Biology subjects

Hashim, S.

Publications and source records attributed to Hashim, S..

5 recordsLinked to original sources

bioRxiv2025

SPONTANEOUS VISUAL IMAGERY DURING EXTENDED MUSIC LISTENING IS ASSOCIATED WITH RELIABLE ALPHA SUPPRESSION

Music is widely recognised as being able to evoke images in the minds eye. However, the neural basis of visual imagery experiences during music listening remains poorly understood. Here, we combined probe-caught experience sampling methodology with 32-channel electroencephalography (EEG) recordings in order to investigate the neuro-oscillatory correlates of music-evoked visual imagery and examine how spontaneously generated imagery compares to more deliberately generated forms. Thirty participants listened with closed eyes to four blocks of music, differing in their familiarity and relaxation potential and spanning a range of genres. In response to probes sent throughout listening, participants indicated whether or not they had been experiencing visual imagery and, if they had, whether the experienced visual imagery had been spontaneous or deliberate. Cluster permutation analyses on the time-frequency decomposed EEG data revealed alpha power suppression during visual imagery that was more reliable during spontaneous than deliberate imagery. Further, while theta and delta bands did not discriminate the presence or absence of the visual imagery experience or its intentionality subtypes, we observed that gamma power suppression in fronto-central areas was present during visual imagery experiences. Our results extend prior findings of a role of posterior alpha suppression in visual imagery to show its reliability in music-evoked spontaneous imagery specifically. We consider plausible interpretations of the presence and absence of other oscillatory signatures in relation to the listening conditions used in the current study. HighlightsO_LIProbe-caught method shown to be effective in capturing moments of music-evoked visual imagery C_LIO_LIEvidence for a high prevalence of spontaneous music-evoked imagery C_LIO_LISpontaneous music-evoked visual imagery shown to be associated with posterior alpha suppression C_LI

neuroscience↗

bioRxiv2025

Matrix tropism influences endometriotic cell attachment patterns

Due to the extended period for clinical diagnosis, the etiology of endometriotic lesion initiation is not well understood or characterized. Endometriotic lesions are most often found on pelvic tissues and organs, especially the ovaries. To investigate the role of tissue tropism on ovarian endometrioma initiation, we adapted a well-characterized polyacrylamide microarray system to investigate the role of tissue-specific extracellular matrix and adhesion motifs on endometriotic cell attachment, morphology, and size. We report the influence of cell origin (endometriotic vs. non-endometriotic), substrate stiffness mimicking aging and fibrosis, and the role of multicellular (epithelial-stromal) cohorts on cell attachment patterns. We identify multiple ovarian-specific attachment motifs that significantly increase endometriotic (vs. non-endometriotic) cell cohort attachment that could be implicated in early disease etiology.

bioengineering↗

bioRxiv2023

Assessing HLA imputation accuracy in a West African population

The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic region and thus difficult to impute. We therefore sought to evaluate HLA imputation accuracy, specifically in a West African population, since they are understudied and are known to harbor high genetic diversity. The study sets were selected from Gambian individuals within the Gambian Genome Variation Project (GGVP) Whole Genome Sequence datasets. Two different arrays, Illumina Omni 2.5 and Human Hereditary and Health in Africa (H3Africa), were assessed for the appropriateness of their markers, and these were used to test several imputation panels and tools. The reference panels were chosen from the 1000 Genomes dataset (1kg-All), 1000 Genomes African dataset (1kg-Afr), 1000 Genomes Gambian dataset (1kg-Gwd), H3Africa dataset and the HLA Multi-ethnic dataset. HLA-A, HLA-B and HLA-C alleles were imputed using HIBAG, SNP2HLA, CookHLA and Minimac4, and concordance rate was used as an assessment metric. Overall, the best performing tool was found to be HIBAG, with a concordance rate of 0.84, while the best performing reference panel was the H3Africa panel with a concordance rate of 0.62. Minimac4 (0.75) was shown to increase HLA-B allele imputation accuracy compared to HIBAG (0.71), SNP2HLA (0.51) and CookHLA (0.17). The H3Africa and Illumina Omni 2.5 array performances were comparable, showing that genotyping arrays have less influence on HLA imputation in West African populations. The findings show that using a larger population-specific reference panel and the HIBAG tool improves the accuracy of HLA imputation in West African populations. Author SummaryFor studies that associate a particular HLA type to a phenotypic trait for instance HIV susceptibility or control, genotype imputation remains the main method for acquiring a larger sample size. Genotype imputation, process of inferring unobserved genotypes, is a statistical technique and thus deals with probabilities. Also, the HLA region is highly variable and therefore difficult to impute. In view of this, it is important to assess HLA imputation accuracy especially in African populations. This is because the African genome has high diversity, and such studies have hardly been conducted in African populations. This work highlights that using HIBAG imputation tool and a larger population-specific reference panel increases HLA imputation accuracy in an African population.

bioinformatics↗

bioRxiv2020

Cytolethal Distending Toxin: from mitotic DNA damage to cGAS-dependent pro-inflammatory response

The Cytolethal Distending Toxin (CDT) is a bacterial genotoxin that activates the DNA damage response and induces inflammatory signatures in host cells, but the precise relationship between these outcomes has not been addressed so far. CDT induces a singular time-dependent increase of DNA damage and cell cycle defects, questioning on possible impaired response to this toxin over the cell cycle. Here, we identify mitosis as a crucial phase during CDT intoxination. Despite active cell cycle checkpoints and in contrast to other DNA damaging agents, CDT-exposed cells reach mitosis where they accumulate massive DNA damage, resulting in chromosome fragmentation and micronucleus formation. These micronuclei are recognized by cGAS that elicits an inflammatory signature resulting in cell distention and senescence. Our results unravel for the first time the mitotic consequences of CDT genotoxic activity and relate them to pro-inflammatory cellular response. These findings may have important implications during bacterial infection regarding CDT-mediated immunomodulatory and tumorigenic processes.

cell biology↗

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↗