Biology subjects

Khan, M. I.

Publications and source records attributed to Khan, M. I..

12 recordsLinked to original sources

bioRxiv2026

A novel role for TRPV1 in macrophage giant cell formation

TRPV1 (transient receptor potential vanilloid 1) is a non-selective cation channel with high permeability to Ca2+ and is best known for its roles in sensory signaling. However, its function in immune cell biology, particularly in macrophage fusion, remains unknown. Cell fusion is a critical process in both physiological and pathological contexts, including development, tissue remodeling, and the foreign body response (FBR) to implanted biomaterials. During FBR, macrophages undergo fusion to form multinucleated foreign body giant cells (FBGCs), which contribute to implant degradation and fibrotic encapsulation. Here, we identify TRPV1 as a key regulator of macrophage multinucleation and FBGC formation. We demonstrate that TRPV1 is endogenously expressed in bone marrow-derived macrophages (BMDMs) and is upregulated in response to fusogenic cytokines and inflammatory stimuli. Functionally, TRPV1 promotes matrix stiffness-dependent macrophage adhesion and spreading, indicating a role in mechanosensitive signaling. We show that TRPV1 is required for efficient macrophage fusion under both cytokine-driven and matrix stiffness-mediated conditions. Mechanistically, TRPV1 links extracellular mechanical cues and cytokine signaling to cytoskeletal remodeling, facilitating the actin reorganization necessary for cell fusion. Importantly, TRPV1 deficiency does not alter TRPV4-mediated Ca2+ signaling, demonstrating that TRPV1 operates independently of TRPV4, a known mechanosensitive channel implicated in FBR and FBGC formation. Collectively, these findings suggest TRPV1 as a previously unrecognized mechanosensitive regulator of macrophage fusion and FBGC formation. This work provides new insight into the molecular mechanisms governing FBR and identifies TRPV1 as a potential therapeutic target for improving biomaterial biocompatibility and mitigating fibrosis.

cell biology↗

bioRxiv2026

Particle Swarm Optimization with Random Forest Surrogates Modelling for Rational Design of Antimicrobial Fluoride Toothpaste Formulations against Clinically Significant Oral Pathogens

To make effective antimicrobial toothpastes, you need to optimize many parts that work together. Creating new formulations the old-fashioned way takes a lot of time and money. This research formulates and substantiates a methodological framework that combines systematic antimicrobial susceptibility testing with Particle Swarm Optimization (PSO) to enhance toothpaste formulations against clinically significant oral pathogens. Using a D-optimal mixture design, we made 24 different toothpaste formulations by changing the type of fluoride (NaF, MFP, SnF2), the concentration of fluoride (1000-1500 ppm), the concentration of SLS (0.5-2.5%), the type of abrasive (silica, calcium carbonate, dicalcium phosphate), and the concentration of abrasive (10-30%). We used agar well diffusion and minimum inhibitory concentration (MIC) tests to see how well the drugs worked against Streptococcus mutans ATCC 25175, Porphyromonas gingivalis ATCC 33277, and Lactobacillus acidophilus ATCC 4356. A Random Forest surrogate model was trained on 120 experimental data points (24 formulations x 5 concentrations) and validated through 10-fold cross-validation. Multi-objective PSO was used to improve the effectiveness of antimicrobials, the availability of fluoride, and the cost of the formulation. Chosen PSO-predicted formulations underwent experimental validation. The antimicrobial activity changed a lot (p < 0.001) depending on the formulation parameters. The optimized formulation (sodium fluoride 1120 ppm, SLS 2.3%, hydrated silica 18%, pH 7.2) showed 28.4 {+/-} 1.2 mm of inhibition against S. mutans, 26.8 {+/-} 1.4 mm against P. gingivalis, and 24.2 {+/-} 1.1 mm against L. acidophilus. These were improvements of 18.5%, 22.3%, and 19.8%, respectively, over the best commercial comparator. Experimental validation corroborated PSO predictions with a mean absolute error of 5.2%. Multi-objective Optimization found Pareto-optimal formulations that let you choose based on trade-offs between effectiveness, safety, and cost. Combining systematic experimental design with PSO gives a tested framework for making rational toothpaste formulations. This method significantly lowers the amount of work needed for experiments while also allowing for the Optimization of multiple competing formulation goals.

microbiology↗

bioRxiv2026

A novel endosome-escaping, macrophage-targeted nanoparticle platform for miR-146a delivery with favorable in vivo biodistribution and biocompatibility

Advanced nanocarrier technologies have reshaped treatment paradigms for inflammatory and degenerative disorders by facilitating cell-specific delivery of bioactive molecules, including nucleic acids. Despite this progress, therapeutic application of microRNAs (miRs) has been hindered by rapid degradation, limited stability in circulation, and suboptimal cytosolic delivery within complex biological environments. In this study, we engineered and validated a macrophage-directed lipid nanoparticle (LNP) system designed to efficiently deliver the anti-inflammatory microRNA miR-146a (MacLNP-miR146a). Mannose-functionalized LNPs were generated through a scalable lipid injection formulation approach, producing highly uniform nanoparticles with strong physicochemical integrity across diverse pH conditions and in serum-rich environments. The optimized four-lipid composition supports efficient miR-146a encapsulation, promotes endosomal escape, and enhances intracellular trafficking, leading to effective cellular uptake and favorable tissue distribution in both in vitro and in vivo models. Notably, MacLNP-miR146a demonstrates strong biocompatibility in primary cell systems and animal studies. Together, these findings position MacLNP-miR146a as a robust and translational nanotherapeutic strategy for modulating macrophage-driven inflammation, including biomaterial-associated foreign body responses and related inflammatory pathologies.

bioengineering↗

bioRxiv2026

Basella alba L. var. Rubra L-DOPA/dopamine-4,5-dioxygenase 1 prefers L-DOPA over dopamine and ascorbic acid enhances its activity

Betalamic acid is the chromophore of betalains, which are pigments of chemotaxonomic and physiological importance. This study involves RACE-PCR-based gene cloning, heterologous expression, protein purification, and steady-state kinetics of B. alba L. var. Rubra L-DOPA/dopamine-4,5-dioxygenase 1 (BrDOD1). BrDOD1 is a unique high betalamic acid-forming LigB homolog in plants having comparable affinity for both L-DOPA and dopamine (KM < 50 M). Ascorbic acid (10 mM) shifted the steady-state kinetics from inhibitory to activator at a particular substrate concentration of both L-DOPA and dopamine. This increased both KM and Vmax by more than 6.5-fold, indicating that ascorbic acid acted as a molecular crowding agent in the enzyme assay. BrDOD1s physiological substrate is L-DOPA as the reaction rate for L-DOPA was 6.6-fold higher than dopamine, L-DOPA was present in higher concentration than that of dopamine in the same plant, and molecular dynamic simulations showed better stability of BrDOD1-L-DOPA complex than that of dopamine. Further, two more LigB homologs from the same plant have also been cloned. Based on the betalamic acid-forming activity, molecular phylogeny, conserved structural regions, and theoretical pI, betalainic plant LigB homologs have been classified into three groups to better understand the evolutionary trajectory of the LigB homologs in plants.

plant biology↗

bioRxiv2026

Endosome-escaping engineered LNP-miR146a with in vivo biodistribution to mitigate inflammation and foreign body giant cell formation

Nanomaterial-enabled delivery systems have transformed therapeutic strategies for treating inflammatory and degenerative diseases by enabling targeted delivery of small molecules and nucleic acids. However, the clinical translation of microRNA (miR) therapeutics remains limited by instability, enzymatic degradation, and inefficient intracellular delivery in biological environments. Here, we present the design and validation of a next-generation lipid nanoparticle (LNP) platform optimized for the stable and effective delivery of the anti-inflammatory microRNA miR-146a. This LNP system is produced using a scalable lipid injection-based formulation method and yields nanoparticles with uniform size distribution and exceptional physicochemical stability across a wide pH range (2.5-8) and in serum-containing conditions. The four-component lipid architecture enables high miR-146a loading efficiency, efficient endo/lysosomal escape, and robust cellular internalization, resulting in effective tissue uptake and biodistribution both in vitro and in vivo. Importantly, LNP-mediated delivery of miR-146a exhibits excellent biocompatibility and potent anti-inflammatory activity in primary cells and animal models. Collectively, these results suggest this LNP-miR146a platform as a stable, efficient, and translatable approach for modulating inflammation and addressing biomaterial-associated inflammatory responses.

bioengineering↗

bioRxiv2022

NAT10, an RNA acetyl cytidine transferase restrains ferroptosis in cancer cells by maintaining SLC7A11 RNA stability

Recently, we reported that N-acetyltransferase 10 (NAT10) regulates fatty acid metabolism through ac4C-dependent RNA modification of key genes in cancer cells. During this work, we noticed ferroptosis as one of the most negatively enriched pathways among other pathways in NAT10 depleted cancer cells. In the current work, we explored the possibility of whether NAT10 acts as an epitrancriptomic regulator of ferroptosis pathway in cancer cells. Global ac4C levels and expression of NAT10 with other ferroptosis-related genes were assessed via dotblot and RT-qPCR respectively. Flow cytometry and biochemical analysis were used to assess oxidative stress and ferroptosis features. The ac4C mediated mRNA stability was conducted RIP-PCR and mRNA stability assay. Metabolites were profiled using LC-MS/MS. Our results showed significant downregulation in expression of essential genes related to ferroptosis namely SLC7A11, GCLC, MAP1LC3A, and SLC39A8 in NAT10 depleted cancer cells. Further, we noticed a reduction in cystine uptake and reduced GSH levels along with elevated ROS, and lipid peroxidation levels in NAT10 depleted cells. Consistently, overproduction of oxPLs as well as increased mitochondrial depolarization and decreased activities of antioxidant enzymes support the notion of ferroptosis induction in NAT10 depleted cancer cells. Mechanistically, reduced ac4C level shortens the half-life of GCLC and SLC7A11 mRNA, resulting in low levels of intracellular cystine and reduced GSH, failing to detoxify ROS leading to increased cellular oxPLs which facilitates ferroptosis induction. Collectively, our findings suggest that NAT10 restrains ferroptosis by stabilizing the SLC7A11 mRNA transcripts to avoid oxidative stress that induces oxidation of phospholipids to initiate ferroptosis.

cancer biology↗

bioRxiv2021

Proteomic insight into soybean response to flooding stress reveals changes in basic energy metabolism and cell wall modifications

Soybean is a legume crop enriched with proteins and oil. It is frequently exposed to anthropogenic and natural flooding that limits its growth and yield. Current study applied gel-free proteomic techniques to unravel soybean response mechanism to flooding stress. Two-days-old soybeans were flooded for 4 days continuously and root samples were collected at days 2 to 6 for proteomic and enzymatic analyses. Age-matched untreated soybeans were collected as control. After protein extraction, purification and tryptic digestion, the peptides were analyzed on nano-liquid chromatography-mass spectrometry. A total of 539 and 472 proteins with matched peptides 2 or more were identified in control and flooded seedlings, respectively. Among these 364 proteins were commonly identified in both control and flooded soybeans. Fourty-two proteins abundances were changed 4-fold after 2-days of flooding stress as compared to starting point. The cluster analysis showed that highly increased proteins included cupin family proteins, enolase, pectin methylesterase inhibitor, glyoxalase II, alcohol dehydrogenase and aldolase. The enzyme assay of enolase and pectin methylesterase inhibitor confirmed protein abundance changes. These findings suggest that soybean adopts the less energy consuming strategies and brings biochemical and structural changes in the cell wall to effectively respond to flooding stress and for the survival.

biochemistry↗

bioRxiv2021

Large scale genomic and evolutionary study reveals SARS-CoV-2 virus isolates from Bangladesh strongly correlate with European origin and not with China.

RationaleThe global public health is in serious crisis due to emergence of SARS-CoV-2 virus. Studies are ongoing to reveal the genomic variants of the virus circulating in various parts of the world. However, data generated from low- and middle-income countries are scarce due to resource limitation. This study was focused to perform whole genome sequencing of 151 SARS-CoV-2 isolates from COVID-19 positive Bangladeshi patients. The goal of this study was to identify the genomic variants among the SARS-CoV-2 virus isolates in Bangladesh, to determine the molecular epidemiology and to develop a relationship between host clinical trait with the virus genomic variants. MethodSuspected patients were tested for COVID-19 using one step commercial qPCR kit for SARS-CoV-2 Virus. Viral RNA was extracted from positive patients, converted to cDNA which was amplified using Ion AmpliSeq SARS-CoV-2 Research Panel. Massive parallel sequencing was carried out using Ion AmpliSeq Library Kit Plus. Assembly of raw data is done by aligning the reads to a pre-defined reference genome (NC_045512.2) while retaining the unique variations of the input raw data by creating a consensus genome. A random forest-based association analysis was carried out to correlate the viral genomic variants with the clinical traits present in the host. ResultAmong the 151 viral isolates, we observed the 413 unique variants. Among these 8 variants occurred in more than 80 % of cases which include 241C to T, 1163A to T, 3037C to T,14408C to T, 23403A to G, 28881G to A, 28882 G to A, and finally the 28883G to C. Phylogenetic analysis revealed a predominance of variants belonging to GR clade, which have a strong geographical presence in Europe, indicating possible introduction of the SARS-CoV-2 virus into Bangladesh through a European channel. However, other possibilities like a route of entry from China cannot be ruled out as viral isolate belonging to L clade with a close relationship to Wuhan reference genome was also detected. We observed a total of 37 genomic variants to be strongly associated with clinical symptoms such as fever, sore throat, overall symptomatic status, etc. (Fishers Exact Test p-value<0.05). The most mention-worthy among those were the 3916CtoT (associated with causing sore throat, p-value 0.0005), the 14408C to T (associated with protection from developing cough, p-value= 0.027), and the 28881G to A, 28882G to A, and 28883G to C variant (associated with causing chest pain, p-value 0.025). ConclusionTo our knowledge, this study is the first large scale phylogenomic studies of SARS-CoV-2 virus circulating in Bangladesh. The observed epidemiological and genomic features may inform future research platform for disease management, vaccine development and epidemiological study.

genetics↗

bioRxiv2019

Differential detection of Entamoeba species in stool samples collected from children in District Swat, Khyber Pakhtunkhwa Pakistan

BackgroundAmoebiasis is an intestinal disease caused by enteric protozoan called Entamoeba histolytica belongs to the Genus Entamoeba. The main reason of infection is the contamination of food and water due to the poor sanitation. Among Entamoeba species, Entamoeba histolytica is highly pathogenic while the other species are non-pathogenic and needs no medical treatment.\n\nMethodologyA total of 400 stool samples were collected from different areas of district Swat and were processed for screening of amoebic cells. Microscopically identified samples containing amoebic cells were stored at -20 {degrees}C till DNA extraction. Extracted DNA was used in a PCR reaction with specific reference primers to amplify the target DNA.\n\nResultsOut of all 400 stool samples 111 (27.7%) were found positive through microscopy while PCR reaction confirmed 80 out of microscope positive samples. Among 80 PCR positive samples, the infection with Entamoeba dispar was most common (57.5%) followed by E. histolytica (47.5%) and Entamoeba moshkovskii (20%). The positive cases for mono-infection of E. dispar were 33 (41.25%), followed by E.histolytica 25 (31.25%) and E. moshkovskii 7 (8.75%). The co-infection of E. histolytica with E. dispar and E. moshkovskii was 6 (7.5%) and 2 (2.5%), respectively. Similarly the co-infection of Entamoeba dispar with Entamoeba moshkovskii was also 2 (2.5%) while 5 (6.25%) samples were observed with mixed infection of E. histolytica, E. dispar and E. moshkovskii.\n\nSignificance of the studyThe aim of the study was to detect and differentiate the E. histolytica, Entamoeba dispar and Entamoeba moshkovskii using conventional microscopy and polymerase chain reaction. The results suggested that the use of PCR is necessary to differentiate E. histolytica from E. dispar and E. moshkovskii and therefore, to avoid unnecessary treatment the present study recommend the use of PCR for the routine diagnosis of amoebiasis in the study area. It is also suggested that further studies from this area may also facilitate the understanding of genetic diversity of these pathogens.

microbiology↗

bioRxiv2018

Molecular and clinical analysis of 27 German patients with Leber congenital amaurosis

Leber congenital amaurosis (LCA) is the earliest and most severe form of all inherited retinal dystrophies (IRD) and the most frequent cause of inherited blindness in children. The phenotypic overlap with other early-onset and severe IRDs as well as difficulties associated with the ophthalmic examination of infants can complicate the clinical diagnosis. To date, 25 genes have been implicated in the pathogenesis of LCA. The disorder is usually inherited in an autosomal recessive fashion, although rare dominant cases have been reported. We report the mutation spectra and frequency of genes in 27 German index patients initially diagnosed with LCA. A total of 108 LCA- and other genes implicated in IRD were analysed using a cost-effective targeted next-generation sequencing procedure based on molecular inversion probes (MIPs). Sequencing and variant filtering led to the identification of putative pathogenic variants in 25 cases, thereby leading to a detection rate of 93%. The mutation spectrum comprises 34 different alleles, 17 of which are novel. In line with previous studies, the genetic results led to a revision of the initial clinical diagnosis in a substantial proportion of cases, demonstrating the importance of genetic testing in IRD. In addition, our detection rate of 93% shows that MIPs are a cost-efficient and sensitive tool for targeted next-generation sequencing in IRD.

genetics↗

bioRxiv2018

S100A4 inhibits cell proliferation by interfering with the RAGE V domain-S100A1

The Ca2+-dependent human S100A4 (Mts1) protein is part of the S100 family, and the S100A1 protein is the target of S100A4. Here, we studied the interactions of S100A1 with S100A4 using nuclear magnetic resonance (NMR; 700 MHz) spectroscopy. We used HADDOCK software to model S100A4 and S100A1, and we observed that S100A1 and the RAGE V domain have an analogous binding area in S100A4. We discovered that S100A4 acts as an antagonist among the RAGE V domain and S100A1, which inhibits tumorigenesis and cell proliferation. We used a WST-1 assay to examine the bioactivity of S100A1 and S100A4. This study could possibly be beneficial for evaluating new proteins for the treatment of cancer.

biochemistry↗

bioRxiv2018

Prokaryotic Diversity from Extreme Environments of Pakistan and its Potential Applications at Regional Levels

Extremophiles, the microorganisms thriving in extreme environments, provide valuable resources for practicing novel biotechnological processes. Pakistan homes a wide spectrum of extreme environments which harbor various biotechnologically significant microorganisms. This review gauges the structural and functional bacterial diversity of several extreme environments, emphasizing their potentials as a source of extremozymes, and in bioleaching, bioremediation, and bioenergy production at regional level. Further, this review highlights a panoramic account of the local natural conservatories of extremophiles. The inadequacies of current fragmental research are discussed with suggestions to quantitatively define the structural and functional diversity of unexplored extreme localities.

microbiology↗