Biology subjects

Hassan, M.

Publications and source records attributed to Hassan, M..

6 recordsLinked to original sources

bioRxiv2018

Probing the circuits of conscious perception with magnetophosphenes

BackgroundConscious perception is thought to involve the large-scale, coordinated activation of distant brain regions, a process termed ignition in the Global Workspace Theory and integration in Integrated Information Theory, which are two of the major theories of consciousness.\n\nMethodsHere, we provide evidence for this process in humans by combining a magnetically-induced phosphene perception task with electroencephalography. Functional cortical networks were identified and characterized using graph theory to quantify the impact of conscious perception on local (segregation) and distant (integration) processing.\n\nResultsConscious phosphene perception activated frequency-specific networks, each associated with a specific spatial scale of information processing. Integration increased within an alpha-band functional network, while segregation occurred in the beta band.\n\nConclusionsThese results bring novel evidence for the functional role of distinct brain oscillations and confirm the key role of integration processes for conscious perception in humans.

neuroscience↗

bioRxiv2018

Immunoinformatics Prediction of Epitope Based Peptide Vaccine Against Madurella mycetomatis Translationally Controlled Tumor Protein

BackgroundMadurella. mycetomatis is most common causative agent of mycetoma in Sudan and worldwide. No vaccines are available till now so design of effective vaccine is essential as protection tool. Peptide vaccine can overcome the common side effects of the conventional vaccines. The aim of this study was to design peptide based vaccine for M.Mycetomatis Translationally Controlled Tumor Protein (TCTP) using immunoinformatics tools.\n\nMaterials and methodsTCTP sequences were retrieved from NCBI and then processed using BioEdit program to determine conserved regions and different immunoinformatics tools from IEDB. Population coverage analysis was performed for the most promising epitopes. Homology modelling was performed to show their structural positions in TCTP. Protein analysis was done using Expasy (ProtParamsotware).\n\nResults and conclusionFour epitopes passed the Bepipred, Emini, Kolaskar and Tongaonkar tools. 111 epitopes were predicted to interact with MHCI alleles with IC50 < 500 nM, three of them were most promising. 274 predicted epitopes were interacted with MHCII alleles with IC50 < 100 nM, four of them were most promising. The epitope (YMKSVKKAL) was the most promising one concerning its binding with MHCI alleles, while (FRLQSTSFD) was the most promising for MHC II. The epitope (YLKAYMKSV) is shared betweenMHC I and II. For the population coverage of M. Mycetomatis TCTP vaccine Sudan (90.39%) had the highest percentage for MHC I. This is the first computational vaccinology study conducted in mycetoma caused by M. Mycetomatis using TCTP.

bioinformatics↗

bioRxiv2018

Psychological resilience correlates with EEG source-space brain network flexibility

ObjectiveWe aimed at identifying the potential relationship between the dynamical properties of the human functional network at rest and one of the most prominent traits of personality, namely resilience.\n\nApproachTo tackle this issue, we used resting-state EEG data recorded from 45 healthy subjects. Resilience was quantified using the 10-items Connor-Davidson Resilience Scale (CD-RISC). Using a sliding windows approach, brain networks in each EEG frequency band (delta, theta, alpha and beta) were constructed using the EEG source-space connectivity method. Brain networks dynamics were evaluated using the network flexibility, linked with the tendency of a given node to change its modular affiliation over time.\n\nMain ResultsThe results revealed a negative correlation between the psychological resilience and the brain network flexibility for a limited number of brain regions within the delta, alpha and beta bands.\n\nSignificanceThis study provides evidence that network flexibility, a metric of dynamic functional networks, is strongly correlated with psychological resilience as assessed from personality testing. Beyond this proof-of-principle that reliable EEG-based quantities representative of personality traits can be identified, this motivates further investigation regarding the full spectrum of personality aspects and their relationship with functional networks.

neuroscience↗

bioRxiv2018

Novel deleterious nsSNPs within MEFV gene that could be used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using bioinformatics analysis

BackgroundFamilial Mediterranean Fever (FMF) is the most common auto inflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin, we aimed to identify the pathogenic SNPs in MEFV by computational analysis software.\n\nMethodsWe carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function.\n\nResult23 novel mutations out of 857 nsSNPs that are found to be deleterious effect on the MEFV structure and function.\n\nConclusionThis is the first in silico analysis in MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

bioinformatics↗

bioRxiv2018

Diagnostic Use of PCR in Carbapenamase-producing Enterobacteriaceae (CPE): An Improved Method to Overcome the presence of inhibitors for DNA Extraction from Blood Cultures

BackgroundCarpanenamase-producing Enterobacteriaceae (CPE) has emerged as a threat to hospitalized patients. Phenotypic test such as Modified hodge test was less sensitive and specific especially to detect blaNDM-1 which is the most predominant genotype in this region. Nucleic acid amplification technology offers improved specificity and sensitivity. However, there is limitation in this method which is failed amplification due to the presence of inhibitors. In this study, we try to use previous method described by Villumseen et al with some modification using another DNA extraction kit.\n\nMethodology/Principle findingsThree confirmed isolates of blaNDM-1 carbapenamase-producing Klebsiella pneumoniae was spiked with 10 mls sterile whole blood in an aerobic Bactec Plus until the growth was detected. The blood specimen was taken and was subjected to DNA extraction method using two commercialized kits followed with multiplex PCR. All the three isolates revealed blaNDM-1 genotypes. Internal control was amplified in all three isolates.\n\nConclusion/significanceThis study proved that we can get a specific and early diagnosis of CPE by using nucleic acid amplification technique directly from blood culture bottle and eliminate the effect of inhibitors.

microbiology↗

bioRxiv2018

Competing endogenous RNA network: Potential entrants to gene editing in Hepatocellular Carcinoma

BackgroundHepatocellular Carcinoma (HCC) is the leading cause of cancer deaths worldwide as well as in Egypt. We aimed to use Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR) gene editing technique to induce forced down-regulation of the circRNA which consequently modified miRNA expression in HepG2 cell line to prove the regulatory relationship between the RNA parts of an in silico-detected competing endogenous RNA network in HCC\n\nMethodWe first retrieved hsa_circ_0000064-miR-1285-TRIM2 mRNA from public microarray databases followed by in silico modelling to mimic the regulation kinetics of cirRNA associated ceRNA network. Secondly, we performed polymerase chain reaction (PCR)-based amplification of synthetic fragments, Gibson assembly of both CRISPR and non CRISPR based circuits, E-coli transformation, plasmid purification, HePG2 cell line transfection. Finally Expression levels of the chosen RNAs in hepatocellular carcinoma (HCC) cell line, HepG2, were examined by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the cytotoxic effect was validated by viability assay.TRIM2 protein expression was proved by immunohistochemistry and flowcytometry.\n\nResultsInduction of hsa_circ_0000064 into HepG2 cell line via CRISPR-and non-CRISPR mediated synthetic circuit resulted in statistically significant decrease in cell number and, then, cellular viability with marked increase in hsa_circ_0000064 and TRIM2 mRNA levels and concomitant decrease in miR-1285 expression in HepG2 cell line compared with control (p<0.0). Moreover exogenous expression of hsa_circ_0000064 in HepG2 cell line showed increased expression of the tumor suppressor protein, TRIM2.\n\nConclusionsOur integrative approach, including in silico data analysis and experimental validation proved that CRISPR-mediated synthetic circuit-based overexpression of hsa_circ_0000064 was more efficient than conventional transient transfection, representing a promising therapeutic strategy for HCC.\n\nData AvailabilityOur Data was made available online on the IGEM wiki of team AFCM-EGYPT: http://2017.igem.org/Team:AFCM-Egypt. Synthetic parts have been submitted to IGEM Parts Registry.\n\nFinancial DisclosureThe project was funded by Armed Forces College of Medicine AFCM, Zewail City of Science and Technology, National Research Center NRC, VitaBiotics, PHARCO Pharmaceuticals, Sim Era and DANUB Paintings. IDT provided 20 kb of DNA synthesis. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

bioengineering↗