Biology subjects

Bashir, S.

Publications and source records attributed to Bashir, S..

9 recordsLinked to original sources

bioRxiv2026

Genetic Diversity of Cytochrome P450 Genes in Apis mellifera Subspecies

The western honey bee (Apis mellifera) is an essential pollinator facing unprecedented threats from pesticide exposure. While pesticide resistance evolution is well documented in agricultural pests, our understanding of genetic variation in honey bee detoxification systems remains limited. This represents a missed opportunity, as harnessing naturally occurring detoxification diversity could provide new avenues for pollinator protection. Cytochrome P450 monooxygenases (CYPs), which are central to xenobiotic metabolism, offer a promising starting point. Here, we present the first comprehensive analysis of CYP genetic diversity in A. mellifera. We analysed the CYPome of 1,467 individuals representing 18 A. mellifera subspecies from 25 countries and identified 5,756 single-nucleotide polymorphisms (SNPs) in 46 CYP genes. Imputed McDonald-Kreitman testing revealed that 56% of non-synonymous CYP substitutions were driven by positive selection. Of the 1,302 haplotypes identified, 84% resided in CYP3, concentrated in the CYP9 and CYP6AS subfamilies implicated in xenobiotic detoxification. Population-level analysis of nucleotide diversity, Tajimas D selection signatures, FST-based differentiation, and McDonald-Kreitman testing pointed to CYP3 clan genes as the primary locus of adaptive variation. This work provides the first step toward building a comprehensive pharmacogenomic resource for honey bees, enabling the prediction of population-specific pesticide vulnerabilities and leveraging naturally occurring detoxification variants to enhance pollinator resilience - a critical step toward sustainable pollinator management.

genomics↗

bioRxiv2026

ACTIVATED CASO₄-INDUCED VACUOLATION AS A QUANTITATIVE PLATFORM FOR PHAGOCYTOSIS-DRIVEN DRUG SCREENING

Cytoplasmic vacuolization is a fundamental process associated with phagocytosis, lysosomal acidification, and autophagy, yet robust in-vitro models for its quantification and pharmacological screening remainlimitedor insufficiently established. In this study, we demonstrate that thermally activated calcium sulfate (ACS) induces extensive vacuolation across mammalian cell lines including HeLa, RAW 264.7, 3T3-L1, and SH-SY5Y, thereby establishing a versatile platform to study vacuole biogenesis. To ensure reproducibility, particle heterogeneity was addressed using sedimentation-based fractionation, with homogeneous suspensions obtained at the 5th minute producing stable and consistent vacuole formation. Vacuolation was subsequently quantified by Neutral Red (NR) uptake, dose and time dependent response analyses confirmed direct correlation between ACS concentration and vacuole induction. The assay was validated with bafilomycin A1 (BFA1), a selective V-ATPase inhibitor, which served as a positive control and demonstrated concentration and time dependent inhibition of vacuole formation and acidification. Building on this framework, ten commercially available drugs were screened, revealing distinct profiles ranging from early cytotoxicity, strong vacuole inhibition to partial suppression or negligible effects. This dual capacity to discriminate between vacuole inhibition and cytotoxic responses highlights the utility of ACS-induced vacuolization as a sensitive and scalable in vitro platform. Collectively, our findings position this system as a tractable assay for mechanistic studies of vacuole biology and a functional screening tool for identifying modulators of lysosomal and phagocytic pathways relevant to infection, Lysosomal Disorders, and Phagocytotic dysfunction disorders. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/711143v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@e5b920org.highwire.dtl.DTLVardef@1dd1072org.highwire.dtl.DTLVardef@62ae59org.highwire.dtl.DTLVardef@a468bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Causality Mapping Using Resting-state fMRI Reveals Hyperactivity and Hypoconnectivity in Schizophrenia Patients

Schizophrenia (SZ) is a debilitating disorder in which patients exhibit psychotic behavior due to aberrant connectivity between different regions of the brain. Advances in neuroimaging have now enabled the diagnosis and analysis of SZ in order to elucidate the whole brain functional connectivity networks. In the present study, we have used resting-state functional magnetic resonance imaging (rs-fMRI) to elucidate the causal relationships amongst the differentially activated brain regions between SZ patients (n=10) and healthy controls (n=10). Vector auto-regression (VAR) model and Granger causality (GC) were then applied to construct a functional connectivity network and analyze the causal effects in SZ patients. Our results revealed that the average voxel activation in the frontal lobe (FL), basal ganglia (BG), and ventricular system (VS) was significantly higher in patients indicating hyper-activity as compared to controls. Conversely, cerebellum white matter (CBWM) showed higher activation in the controls as compared to patients. A higher Pearson correlation was observed between the controls as compared to patients while VAR and GC showed higher functional connectivity among all the regions of interest (ROIs) along with more causal relations in the controls. Finally, mediation analysis showed that right middle superior frontal gyrus acts as a strong partial mediator between left accumbens area and left middle superior frontal gyrus. Taken together, this study decodes the dysregulated brain activity in schizophrenia showing hyperactivation in patients when compared with the healthy controls which leads to alterations in neural connections resulting in hypoconnectivity.

neuroscience↗

bioRxiv2023

Size-Dependent Expression of the Fission Yeast Cdc13 Cyclin is Conferred by Translational Regulation

The major fission yeast cyclin, Cdc13, has been shown to increase in concentration in correlation with cell size, and has been proposed to thereby regulate cell size at division. However, the mechanism of its cell-size regulation has been unknown. Here, we show that Cdc13 is regulated post-transcriptionally. Its transcript is not expressed in a size-dependent manner, rather a size-dependent concentration of protein is expressed from a size-independent concentration of mRNA. Moreover, we show that the expression of Cdc13 is, in fact, size dependent, as opposed to simply size-correlated due to time-dependent expression. We identify a 20-amino-acid motif, which includes the APC D-box degron, as necessary and sufficient for size-dependent expression, which allowed us to construct a size-independent allele of cdc13. Using this allele, we show that size-dependent expression of Cdc13 is not required for size control in fission yeast cells.

cell biology↗

bioRxiv2021

Metabolic engineering of Bacillus subtilis with an Endopolygalacturonase gene Isolated from Pectobacterium carotovorum; a Plant Pathogenic bacterial strain.

Pectinolytic enzymes (pectinases) produced by microbes are highly important for their biotechnological use in processing of vegetables and fruits beverages and use in pulp and paper industry. A pectinase, namely endo-polygalacturonase (endo-PGase), encoding gene isolated from Pectobacterium carotovorum, a plant pathogenic strain of bacteria was successfully cloned into a secretion vector pHT43 having {sigma}A-dependent promoter P grac. For enhanced expression analysis, competent cells of Bacillus subtilis (WB800N) were prepared at stationary phase using high salt medium. The recombinant B. subtilis competent cells, harbouring the engineered pHT43 with the endo-PGase gene were cultured in 2X-yeast extract tryptone medium. The recombinant endo-PGase enzyme was secreted directly into the medium after 72 hours of the first IPTG induction. The recombinant endo-PGase was screened for its activity at various temperatures and pH ranges. Optimal activity was found at pH 5.0 and a temperature of 40{degrees}C with a stability ranging from pH 5.0-9.0. For detection of metal ion effect, recombinant enzyme was incubated with 1mM concentration of; Ca++, Mg++, Zn++, EDTA, K++ for 45 minutes. Resultantly, Ca++, EDTA and Zn++ strongly inhibited the enzyme activity. The chromatographic analysis of enzymatic hydrolysate of polygalacturonic acid (PGA) and pectin substrates using HPLC and TLC revealed that tri and tetra-galacturonates were the end products of hydrolysis. The study led to the conclusion that endo-PGase gene from the plant pathogenic strain was successfully expressed in Bacillus subtilis and could be assessed for enzyme production using a very simple medium with IPTG induction. These findings proposed that the Bacillus expression system might be safe for commercial enzyme production as compared to yeast and fungi to escape endotoxins.

bioengineering↗

bioRxiv2021

sMEK1 promotes crosstalk between IRE1 and Akt signaling pathway: Evidence for a novel IRE1/sMEK1/Akt complex

The Unfolded Protein Response (UPR) is a dynamic cellular pathway that helps maintain proteostasis during endoplasmic reticulum (ER) stress. One of the key UPR sensors is IRE1, which plays a central role in managing ER stress and interacts with other cellular pathways to regulate cell homeostasis. The Akt signalling pathway, on the other hand, is a crucial survival pathway involved in diverse cellular functions like growth, proliferation, glucose metabolism, and survival. This study explores the interplay between these two important cell signalling pathways. Specifically, our study revealed that IRE1 negatively regulates Akt through the protein phosphatase sMEK1. We identified sMEK1 and Akt as novel interacting partners of IRE1, which together form a ternary complex that helps coordinate the IRE1 and Akt signalling networks. The IRE1/sMEK1/Akt ternary complex results in the dephosphorylation of Akt by sMEK1 in the presence of activated IRE1. Together, this study sheds light on the molecular mechanism underlying the UPR/Akt link and provides valuable insights into the overall impact of their interaction.

cell biology↗

bioRxiv2020

Causality Mapping Using Resting-State fMRI reveals Suppressed Functional Connectivity in Schizophrenia Patients

Schizophrenia is a psychotic brain disorder in which patients exhibit aberrant connectivity between different regions of the brain. Neuroimaging is a state-of-the-art technique that is now increasingly been employed in clinical investigation of Schizophrenia. In the present study, we have used resting-state functional magnetic resonance neuroimaging (rsfMRI) to elucidate the cause-and-effect relationships among four regions of the brain including occipital, temporal, and frontal lobes and hippocampus in Schizophrenia. For that, we have employed independent component analysis, a seed-based temporal correlation analysis, and Granger causality analysis for measuring causal relationships amongst four regions of the brain in schizophrenia patients. Eighteen subjects with nine patients and nine controls were evaluated in the study. Our results show that Schizophrenia patients exhibit significantly different activation patterns across the selected regions of the brain in comparison with the control. In addition to that, we also observed an aberrant causal relationship between these four regions of the brain. In particular, the temporal and frontal lobes of patients with schizophrenia had a significantly lowered causal relationship with the other areas of the brain. Taken together, the study elucidates the dysregulated brain activity in Schizophrenia patients, decodes its causal mapping and provides novel insights towards employment in clinical evaluation of Schizophrenia.

neuroscience↗

bioRxiv2019

Bid as a novel interacting partner of IRE1 differentially regulating its RNAse activity

Unfolded protein response is a dynamic signalling pathway, which is involved in the maintenance of proteostasis and cellular homeostasis. IRE1, a transmembrane signalling protein represents the start point of a highly conserved UPR signalling cascade. IRE1 is endowed with kinase and endoribonuclease activities. The activation of the kinase domain of IRE1 by trans-autophosphorylation leads to the activation of its RNAse domain. RNAse domain performs atypical splicing of Xbp1 mRNA and degradation of mRNAs by an effector function known as Regulated IRE1 Dependent Decay (RIDD). The regulation of the distinctive nature of the IRE1 ribonuclease function is potentially mediated by a dynamic protein structure UPRosome that is an assembly of a huge number of proteins on IRE1. Here, we reported that Bid is a novel recruit to UPRosome, which directly interacts with the cytoplasmic domain of IRE1. Bid controls the auto-phosphorylation of IRE1 in a negative manner where Bid overexpression conditions displayed reduced phosphorylation levels of IRE1 and Bid knockdown cells showed slightly enhanced IRE1 phosphorylation. This effect was reciprocated with JNK, a downstream target of IRE1. Our Insilico analysis revealed that Bid binding to IRE1 dimer averts its structural flexibility and thereby preventing its trans-autophosphorylation activity. We found that the effect of Bid is specific to the IRE1 branch of UPR signalling and competitive in nature. The highlighting observation of the study was that Bid stimulated a differential activity of the IRE1 RNAse domain towards Xbp1 splicing and RIDD. These results together establish that Bid is a part of the UPRosome and modulates IRE1 in a way to differentially regulate its RNAse outputs.

cell biology↗

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↗