodium taurocholate cotransporting polypeptide receptor (NTCP), Using bioinformatics tools and servers. Material and method: Using CHemSketch the drug molecule was drawn and determined and using OpenBabel software the molecule was transferred and designed into MOL 2 format to be applied in the SwissDock server. The target protein from the protein database bank using the PDB ID of NTCP receptor protein was retrieved and then inserted it into SwissDock. The result of docking was the...
This study pathogenomic to gain genetic characterizations of the first pathogenic strains of Macr... more This study pathogenomic to gain genetic characterizations of the first pathogenic strains of Macrococcus caseolyticus, obtained from the donkey in Sudan. The in-silico analysis revealed that a total of (714 genes) were associated with carbohydrate metabolism (187 genes), amino acid and derivatives (138 genes), protein metabolism (163 genes), cofactors, vitamins, prosthetic groups, pigments (103 genes), membrane transport (26 genes), RNA metabolism (37 genes) and stress response (29 genes). In addition, (31 genes) identified in the strain were involved in virulence, disease, and defense. Multiple antibiotic resistances were revealed (13gens) including methicillin resistance (mecI, mecA, mecR1) penicillin binding (PonA, pbpA, pbpH, pbpF and pbpB), Multidrug resistance (mdtH_1, ykka, ykkc and mdtH_2), Tetracycline resistance (tetA, tet38), multidrug export (emrB), multidrug efflux pump (sdrM, sepA) and putative multidrug resistance (emrK). Also, stress responses were (yug1_1, yug1_2, y...
Background: The aim of this study was to investigate the possible risk factors and mutations in V... more Background: The aim of this study was to investigate the possible risk factors and mutations in VIM gene among Sudanese's breast cancer women in Khartoum State. Methods: This case-control study involved 45 patients with breast cancer and 45controls. It was conducted across three hospitals and two laboratories in Khartoum State. A structural questionnaire was used to obtain data regarding age, family history, menarche, marriage, menopause, pregnancy, nulliparous and parous women, breast-feeding, use of fertility or contraceptive drugs and grade of the disease. DNA from patient and control tissues was extracted using extraction kits. PCR was conducted to amplify VIM gene using specific primers. PCR products were sequenced in order to detect the mutation in VIM gene. Data was analyzed using Pearson's Chi-square tests to identify risk factors associated with breast cancer. Results: The study showed that the main risk factors associated with breast cancer were family history with first degree relative, menarche, irregularity of menarche, reproductive factors such as pregnancy, breast-feeding and nulliparous. DNA sequencing revealed no mutations in VIM gene associated with breast cancer in Sudanese women in Khartoum State. Conclusion: The association of other risk factors such as menopausal status, age of menopausal, oral contraceptive birth control and fertility hormones needs more illumination and further work. Other genes associated with breast cancer can be investigated.
GATA2 or GATA-binding factor 2 is a transcription factor, which regulates the expression of genes... more GATA2 or GATA-binding factor 2 is a transcription factor, which regulates the expression of genes that are critical for the embryonic development, self-renewal, maintenance, and functionality of blood-forming lymphatic system-forming, and other tissue-forming stem cells. GATA2 protein is encoded by the GATA2 gene which often suffers germ line and somatic mutations which lead to a wide range of familial and sporadic diseases. Association of data including protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity were predicted using Gene MANIA software. This gene was investigated in NCBI database and the Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) were analyzed by computational software, (SIFT, PROVEAN, Polyphen-2, SNPs&GO, PHD-SNPs, I-Mutant and MUpro). The Protein structural analysis was done by modelling of amino acid substitutions using Project Hope for all predicted pathological polymorphisms. GeneMANIA results showed th...
Background: The FOXP3 gene provides instructions for producing the forkhead box P3 (FOXP3) protei... more Background: The FOXP3 gene provides instructions for producing the forkhead box P3 (FOXP3) protein. The FOXP3 protein attaches (binds) to specific regions of DNA and helps control the activity of genes that are involved in regulating the immune system. Aim: This study intended to analyze SNPs in FOXP3 gene in the coding region, 5`UTR and 3`UTR using bioinformatics tools and visualizing the 3D structure of the gene. Methods: SNPs were retrieved from NCBI, and the protein sequences were retrieved from UniprotKB. SIFT and Provean software was used to predict whether the nsSNPs were tolerated or deleterious. Polyphen2 for nsSNPs function prediction on the produced protein.I-mutant and Mupro software to check the protein stability, finally PHD software to see whether the nsSNPs were related to a disease or not.Regulomedb to predict the regulatory element for 5`UTR region. For the 3`UTR PolymiRTs database to predict the variation in microRNA (miRNA). FuncPred software to show the unknown ...
DHCR7 gene (7-dehydrocholesterol reductase) provides the necessary instruction for synthesis of t... more DHCR7 gene (7-dehydrocholesterol reductase) provides the necessary instruction for synthesis of the enzyme 7-dehydrocholesterol reductase which is needed for cholesterol synthesis. Cholesterol plays an important role as a precursor for synthesis of hormones, bile acids and acts as a structural component of cell membranes and myelin. One of the main health problems resulting from mutations in this gene is Smith–Lemli–Opitz syndrome. It is an autosomal recessive inheritance disease characterized by failure to thrive, intellectual disability and multiple anomaly. Aims: This study aimed to investigate the effect of non-synonymous SNPs (ns SNPs) of DHCR7 gene in protein function and structure using different computational software. Materials and Methods: Different nsSNPs and protein related sequences were obtained from NCBI and ExPASY database. Deleterious and damaging effect of SNPs were analyzed using SIFT, Polyphen 2, Provean and SNPs & GO software. Protein stability was investigated ...
Background: Chicken caecal coccidiosis is an invasion and destruction of caecal mucosa by the pro... more Background: Chicken caecal coccidiosis is an invasion and destruction of caecal mucosa by the protozoa Eimeria tenella. The infection is characterized by extreme caecal damage resulting in diarrhea, morbidity and mortality with consequent serious economic losses. Aim: The aim of this study was to characterize the Eimeria tenella existing in Khartoum State, using oocyst measurements and molecular barcoding approach. Materials and Methods: Oocysts of E. tenella were collected from 10 positive samples. The supernatant containing the oocysts (after being sporulated) was used for length measurements using light microscope equipped with calibrated ocular micrometer. DNA was extracted using modified Cetyl-Trimethyl Ammonium Bromide (CTAB) method. The CO1 positive PCR products were purified and sequenced by Sanger sequencing method. The edited sequences were aligned with ClustalW using BioEdit software. A bootstrap Niebuhr-Joining tree (500 replicates) was created using MEGA7 software. Results: The average length of the oocyst was 19.63 μm and the width was 17.02 μm. The shape index was 1.13 μm. The positive CO1 isolates showed 100% identity with E. tenella from GenBank with zero P-distance value. Conclusion: E. tenella was successfully identified by CO1 barcoding primer, and the sequences showed identity to the global isolates forming sister clades. 32. El-Sherry., et al. "Divergent nuclear 18S rDNA paralogs in a turkey coccidium, Eimeria meleagrimitis, complicate molecular systematics and identification".
International Journal of Genetics and Genomics, 2019
N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xeno... more N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xenobiotics and drugs components. It is a critical enzyme in clinical pharmacology. It has remarkable genetic polymorphisms, which is associated with the risk of developing cancer due to the change of normally fast acetylation of substrates to slow acetylation. This study assessed single nucleotide polymorphisms (SNPs) in the coding region and (3ʹUTR) of NAT2. Computational approaches were used in this study for functional and structural effects of NAT2 gene. SNPs. Were retrieved from NCBI SNPsdatabase. TheNAT2 protein sequence and amino acid change were used as an input to the SIFT, PolyPhen-2, PhD-SNP, SNPs& GO, SNP Analyzer, I-Mutant 3.0 and PMut to determine the deleterious and SNPs conditions. Other software for predication of the structural change were Mutation3D, Chimera and Project HOPE. GeneMANIA software was used to show gene-gene interaction. PolymiRTs was used to investigate the disruption or creation of SNPs of miRNA region. In Homosapiens182 were nonsynonymous SNPs (nsSNPs), 60 synonymous SNPs, 48 3ʹUTRSNPs and 19 5ʹUTR SNPs. A total, 65 of those nsSNPs were predicted to be highly damaging with 3-6 score rates when analyzed with six software. Recomputation of results with I-Mutant 3.0 showed adecrease in the effective stability of the protein due to 55 nsSNPs. Consequent structural changes were shown using Project HOPE and Chimera. NAT2 is a highly polymorphic gene; the majority of deleterious NAT2SNPs are nsSNPs that alter the physiochemical and structural properties of the protein, possibly leading to the loss or distortion of the protein's ability to detoxify and metabolize xenobiotic and aromatic amine compounds. There were three SNPs at the 3ʹUTR that changed the miRNA binding sites, which might affect the gene regulation.
International Journal of Genetics and Genomics, 2020
Roberts's syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected... more Roberts's syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion Nacetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
International Journal of Genetics and Genomics, 2020
Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen whi... more Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen which regulates blood pressure and balances fluids in the body. Hypertension happens due to many causes one of this is the defect in AGT gene. Hypertension usually has no symptoms. However, it is a major risk factor for heart diseases, stroke, kidney failure, and eye problems. Objectives: in this study we use software to analyze the gene using different software and represented statistically and to detect the SNPs that can cause the disease. Material and Method: In this analysis using many software tools that can analyze the nsSNPs retrieved from NCBI website. These software include SIFT, I-mutant, Polyphen-2, PHD SNP and SNP& Go, Projecthop and GeneMANIA. Results: The study showed that from 172 nsSNPs only 46 nsSNPs were deleterious while 126 were tolerated using SIFT. Two were benign, 11 were possibly damaging and 33 were probably damaging by Polyphen-2. Using Provean, 19 nsSNPs were neutral and 27 were deleterious. For PHD-SNP software 20 nsSNPs were disease related and 18 were neutral. Also SNPs were checked using SNP & Go software that showed 32 neutral nsSNPs and 14 nsSNPs were disease associated variants. Using I-Mutant software 13 nsSNPs increase the stability of the protein and 33 decrease the protein stability. Conclusions: In conclusion, extensive functional and structural analyses are carried out to predict potentially damaging and deleterious nsSNPs of AGT gene using bioinformatics and computational methods. In the study, 14 high confidence damaging nsSNPs are identified from 172 nsSNPs. Although bioinformatics tools have their limitations, the results from the present study may be convenient in future for further population based research activities and towards development of accuracy medicines.
Introduction: Dopa responsive dystonia (DRD) is an inherited movement disorder. Mutations in GCH1... more Introduction: Dopa responsive dystonia (DRD) is an inherited movement disorder. Mutations in GCH1 gene is the most common root of autosomal dominant, early onset of DRD. This study aimed to analyze the genetic variation that can alter the expression and the function of the GCH1 gene using computational methods. Materials and methods: All SNPs were retrieved from the dbSNP database. GeneMANIA software was used to show gene-gene interaction. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) were analyzed using different tools (SIFT, PolyPhen-2, PROVEAN, SNPs & GO, I-Mutant, MUpro, Swiss-PdbViewer and Project HOPE). The SNPs in 3 ′ UTR and 5 ′ UTR regions were analyzed using PolymiRTs and SNP Function Prediction tools, respectively. Results: According to dbSNP database, the human GCH1 gene contained 178 SNPs in the coding region, 451 in the 3 ′ UTR and 63 in the 5 ′ UTR. GeneMania revealed that GCH1 had strong interactions with other genes involved in phenol-containing compound and catecholamine biosynthetic process, regulation of monooxygenase activity and nitric-oxide synthase activity. A total of seven nsSNPs (R88W, G108D, D134V, G201E, H144P, I135K and R184H) were predicted to have the most damaging effects on structure, function and affecting the GCH1 protein stability. Modeling was done using Project HOPE and Swiss-PdbViewer. Regarding the non-coding region, 33 SNPs out of 451 in 3 ′ UTR were predicted by PolymiRTs to induce disruption or creation of miRNA binding sites while two SNPs were predicted by SNP Function Prediction to be functionally significant in the 5 ′ UTR. Conclusion: Functional and structural impacts of SNPs in the GCH1gene were studied using computational prediction tools. Pathogenic SNPs predicted in this study can be considered as important candidates inducing Dopa responsive dystonia and could be used as diagnostic markers.
N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xeno... more N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xenobiotics and drugs components. It is a critical enzyme in clinical pharmacology. It has remarkable genetic polymorphisms, which is associated with the risk of developing cancer due to the change of normally fast acetylation of substrates to slow acetylation. This study assessed single nucleotide polymorphisms (SNPs) in the coding region and (3ʹUTR) of NAT2. Computational approaches were used in this study for functional and structural effects of NAT2 gene. SNPs. Were retrieved from NCBI SNPsdatabase. TheNAT2 protein sequence and amino acid change were used as an input to the SIFT, PolyPhen-2, PhD-SNP, SNPs& GO, SNPAnalyzer, I-Mutant 3.0 and PMut to determine the deleterious and SNPs conditions. Other software for predication of the structural change were Mutation3D, Chimera and Project HOPE. GeneMANIA software was used to show gene-gene interaction. PolymiRTs was used to investigate the disruption or creation of SNPs of miRNA region. In Homosapiens182 were nonsynonymous SNPs (nsSNPs), 60 synonymous SNPs, 48 3ʹUTRSNPs and 19 5ʹUTR SNPs. A total, 65 of thosensSNPs were predicted to be highly damaging with 3-6 score rates when analyzed with six software. Recomputation of results with I-Mutant 3.0 showed adecrease in the effective stability of the protein due to 55 nsSNPs. Consequent structural changes were shown using Project HOPE and Chimera. NAT2 is a highly polymorphic gene; the majority of deleterious NAT2SNPs are nsSNPs that alter the physiochemical and structural properties of the protein, possibly leading to the loss or distortion of the protein's ability to detoxify and metabolize xenobiotic and aromatic amine compounds. There were three SNPs at the 3ʹUTR that changed the miRNA binding sites, which might affect the gene regulation.
Background Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis, a pote... more Background Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis, a potentially fatal disease in humans and dogs. The epidemiology and transmission dynamics of L. donovani in Sudan are poorly understood. Objective To determine the prevalence and characterization of L. donovani in human hospital cases and domestic dogs using different diagnostic methods in two localities in Gadarif State, Sudan. Material and method: A cross-sectional study was conducted from October 2019 to April 2020 Whole blood samples and lymph node aspirates were collected from 69 human and 32 dog participants for parasitological, immunological, and molecular tests. Results No parasites were detected in blood samples from either humans or dogs. Lymph node microscopy revealed 71.01% positivity in humans and 9.4% in dogs. The IT Leish test showed 82.6% positivity in humans and 43.75% in dogs. PCR confirmed L. donovani infection in all six selected samples (three from humans and three from d...
Aim: This study aimed to investigate the effect of non-synonymous SNPs
(nsSNPs) of the Glucago... more Aim: This study aimed to investigate the effect of non-synonymous SNPs
(nsSNPs) of the Glucagon-like peptide-1 Receptor (GLP-1R) gene in protein
function and structure using different computational software. Introduction:
The GLP1R gene provides the necessary instruction for the synthesis of the
insulin hormones which is needed for glucose catabolism. Polymorphisms in
this gene are associated with diabetes. The protein is an important drug target
for the treatment of type-2 diabetes and stroke. Material and Methods: Different
nsSNPs and protein-related sequences were obtained from NCBI and
ExPASY database. Gene associations and interactions were predicted using
GeneMANIA software. Deleterious and damaging effects of nsSNPs were analyzed
using SIFT, Provean, and Polyphen-2. The association of the nsSNPs
with the disease was predicted using SNPs & GO software. Protein stability
was investigated using I-Mutant and MUpro software. The structural and
functional impact of point mutations was predicted using Project Hope software.
Project Hope analyzes the mutations according to their size, charge,
hydrophobicity, and conservancy. Results: The GLP1R gene was found to
have an association with 20 other different genes. Among the most important
ones is the GCG (glucagon) gene which is also a trans membrane protein.
Overall 7229 variants were seen, and the missense variants or nsSNPs (146)
were selected for further analysis. The total number of nsSNPs obtained in
this study was 146. After being subjected to SIFT software (27 Deleterious
and 119 Tolerated) were predicted. Analysis with Provean showed that (20
deleterious and 7 neutral). Analysis using Polyphen-2 revealed 17 probably
damaging, 2 possibly damaging and 1 benign nsSNPs. Using two additional
software SNPs & GO and PHD-SNPs showed that 14 and 17 nsSNPs had a
A pathogenic strain of Macrococcus caseolyticus (M. caseolyticus) was isolated from wounds infect... more A pathogenic strain of Macrococcus caseolyticus (M. caseolyticus) was isolated from wounds infection during an investigation on donkeys in Khartoum State. (122) samples were collected from external wounds (head, abdomen, back and leg) during different seasons. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified 31 virulent genes of disease and defense, including methicillin-resistant genes, TatR family and ANT(4′)-Ib. Plasmid rep22 was identified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel M. caseolyticus strain (DaniaSudan). The MLST−tree−V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain DaniaSudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. Mice modeling showed bacteremia and many clinical signs (swelling, allergy, wounds, and hair loss). Enlargement, hyperemia, adhesions and abscesses wer...
Background: Hepatitis B Virus (HBV) is a viral infection that attacks the liver and can cause bot... more Background: Hepatitis B Virus (HBV) is a viral infection that attacks the liver and can cause both acute and chronic disease. The virus is most commonly transmitted from mother to child during birth and delivery. Also, by contact with patient blood or other fluids during sex with an infected partner. The virus enters the cell body by sodium taurocholate cotransporting polypeptide receptor (NTCP), then it replicate and invade other healthy cells. Aim: the aim of this study is to design a drug that can block sodium taurocholate cotransporting polypeptide receptor (NTCP), Using bioinformatics tools and servers. Material and method: Using CHemSketch the drug molecule was drawn and determined and using OpenBabel software the molecule was transferred and designed into MOL 2 format to be applied in the SwissDock server. The target protein from the protein database bank using the PDB ID of NTCP receptor protein was retrieved and then inserted it into SwissDock. The result of docking was the...
This study pathogenomic to gain genetic characterizations of the first pathogenic strains of Macr... more This study pathogenomic to gain genetic characterizations of the first pathogenic strains of Macrococcus caseolyticus, obtained from the donkey in Sudan. The in-silico analysis revealed that a total of (714 genes) were associated with carbohydrate metabolism (187 genes), amino acid and derivatives (138 genes), protein metabolism (163 genes), cofactors, vitamins, prosthetic groups, pigments (103 genes), membrane transport (26 genes), RNA metabolism (37 genes) and stress response (29 genes). In addition, (31 genes) identified in the strain were involved in virulence, disease, and defense. Multiple antibiotic resistances were revealed (13gens) including methicillin resistance (mecI, mecA, mecR1) penicillin binding (PonA, pbpA, pbpH, pbpF and pbpB), Multidrug resistance (mdtH_1, ykka, ykkc and mdtH_2), Tetracycline resistance (tetA, tet38), multidrug export (emrB), multidrug efflux pump (sdrM, sepA) and putative multidrug resistance (emrK). Also, stress responses were (yug1_1, yug1_2, y...
Background: The aim of this study was to investigate the possible risk factors and mutations in V... more Background: The aim of this study was to investigate the possible risk factors and mutations in VIM gene among Sudanese's breast cancer women in Khartoum State. Methods: This case-control study involved 45 patients with breast cancer and 45controls. It was conducted across three hospitals and two laboratories in Khartoum State. A structural questionnaire was used to obtain data regarding age, family history, menarche, marriage, menopause, pregnancy, nulliparous and parous women, breast-feeding, use of fertility or contraceptive drugs and grade of the disease. DNA from patient and control tissues was extracted using extraction kits. PCR was conducted to amplify VIM gene using specific primers. PCR products were sequenced in order to detect the mutation in VIM gene. Data was analyzed using Pearson's Chi-square tests to identify risk factors associated with breast cancer. Results: The study showed that the main risk factors associated with breast cancer were family history with first degree relative, menarche, irregularity of menarche, reproductive factors such as pregnancy, breast-feeding and nulliparous. DNA sequencing revealed no mutations in VIM gene associated with breast cancer in Sudanese women in Khartoum State. Conclusion: The association of other risk factors such as menopausal status, age of menopausal, oral contraceptive birth control and fertility hormones needs more illumination and further work. Other genes associated with breast cancer can be investigated.
GATA2 or GATA-binding factor 2 is a transcription factor, which regulates the expression of genes... more GATA2 or GATA-binding factor 2 is a transcription factor, which regulates the expression of genes that are critical for the embryonic development, self-renewal, maintenance, and functionality of blood-forming lymphatic system-forming, and other tissue-forming stem cells. GATA2 protein is encoded by the GATA2 gene which often suffers germ line and somatic mutations which lead to a wide range of familial and sporadic diseases. Association of data including protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity were predicted using Gene MANIA software. This gene was investigated in NCBI database and the Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) were analyzed by computational software, (SIFT, PROVEAN, Polyphen-2, SNPs&GO, PHD-SNPs, I-Mutant and MUpro). The Protein structural analysis was done by modelling of amino acid substitutions using Project Hope for all predicted pathological polymorphisms. GeneMANIA results showed th...
Background: The FOXP3 gene provides instructions for producing the forkhead box P3 (FOXP3) protei... more Background: The FOXP3 gene provides instructions for producing the forkhead box P3 (FOXP3) protein. The FOXP3 protein attaches (binds) to specific regions of DNA and helps control the activity of genes that are involved in regulating the immune system. Aim: This study intended to analyze SNPs in FOXP3 gene in the coding region, 5`UTR and 3`UTR using bioinformatics tools and visualizing the 3D structure of the gene. Methods: SNPs were retrieved from NCBI, and the protein sequences were retrieved from UniprotKB. SIFT and Provean software was used to predict whether the nsSNPs were tolerated or deleterious. Polyphen2 for nsSNPs function prediction on the produced protein.I-mutant and Mupro software to check the protein stability, finally PHD software to see whether the nsSNPs were related to a disease or not.Regulomedb to predict the regulatory element for 5`UTR region. For the 3`UTR PolymiRTs database to predict the variation in microRNA (miRNA). FuncPred software to show the unknown ...
DHCR7 gene (7-dehydrocholesterol reductase) provides the necessary instruction for synthesis of t... more DHCR7 gene (7-dehydrocholesterol reductase) provides the necessary instruction for synthesis of the enzyme 7-dehydrocholesterol reductase which is needed for cholesterol synthesis. Cholesterol plays an important role as a precursor for synthesis of hormones, bile acids and acts as a structural component of cell membranes and myelin. One of the main health problems resulting from mutations in this gene is Smith–Lemli–Opitz syndrome. It is an autosomal recessive inheritance disease characterized by failure to thrive, intellectual disability and multiple anomaly. Aims: This study aimed to investigate the effect of non-synonymous SNPs (ns SNPs) of DHCR7 gene in protein function and structure using different computational software. Materials and Methods: Different nsSNPs and protein related sequences were obtained from NCBI and ExPASY database. Deleterious and damaging effect of SNPs were analyzed using SIFT, Polyphen 2, Provean and SNPs & GO software. Protein stability was investigated ...
Background: Chicken caecal coccidiosis is an invasion and destruction of caecal mucosa by the pro... more Background: Chicken caecal coccidiosis is an invasion and destruction of caecal mucosa by the protozoa Eimeria tenella. The infection is characterized by extreme caecal damage resulting in diarrhea, morbidity and mortality with consequent serious economic losses. Aim: The aim of this study was to characterize the Eimeria tenella existing in Khartoum State, using oocyst measurements and molecular barcoding approach. Materials and Methods: Oocysts of E. tenella were collected from 10 positive samples. The supernatant containing the oocysts (after being sporulated) was used for length measurements using light microscope equipped with calibrated ocular micrometer. DNA was extracted using modified Cetyl-Trimethyl Ammonium Bromide (CTAB) method. The CO1 positive PCR products were purified and sequenced by Sanger sequencing method. The edited sequences were aligned with ClustalW using BioEdit software. A bootstrap Niebuhr-Joining tree (500 replicates) was created using MEGA7 software. Results: The average length of the oocyst was 19.63 μm and the width was 17.02 μm. The shape index was 1.13 μm. The positive CO1 isolates showed 100% identity with E. tenella from GenBank with zero P-distance value. Conclusion: E. tenella was successfully identified by CO1 barcoding primer, and the sequences showed identity to the global isolates forming sister clades. 32. El-Sherry., et al. "Divergent nuclear 18S rDNA paralogs in a turkey coccidium, Eimeria meleagrimitis, complicate molecular systematics and identification".
International Journal of Genetics and Genomics, 2019
N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xeno... more N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xenobiotics and drugs components. It is a critical enzyme in clinical pharmacology. It has remarkable genetic polymorphisms, which is associated with the risk of developing cancer due to the change of normally fast acetylation of substrates to slow acetylation. This study assessed single nucleotide polymorphisms (SNPs) in the coding region and (3ʹUTR) of NAT2. Computational approaches were used in this study for functional and structural effects of NAT2 gene. SNPs. Were retrieved from NCBI SNPsdatabase. TheNAT2 protein sequence and amino acid change were used as an input to the SIFT, PolyPhen-2, PhD-SNP, SNPs& GO, SNP Analyzer, I-Mutant 3.0 and PMut to determine the deleterious and SNPs conditions. Other software for predication of the structural change were Mutation3D, Chimera and Project HOPE. GeneMANIA software was used to show gene-gene interaction. PolymiRTs was used to investigate the disruption or creation of SNPs of miRNA region. In Homosapiens182 were nonsynonymous SNPs (nsSNPs), 60 synonymous SNPs, 48 3ʹUTRSNPs and 19 5ʹUTR SNPs. A total, 65 of those nsSNPs were predicted to be highly damaging with 3-6 score rates when analyzed with six software. Recomputation of results with I-Mutant 3.0 showed adecrease in the effective stability of the protein due to 55 nsSNPs. Consequent structural changes were shown using Project HOPE and Chimera. NAT2 is a highly polymorphic gene; the majority of deleterious NAT2SNPs are nsSNPs that alter the physiochemical and structural properties of the protein, possibly leading to the loss or distortion of the protein's ability to detoxify and metabolize xenobiotic and aromatic amine compounds. There were three SNPs at the 3ʹUTR that changed the miRNA binding sites, which might affect the gene regulation.
International Journal of Genetics and Genomics, 2020
Roberts's syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected... more Roberts's syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion Nacetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
International Journal of Genetics and Genomics, 2020
Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen whi... more Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen which regulates blood pressure and balances fluids in the body. Hypertension happens due to many causes one of this is the defect in AGT gene. Hypertension usually has no symptoms. However, it is a major risk factor for heart diseases, stroke, kidney failure, and eye problems. Objectives: in this study we use software to analyze the gene using different software and represented statistically and to detect the SNPs that can cause the disease. Material and Method: In this analysis using many software tools that can analyze the nsSNPs retrieved from NCBI website. These software include SIFT, I-mutant, Polyphen-2, PHD SNP and SNP& Go, Projecthop and GeneMANIA. Results: The study showed that from 172 nsSNPs only 46 nsSNPs were deleterious while 126 were tolerated using SIFT. Two were benign, 11 were possibly damaging and 33 were probably damaging by Polyphen-2. Using Provean, 19 nsSNPs were neutral and 27 were deleterious. For PHD-SNP software 20 nsSNPs were disease related and 18 were neutral. Also SNPs were checked using SNP & Go software that showed 32 neutral nsSNPs and 14 nsSNPs were disease associated variants. Using I-Mutant software 13 nsSNPs increase the stability of the protein and 33 decrease the protein stability. Conclusions: In conclusion, extensive functional and structural analyses are carried out to predict potentially damaging and deleterious nsSNPs of AGT gene using bioinformatics and computational methods. In the study, 14 high confidence damaging nsSNPs are identified from 172 nsSNPs. Although bioinformatics tools have their limitations, the results from the present study may be convenient in future for further population based research activities and towards development of accuracy medicines.
Introduction: Dopa responsive dystonia (DRD) is an inherited movement disorder. Mutations in GCH1... more Introduction: Dopa responsive dystonia (DRD) is an inherited movement disorder. Mutations in GCH1 gene is the most common root of autosomal dominant, early onset of DRD. This study aimed to analyze the genetic variation that can alter the expression and the function of the GCH1 gene using computational methods. Materials and methods: All SNPs were retrieved from the dbSNP database. GeneMANIA software was used to show gene-gene interaction. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) were analyzed using different tools (SIFT, PolyPhen-2, PROVEAN, SNPs & GO, I-Mutant, MUpro, Swiss-PdbViewer and Project HOPE). The SNPs in 3 ′ UTR and 5 ′ UTR regions were analyzed using PolymiRTs and SNP Function Prediction tools, respectively. Results: According to dbSNP database, the human GCH1 gene contained 178 SNPs in the coding region, 451 in the 3 ′ UTR and 63 in the 5 ′ UTR. GeneMania revealed that GCH1 had strong interactions with other genes involved in phenol-containing compound and catecholamine biosynthetic process, regulation of monooxygenase activity and nitric-oxide synthase activity. A total of seven nsSNPs (R88W, G108D, D134V, G201E, H144P, I135K and R184H) were predicted to have the most damaging effects on structure, function and affecting the GCH1 protein stability. Modeling was done using Project HOPE and Swiss-PdbViewer. Regarding the non-coding region, 33 SNPs out of 451 in 3 ′ UTR were predicted by PolymiRTs to induce disruption or creation of miRNA binding sites while two SNPs were predicted by SNP Function Prediction to be functionally significant in the 5 ′ UTR. Conclusion: Functional and structural impacts of SNPs in the GCH1gene were studied using computational prediction tools. Pathogenic SNPs predicted in this study can be considered as important candidates inducing Dopa responsive dystonia and could be used as diagnostic markers.
N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xeno... more N-acetyltransferase 2 (encoded by NAT2) is a phase II enzyme that detoxifies and metabolizes xenobiotics and drugs components. It is a critical enzyme in clinical pharmacology. It has remarkable genetic polymorphisms, which is associated with the risk of developing cancer due to the change of normally fast acetylation of substrates to slow acetylation. This study assessed single nucleotide polymorphisms (SNPs) in the coding region and (3ʹUTR) of NAT2. Computational approaches were used in this study for functional and structural effects of NAT2 gene. SNPs. Were retrieved from NCBI SNPsdatabase. TheNAT2 protein sequence and amino acid change were used as an input to the SIFT, PolyPhen-2, PhD-SNP, SNPs& GO, SNPAnalyzer, I-Mutant 3.0 and PMut to determine the deleterious and SNPs conditions. Other software for predication of the structural change were Mutation3D, Chimera and Project HOPE. GeneMANIA software was used to show gene-gene interaction. PolymiRTs was used to investigate the disruption or creation of SNPs of miRNA region. In Homosapiens182 were nonsynonymous SNPs (nsSNPs), 60 synonymous SNPs, 48 3ʹUTRSNPs and 19 5ʹUTR SNPs. A total, 65 of thosensSNPs were predicted to be highly damaging with 3-6 score rates when analyzed with six software. Recomputation of results with I-Mutant 3.0 showed adecrease in the effective stability of the protein due to 55 nsSNPs. Consequent structural changes were shown using Project HOPE and Chimera. NAT2 is a highly polymorphic gene; the majority of deleterious NAT2SNPs are nsSNPs that alter the physiochemical and structural properties of the protein, possibly leading to the loss or distortion of the protein's ability to detoxify and metabolize xenobiotic and aromatic amine compounds. There were three SNPs at the 3ʹUTR that changed the miRNA binding sites, which might affect the gene regulation.
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Papers by Mona khaier
(nsSNPs) of the Glucagon-like peptide-1 Receptor (GLP-1R) gene in protein
function and structure using different computational software. Introduction:
The GLP1R gene provides the necessary instruction for the synthesis of the
insulin hormones which is needed for glucose catabolism. Polymorphisms in
this gene are associated with diabetes. The protein is an important drug target
for the treatment of type-2 diabetes and stroke. Material and Methods: Different
nsSNPs and protein-related sequences were obtained from NCBI and
ExPASY database. Gene associations and interactions were predicted using
GeneMANIA software. Deleterious and damaging effects of nsSNPs were analyzed
using SIFT, Provean, and Polyphen-2. The association of the nsSNPs
with the disease was predicted using SNPs & GO software. Protein stability
was investigated using I-Mutant and MUpro software. The structural and
functional impact of point mutations was predicted using Project Hope software.
Project Hope analyzes the mutations according to their size, charge,
hydrophobicity, and conservancy. Results: The GLP1R gene was found to
have an association with 20 other different genes. Among the most important
ones is the GCG (glucagon) gene which is also a trans membrane protein.
Overall 7229 variants were seen, and the missense variants or nsSNPs (146)
were selected for further analysis. The total number of nsSNPs obtained in
this study was 146. After being subjected to SIFT software (27 Deleterious
and 119 Tolerated) were predicted. Analysis with Provean showed that (20
deleterious and 7 neutral). Analysis using Polyphen-2 revealed 17 probably
damaging, 2 possibly damaging and 1 benign nsSNPs. Using two additional
software SNPs & GO and PHD-SNPs showed that 14 and 17 nsSNPs had a
(nsSNPs) of the Glucagon-like peptide-1 Receptor (GLP-1R) gene in protein
function and structure using different computational software. Introduction:
The GLP1R gene provides the necessary instruction for the synthesis of the
insulin hormones which is needed for glucose catabolism. Polymorphisms in
this gene are associated with diabetes. The protein is an important drug target
for the treatment of type-2 diabetes and stroke. Material and Methods: Different
nsSNPs and protein-related sequences were obtained from NCBI and
ExPASY database. Gene associations and interactions were predicted using
GeneMANIA software. Deleterious and damaging effects of nsSNPs were analyzed
using SIFT, Provean, and Polyphen-2. The association of the nsSNPs
with the disease was predicted using SNPs & GO software. Protein stability
was investigated using I-Mutant and MUpro software. The structural and
functional impact of point mutations was predicted using Project Hope software.
Project Hope analyzes the mutations according to their size, charge,
hydrophobicity, and conservancy. Results: The GLP1R gene was found to
have an association with 20 other different genes. Among the most important
ones is the GCG (glucagon) gene which is also a trans membrane protein.
Overall 7229 variants were seen, and the missense variants or nsSNPs (146)
were selected for further analysis. The total number of nsSNPs obtained in
this study was 146. After being subjected to SIFT software (27 Deleterious
and 119 Tolerated) were predicted. Analysis with Provean showed that (20
deleterious and 7 neutral). Analysis using Polyphen-2 revealed 17 probably
damaging, 2 possibly damaging and 1 benign nsSNPs. Using two additional
software SNPs & GO and PHD-SNPs showed that 14 and 17 nsSNPs had a