Biology subjects

Hossain, M. F.

Publications and source records attributed to Hossain, M. F..

8 recordsLinked to original sources

bioRxiv2026

Establishment of a cochlear lymphatic vascular network and immune surveillance system following cochlear implantation

Hearing loss is a highly prevalent sensory abnormality often addressed with cochlear implants (CI) that provide auditory rehabilitation for deaf patients. However, a universal inflammatory foreign body response (FBR) to the implanted materials negatively impacts CI outcomes. The mechanistic basis for immune cell infiltration and propagation of the FBR directed against CIs is not defined. Using mouse CI models and quantitative, highly tractable reporters for lymphatics, blood vessels, and immune cells, we identify inner ear lymphatic vessels and changes to the immune surveillance system following cochlear implantation. Histopathological analysis of implanted temporal bones from human subjects shows that both blood vessels and lymphatics are evident within the scala tympani of the implanted cochlea. Our data reveal a rich lymphatic vascular network in the inner ear, closely associated with the perilymphatic and endolymphatic spaces. Lymphatics proliferate within the perilymphatic space of the implanted cochleae and appear to traffic immune cells. Together, our data provide direct evidence that concurrent proliferation of blood vessels and recruitment of blood-borne immune cells comprise an 'immune surveillance system' in the implanted cochleae that promotes the FBR. Our findings also highlight potential opportunities to limit adverse FBR outcomes following cochlear implantation.

systems biology↗

bioRxiv2025

Identification of HIV-Associated Gene Expression Biomarkers Using Machine Learning and Interpretable Artificial Intelligence

Despite advances in antiretroviral therapy (ART), the early and accurate diagnosis of Human Immunodeficiency Virus (HIV) infection remains a significant public health challenge. Traditional biomarkers, such as CD4+ T cell counts and viral load, are limited in capturing the complex biological mechanisms underlying HIV pathogenesis. This study proposes a machine learning (ML) and interpretable artificial intelligence (AI) framework to identify transcriptomic biomarkers for HIV diagnosis using immune cell-specific gene expression data. We utilized the GSE6740 dataset, which includes microarray profiles from CD4+ and CD8+ T cells of HIV-positive (treatment-naive) and HIV-negative individuals. Feature selection was performed through differential gene expression analysis, weighted gene co-expression network analysis (WGCNA), and protein-protein interaction (PPI) network construction. Hub genes identified through these methods were used to train six supervised ML classifiers. The best-performing model was selected based on cross-validated metrics, including accuracy, Kappa, ROC, sensitivity, and specificity, and further interpreted using SHapley Additive exPlanations (SHAP) values. Seven co-expression modules were identified, with the red and green modules showing strong positive and negative correlations with HIV status, respectively. From the intersection of WGCNA modules, differentially expressed genes (DEGs), and PPI networks, ten hub genes were prioritized. Among the trained models, the regularized regression model (GLMNET) demonstrated the highest diagnostic performance (ROC = 0.97, accuracy = 91%). SHAP analysis highlighted GBP1, ISG15, OAS2, OAS1, and DDX60 as the most influential genes contributing to model predictions, thereby enhancing interpretability and biological relevance. By integrating transcriptomic profiling with interpretable ML, this study identifies novel gene-based biomarkers for HIV diagnosis and underscores the potential of explainable AI in advancing precision medicine approaches for infectious diseases.

bioinformatics↗

bioRxiv2024

Population dynamics of fruit flies (Diptera: Tephritidae) in a semirural area under subtropical monsoon climate of Bangladesh

Fruit flies belonging to Tephritidae family are highly destructive agricultural pests, posing a significant threat to various fruits and vegetables grown in Bangladesh. A comprehensive year-round survey was conducted at Atomic Energy Research Establishment (AERE) campus located in the central region of Bangladesh. Three types of male lures (methyl eugenol, cue-lure and zingerone) were used to detect and assess the diversity of pest fruit fly species. A total of seventeen species of Tephritidae fruit flies were detected in this survey. The Bactrocera carambolae fruit fly has been discovered for the first time in our survey area, indicating spread of its range towards the north-west region from its previous detection sites (Chattogram and Sylhet Divisions) in Bangladesh. Among the detected pest species, we identified six abundant species: Bactrocera dorsalis, Zeugodacus cucurbitae, Zeugodacus tau, Bactrocera rubigina, Bactrocera zonata, and Dacus longicornis. The most abundant species was the polyphagous fruit pest B. dorsalis, comprising 76.83% of all captured flies. The species Z. cucurbitae was the second most abundant, representing 13.82% of the total trapped flies. The fitted curve to survey data using Gaussian mixture model revealed the existence of overlapped subgroups in the population of B. dorsalis and Z. cucurbitae. In addition, our statistical analysis of the six abundant Tephritidae fruit fly species revealed correlation of population dynamics with several factors including temperature, rainfall, humidity, photoperiod, and fruiting time of host plant species in the selected area.

ecology↗

bioRxiv2024

Effect of different lining paper materials and infusions on oviposition preference of Aedes aegypti (Diptera: Culicidae) gravid mosquitoes

Aedes aegypti (Linnaeus) mosquito is a vector, responsible for increasing global public health concerns due to its rapid geographical spread and increasing vectorial capacity. Understanding the breeding behavior of Ae. aegypti is crucial to control this vector and thereby limiting the spread of diseases. To study this mosquito breeding in the laboratories and ovitraps, different types of lining-papers, surrounding inner surface of a container along with different types of added infusions, are used. Lining-papers serve as surfaces for oviposition and infusions provide the essential environment for nurturing. The types of oviposition surfaces and infusions used in laboratory rearing facilities or ovitraps influence oviposition preference, changing the breeding behavior of Ae. aegypti gravid mosquitoes. This study presents a comparative study on oviposition preferences for six different types of lining-papers and six different types of infusions in a bioassay cage. ANOVA analysis shows a significant effect on oviposition preference of different types of lining-papers that served as oviposition surfaces. The highest oviposition activity was observed for the agri seed germination paper-75 lining-paper when normal tap water infusion was used. Likewise, statistical analysis shows that when a plain printing offset paper 80 GSM lining-paper was used, a highly statistically significant effect on oviposition preference is observed for different types of infusions used in the oviposition cups.

animal behavior and cognition↗

bioRxiv2024

A conserved RNA switch for acetylcholine receptor clustering at neuromuscular junctions in chordates

In mammals, neuromuscular synapses rely on clustering of acetylcholine receptors (AChRs) in the muscle plasma membrane, ensuring optimal stimulation by motor neuron-released acetylcholine neurotransmitter. This clustering depends on a complex pathway based on alternative splicing of Agrin mRNAs by the RNA-binding proteins Nova1/2. Neuron-specific expression of Nova1/2 ensures the inclusion of small "Z" exons in Agrin, resulting in a neural-specific form of this extracellular proteoglycan carrying a short peptide motif that is required for binding to Lrp4 receptors on the muscle side, which in turn stimulate AChR clustering. Here we show that this intricate pathway is remarkably conserved in Ciona robusta, a non-vertebrate chordate in the tunicate subphylum. We use in vivo tissue-specific CRISPR/Cas9-mediated mutagenesis and heterologous "mini-gene" alternative splicing assays in cultured mammalian cells to show that Ciona Nova is also necessary and sufficient for Agrin Z exon inclusion and downstream AChR clustering. We present evidence that, although the overall pathway is well conserved, there are some surprising differences in Nova structure-function between Ciona and mammals. We further show that, in Ciona motor neurons, the transcription factor Ebf is a key activator of Nova expression, thus ultimately linking this RNA switch to a conserved, motor neuron-specific transcriptional regulatory network.

developmental biology↗

bioRxiv2023

Discovery of specific activity of 2-HPA acting on the membrane progestin receptor α (paqr7) by purification of natural products from the marine algae Padina

Membrane progestin receptors (mPRs) are members of the progestin and adipoQ (PAQR) receptor family that are stimulated by endogenous steroids to initiate rapid intracellular signalling through a nongenomic pathway. Previously, water-soluble compounds with mPR-binding activity from the marine algae Padina arborescens were fractionated by HPLC steps. In this study, the structure of one of the major compounds in the fraction was identified as 2-hydroxypentanoic acid (2-HPA) using Nuclear Magnetic Resonance spectroscopy. 2-HPA showed a substantial competitive binding affinity for hmPR in the GQD-hmPR binding assay. In contrast, synthetic structural analogues of 2-HPA showed no competitive binding activity. The physiological activity of 2-HPA and its analogues was then investigated using in vitro goldfish and in vivo zebrafish oocyte maturation and ovulation assays. As with the hmPR binding assay, only 2-HPA showed inhibitory activity on oocyte maturation and ovulation of fish oocytes. Furthermore, the inhibitory activity of 2-HPA was compared between S- and R-type 2-HPA. The results showed that both types had the same level of activity. These results indicate that 2-HPA, found as a secreted compound from Padina arborescens, is a novel mPR antagonist and its chemical structure is highly restricted to show its activity.

biochemistry↗

bioRxiv2018

Analysis of Maize Profilin-4 Isoform as an allergen

Profilin is an actin monomer-binding protein that controls the dynamic turnover of actin filaments and is ubiquitously present in different organisms ranging from prokaryotes to higher eukaryotes. Maize (Zea mays) profilin-4 isoform is a pollen-specific protein. Birch profilin isoform is a known allergen but maize profilin is yet to be characterized. Due to the high cultivation rate of maize, the analysis of the properties of maize profilin-4 isoform as an allergen is a demand of time for developing an effective immune therapy. Here, we analyzed the allergenic potency of profilin-4 by studying of its physicochemical properties, including molecular weight ([~]14kD) and theoretical pI (4.63). We tested the potential B cell epitope candidates of profilin-4 using different immune-informatics tools housed at IEDB analysis resource. For the B cell epitope prediction, potential antigenic sites on the protein surface were predicted by both propensity scale and machine learning method followed by their mapping of 3D structure prediction. We hereby claim that the profilin-4 is a potential allergen and is able to induce allergic responses. However, the wet lab experiments are needed to validate our claim thats beyond our scope.

bioinformatics↗

bioRxiv2018

Prediction of Deleterious Single Nucleotide Polymorphisms in Human p53 Gene

With a variety of accessible Single Nucleotide Polymorphisms (SNPs) data on human p53 gene, this investigation is intended to deal with detrimental SNPs in p53 gene by executing diverse valid computational tools, including Filter, SIFT, PredictSNP, Fathmm, UTRScan, ConSurf, Phyre, Tm-Adjust, I-Mutant, Task Seek after practical and basic appraisal, dissolvable openness, atomic progression, and analysing the energy minimization. Of 581 p53 SNPs, 420 SNPs are found to be missense or non-synonymous and 435 SNPs are in the 3 prime UTR and 112 SNPs are of every 5 prime UTR from which 16 non synonymous SNPs (nsSNPs) as non-tolerable while PredictSNP package predicted 14 (taking consideration SNP colored green by two or more than 2 analyses is neutral). By concentrating on six bioinformatics tools of various dimensions a combined output is generated where 14 nsSNPs are prone to exert a deleterious effect. By using diverse SNP analysing tools we have found 5 missense SNPs in the 3 crucial amino acids position in the DNA binding domain. The underlying discoveries are fortified by I-Mutant and Project HOPE. The ExPASy-PROSITE tools characterized whether the mutations located in the functional part of the protein or not. This study provides a decisive outcome concluding the accessible SNPs information by recognizing the five harming nsSNPs: rs28934573 (S241F), rs11540652 (R248Q), rs121913342 (R248W), rs121913343 (R273C) and rs28934576 (R273H). The findings of this investigation recognize the detrimental nsSNPs which enhance the danger of various kinds of oncogenesis in patients of different populations in genome-wide studies (GWS).

bioinformatics↗