Biology subjects

Akhtar, M.

Publications and source records attributed to Akhtar, M..

8 recordsLinked to original sources

bioRxiv2026

Drosophila orthologues of oculocutaneous albinism-associated genes regulate sleep and circadian rhythm via visual neurotransmission

Melanin is a pigment found in the skin and cuticle of animals. Oculocutaneous albinism (OCA) is a group of autosomal recessive disorders defined by reduced melanin in skin and eyes, and is associated with visual defects such as foveal hypoplasia and infantile nystagmus. Sleep disturbance has been documented in children with OCA, and oca2 loss-of-function in cavefish causes constitutive sleep loss, indicating a sleep regulatory function of OCA-associated genes in the visual system. To test potential roles of OCA-associated genes in regulating sleep and vision through evolutionarily conserved mechanisms, we used Drosophila melanogaster, a high-throughput phenotyping system to screen sleep and visual phenotypes for genetic mutants of OCA-associated genes. Among the OCA-associated genes, bidirectional DRSC Integrative Ortholog Prediction Tool identified Drosophila orthologues for OCA2, SLC45A2, SLC24A5 and LRMDA. RNAi-mediated knockdown in developing Drosophila eye tissue identified the OCA2 orthologues hoe1, hoe2, and the SLC45A2 orthologue lovit as candidate genes required for normal sleep. Moreover, hoe1, hoe2 and lovit1 null alleles reduced sleep and circadian rhythmicity, and showed altered photoreceptor neurotransmission. Consistently, the enhancer-trap reporter assay and scRNA dataset revealed that these OCA orthologues express in brain regions critical for sleep and vision regulation. Collectively the data indicate evolutionarily conserved neuronal function of OCA2 and SLC45A2 orthologues that regulate sleep and photoreceptor neurotransmission. Significance StatementOculocutaneous albinism (OCA) is a pigmentation disorder of the skin and eyes accompanied by reduced visual acuity. Children with albinism also report sleep disturbance, and the mechanism is unclear. We tested whether genes mutated in albinism regulate sleep in the fruit fly Drosophila melanogaster, an organism that has a divergent melanin synthesis pathway and lacks tyrosinase, the principal pigmentation enzyme in mammals. We found Drosophila OCA orthologues, hoe1, hoe2 and lovit express widely in the nervous system and control sleep, circadian rhythmicity and neural activity of photoreceptors. Importantly no pigmentation defects were detected in aforementioned mutants, our finding is consistent with the proposal that pleiotropic neuronal function of OCA2 and SLC45A2 underlies the sleep and vision symptoms in albinism.

neuroscience↗

bioRxiv2026

In silico analysis of the human titin protein (Immunoglobulin-like, fibronectin type III, and Protein kinase domains) as a potential forensic marker for postmortem interval (PMI) estimation

Due to the limited availability of reliable and well-validated molecular markers, the determination of postmortem interval (PMI) is still a major obstacle for forensic investigators to resolve a case. The largest human protein, known as titin, has never undergone at domain level examination of postmortem degradation patterns. This study focused on the In-silico analysis of the Immunoglobulin-like, fibronectin-type III, and Protein kinase domains of human titin to assess their potential utility in PMI estimation. Sequence data for the studied domains were retrieved from UniProt, 2D & 3D models were generated by PSIPRED and SWISS-MODEL, respectively, followed by physicochemical properties, solubility assessment, and structural comparison. This study revealed that the Ig-like domain is the most stable, followed by the Fn-III and Protein kinase domains. These findings indicate that Titin domains may degrade at different rates in the postmortem period. This study introduces the first computational basis for considering Titin as a multi-domain candidate biomarker for PMI estimation, laying the groundwork for upcoming laboratory validation.

bioinformatics↗

bioRxiv2025

A sleep promoting role of phototransduction in Drosophila melanogaster

The daily sleep-wake cycle is a conserved behaviour defined by locomotion quiescence and enhanced responsive threshold to sensory stimuli. Both the circadian clock and sleep-homeostasis determine the daily sleep profile. Environmental light is a major sensory input and also regulates circadian clock and the balance between sleep and wakefulness. In Drosophila, the cellular mechanism and neural circuitry underlying light-mediated circadian synchronization are well-established, yet the direct relationship between light/visual input and sleep remains unclear. To address this knowledge gap, we measured sleep behaviour in Drosophila with mutations in genes involved in phototransduction and downstream neural transmission. We observed consistent day sleep fragmentation in flies with mutations in multiple phototransduction components. We also found that mutation that led to hyperpolarised Drosophila photoreceptors resulted in shorter day sleep. We found a severe reduction in locomotor speed in several visual mutants during normal waking time preventing assessment of their sleep-linked immobility. Taken together, our rigorous quantification of sleep in phototransduction genetic mutants reveals the key role of visual input in promoting sleep.

neuroscience↗

bioRxiv2024

Host-derived CEACAM-laden vesicles engage enterotoxigenic E. coli for elimination and toxin neutralization.

Enterotoxigenic Escherichia coli (ETEC) cause hundreds of millions of diarrheal illnesses annually ranging from mildly symptomatic cases to severe, life-threatening cholera-like diarrhea. Although ETEC are associated with long-term sequelae including malnutrition, the acute diarrheal illness is largely self-limited. Recent studies indicate that in addition to causing diarrhea, the ETEC heat-labile toxin (LT) modulates the expression of many genes in intestinal epithelia, including carcinoembryonic cell adhesion molecules (CEACAMs) which ETEC exploit as receptors, enabling toxin delivery. Here however, we demonstrate that LT also enhances the expression of CEACAMs on extracellular vesicles (EV) shed by intestinal epithelia and that CEACAM-laden EV increase in abundance during human infections, mitigate pathogen-host interactions, scavenge free ETEC toxins, and accelerate ETEC clearance from the gastrointestinal tract. Collectively, these findings indicate that CEACAMs play a multifaceted role in ETEC pathogen-host interactions, transiently favoring the pathogen, but ultimately contributing to innate responses that extinguish these common infections. Significance statementEnterotoxigenic E. coli, characterized by the production of heat-labile (LT) and heat-stable (ST) toxins, are a very common cause of diarrhea in low-income regions responsible for hundreds of millions of infections each year, and the major cause of diarrhea in travelers to endemic areas. Although these infections may be severe and cholera-like, they are typically self-limited. These studies demonstrate that extracellular vesicles produced by host intestinal cells can capture the bacteria and its secreted toxins at a distance from the cell surface, potentially acting as molecular decoys to neutralize the enterotoxins and extinguish the infection.

microbiology↗

bioRxiv2024

Repeat modules and N-linked glycans define structure and antigenicity of a critical enterotoxigenic E. coli adhesin

Enterotoxigenic Escherichia coli (ETEC) cause hundreds of millions of cases of infectious diarrhea annually, predominantly in children from low-middle income regions. Notably, in children, as well as human volunteers challenged with ETEC, diarrheal severity is significantly increased severity in blood group A (bgA) individuals. EtpA, is a secreted glycoprotein adhesin that functions as a blood group A lectin to promote critical interactions between ETEC and blood group A glycans on intestinal epithelia for effective bacterial adhesion and toxin delivery. EtpA is highly immunogenic resulting in robust antibody responses following natural infection and experimental challenge of human volunteers with ETEC. To understand how EtpA directs ETEC-blood group A interactions and stimulates adaptive immunity, we mutated EtpA, mapped its glycosylation by mass-spectrometry (MS), isolated polyclonal (pAbs) and monoclonal antibodies (mAbs) from vaccinated mice and ETEC-infected human volunteers, and determined structures of antibody-EtpA complexes by cryo-electron microscopy. Both bgA and mAbs that inhibited EtpA-bgA interactions and ETEC adhesion, bound to the C-terminal repeat domain highlighting this region as crucial for ETEC pathogen-host interaction. MS analysis uncovered extensive and heterogeneous N-linked glycosylation of EtpA and cryo-EM structures revealed that mAbs directly engage these unique glycan containing epitopes. Finally, electron microscopy-based polyclonal epitope mapping revealed antibodies targeting numerous distinct epitopes on N and C-terminal domains, suggesting that EtpA vaccination generates responses against neutralizing and decoy regions of the molecule. Collectively, we anticipate that these data will inform our general understanding of pathogen-host glycan interactions and adaptive immunity relevant to rational vaccine subunit design. Author summaryEnterotoxigenic E. coli (ETEC), a leading cause of diarrhea disproportionately affecting young children in low-income regions, are a priority for vaccine development. Individuals possessing A blood-type are more susceptible to severe cholera-like disease. EtpA, a secreted, immunogenic, blood group A binding protein, is a current vaccine target antigen. Here, we determined the atomic structure of EtpA in complex with protective as well as non-protective monoclonal antibodies targeting two different domains of the protein, allowing us to pinpoint key regions involved in blood-group A antigen recognition and uncover the mechanism of antibody-based protection. In addition, we show through mass-spectrometry that EtpA is extensively and heterogeneously glycosylated at surface-exposed asparagine residues by a promiscuous and low-fidelity glycosyltransferase, EtpC, and that this unique form of bacterial glycosylation is critical for to development of protective immune responses. Lastly, polyclonal antibodies from vaccinated mice as well as monoclonal antibodies obtained from ETEC-infected human volunteers revealed that the highly antigenic surface of EtpA exhibits both protective and non-protective epitopes. These results greatly expand our understanding of ETEC pathogenesis, and the immune responses elicited by these common infections, providing valuable information to aid in the rational design and testing of subunit vaccines.

microbiology↗

bioRxiv2021

EMS-based mutants are useful for enhancing drought tolerance in spring wheat

Sustainable wheat production in drought prone areas can be achieved by developing resilient wheat varieties. In the present study, chemical mutagenesis was used to induce mutations in a cultivated wheat variety NN-Gandum-1. In total, 44 mutants were selected based on their high yield potential for exposing to well-watered (W1) and rainfed (W2) conditions for one season. Then 24 mutants were selected, and were exposed to W1 and W2 regimes. On the basis of least relative reduction in physiological parameters under W2 regime, five mutants were selected for conducting exome capturing assays. In total, 184 SNPs were identified in nine genes (ABC transporter type 1, Aspartic peptidase, Cytochrome P450, transmembrane domain, Heavy metal-associated domain, HMA, NAC domain, NAD (P)-binding domain, S-type anion channel, Ubiquitin-conjugating enzyme E2 and UDP-glucuronosyl/UDP-glucosyltransferase). Maximum number of mutations were observed in chr.2D, which contained mutations in three genes i.e. ABC transporter type 1, NAD (P)-binding domain and UDP-glucuronosyl/UDP-glucosyltransferase which may have a role in conferring drought tolerance. The selected mutants were further tested for studying their biochemical responses under both the regimes for two years. The extent of membrane damage was estimated through malondialdehydeand hydrogen per oxidase and tolerance to drought stress was assessed via antioxidant enzymes in leaves. The selected mutants under drought stress increased the accumulation of proline content, total soluble sugars, total free amino acids, while decreased total chlorophyll content, carotenoids and total soluble protein. Finally, the procedure of narrowing down the number of developed mutants from a large mutation population (>4000) is found useful for exploring the complex trait like drought without compromising yield potential. These mutants can further be explored to understand the genetic circuits of drought tolerance in wheat which will pave the way towards improving livelihood of resource poor farming community mostly relying on cereal food.

plant biology↗

bioRxiv2020

Contribution of noncanonical antigens to virulence and adaptive immunity in human infection with enterotoxigenic E. coli

Enterotoxigenic E. coli (ETEC) contribute significantly to the substantial burden of infectious diarrhea among children living in low and middle income countries. In the absence of a vaccine for ETEC, children succumb to acute dehydration as well as non-diarrheal sequelae related to these infections including malnutrition. The considerable diversity of ETEC genomes has complicated canonical vaccine development approaches focused on a subset of antigens known as colonization factors (CFs). To identify additional conserved immunogens, we mined genomic sequences of 89 ETEC isolates, bioinformatically selected potential surface-exposed pathovar-specific antigens conserved in more than 40% of the genomes (n=118), and assembled the representative proteins onto microarrays, complemented with known or putative colonization factor subunit molecules (n=52), and toxin subunits to interrogate samples from individuals with acute symptomatic ETEC infections. Surprisingly, in this open-aperture approach, we found that immune responses were largely constrained to a small number of antigens including individual colonization factor antigens and EtpA, an extracellular adhesin. In a Bangladeshi cohort of naturally infected children < 2 years of age, both EtpA and a second noncanonical antigen, EatA, elicited significant serologic responses that were associated with protection from symptomatic illness. In addition, children infected with ETEC isolates bearing either etpA or eatA genes were significantly more likely to develop symptomatic disease. These studies support a role for more recently discovered noncanonical antigens in virulence and the development of adaptive immune responses during ETEC infections, findings that may inform vaccine design efforts to complement existing approaches.

microbiology↗

bioRxiv2018

A dynamic neural network model for real-time prediction of the Zika epidemic in the Americas

BackgroundIn 2015 the Zika virus spread from Brazil throughout the Americas, posing an unprecedented challenge to the public health community. During the epidemic, international public health officials lacked reliable predictions of the outbreaks expected geographic scale and prevalence of cases, and were therefore unable to plan and allocate surveillance resources in a timely and effective manner.\n\nMethodsIn this work we present a dynamic neural network model to predict the geographic spread of outbreaks in real-time. The modeling framework is flexible in three main dimensions i) selection of the chosen risk indicator, i.e., case counts or incidence rate, ii) risk classification scheme, which defines the relative size of the high risk group, and iii) prediction forecast window (one up to 12 weeks). The proposed model can be applied dynamically throughout the course of an outbreak to identify the regions expected to be at greatest risk in the future.\n\nResultsThe model is applied to the recent Zika epidemic in the Americas at a weekly temporal resolution and country spatial resolution, using epidemiological data, passenger air travel volumes, vector habitat suitability, socioeconomic and population data for all affected countries and territories in the Americas. The model performance is quantitatively evaluated based on the predictive accuracy of the model. We show that the model can accurately predict the geographic expansion of Zika in the Americas with the overall average accuracy remaining above 85% even for prediction windows of up to 12 weeks.\n\nConclusionsSensitivity analysis illustrated the model performance to be robust across a range of features. Critically, the model performed consistently well at various stages throughout the course of the outbreak, indicating its potential value at the early stages of an epidemic. The predictive capability was superior for shorter forecast windows, and geographically isolated locations that are predominantly connected via air travel. The highly flexible nature of the proposed modeling framework enables policy makers to develop and plan vector control programs and case surveillance strategies which can be tailored to a range of objectives and resource constraints.

epidemiology↗