Biology subjects

Hassan, M. A.

Publications and source records attributed to Hassan, M. A..

At least 37 records · Page 2Linked to original sources

bioRxiv2020

Contamination of Currency Notes with Kanamycin Resistant Shigella flexneri

Shigella flexneri is the main causative agent of shigellosis commonly distributed in developing countries with high morbidity and mortality rates. This study aimed to examine the presence of Shigella species in Sudanese currency notes using both traditional and molecular techniques. One hundred thirty five currency notes were collected and their contaminants were isolated and identified conventionally and genetically using 16S rRNA gene amplification and sequencing. Eight isolates were identified as Shigella species in different notes, and 3 of them were resistant to penicillin, kanamycin and nitrofurantoin. One S. flexneri isolate has insertion mutation of guanine nucleotide at position 730 of lifes essential gene 16S rRNA which known evolutionarily to be stable gene. Banknotes are highly circulating items and therefore, appropriate measures such as regular replacement of the dirty notes with new papers are necessary to protect peoples from being infected with drug resistant pathogens.

microbiology↗

bioRxiv2019

Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two lineages of H. pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution

BackgroundH. pylori is ubiquitous among humans, and one of the best studied examples of an intimate association between bacteria and humans. Under several diverse socio-demographic factors in Sudan, a continuous increase in the prevalence rate of H. pylori infection has been noticed which represents a major public health challenge. In this study, we analyzed the molecular evolution of H. pylori Strains detected from different ethnic and regions of Sudan using 16S rRNA gene and phylogenetic approach. Materials and methodsA total of 75 gastric biopsies taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was done by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was performed; then Blast these sequences with those available in the NCBI nucleotide database. The evolutionary aspects were analyzed using a MEGA7 software. ResultMolecular detection of H. pylori has shown that 28 (37.33%) of patients were positive for H. pylori. Bivariate analysis has found no significant differences exhibited across sociodemographic, endoscopy series and H. pylori infection. Nucleotide variations were found at five nucleotide positions (positions 219, 305, 578, 741 and 763-764) and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. The phylogenetic tree diverged into two lineages. ConclusionThe phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. Sex mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites. 66.67% of them were located in the central domain of 16S rRNA. Studying the effect of these mutations on the functions of 16S rRNA molecules in protein synthesis and antibiotic resistance is of great importance.

microbiology↗

bioRxiv2019

A genome-wide loss-of-function screen identifies Toxoplasma gondii genes that determine fitness in interferon gamma-activated murine macrophages

Macrophages play an essential role in the early immune response against Toxoplasma and are the cell type preferentially infected by the parasite in vivo. Interferon gamma (IFN{gamma}) elicits a variety of anti-Toxoplasma activities in macrophages. Using a genome-wide CRISPR screen we identified [~]130 Toxoplasma genes that determine parasite fitness in naive macrophages and [~]466 genes that determine fitness in IFN{gamma}-stimulated murine macrophages, seven of which we investigated and confirmed. We show that one of these genes encodes dense granule protein GRA45, which contains a putative chaperone-like domain, and which we show is critical in preventing other GRA effectors from aggregating. Parasites lacking GRA45 mislocalize GRA effectors upon secretion, are more susceptible to IFN{gamma}-mediated growth inhibition, and have reduced virulence in mice. Our results provide a resource for the community to further explore the function of Toxoplasma genes that determine fitness in IFN{gamma}-stimulated macrophages. IMPORTANCEThe intracellular parasite Toxoplasma gondii can cause congenital infections and severe disease in immunocompromised patients. The cytokine IFN{gamma} can block parasite replication by upregulating a variety of toxoplasmacidal mechanisms in many cells, including macrophages. Toxoplasma preferentially infects macrophages. Therefore, the parasite has evolved mechanisms to survive in these cells in the presence of IFN{gamma}. Here, we generated pools of Toxoplasma mutants for every gene and determined which mutants were specifically depleted in IFN{gamma}-stimulated macrophages, thus identifying parasite genes determining fitness in these cells. We show that one of these genes encodes for a dense granule protein (GRA45) that plays an important role in preventing other GRA effectors from aggregating. Parasites without GRA45 mislocalize GRA effectors upon secretion, have enhanced susceptibility to IFN{gamma}-mediated growth inhibition, and are avirulent in mice. Thus, our screen provides a resource to the Toxoplasma community to determine the function of Toxoplasma genes that affect its fitness in IFN{gamma}-stimulated macrophages.

microbiology↗

bioRxiv2019

Single-cell RNA-seq reveals CD16- monocytes as key regulators of human monocyte transcriptional response to Toxoplasma

Monocytes are among the major myeloid cells that respond to Toxoplasma, a ubiquitous foodborne that infects [≥]1 billion people worldwide, in human peripheral blood. As such, a molecular understanding of human monocyte-Toxoplasma interactions can expedite the development of novel human toxoplasmosis control strategies. Current molecular studies on monocyte-Toxoplasma interactions are based on average cell or parasite responses across bulk cell populations. Although informative, population-level averages of monocyte responses to Toxoplasma have sometimes produced contradictory results, such as whether CCL2 or IL12 define effective monocyte response to the parasite. Here, we used single-cell dual RNA sequencing (scDual-Seq) to comprehensively define, for the first time, the monocyte and parasite transcriptional responses that underpin human monocyte-Toxoplasma encounters at the single cell level. We report extreme transcriptional variability between individual monocytes. Furthermore, we report that Toxoplasma-exposed and unexposed monocytes are transcriptionally distinguished by a reactive subset of CD14++CD16- monocytes. Functional cytokine assays on sorted monocyte populations show that the infection-distinguishing monocytes secrete high levels of chemokines, such as CCL2 and CXCL5. These findings uncover the Toxoplasma-induced monocyte transcriptional heterogeneity and shed new light on the cell populations that largely define cytokine and chemokine secretion in human monocytes exposed to Toxoplasma.

genomics↗

bioRxiv2019

Comprehensive Analysis of HEXB Protein Reveal Forty Two Novel nsSNPs That May Lead to Sandhoff disease (SD) Using Bioinformatics

BackgroundSingle Nucleotide Polymorphisms (SNPs) in the HEXB gene are associated with a neurodegenerative disorder called Sandhoff disease (SD) (GM2 gangliosidosis-O variant). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools. MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of beta subunit beta subunit of both hexosaminidase A and hexosaminidase B proteins. ResultsForty nine mutations were found to be extremely damaging to the structure and function of the HEXB gene protein. ConclusionAccording to this study, forty two novel nsSNP in HEXB are predicted to have possible role in Sandhoff disease using different bioinformatics tools, beside two SNPs found to have effect on miRNAs binding site affecting expression of HEXB gene. Our findings may assist in genetic study and diagnosis of Sandhoff disease.

bioinformatics↗

bioRxiv2019

Insilico Analysis Reveal Three novel nsSNPs May effect on GM2A protein Leading to AB variant of GM2 gangliosidosis

BackgroundAB variant of GM2 gangliosidosis caused as a result of mutations in GM2 activator gene (GM2A) which is regarded as neurodegenerative disorder. This study aimed to predict the possible damaging SNPs of this gene and their impact on the protein using different bioinformatics tools. MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different tools collectively predicted the effect of single nucleotide substitution on both structure and function of GM2 activator. ResultsThree novel mutations were found to be highly damaging to the structure and function of the GM2A gene. ConclusionFour SNPs were found to be highly damaging SNPs that affect function, structure and stability of GM2A protein, which they are: C99Y, C112F, C138S and C138R, three of them are novel SNPs (C99Y, C112F and C138S). Also 46 SNPs were predicted to affect miRNAs binding sites on 3UTR leading to abnormal expression of the resulting protein. These SNPs should be considered as important candidates in causing AB variant of GM2 gangliosidosis and may help in diagnosis and genetic screening of the disease.

bioinformatics↗

bioRxiv2019

The Association between SLC25A15 Gene Polymorphisms and Hyperornithinemia-hyperammonemia-homocitrullinuria Syndrome: Using In Silico Analysis

BackgroundHyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome is an autosomal recessive inborn error of the urea cycle. It is caused by mutations in the SLC25A15 gene that codes the mitochondrial ornithine transporter. The aim of this study is to detect and identify the pathogenic SNPs in SLC25A15 gene through a combination set of bioinformatics tools and their effect on the structure and function of the protein.\n\nMethodsThe deleterious SNPs in SLC25A15 are detected by various bioinformatics tools, with addition to identifying their effects on the structure and function of this gene.\n\nResults20 deleterious SNPs out 287of were found to have their own damaging effects on the structure and function of the SLC25A15 gene.\n\nConclusionThis study is the first in silico analysis of SLC25A15 using a selection of bioinformatics tools to detect functional and structural effects of deleterious SNPs. Finding the pathogenic SNPs is a promising start to innovate new, useful SNP diagnostic markers for medical testing and for safer novel therapies specifically targeting mutant SLC25A15.

bioinformatics↗

bioRxiv2019

Thirty two novel nsSNPs May effect on HEXA protein Leading to Tay-Sachs disease (TSD) Using a Computational Approach

BackgroundGenetic polymorphisms in the HEXA gene are associated with a neurodegenerative disorder called Tay-Sachs disease (TSD) (GM2 gangliosidosis type 1). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools.\n\nMethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of the hexosaminidase A protein.\n\nResultsFifty nine mutations were found to be highly damaging to the structure and function of the HEXA gene protein.\n\nConclusionAccording to this study, thirty two novel nsSNP in HEXA are predicted to have possible role in Tay-Saches Disease using different bioinformatics tools. Our findings could help in genetic study and diagnosis of Tay-Saches Disease.

bioinformatics↗

bioRxiv2019

Thirty five novel nsSNPs may effect on ADAMTS13 protein leading to Thrombotic thrombocytopenic purpura (TTP) using bioinformatics approach

BackgroundGenetic polymorphisms in the ADAMTS13 gene are associated with thrombotic thrombocytopenic purpura or TTP, a life-threatening microangiopathic disorder. This study aims to predict the possible pathogenic SNPs of this gene and their impact on the protein structure and function using insilico methods.\n\nMethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms applied collectively to predictthe effect of single nucleotide substitution on both structure and function of the ADAMTS13 protein.\n\nResultsFifty one mutations were found to be highly damaging to the structure and function of the protein. Of those, thirty five were novel nsSNPs not previously reported in the literature.\n\nConclusionAccording to our analysis we found thirty five nsSNPs effects on ADAMTS13 protein leading to thrombotic thrombocytopenic purpura using computational approach. Bioinformatics tools are vital in prediction analysis, making use of increasingly voluminous biomedical data thereby providing markers for screening or for genetic mapping studies.

bioinformatics↗

bioRxiv2019

In silico analysis of CDC73 gene revealing 11 novel SNPs associated with Jaw Tumor Syndrome

Back groundhyperparathyroidism-jaw tumor (HPT-JT) is an autosomal dominant disorder with variable expression, with an estimated prevalence of 6.7 per 1,000 population. Genetic testing for predisposing CDC73 (HRPT2) mutations has been an important clinical advance, aimed at early detection and/or treatment to prevent advanced disease. The aim of this study is to assess the effect of SNPs on CDC73 structure and function using different bioinformatics tools.\n\nMethodComputational analysis using eight different in-silico tools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, PMut and Imutant were used to identify the impact on the structure and/or function of CDC73 gene that might be causing jaw tumour.\n\nResultsFrom (733) SNPs identified in the CDC73 gene we found that only Eleven were deleterious to the function and structure of protein and expected to cause syndrome.\n\nConclusionEleven substantial genetic/molecular aberrations in CDC73 gene were identified that could serve as actionable targets for chemotherapeutic intervention in patients whose disease is no longer surgically curable.

bioinformatics↗

bioRxiv2019

Physiological and pathophysiological homeostasis of astroglial channel proteins by Nedd4-2

Nedd4-2 is an E3 ubiquitin ligase, missense mutation of which is related to familial epilepsy, indicating its critical role in regulating neuronal network activity. However, Nedd4-2 substrates involved in neuronal network function have yet to be identified. Using mouse lines lacking Nedd4-1 and Nedd4-2, we identified astrocytic channel proteins inwardly rectifying K+ channel 4.1 (Kir4.1) and Connexin43 as Nedd4-2 substrates. We found that the expression of Kir4.1 and Connexin43 is increased upon conditional deletion of Nedd4-2 in astrocytes, leading to an elevation of astrocytic membrane ion permeability and gap junction activity, with a consequent reduction of {gamma}-oscillatory neuronal network activity. Interestingly, our biochemical data demonstrate that missense mutations found in familial epileptic patients produce gain-of-function of Nedd4-2 gene product. Our data reveal a process of coordinated astrocytic ion channel proteostasis that controls astrocyte function and astrocyte-dependent neuronal network activity, and elucidate a potential mechanism by which aberrant Nedd4-2 function leads to epilepsy.\n\nCONDENSED TITLEUbiquitination of Astrocytic Channels by Nedd4-2\n\nSUMMARYUbiquitination is a key regulatory machinery for protein expression. Our present work provides evidence that astrocytic ion channel proteostasis coordinated by an E3 ubiquitin ligase Nedd4-2 is of particular importance for the maintenance of neuronal network activity.

neuroscience↗

bioRxiv2019

Epitope-based peptide vaccine against glycoprotein G of Nipah henipavirus using immunoinformatics approaches

BackgroundNipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia, first emerged in Malaysia in 1998. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Clinical presentation ranges from asymptomatic infection to fatal encephalitis. Bats are the main reservoir for this virus, which can cause disease in humans and animals. The last investigated NiV outbreak has occurred in May 2018 in Kerala.\n\nObjectiveThis study aims to predict effective epitope-based vaccine against glycoprotein G of Nipah henipavirus using immunoinformatics approaches.\n\nMethods and MaterialsGlycoprotein G of Nipah henipavirus sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominees epitopes in BepiPred-2.0: Sequential B-Cell Epitope Predictor for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.\n\nResults and ConclusionsPeptide TVYHCSAVY shows a very strong binding affinity to MHC I alleles while FLIDRINWI shows a very strong binding affinity to MHC II and MHC I alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FLIDRINWI that is likely to be the first proposed epitope-based vaccine against glycoprotein G of Nipah henipavirus. This study recommends an in-vivo assessment for the most promising peptides especially FLIDRINWI.

bioinformatics↗

bioRxiv2019

Immunoinformatics Prediction of Epitope Based Peptide Vaccine Against Listeria Monocytogenes Fructose Bisphosphate Aldolase Protein

Listeria Monocytogenes represents an important food-borne pathogen worldwide that can cause life-threatening listeriosis disease especially in pregnant women, fetuses, elderly people, and immuno-compromised individuals with high mortality rates. Moreover, no vaccine against it exists. This study predicts an effective epitope-based vaccine against Fructose 1,6 Bisphosphate Aldolase (FBA) enzyme of Listeria Monocytogenes using immunoinformatics approaches. The sequences were retrieved from NCBI and several prediction tests were conducted to analyze possible epitopes for B-cell, T-cell MHC class I and II. 3D structure of the promising epitopes was obtained. Two epitopes showed high binding affinity for B-cells, while four epitopes showed high binding affinity for MHCI and MHCII. The results were promising to formulate a vaccine with more than 98% population coverage. We hope that these promising epitopes serves as a preventive measure for the disease in the future and recommend invivo and invitro studies.

bioinformatics↗

bioRxiv2019

Rapid and highly sensitive detection of pyocyanin biomarker in different Pseudomonas aeruginosa infections using gold nanoparticles modified sensor

Successful antibiotic treatment of infections relies on accurate and rapid identification of the infectious agents. Pseudomonas aeruginosa is implicated in a wide range of human infections that almost complicated and become life threating especially in immunocompromised and critically ill patients. Conventional microbiological methods take more than 3 days to obtain accurate results. Pyocyanin is a distinctive electroactive biomarker for Pseudomonas aeruginosa. Here, we have developed a rapid diagnostic (polyaniline) PANI gold nanoparticles (Au NPs) modified indium tin oxide (ITO) electrode that showed 100% sensitivity for pyocyanin in culture of Pseudomonas aeruginosa clinical isolates and high selectivity for pyocyanin at low concentration when measured in the presence of other substances like ascorbic acid, uric acid, and glucose as interferences. The constructed electrode was characterized using scanning electron microscopy and cyclic voltammetry. The determined linear range for pyocyanin detection was from 238 {micro}M to 1.9 {micro}M with a detection limit of 500 nM. Compared to the screen-printed electrode used before, the constructed electrode showed a 4-fold enhanced performance.

biochemistry↗

bioRxiv2019

Genetic Monitoring and Molecular Phylogeny for Cymothoid Isopod Invasion in Egyptian Lake Qarun Fishes by Using adopted taxonomic marker (COI)

Different types of aquatic ecosystem is abundant by a lot of crustaceans. There are species adapted to maximum of temperature, pressure and salinity. Isopods are a marine parasitic organism and commonly live in warmer seas. They are feeding on blood. Several species settle in the buccal cavity of fish. Parasite became a morbidity case in lake Qarun, GAFRD (General Authority for fish resources development, Fish Statistics yearbook, 2015). DNA barcoding gene (COI gene) was used to make the genetic characterization for the invasive species of Cymothoidae, Cymothoidae sp and recorded in the Genbank. Constructing a phylogeny depending on the degree of similarity between the new record (LC138010.1) and the other records of Cymothoidae species in the Genebank then the environmental conditions were compared according to the analysis of the constructed tree. Suez canal is the primary resource for the fingers of mullet which transferred to Qarun Lake (salinity, 49 ppt). Ballast water have an environmental effect by transferring the alien species in the Suez Gulf which have a warm weather. This study suggests that the Cymothoidae is expanded invasive species came from its habitat regions to a closed lakes which have a similar condition of water environment, temperature and depth to live and to be a morbidity in Lake Quran. Ballast water is a risky way to transfer the invasive species to Suez Canal then New Suez Canal poses and lead to biodiversity risks. Using eDNA techniques to diagnose the invasive species is very important unit which must be established in general authorities of fish resources and development in Egypt and other countries which invaded by different alien species.

genetics↗

bioRxiv2019

Identification of novel key biomarkers in Simpson-Golabi-Behmel Syndrome: Evidence from bioinformatics analysis

BackgroundThe Simpson-Golabi-Behmel Syndrome (SGBS) or overgrowth Syndrome is a rare inherited X-linked condition characterized by pre- and postnatal overgrowth. The aim of the present study is to identify functional non-synonymous SNPs of GPC3 gene using various in silico approaches. These SNPs are supposed to have a direct effect on protein stability through conformation changes.\n\nMaterial and methodsThe SNPs were retrieved from the Single Nucleotide Polymorphism database (dbSNP) and further used to investigate a damaging effect using SIFT, PolyPhen, PROVEAN, SNAP2, SNPs&GO, PHD-SNP and P-mut, While we used I-mutant and MUPro to study the effect of SNPs on GPC3 protein structure. The 3D structure of human GPC3 protein is not available in the Protein Data Bank, so we used RaptorX to generate a 3D structural model for wild-type GPC3 to visualize the amino acids changes by UCSF Chimera. For biophysical validation we used project HOPE. Lastly we run conservational analysis by BioEdit and Consurf web server respectively.\n\nResultsour results revealed three novel missense mutations (rs1460413167, rs1295603457 and rs757475450) that are found to be the most deleterious which effect on the GPC3 structure and function.\n\nConclusionThis present study could provide a novel insight into the molecular basis of overgrowth Syndrome.

bioinformatics↗

bioRxiv2019

In Silico Genetics Revealing Novel Mutations in CEBPA Gene Associated with Acute Myeloid Leukemia

BackgroundMyelodysplastic syndrome/Acute myeloid leukemia (MDS/AML) is a highly heterogeneous malignant disease; affects children and adults of all ages. AML is one of the main causes of death in children with cancer. However, It is the most common acute leukemia in adults, with a frequency of over 20 000 cases per year in the United States of America alone.\n\nMethodsThe SNPs were retrieved from the dbSNP database. this SNPs were submitted into various functional analysis tools that done by SIFT, PolyPhen-2, PROVEAN, SNAP2, SNPs&GO, PhD-SNP and PANTHER, while structural analysis were done by I-mutant3 and MUPro. The most damaging SNPs were selected for further analysis by Mutation3D, Project hope, ConSurf and BioEdit softwares.\n\nResultsA total of five novel nsSNPs out of 248 missense mutations were predicted to be responsible for the structural and functional variations of CEBPA protein.\n\nConclusionIn this study the impact of functional SNPs in the CEBPA gene was investigated through different computational methods, which determined that (R339W, R288P, N292S N292T and D63N) are novel SNPs have a potential functional effect and can thus be used as diagnostic markers and may facilitate in genetic studies with a special consideration of the large heterogeneity of AML among the different populations.

bioinformatics↗

bioRxiv2019

Genetic analysis of TP53 gene mutations in exon 4 and exon 8 among esophageal cancer patients in Sudan

BackgroundEsophageal carcinoma (EC) represents the 1st rank among all gastrointestinal cancers in Sudan. Despite little publications, there is a deep absence of literature about the molecular pathogenesis of EC considering TP53 gene from Sudanese population.\n\nAimsIn this study, we performed the expression analysis on p53 protein level by immunohistochemical staining and examined its overexpression with p53 mutations in exons 4 and 8 among esophageal cancer patients in Sudan.\n\nMaterial and MethodsFixed tissue with 10% buffered formalin was stained by Hematoxlin and Eosin (H&E), Alcian blue-Periodic Acid Schiff (PAS) and Immunohistochemistry stain. PCR-RFLP was used to study the frequencies of p53 codon 72 R/P polymorphism. Conventional PCR and sanger sequencing were applied for exon 4 and exon 8. Then detection and functional analysis of SNPs and mutations were performed using various in bioinformatics tools.\n\nResultNuclear accumulations for p53 protein was detected in all of the esophageal carcinomas examined while no accumulations were observed in normal control sections. Four patients with immune-positive for p53 showed no mutations in p53 gene (exon4 and exon8). The incidence of the homozygous mutant variant Pro/Pro was higher in esophageal cancerous patients comparing to healthy control subject 20(71. 4%) vs. 1(10%), respectively (p=0.0026). In exon 4, no mutation was detected other than NG_017013.2:g. 16397C>G. While in exon 8, g.18783-18784AG>TT, g.18803A>C, g.18860A>C, g.18845A>T and g.18863_ 18864 InsT were observed.\n\nConclusionwe found a significant association between the overexpression of TP53 protein and mutation in exon 4 and 8. A silent mutation P301P was detected in all of examined cases. Two patients who diagnosed with small cell sarcoma have shared the same mutations in exon8. Further studies with large sample size are required to demonstrate the usefulness of these mutations in the screening of EC especially SCCE.

cancer biology↗