Biology subjects

Hassan, M. A.

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

50 records · Page 3Linked to original sources

bioRxiv2019

Comprehensive bioinformatics analysis of L1CAM gene revealed Novel Pathological mutations associated with L1 syndrome

BackgroundMutations in the human L1CAM gene cause a group of neurodevelopmental disorders known as L1 syndrome (CRASH syndrome). The L1CAM gene provides instructions for producing the L1 protein, which is found all over the nervous system on the surface of neurons. L1 syndrome involves a variety of characteristics but the most common characteristic is muscle stiffness. Patients with L1 syndrome can also suffer from difficulty speaking, seizures, and underdeveloped or absent tissue connecting the left and right halves of the brain. MethodThe human L1CAM gene was studied from dbSNP/NCBI, 1499 SNPs were Homo sapiens; of which 450 were missense mutations. This selected for Comprehensive bioinformatics analysis by several in silico tools to investigate the effect of SNPs on L1CAM proteins structure and function. Results34 missense mutations (26 novel mutations) out of 450 nsSNPs that are found to be the most deleterious that effect on the L1CAM structural and functional level. ConclusionBetter understanding of L1 syndrome caused by mutations in L1CAM gene was achieved using Comprehensive bioinformatics analysis. These findings describe 35 novel L1 mutations which improve our understanding on genotype-phenotype correlation. And can be used as diagnostic markers for L1 syndrome and besides in cancer diagnosis specifically in breast cancer.

bioinformatics↗

bioRxiv2019

In silico analysis of IDH3A gene revealed Novel mutations associated with Retinitis Pigmentosa

BackgroundRetinitis Pigmentosa (RP) refers to a group of inherited disorders characterized by the death of photoreceptor cells leading to blindness. The aim of this study is to identify the pathogenic SNPs in the IDH3A gene and their effect on the structure and function of the protein. Methodwe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. Result20 deleterious SNPs out of 178 were found to have a damaging effect on the protein structure and function. Conclusionthis is the first in silico analysis of IDH3A gene and 20 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for Retinitis Pigmentosa.

bioinformatics↗

bioRxiv2019

In Silico Analysis and Modeling of Novel Pathogenic Single Nucleotide Polymorphisms (SNPs) in Human CD40LG Gene

AbstractO_ST_ABSBackgroundC_ST_ABSThe X-linked hyper-immunoglobulin M syndrome (XHIGM) is a rare, inherited immune deficiency disorder. It is more common in males. Characterized by elevated serum IgM levels and low to undetectable levels of serum IgG, IgA and IgE. Hyper-IgM syndrome is caused by mutations in the CD40LG gene. Located in human Xq26. CD40LG acts as an immune modulator in activated T cells. MethodWe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. Result8 novel SNPs out of 233 were found to have most deleterious effect on the protein structure and function. While modeling of nsSNPs was studied by Project HOPE software. ConclusionBetter understanding of Hyper-IgM syndrome caused by mutations in CD40LG gene was achieved using in silico analysis. This is the first in silico functional analysis of CD40LG gene and 8 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for hyper-IgM syndrome. These 8 novel SNPs may be important candidates for the cause of different types of human diseases by CD40LG gene.

bioinformatics↗

bioRxiv2019

In Silico Genetics: Identification of pathogenic nsSNPs in human STAT3 gene associated with Job's syndrome

BackgroundAutosomal dominant hyper-IgE syndrome (AD-HIES) or Jobs syndrome is a rare immunodeficiesncy disease that classically presents in early childhood, characterized by eczematoid dermatitis, characteristic facies, pneumatoceles, hyperextensibility of joints, multiple bone fractures, scoliosis, atopic dermatitis and elevated levels of serum IgE (>2000 IU/ml). The term Autosomal dominant hyper-IgE syndrome has primarily been associated with mutations in STAT3 gene, Located in human chromosome 17q21. MethodsThe human STAT3 gene was investigated in dbSNP/NCBI, 962 SNPs were Homo sapiens; of which 255 were missense SNPs. This selected for in silico analysis by multiple in silico tools to investigate the effect of SNPs on STAT3 proteins structure and function. ResultEleven novel mutations out of 255 nsSNPs that are found to be deleterious effect on the STAT3 structure and function. ConclusionA total of eleven novel nsSNPs were predicted to be responsible for the structural and functional modifications of STAT3 protein. The newly recognized genetic cause of the hyper-IgE syndrome affects complex, compartmentalized somatic and immune regulation. This study will opens new doors to facilitate the development of novel diagnostic markers for associated diseases.

bioinformatics↗

bioRxiv2019

Unmasking of novel mutations within XK gene that could be used as Diagnostic Markers to Predict McLeod syndrome: Using in silico analysis

BackgroundMcLeod neuroacanthocytosis syndrome is a rare X-linked recessive multisystem disorder affecting the peripheral and central nervous systems, red blood cells, and internal organs. MethodsWe carried out in silico analysis of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structural and functional level. Result2 novel mutations out of 104 nsSNPs that are found to be deleterious effect on the XK structure and function. ConclusionThe present study provided a novel insight into the understanding of McLeod syndrome, SNPs occurring in coding and non-coding regions, may lead to RNA alterations and should be systematically verified. Functional studies can gain from a preliminary multi-step approach, such as the one proposed here; we prioritize SNPs for further genetic mapping studies. This will be a valuable resource for neurologists, hematologists, and clinical geneticists on this rare and debilitating disease.

bioinformatics↗

bioRxiv2019

Computational vaccinology approach: Designing an efficient multi-epitope peptide vaccine against Cryptococcus neoformans var. grubii heat shock 70KDa protein

IntroductionCryptococcosis is a ubiquitous opportunistic fungal disease caused by Cryptococcus neoformans var. grubii. It has high global morbidity and mortality among HIV patients and none-HIV carriers with 99% and 95% respectively. Furthermore, the increasing prevalence of undesired toxicity profile of antifungal, multi-drug resistant organism, and the scarcity of FDA authorized vaccines, where the hallmark in the present days. This study was undertaken to design a reliable multi-epitope peptide vaccine against highly conserved immunodominant heat shock 70KDa protein of Cryptococcus neoformans var. grubii that covers a considerable digit of the world population through implementing computational vaccinology approach. Materials and MethodsA total of 38 Sequences of Cryptococcus neoformans var. grubiis heat shock 70KDa protein were retrieved from NCBI protein database. Different prediction tools were used to analyze the aforementioned protein at Immune Epitope Database (IEDB) to discriminate the most promising T-cell and B-cell epitopes. Then the proposed epitopes were subjected to Population coverage analysis tool to compute global populations coverage. Finally, the projected epitopes were ranked based on their scores and binding modes through using Moe 2007 program. Outstanding Results and ConclusionOur prime vaccine candidate was a putative ten promising epitopes (ANYVQASEK, NYVQASEK, KSVEKPAS, TPQQPPAQ, YVYDTRGKL, FYRQGAFEL, FTQLVAAYL, FFGGKVLNF, FDYALVQHF, and FINAQLVDV). Together, these epitopes are forecasted to trigger T lymphocytes, B lymphocytes, and immunological memory with overall population coverage above 90%. Accordingly, our in silico vaccine is expected to be the future multi-epitope peptide vaccine against Cryptococcus neoformans var. grubiis heat shock 70KDa protein that covers a significant figure of the entire world citizens. Therefore, there is a definite need for experimental validation for the carefully chosen vaccine candidates in vitro and in vivo to fortify their antigenic and immunogenic potentials. Additionally, further computational studies are needed to be conducted in pathogens-derived Heat shock 70KDa protein family, as it believed to find universal epitopes that might be overlapped with other pathogens-derived Hsp70.

bioinformatics↗

bioRxiv2019

Computational Analysis Revealed Five Novel Mutations in Human IL2RG gene Related to X-SCID

BackgroundX linked severe combined immunodeficiency (X-SCID) is a life-threatening disorder. It is due to mutation of the interleukin two receptor gamma-chain (IL2RG) gene. Nonsynonymous SNPs (nsSNPs) are the most common polymorphism, known to be deleterious or disease-causing variations because they alter protein sequence, structure, and function. Objective: is to reveal the effect of harmful SNPs in the function and structure of IL2RG protein. MethodData on IL2RG was investigated from dbSNP/NCBI database. Prediction of damaging effect was done using sift, polyphen, provean and SNAP2.more software were used for more analysis: phd-snp, and and go, Pmut, Imutant.modeling was done using chimera and project hope. Gene interaction was done by gene mania.3UTR prediction was done using polymiRTS software. ResultThe in-silico prediction identified 1479 SNPs within IL2RG gene out of which 253 were coding SNPs, 50 took place in the miRNA 3 UTR, 21 occurred in 5 UTR region and 921 occurred in intronic regions. a total of 12 missense nsSNPs were found to be damaging by both a sequence homology-based tool (SIFT) and a structural homology-based method (PolyPhen), Five of them were novel; rs1322436793(G305R), rs1064794027(C182Y), rs111033620(G114D), rs193922347 (Y105C) and rs1293196743(Y91C), Two SNPs(Rs144075871 and rs191726889) out of 50 in the 3UTR region were predicted to disrupt miRNAs binding sites and affect the gene expression. ConclusionsComputational analysis of SNPs has become a very valuable tool in order to discriminate neutral SNPs from damaging SNPs. This study revealed 5 novel nsSNPs in the IL2RG gene by using different software and 21 SNPs in 3UTR. These SNPs could be considered as important candidates in causing diseases related to IL2RG mutation and could be used as diagnostic markers.

bioinformatics↗

bioRxiv2019

Novel mutations within PRSS1 Gene that could potentially cause hereditary pancreatitis: Using Comprehensive in silico Approach

BackgroundHereditary pancreatitis (HP) is an autosomal dominant disorder with incomplete penetrance characterized by recurring episodes of severe abdominal pain often presenting in childhood. The comprehensive in silico analysis of coding SNPs, and their functional impacts on protein level, still remains unknown. In this study, we aimed to identify the pathogenic SNPs in PRSS1 gene by computational analysis approach.\n\nMaterials and MethodsWe carried out in silico analysis of structural effect of each SNP using different bioinformatics tools to predict Single-nucleotide polymorphisms influence on protein structure and function.\n\nResultTwo novel mutations out of 339 nsSNPs that are found be deleterious effect on the PRSS1 structure and function.\n\nConclusionThis is the first in silico analysis in PRSS1 gene, which will be a valuable resource for future targeted mechanistic and population-based studies.

bioinformatics↗

bioRxiv2019

Molecular Genetic Analysis of RB1 gene among Sudanese children with Retinoblastoma

BACKGROUNDRetinoblastoma (RB), the commonest early childhood intraocular tumor, is most often related to mutations in the RB1 gene with an incidence of 3% of all pediatric tumors. It has good prognosis if diagnosed early but it is life-threatening when diagnosed late.\n\nOBJECTIVETo study the Molecular Genetic Analysis of Retinoblastoma (RB) in Sudanese families.\n\nMETHODSThirty one (n=31) clinically and histopathologically diagnosed cases of RB attending Makkah Eye Complex (MEC) Orbit clinic (Khartoum, Sudan) were included in this Molecular Genetic RB Analysis. Fresh blood samples extracted from seven RB patients and 15 close families for DNA extraction and PCR were sent for Genetic Sequencing and In silico approach for \"Exon 18 mutations\" which is one of the highly mutated exons worldwide.\n\nRESULTSThe majority of patients (41.9%) were below five years old. Females were 58.1%, males were 41.9%. Leukocoria was the commonest sign at presentation (41.9%). RB Unilaterality were in (77.4%) while Bilaterality in 19.4%. Both eyes were equally affected 50% each. The age at diagnosis time ranged from 0.02 to five years. Consanguinity of parents was very high (85.7%), the 1st degree cousins were less (28.6%) while the 2nd degree was high (57.1%). The patients ethnic background and geographical area were from seven different tribes; all belong to the Western Sudan. The molecular genetic study showed that exon 18 was free of mutation among the seven patients + their three relatives. The Functional Analysis and (SNPs) prediction study of exon 18 from NCBI data base showed that the various computational approaches used (SIFT, PolyPhen-2, I-mutant and Project hope) identified 16 reported mutations worldwide, three of which (rs137853292, rs375645171 and rs772068738) are major nsSNPs (non-synonymous) which might contribute to native RB1 protein malfunction and ultimately causing carcinoma.\n\nCONCLUSIONRB mainly affected children under five years and both sexes are equally affected. Unilaterality was predominant. Consanguinity plays a role in inheritance and the majority of patients were from Western Sudan. The most commonly detected deleterious mutations worldwide in exon 18 were not found in the Sudanese studies samples. Further screening for the highly reported mutations in exons 8, 10 and 14 or Next Generation Sequencing (NGS) are recommended. In silico tools are useful in studying the functional analysis of SNPs.

molecular biology↗

bioRxiv2018

Translationally Controlled Tumor Protein TCTP as Peptide Vaccine against Schistosoma japonicum: an Immunoinformatics Approach

Schistosoma japonicum is the most pathogenic causative form of schistosomiasis that causes a major health problem in its endemic countries. Until now, praziquantel is the only drug used to treat Schistosomiasis, but it does not prevent re-infection. So, repetition of the treatment is needed. Moreover, there is no effective vaccine against S. japonicum. Therefore, an urgent need for the development of vaccines is mandatory. This study aimed to analyze an immunogenic protein, Transitionally Controlled Tumor Protein (TCTP) using an immunoinformatics approach to design a universal peptide vaccine against Schistosoma japonicum. A set of 22 of TCTP sequences were retrieved from NCBI database. Conservancy of these sequences was tested and then conserved B cell and T cell epitopes were predicted using different tools available in IEBD. Epitopes having high scores in both B and T cell predicting tools were proposed. An epitope 129YEHYI133 was predicted as a most promising epitope with good prediction scores in surface accessibility and antigenicity. Besides that, epitopes 129YEHYIGESM 137and 92YLKAIKERL100 were predicted as the most promising epitopes concerning their binding to MHC I and MHC II allele respectively. The study revealed that our predicted epitopes could be used to develop an efficacious vaccine against Schistosoma japonicum in the future especially epitope YEHYIGESM as it is shared between MHC I and II alleles and overlapped with the most promising B cell epitope. Both in vitro and in vivo studies is recommended to confirm the efficacy of YEHYIGESM as a peptide vaccine.

bioinformatics↗

bioRxiv2018

Computational Analysis of Single Nucleotide polymorphisms (SNPs) in Human T-Cell Acute Lymphocytic Leukemia Protein 1 (TAL1) Gene/ Comprehensive Study

BackgroundTAL1 is a proto-oncogene whose distorted modifications in committed T-cell Precursors is related with the development of T-ALL, it also found to be related to many other human hematological diseases such as lymphoblastic lymphoma, immunodeficiency 18, acute myeloid leukemia and diamond-blackfan Anemia.\n\nObjectivesThis study aims to predict the effect of nsSNPs on TAL1 protein structure function\n\nMethodsRetrieved nSNPs in the coding and 3UTR regions were analyzed using different in silico tools. Interactions of TAL1 with functionally similar genes were investigated using Genemania. Post-translational modifications in several sites of the protein were also investigated.\n\nResultsOut of ninety nsSNPs identified, only eight were found damaging to protein function of which one is located in the basis helix-loop-helix domain (bHLH). Two SNPs were anticipated by PolymiRTs to prompt disturbance or creation of miR binding sites.\n\nConclusionThe present study is the first ever computational analysis of TAL1s nsSNPs hence this effort might be of help in the near future for inventing early diagnostic and therapeutic measures for T-ALL

bioinformatics↗

bioRxiv2018

Comprehensive in silico Analysis of IKBKAP gene that could potentially cause Familial dysautonomia

BackgroundFamilial dysautonomia (FD) is a rare neurodevelopmental genetic disorder within the larger classification of hereditary sensory and autonomic neuropathies. We aimed to identify the pathogenic SNPs in IKBKAP gene by computational analysis softwares, and to determine the structure, function and regulation of their respective proteins.\n\nMaterials and MethodsWe carried out in silico analysis of structural effect of each SNP using different bioinformatics tools to predict SNPs influence on protein structure and function.\n\nResult41 novel mutations out of 973 nsSNPs that are found be deleterious effect on the IKBKAP structure and function.\n\nConclusionThis is the first in silico analysis in IKBKAP gene to prioritize SNPs for further genetic studies.

bioinformatics↗

bioRxiv2018

Lewis rat NLRP1 inflammasome activation is mediated by three Toxoplasma gondii dense granule proteins

The Lewis rat is the only known warm-blooded animal that has sterile immunity to Toxoplasma. Upon invasion of Lewis rat macrophages Toxoplasma rapidly activates the nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing 1 (NLRP1) inflammasome resulting in interleukin (IL)-1{beta} secretion and a form of cell death known as pyroptosis, which prevents Toxoplasma replication. Using a chemical mutagenesis screen we identified Toxoplasma mutants that no longer induced pyroptosis. Whole genome sequencing led to the identification of three Toxoplasma parasitophorous vacuole-localized dense granule proteins, GRA35, GRA42 and GRA43 that are individually required for inflammasome activation in Lewis rat macrophages. Macrophage infection with {Delta}gra35, {Delta}gra42, and {Delta}gra43 parasites leads to greatly reduced cell death and reduced IL-1{beta} secretion. Lewis rat macrophage infected with parasites containing single, double or triple deletion of these GRAs showed similar levels of cell viability suggesting the three GRAs function in the same pathway that activates the inflammasome. Deletion of GRA42 and GRA43 resulted in GRA35, and other GRAs, being retained inside the parasitophorous vacuole instead of being localized to the parasitophorous vacuole membrane. Toxoplasma deficient in GRA35, GRA42 or GRA43 do not establish chronic infection in Lewis rats, but have reduced cyst number in parasite-susceptible F344 rats, in which Toxoplasma does not activate the NLRP1 inflammasome, revealing these GRAs determine parasite in vivo fitness independent of their role in inflammasome activation. Overall, our data suggest that Toxoplasma dense granule proteins that localize to the parasitophorous vacuole membrane are novel mediators of host NLRP1 inflammasome activation.\n\nImportanceInflammasomes are a major component of the innate immune system and responsible for detecting various microbial and environmental danger signals. The Lewis rat has sterile immunity to Toxoplasma because upon invasion of Lewis rat macrophages the parasite rapidly activates the NLRP1 inflammasome resulting in cell death and parasite elimination. The work reported here identified that Toxoplasma GRA35, GRA42 and GRA43 are required for activation of the Lewis rat NLRP1 inflammasome. GRA42 and GRA43 mediate the correct localization of other GRAs, including GRA35, to the parasitophorous vacuole membrane. In addition to their role in inflammasome activation, these three GRAs are also important for parasite in vivo fitness in a Toxoplasma-susceptible rat strain. Thus, these results give new insight into NLRP1 inflammasome activation by Toxoplasma effectors and identified three GRAs that are required for pathogenesis of the parasite.

microbiology↗

bioRxiv2018

Epitope - based peptide vaccine against Fructose-bisphosphate aldolase (FBA) of Madurella mycetomatis using immunoinformatics approaches

BackgroundMycetoma is a distinct flesh eating and destructive neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections (actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi (eumycetoma) such as Madurella mycetomatis. Until date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma.\n\nThe aim of this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches.\n\nMethods and MaterialsFructose-bisphosphate aldolase of Madurella mycetomatis Sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominees epitopes in Immune Epitope Database for B-cell, T-cell MHC class II & I. Then the proposed peptides were docked using Autodock 4.0 software program.\n\nResults and ConclusionsThe proposed and promising peptides KYLQ shows a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC1 alleles and FFKEHGVPL that show a very strong binding affinity to MHC11and MHC1 alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against Fructose-bisphosphate aldolase of Madurella mycetomatis. This study recommends an in-vivo assessment for the most promising peptides especially FFKEHGVPL.

bioinformatics↗