Computational Analysis of Deleterious nsSNPs in INS Gene Associated with Permanent Neonatal Diabetes Mellitus.

Insulin gene mutations affect the structure of insulin and are considered a leading cause of neonatal diabetes and permanent neonatal diabetes mellitus PNDM. These mutations can affect the production and secretion of insulin, resulting in inadequate insulin levels and subsequent hyperglycemia. Early discovery or prediction of PNDM can aid in better management and treatment. The current study identified potential deleterious non-synonymous single nucleotide polymorphisms nsSNPs in the INS gene. The analysis of the nsSNPs in the INS gene was conducted using bioinformatics tools by implementing computational algorithms including SIFT, PolyPhen2, SNAP2, SNPs & GO, PhD-SNP, MutPred2, I-Mutant, MuPro, and HOPE tools to investigate the prediction of the potential association between nsSNPs in the INS gene and PNDM. Three mutations, C96Y, P52R, and C96R, were shown to potentially reduce the stability and function of the INS protein. These mutants were subjected to MDSs for structural analysis. Results suggested that these three potential pathogenic mutations may affect the stability and functionality of the insulin protein encoded by the INS gene. Therefore, these changes may influence the development of PNDM. Further researches are required to fully understand the various effects of mutations in the INS gene on insulin synthesis and function. These data can aid in genetic testing for PNDM to evaluate its risk and create treatment and prevention strategies in personalized medicine.

Molecular detection of Epstein-Barr virus among Sudanese patients diagnosed with Hashimoto's thyroiditis.

OBJECTIVES: Hashimoto's thyroiditis (HT) is the most common cause of hypothyroidism. The exact mechanism initiating the development of HT is not yet clear. This study aimed to investigate the correlation between HT and the presence of Epstein-Barr virus (EBV) in a Sudanese population. RESULTS: EBV-LMP1 was detected in 11.1% of HT cases, which is consistent with previous studies. Studies have reported a wide range of frequencies indicating the presence of EBV in HT, and patients with autoimmune thyroiditis have increased titers of anti-EBV antibodies in their sera compared to healthy subjects. Intrathyroidal EBV-infected B cells may be responsible for the increased risk of development of B-cell lymphoma in the thyroid gland in patients with autoimmune thyroiditis. Our study suggests that regular follow-up is necessary for patients diagnosed with HT and are positive for EBV, as antiviral therapy is not applicable due to the risk of thyroid dysfunction. The study suggests an association between EBV and HT, but causation cannot be determined. The study also highlights the need for further research to determine the viral role and correlate it with the severity and progression of HT.

In Silico Evaluation of the Potential Association of the Pathogenic Mutations of Alpha Synuclein Protein with Induction of Synucleinopathies.

Alpha synuclein (α-Syn) is a neuronal protein encoded by the SNCA gene and is involved in the development of Parkinson's disease (PD). The objective of this study was to examine in silico the functional implications of non-synonymous single nucleotide polymorphisms (nsSNPs) in the SNCA gene. We used a range of computational algorithms such as sequence conservation, structural analysis, physicochemical properties, and machine learning. The sequence of the SNCA gene was analyzed, resulting in the mapping of 42,272 SNPs that are classified into different functional categories. A total of 177 nsSNPs were identified within the coding region; there were 20 variants that may influence the α-Syn protein structure and function. This identification was made by employing different analytical tools including SIFT, PolyPhen2, Mut-pred, SNAP2, PANTHER, PhD-SNP, SNP&Go, MUpro, Cosurf, I-Mut, and HOPE. Three mutations, V82A, K80E, and E46K, were selected for further examinations due to their spatial positioning within the α-Syn as determined by PyMol. Results indicated that these mutations may affect the stability and function of α-Syn. Then, a molecular dynamics simulation was conducted for the SNCA wildtype and the four mutant variants (p.A18G, p.V82A, p.K80E, and p.E46K). The simulation examined temperature, pressure, density, root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (Rg). The data indicate that the mutations p.V82A, p.K80E, and p.E46K reduce the stability and functionality of α-Syn. These findings highlight the importance of understanding the impact of nsSNPs on α-syn structure and function. Our results required verifications in further protein functional and case-control studies. After being verified these findings can be used in genetic testing for the early diagnosis of PD, the evaluation of the risk factors, and therapeutic approaches.

Obstacles faced by healthcare providers during COVID-19 pandemic in Sudan.

The impacts of COVID -19 pandemic have been quite significant on healthcare providers. I was particularly challenging for those in Low and Middle-Income Countries including Sudan . Unfortunately, the pandemic has hit Sudan on extremely difficult time for the country and its people. The country was coming out of long-brutal and devastating dictatorship and transitioning to new democracy with civilian leadership. In addition to the pandemic related issues, trying to rebuild the health system during socioeconomic crisis, healthcare providers  in the country were challenged personally and professionally. These challenges include the stress of working in under-resourced settings with limited access to personal-protection equipment and testing kits raised the fear of contracting the virus and spreading it to their families. The professional, social, and personal life of healthcare providers have been dramatically changed by the ongoing pandemic, however, they are heroically accepting this change in a hope that, this will save the life of many more people. Nevertheless, their fights and sacrifices should at least be rewarded by governments and communities altogether strictly enforce the implementation of other preventive measures including vaccination, face masking, and social distancing and get all protected. We should all understand that, unless we are all protected no one is protected, so all must adapt to the new norm of life and collaborate not only on ending this pandemic but to prevent similar ones in the future.

Association of interleukin-17A rs2275913 polymorphism with rheumatoid arthritis susceptibility in Sudanese population.

OBJECTIVES: Rheumatoid arthritis is a chronic inflammatory autoimmune disease. This study aimed to determine the association of interleukin-17A-197G/A polymorphism with rheumatoid arthritis in Sudanese patients. METHODS: A case-control study was conducted between March and December 2018. Clinical and demographic data of the study participants were collected and analyzed. Polymerase chain reaction restriction fragment length polymorphism molecular technique was done to investigate interleukin-17A-197G/A polymorphisms. All statistical tests were considered statistically significant when p < 0.05. RESULTS: The study population included 266 participants aged between 1 and 85 years, with an average of 40 years, classified into 85 (31.2%) cases (mean age 48.5 ± 11.3 years), and 181 (68.8%) controls (mean age 35.3 ± 15.9 years). The interleukin-17A homozygote AA genotype was more frequent among the control group compared to the case group; 95 (52.5%) and 7 (8.2%), respectively. The homozygote GG and the heterozygote AG genotypes were proportionally not different among the cases and control groups; 13 (54.2%) and 11 (45.8%), and 65 (46.4%) and 75 (53.6%), respectively. According to the distribution of interleukin-17A genotypes, a statistically significant difference was observed among cases with the interleukin-17A AA and AG genotypes, p values 0.001 and 0.004, respectively. For the association interleukin-17A genotypes and family history a negatively significant association was reported (95% confidence interval, -0.219, p value = 0.001). There was also a negatively significant association of interleukin-17A genotypes and anti-cyclic citrullinated peptide (95% confidence interval, -0.141, p value = 0.002). CONCLUSION: This study is the first study in Sudan established the association between interleukin-17A-197G/A (rs2275913) polymorphisms and susceptibly to rheumatoid arthritis. These findings appeal for further research in Sudan to investigate the exact role of IL-17A in immunopathology and disease severity among Sudanese rheumatoid arthritis.

Molecular detection of human papillomavirus-16 among Sudanese patients diagnosed with squamous cell carcinoma and salivary gland carcinoma.

OBJECTIVE: Human papillomavirus (HPV) gained momentum as a potential etiological factor for many types of cancers. Therefore, the aim of this study was to assess the prevalence of HPV-16 infection among Sudanese patients diagnosed with Squamous Cell Carcinoma (SCC) and Salivary Gland Carcinoma. A descriptive, hospital-based study was conducted. 150 formalin-fixed paraffin-embedded blocks were collected. RESULTS: The study population included a total of 150 patients aged between 18 to 87 years with a mean age of 48.8 ± 11.9 years. Based on gender, females constituted 46.7% while males constituted 53.3%. The 150 patients were classified into 40 (26.0%) esophageal, 30 (20.0%) nasopharyngeal, 18 (12.0%) conjunctival, 18 (12.0%) tongue 12 (8.0%) laryngeal, 8 (5.3%) lip, 6 (4.0%) oropharyngeal, 6 (4.0%) mucoepidermoid, and 6 (4.0%) adenoid cystic, and 6 (4.0%) myoepithelial carcinomas. Odds ratio for male and female diagnosed with carcinoma was 1.025 [0.439-2.394, 95% CI]. Molecular detection of HPV-16 revealed a prevalence of 26 (17.3%) patients were positive for HPV-16. According to cancer diagnosis, esophageal SCC patients showed a high proportion of HPV-16; 14/40 (35.0%). A statistically significant difference was seen for the distribution of HPV-16 positive patients based on cancer diagnosis, P value 0.001.

Frequency distribution of IL-17A G197A (rs2275913) and IL-17F A7488G (rs763780) polymorphisms among healthy Sudanese population.

OBJECTIVES: IL-17A G197A and IL-17F A7488G polymorphisms has been identified to be associated with the susceptibility to many diseases. This study aimed to investigate the frequency distribution of IL-17A G197A and IL-17F A7488G polymorphisms among healthy Sudanese population. A descriptive cross-sectional hospital-based molecular study conducted in different sites throughout Sudan. Two ml blood samples were collected from 717 healthy participants. Demographic data and the medical history of the participants were collected. RESULTS: Of the 717 participants, 355 (49.5%) were males and 362 (50.5%) were females, their mean age was 30.2 ± 17.2 and 32.2 ± 16.5, respectively. For IL-17A, the most frequent genotype detected among males and females was IL-17A heterozygote allele (AG); 215 (60.6%) and 194 (53.6%), respectively. Whereas, for IL-17F, the most frequent allele among males and females was the homozygote allele (AA); 298 (83.9%) for males and 322 (89.0%) for females. HWE for genotype distributions of IL-17A was showing statistical insignificance for IL-17A among males and females, P value 0.614. While HWE for IL-17F reached the equilibrium level, P value 0.048. The most frequent age group was those aged between 21 to 40 years; 281 (39.2%). Arab constituted the major ethnicity of the study participants; 418 (58.3%), P value 0.034.

Prevalence of Helicobacter pylori among Sudanese patients diagnosed with colon polyps and colon cancer using immunohistochemistry technique.

OBJECTIVES: Infection with the bacteria Helicobacter pylori has been classified as class one carcinogen associated with increasing susceptibility of gastritis and gastric carcinoma. This study is aiming at investigating the prevalence of H. pylori among colon polyps and colon cancer patients. A descriptive cross-sectional hospital-based study was conducted between February and June 2017. Sixty-nine formalin-fixed paraffin blocks collected from colon polyps and colon cancer patients to detect H. pylori using immunohistochemistry technique. RESULTS: Of the 69 patients included in the study, 39 (56.5%) males and 30 (43.5%) were females, their age ranged from 21 to 80 years with a mean age of 47.1 ± 19.7. Of the 69 colon polyps and colon cancer patients, 44 (63.8%) were diagnosed as adenocarcinoma, 10 (14.5%) colitis, 15 (21.7%) juvenile polyposis syndrome. The results of immunohistochemistry technique showed the presence of 16 (23.2%) positive patients for H. pylori infection. Of these 16, 13 (81.3%) patients were diagnosed with adenocarcinoma and 3 (18.7%) patients were diagnosed with juvenile polyps. The results of H. pylori detection among the different colon polyps and colon cancer patients were showing a statistically significant association for H. pylori infection and adenocarcinoma, P value 0.028.

Immunohistochemical expression of Cyclin D1 among Sudanese patients diagnosed with benign and malignant prostatic lesions.

OBJECTIVES: Prostate cancer (PC) is common cancer worldwide. Several markers have been developed to differentiate between benign prostatic hyperplasia (BPH) from PC. A descriptive retrospective hospital-based study aimed at determining the expression of Cyclin D1 in BPH and PC. The study took place at different histopathology laboratories in Khartoum state, Sudan, from December 2016 to January 2019. Formalin-fixed paraffin-embedded blocks were sectioned and fixed in 3-aminopropyltriethoxysilane coated slides incubated into primary antibody for Cyclin D1. The assessment of immunoreactivity of Cyclin D1 of each section was done using the Gleason scoring system. RESULTS: A total of 153 males' prostate sections included in this study, of them, 120 (78.4%) were PC, and 33 (21.6%) were BPH. Their age ranged from 45 to 88 years, mean age was 66.19 ± 8.599. 142 (92.8%) did not have a family history of PC, while 11 (7.2%) patients reported having a family history. The Gleason scoring showed a total of 81 (52.9%) patients with high-grade and 39 (25.5%) with low-grade. 118 (97.5%) patients had PC showed positive results for Cyclin D1, while BPH was 3 (2.5%). P value < 0.001. Cyclin D1 staining was associated with high-grade Gleason score and perineural invasion, P value 0.001.

Immunohistochemical expression of interleukin-17 and hormonal receptors in benign and malignant breast lesions.

OBJECTIVES: IL17 is a critical pro-inflammatory cytokine that is involved in inflammation, multidrug resistance and growth persistence pathways in cancer. This study is aiming at studying the expression of IL17 and hormonal receptors expression in benign and malignant breast lesions using immunohistochemical staining methods. RESULTS: A total of 137 cases of breast lesions were studied, 97 (70.8%) were malignant and 40 (29.2%) were benign cases. Age range for malignant and benign cases were between 26 and 80 years [mean age 50 ± 2 years], and 20 to 70 years [mean age 41 ± 4 years], respectively, Odds ratio = 2.3 [1.78-1.99, 95% CI]. The majority of the histopathological diagnosis of the benign and malignant lesions were 21 (15.3%) fibro-adenomas and 87 (63.5%) invasive ductal carcinoma, respectively. Expression of IL17 and age were insignificantly negatively correlated for both groups; benign cases [r = - 0.054, P value 0.742] and malignant cases [r = - 0.080, P value 0.444]. IL17 expression was showing insignificant association with age group, P value 0.065. IL17 expression showed a statistical significance based on the different histopathological diagnosis, P value 0.035. Expression levels of estrogen, progesterone, and human epidermal receptors were showing insignificant difference among IL17 expression categories, P values 0.678, 0.623, and 0.361, respectively.

Interleukin-17 and matrix metalloprotease-9 expression in the mycetoma granuloma.

Mycetoma is a persistent, progressive granulomatous inflammatory disease caused either by fungi or by bacteria. Characteristic of this disease is that the causative agents organise themselves in macroscopic structures called grains. These grains are surrounded by a massive inflammatory reaction. The processes leading to this host tissue reaction and the immunophenotypic characteristics of the mycetoma granuloma are not known. Due to the massive immune reaction and the tissue remodeling involved, we hypothesised that the expression levels of interleukin-17 (IL-17) and matrix metalloprotease-9 (MMP-9) in the mycetoma granuloma formation were correlated to the severity of the disease and that this correlation was independent of the causative agent responsible for the granuloma reaction. To determine the expression of IL-17 and MMP-9 in mycetoma lesions, the present study was conducted at the Mycetoma Research Centre, Sudan. Surgical biopsies from 100 patients with confirmed mycetoma were obtained, and IL-17 and MMP-9 expression in the mycetoma granuloma were evaluated immunohistochemically. IL-17 was mainly expressed in Zones I and II, and far less in Zone III. MMP-9 was detected mainly in Zones II and III, and the least expression was in Zone I. MMP-9 was more highly expressed in Actinomadura pelletierii and Streptomyces somaliensis biopsies compared to Madurella mycetomatis biopsies. MMP-9 levels were directly proportional to the levels of IL-17 (p = 0.001). The only significant association between MMP9 and the patients' characteristics was the disease duration (p<0.001). There was an insignificant correlation between the IL-17 levels and the patients' demographic characteristics.

Enteroparasitosis infections among renal transplant recipients in Khartoum state, Sudan 2012-2013.

OBJECTIVES: Renal transplantation procedure markedly increased over the past few decades. The risk of harboring parasitic diseases may affect transplant recipients during life expectancy. We aimed in this study to determine the enteroparasitosis frequency among renal transplant recipients in Khartoum state, Sudan. A case-control hospital-based study performed between November 2012 and May 2013, on 300 renal transplant recipients attending Sudanese Kidney Association hospital in Khartoum state, Sudan, along with 300 normal healthy individuals matching the case in age and sex. Stool samples were collected for parasitological studies. RESULTS: Out of the 300 renal transplant recipients: 242 (80.7%) were males mean age 43 ± 11.28 and 58 (19.3%) were females mean age 41 ± 13.41. Intestinal parasitic infection was observed in 118 participants and the overall frequency was 19.7%; of which 64 were cases (21.3%) and 54 (18.0%) were controls. Eight different species of intestinal parasites were identified; Entamoeba histolytica/dispar (7.5%), Entamoeba coli (6.5%), Giardia lambelia (3.2%), Cryptosporidium parvum (1.2%), Ascaris lumbricoides (0.6%), Enterobius vermicularis (0.3%), (0.2%) for each of Strongyloides stercoralis and Hymenolepis nana.

Erratum to: Molecular Detection of Epstein - Barr virus in Nasopharyngeal Carcinoma among Sudanese population.

[This corrects the article DOI: 10.1186/s13027-016-0104-7.].

Parasitic contamination of fresh vegetables sold at central markets in Khartoum state, Sudan.

BACKGROUND: Fresh vegetables are considered as vital nutrients of a healthy diet as they supply the body with essential supplements. The consumption of raw vegetables is the main way for transmission of intestinal parasitic organisms. This study was aimed at detecting the parasitic contamination in fresh vegetables sold in two central open-aired markets in Khartoum state, Sudan. METHODS: In this prospective cross-sectional study, a total of 260 fresh vegetable samples and 50 water samples used to sprinkle vegetable(s) were collected from two central open-aired markets (namely; Elshaabi and Central markets) during November 2011 to May 2012. The samples were microscopically examined for detection of parasitic life forms using standardized parasitological techniques for protozoans and helminthes worms. RESULTS: Of the 260 fresh vegetable samples, 35 (13.5 %) were microscopically positive for intestinal parasites whereas 7/50 (14 %) of water samples used to sprinkle vegetable(s) were found positives. Remarkably, high level of contamination in fresh vegetable samples was recorded in lettuce (Lactuca sativa) 36.4 % (4/11) while cayenne pepper (Capsicum annuum) and cucumber (Cucumis sativus) were not contaminated. The identified protozoans and helminthes were Entamoeba histolytica/dispar, Entamoeba coli, Giardia lamblia, Ascaris lumbricoides, Strongyloides stercoralis, T. trichiura and hookworms. The most predominant parasite encountered was E. histolytica/dispar (42.9 %) whereas both T. trichiura and A. lumbricoides (2.9 %) were the least detected parasites. None of the fresh vegetables had single parasitic contamination. The highest percentages found in water samples used to sprinkle vegetable(s) was for Strongyloides larvae 60 % (3/5). It is worth-mentioned that the rate of contamination in Elshaabi market was higher compared with Central market. However, there was no significant correlation between the type of vegetables and existence of parasites in both markets and a high significant relationship was observed between the type of parasite and total prevalence in fresh vegetables (p = 0.000). CONCLUSION: The study has identified a moderate rate of fresh vegetables contaminated with protozoan and helminthes. Contaminated fresh vegetables in central markets of Khartoum state may play a significant role in transmission of intestinal parasitic infections to humans, and the water used by greengrocers to sprinkle vegetable(s) can be implicated in vegetable contamination.

Diagnostic importance of Ultrasound-Guided Fine Needle Aspiration in Diagnosing Hepatic Lesions among Sudanese Patients 2015.

BACKGROUND: Liver cytology is indicated and requested for evaluating hepatic masses in symptomatic or serendipitous cryptic discovered lesions. OBJECTIVE: To determine the cytomorphological patterns of hepatic lesions identified among a group of Sudanese patients. MATERIALS AND METHODS: This is an analytical descriptive hospital-based study included 165 patients undergoing ultrasound-guided fine needle is an aspiration cytology (FNAC)for hepatic lesions, at Al-Amal Military Hospital and Khartoum Teaching Hospital in Khartoum, Sudan. Clinical data were reviewed. Air dried Diff Quick stained smears were grouped into unsatisfactory samples, benign lesions, and malignant neoplasms. RESULTS: Our population were consisted of 35 (21.2%) females and 130 (78.8%) males, with a male to female ratio 3.7:1 and an age ranged between 47 to 80, and a mean age 57±7. Of 165 cases, 57 (34.5%) were benign, no atypia were noticed, 101 (61.2%) were malignant. Most investigated patients were found to have metastatic lesions. CONCLUSION: FNAC is a useful tool for investigating hepatic lesions.

Accuracy of oral exfoliative cytology in Sudanese patients undergoing oral biopsy

Introduction: Early detection of a premalignant or malignant oral lesions promises to improve the survival and the morbidity of patients suffering from these conditions. Oral exfoliative cytology (OEC) is a non-invasive method that is well accepted by the patient, and is therefore, suitable for screening at-risk population for early diagnosis of oral cancer. Objective: The purpose of this study is to investigate the value of OEC in the detection of oral premalignant and malignant lesions. Material and methods: In this hospital-based case-control study, cytological scrapes from buccal mucosa were obtained from 100 individuals, of whom 50 were patients with oral lesions ascertained as "cases" and 50 were clinically healthy volunteers ascertained as "controls". All patients with oral lesions were also subjected to oral biopsy and histological examination. Results: Out of 50 cases studied, histopathology showed the presence of: Oral squamous cell carcinoma OSCC (n = 28), leukoplakia (n = 8), dysplasia (n = 3), and benign normal lesions (n = 11). In cytology, a specificity of 100%, sensitivity of 93% and accuracy of 92% were obtained for OSCC. Leukoplakia gave a specificity of 100%, a sensitivity of 87.5%, and an accuracy of 95%. Conclusion: Despite the small number of cases in this study, OEC is a useful method for detecting oral premalignant and malignant lesions. OEC can detect a number of pathological conditions that require management.

Value of centrifugated liquid-based cytology by Papanicolaou and May-Grünwald in oral epithelial cells.

For many years, liquid-based cytology (LBC) has been developed for cervical cancer screening and not oral cancer, as it requires automated devices. The aim of this study was to compare the utility of centrifugated CLBC preparation with that of direct preparation in oral lesions, by Papanicolaou (Pap) and May Grünwald-Giemsa's (MGG) methods. A total of 100 consecutive cases of oral lesions were investigated. We compared the results obtained by the CLBC performed by cytocentrifugation with those obtained by direct smear applying Pap and MGG methods. The comparison between CLBC and direct smears was based on the thickening or adequacy of the smear, distribution of cells and staining quality. All smears in CLBC and direct preparation were found adequate. For thickness of the smear, 40% and 42% were excellent, 33% and 30% were good, and 27% and 28% were acceptable by LBC and direct preparation, respectively. For the distribution of cells and scantiness of background elements, 92 (92%) smears of the CLBC have revealed clear, well distributed smears, compared to 70 (70%) of those in direct preparation. For the staining quality with the Pap method, 39% and 69% were excellent staining quality, 25% and 20% were good, and 36% and 11% were acceptable for CLBC and direct preparation, respectively. In MGG method, 9% and 22% were excellent staining quality, 23% and 36% were good and 68% and 43% were acceptable for CLBC and direct preparation respectively. CLBC performed by cytocentrifugation is inexpensive, and reduces inadequate smears and background staining.