Biology subjects

Irfan, M.

Publications and source records attributed to Irfan, M..

10 recordsLinked to original sources

bioRxiv2025

Chikungunya virus non-structural protein 2 (nsP2) inhibits RIG-I and TLR-mediated immune response

Chikungunya virus (CHIKV) is a single-stranded positive-sense RNA virus that employs various strategies to evade the hosts immune response. The CHIKV non-structural protein 2 (nsP2) is one of the viral-encoded proteins essential for viral replication as well as modulation of the immune response. In this study, we demonstrate that CHIKV nsP2 suppresses both RIG-I-like receptors (RLR) and Toll-like receptors (TLR) signaling pathways. Domain mapping of the nsP2 identified the N-terminal region encompassing the N-terminal domain and the helicase domain (NH) is responsible for the inhibition. Furthermore, site-directed mutagenesis experiments showed that functional helicase is necessary for inhibiting interferon production, but the C-terminal V-Loop region, previously implicated in host transcriptional shutoff is not. Lastly, we demonstrate that nsP2 disrupts two key immune signaling pathways, RLR and TLRs, by interfering with common proteins, TBK1 and IRF3, involved in both signaling pathways. These findings enhance our understanding of CHIKV immune evasion strategies and offer potential targets for the development of antiviral therapeutics.

immunology↗

bioRxiv2025

RNA sequencing reveals key factors modulating TNFa-stimulated odontoblast-like differentiation of dental pulp stem cells

Inflammation is a complex host response to harmful infections or injuries, playing both beneficial and detrimental roles in tissue regeneration. Notably, clinical dentinogenesis associated with caries development occurs within an inflammatory environment. Reparative dentinogenesis is closely linked to intense inflammation, which triggers the recruitment and differentiation of dental pulp stem cells (DPSCs) into the dentin lineage. Understanding how inflammatory responses influence DPSCs is essential for elucidating the mechanisms underlying dentin and pulp regeneration. Given the limited data on this process, a broad approach is employed here to gain a deeper understanding of the complex mechanisms involved and to identify downstream signaling targets. This study aims to investigate the role of inflammation and the complement receptor C5L2 in the odontoblastic differentiation of DPSCs and the associated transcriptomic changes using poly-A RNA sequencing (RNA-seq). RNA-seq techniques provide insight into the transcriptome of a cell, offering higher coverage and greater resolution of its dynamic nature. Following inflammatory stimulation, DPSCs exhibit significantly altered gene profiles, including marked upregulation of key odontogenic genes, highlighting the critical role of inflammation in dentinogenesis. We demonstrate that TNF-treated odontoblast-like differentiating DPSCs, under C5L2 modulation, exhibit significant differential gene expression and transcriptomic changes. The data presented may provide new avenues for experimental approaches to uncover pathways in dentinogenesis by identifying specific transcription factors and gene profiles.

bioinformatics↗

bioRxiv2024

CRISPR-Edited DPSCs, Constitutively Expressing BDNF Enhance Dentin Regeneration in Injured Teeth

Dental caries, a prevalent global health issue, results from complex bacterial interactions. In response to harmful stimuli, a desirable outcome for the tooth is the formation of tertiary dentin, a protective reparative process that generates new hard tissue. This reparative dentinogenesis is associated with significant inflammation, which triggers the recruitment and differentiation of dental pulp stem cells (DPSCs). Previously, we have demonstrated that brain-derived neurotrophic factor (BDNF) and its receptor TrkB, key mediators of neural functions, are activated during the DPSC-mediated dentin regeneration process. In this study, we further define the role of inflammation in this process and apply stem cell engineering to enhance dentin regeneration in injured teeth. Our data show that TrkB expression and activation in DPSCs rapidly increase during odontogenic differentiation, further amplified by inflammatory inducers and mediators such as TNF, LTA, and LPS. An in vivo dentin formation assessment was conducted using a mouse pulp-capping/caries model, where CRISPR-engineered DPSCs overexpressing BDNF were transplanted into inflamed pulp tissue. This transplantation significantly enhanced dentin regeneration in injured teeth. To further explore potential downstream pathways, we conducted transcriptomic profiling of TNF-treated DPSCs, both with and without TrkB antagonist CTX-B. The results revealed significant changes in gene expression related to immune response, cytokine signaling, and extracellular matrix interactions. Taken together, our study advances our understanding of the role of BDNF in dental tissue engineering using DPSCs and identifies potential therapeutic avenues for improving dental tissue repair and regeneration strategies.

bioengineering↗

bioRxiv2024

Cerebellar white matter development is regulated by fractalkine-dependent microglia phagocytosis of oligodendrocyte progenitor cells

Complex neurodevelopmental disorders involve motor as well as cognitive dysfunction and these impairments are associated with both cerebral and cerebellar maturity. A network of connections between these two brain regions is proposed to underlie neurodevelopmental impairments. The cerebellar gray matter has a protracted developmental timeline compared to the cerebral cortex, however, making the association of these relay pathways unclear for neurodevelopmental disabilities. We show that a population of amoeboid microglia infiltrate the cerebellar white matter through the fourth ventricular zone during early postnatal development. This infiltration is synchronized with the emergence of amoeboid microglia in the ventricular zone of the lateral ventricles and appearance in cerebral white matter. Amoeboid microglia phagocytosed oligodendrocyte progenitor cells (OPCs) in the cerebellar white matter during a restricted early postnatal time window before transitioning to a ramified morphology. Modulating fractalkine receptor signaling, shown to be involved in microglial pruning of synapses, significantly reduced microglial engulfment of OPCs resulting in increased numbers of OLs and altered myelin formation. Variants in the fractalkine receptor are associated with neurodevelopmental disorders including schizophrenia and autism where myelin perturbations have been documented. Overall, these data support that white matter refinement by amoeboid microglia is coordinated in both cerebral and cerebellar development with important implications for altered circuit function in neurodevelopmental disabilities. One sentence summaryMicroglia engulf oligodendrocyte progenitors in the developing cerebellum

neuroscience↗

bioRxiv2024

Time-resolved tracking of cellulose biosynthesis and microfibril network assembly during cell wall regeneration in live Arabidopsis protoplasts

Significance StatementCellulose is a major extracellular matrix component of cells that is critical for plant development and has applications to bioenergy, agricultural food/feed, textile, and wood production. Cellulose is thought to be assembled by the closely coordinated motion of plasma membrane-embedded cellulose synthase enzyme complexes. To date, however, it has not been possible to visualize de novo plant cell wall synthesis at the single cell level with the necessary spatiotemporal resolution to derive a data-driven model of how plant cells can resynthesize and assemble cell wall after its removal. Based on our time-resolved data, we propose a new model for cellulose biosynthesis after successfully performing live protoplast time-lapse imaging to visualize for the first time the complex dynamics of de novo cellulose biosynthesis and assembly into an intertwined microfibril network. Plant cell walls are composed of polysaccharides among which cellulose is the most abundant component. Cellulose is processively synthesized as bundles of linear {beta}-1,4-glucan homopolymer chains via the coordinated action of multiple enzymes in cellulose synthase complexes (CSCs) embedded within the plasma cell membrane. Plant cell walls are composed of multiple layers of cellulose fibrils that form highly intertwined extracellular matrix networks. However, it is not yet clear as to how cellulose fibrils synthesized by multiple CSCs are assembled into the intricate cellulose network deposited on plant cell surfaces. Herein, we have established an in vivo time-resolved imaging platform for visualizing cellulose during its biosynthesis and assembly into a complex fibrillar network on the surface of Arabidopsis thaliana mesophyll protoplasts as the primary cell wall regenerates. We performed total internal reflection fluorescence microscopy (TIRFM) with fluorophore-conjugated tandem carbohydrate binding modules (tdCBMs) that were engineered to specifically bind to nascent cellulose fibrils. Together with a well-controlled environment, it was possible to monitor in vivo cellulose fibril synthesis dynamics in a time-resolved manner for nearly one day of continuous cell wall regeneration on protoplast cell surfaces. Our observations provide the basis for a novel model of cellulose fibril network development in protoplasts driven by complex interplay of multi-scale dynamics that include: rapid diffusion and coalescence of short nascently synthesized cellulose fibrils; processive elongation of single fibrils; and cellulose fibrillar network rearrangement during cell wall maturation. This platform is valuable for exploring mechanistic aspects of cell wall synthesis while visualizing cellulose microfibrils assembly.

plant biology↗

bioRxiv2024

Relaxed selection and horizontal gene transfer fuel underwater adaptation in a water spider

Spiders have primarily adapted to terrestrial life, yet a number of species have made evolutionary transitions to marine and freshwater environments. While its physiological and behavioral adaptations have been characterized, the genetic basis of semi-aquatic and aquatic adaptation in spiders remains poorly understood. Here, we provide a high-quality, chromosome-level genome assembly for the aquatic spider Argyroneta aquatica, alongside a reference transcriptome for the semi-aquatic spider Desis martensi. We performed comparative genomes analyses of 22 spider species, including a unique aquatic spider, two semi-aquatic spiders and 19 terrestrial spider species, with a focus on those in the marronoid clade. By integrating morphological, phylogenomic, comparative genomic, transcriptomic, and metabolomic analyses, we explored the genomic adaptations of aquatic and semi-aquatic spiders. Phylogenomic analysis suggests that aquatic and semi-aquatic spiders have independently evolved from their terrestrial ancestors and represent divergent evolutionary routes We found hundreds of genes tend to experience relaxed selection, positive selection, and evidence of horizontal gene transfer (HGT) associated with the transition to aquatic and semi-aquatic life in spiders. These genes are associated with respiratory, osmoregulatory, fat metabolism and digestion, hypoxia, and thermal functions, putatively facilitate the adaptations to diverse underwater life. Altogether, our findings highlight the divergent evolutionary mechanisms enabling spiders to thrive in diverse aquatic environments, providing insights into the genomic basis of adaptations to semi-aquatic and aquatic habitats.

genomics↗

bioRxiv2023

Nanopore sequencing of antibiotic-resistant Klebsiella pneumoniae JRCGR1 isolate from Pakistan and country scale pan-genomics

Klebsiella pneumoniae is a gram-negative, encapsulated, non-motile bacterium that can cause damage to human lungs. Antibiotic resistance of this strain requires constant monitoring and for this purpose, Oxford nanopore mediated whole genome sequencing was done for a strain acquired from the pleural fluid of a diabetic patient suffering from chronic kidney disease. A genome of 5.98 MB was obtained, with 8,869 CDSs and 110 RNAs. Around 96 proteins were seen as involved in virulence, disease or defense, while 25 antibiotic resistance genes were identified. Pan-genome was inferred as open, with 12,857 and 1,303 CDSs forming respective accessory and core genome of antibiotic resistant Pakistani strains (n=168) of this species. Apart from notable antimicrobial resistance genes like beta-lactamases, a gene conferring resistance to colistin was also mined. To the best of our knowledge, this is first report of nanopore mediated long read sequencing of a hypermucoviscous virulent K. pneumoniae from Pakistan.

genomics↗

bioRxiv2023

Engineering and characterization of carbohydrate-binding modules to enable real-time imaging of cellulose fibrils biosynthesis in plant protoplasts

O_LICarbohydrate binding modules (CBMs) are non-catalytic domains associated with cell wall degrading carbohydrate-active enzymes (CAZymes) that are often present in nature tethered to distinct catalytic domains (CD). Fluorescently labeled CBMs have been also used to visualize the presence of specific polysaccharides present in the cell wall of plant cells and tissues. C_LIO_LIPrevious studies have provided a qualitative analysis of CBM-polysaccharide interactions, with limited characterization of optimal CBM designs for recognizing specific plant cell wall glycans. Furthermore, CBMs also have not been used to study cell wall regeneration in plant protoplasts. C_LIO_LIHere, we examine the dynamic interactions of engineered type-A CBMs (from families 3a and 64) with crystalline cellulose-I and phosphoric acid swollen cellulose (PASC). We generated tandem CBM designs to determine their binding parameters and reversibility towards cellulose-I using equilibrium binding assays. Kinetic parameters - adsorption (kon) and desorption (koff) rate constants-for CBMs towards nanocrystalline cellulose were determined using quartz crystal microbalance with dissipation (QCM-D). Our results indicate that tandem CBM3a exhibits a five-fold increased adsorption rate to cellulose compared to single CBM3a, making tandem CBM3a suitable for live-cell imaging applications. We next used engineered CBMs to visualize Arabidopsis thaliana protoplasts with regenerated cell walls using wide-field fluorescence and confocal laser scanning microscopy (CLSM). C_LIO_LIIn summary, tandem CBMs offer a novel polysaccharide labeling probe for real-time visualization of growing cellulose chains in living Arabidopsis protoplasts. C_LI

plant biology↗

bioRxiv2021

Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic

Surveillance of genetic diversity in the SARS-CoV-2 is extremely important to detect the emergence of more infectious and deadly strains of the virus. In this study, we monitored mutational events in the SARS-CoV-2 genome through whole genome sequencing. The samples (n=48) were collected from the hot spot regions of the metropolitan city Karachi, Pakistan during the four months (May 2020 to August 2020) of first wave of the COVID-19 pandemic. The data analysis highlighted 122 mutations, including 120 single nucleotide variations (SNV), and 2 deletions. Among the 122 mutations, there were 71 singletons, and 51 recurrent mutations. A total of 16 mutations, including 5 nonsynonymous mutations, were detected in spike protein. Notably, the spike protein missense mutation D614G was observed in 31 genomes. The phylogenetic analysis revealed majority of the genomes (36) classified as B lineage, where 2 genomes were from B.6 lineage, 5 genomes from B.1 ancestral lineage and remaining from B.1 sub-lineages. It was noteworthy that three clusters of B.1 sub-lineages were observed, including B.1.36 lineage (10 genomes), B.1.160 lineage (11 genomes), and B.1.255 lineage (5 genomes), which represent independent events of SARS-CoV-2 transmission within the city. The sub-lineage B.1.36 had higher representation from the Asian countries and the UK, B.1.160 correspond to the European countries with highest representation from the UK, Denmark, and lesser representation from India, Saudi Arabia, France and Switzerland, and the third sub-lineage (B.1.255) correspond to the USA. Collectively, our study provides meaningful insight into the evolution of SARS-CoV-2 lineages in spatio-temporal local transmission during the first wave of the pandemic.

genomics↗

bioRxiv2019

Developmental time course of SNAP-25 isoform regulation of hippocampal long-term synaptic plasticity and hippocampus-dependent learning

SNAP-25 is essential in activity-dependent vesicle fusion and neurotransmitter release in the nervous system. During development and adulthood, SNAP-25 appears to have differential influences on long- and short-term synaptic plasticity in the hippocampus. The involvement of SNAP-25 in this process may be altered by two different splice variants expressed in adolescences versus adulthood in hippocampal neurons. This study suggests that the adolescent isoform, SNAP-25a can contribute to developmental regulation of the expression of LTD and LTP. In mice deficient in SNAP-25b, the adult isoform, Schaffer collateral-CA1 synapses showed slower release kinetics, reduced initial release probabilities, decreased LTP and enhanced LTD at 1 month. By 4 months of age, when mice have fully developed in the absence of SNAP-25b, the gene targeted mice appear to have compensated for the lack of the adult SNAP-25b isoform. Moreover, hippocampal-dependent training reversed reductions in LTP, but not LTD, seen at 1 month. In 4 month old adult mice, training prevented the compensatory reversal of LTD that had been observed prior to training. These findings support the hypothesis that immature SNAP-25a plays a strong role in the expression of plasticity at Schaffer collateral-CA1 synapses in adolescent mice, but compensatory mechanisms that reverse alterations in synaptic plasticity once mice reach adulthood.

neuroscience↗