Search bioRxivSearch

Biology subjects

Hassan, M. A.

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

4 recordsLinked to original sources

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

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

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

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