Biology subjects

Ali, I.

Publications and source records attributed to Ali, I..

16 recordsLinked to original sources

bioRxiv2026

Spatial transcriptomics reveals epithelial-immune remodeling preceding malignant transformation of oral premalignant lesions

Oral premalignant lesions (OPLs) are common; however, histopathological grading incompletely identifies lesions destined for cancer. To define tissue ecosystems that precede malignant transformation, we integrated single-cell-resolution Xenium spatial transcriptomics of 20 HPV-negative biospecimens from 16 patients, with independent single-cell RNA sequencing and immunofluorescence data from 38 patients with OPLs after quality control. Progressive OPLs exhibit a coordinated epithelial-immune program comprising MX1/NOTCH3-high KRT14+/KRT15+ basal epithelial states, S100A9-high inflammatory macrophages, TIGIT-high, exhaustion-associated T cells, and altered dendritic cell states. Spatial analyses showed that T cells and dendritic cells were displaced from the basal epithelial interface, and that epithelial neighborhoods were depleted of dendritic cells but enriched for TIGIT-high T cells, revealing immune reorganization not captured by cellular abundance alone. Independent single-cell and protein-level analyses reproduced basal epithelial interferon/stress programs, S100A9-associated myeloid inflammation, TIGIT-high, exhaustion-associated T-cell programs, and dendritic cell redistribution. Ligand-receptor inference suggested convergent myeloid and lymphoid signals linked to epithelial stress, checkpoint regulation, and extracellular matrix remodeling. Functionally, recombinant S100A9 accelerated wound closure in oral epithelial and cancer cells, whereas S100A9 and S100A8/S100A9 enhanced oral cancer cell proliferation. These responses were attenuated by pharmacologic inhibition of TLR4 or RAGE. Together, these data define a spatially organized, myeloid-skewed, checkpoint-enriched ecosystem present before invasion and suggest S100A9-TLR4/RAGE signaling and epithelial-immune geometry as candidate mechanisms and biomarkers for oral cancer interception.

immunology↗

bioRxiv2026

Regulatory plasticity of the rdar biofilm morphotype in clinical uropathogenic Escherichia coli and its modulation by ciprofloxacin

Red, dry and rough (rdar) biofilm formation in Escherichia coli is characterized by the coordinated production of extracellular cellulose and amyloid curli fimbriae. Although rdar biofilm formation has been extensively characterized in laboratory strains, its clinical relevance and implications for antimicrobial treatment remain poorly understood. Here, we systematically investigate rdar biofilm formation of 150 consecutively isolated E. coli strains recovered from patients with urinary tract infections and correlate it to antimicrobial resistance. Genetic analysis of rdar regulation revealed distinct nucleotide signatures within the csgD promoter region that discriminate semi-constitutive rdar expression from temperature-dependent phenotypes, highlighting regulatory plasticity among clinical isolates. Whole-genome sequencing-based phylogenetic analysis further demonstrated that rdar-positive isolates are distributed across diverse E. coli phylogroups and sequence types, indicating that rdar biofilm formation is not restricted to specific clonal lineages. Strikingly, phenotypic assays revealed that the fluoroquinolone antibiotic ciprofloxacin suppresses rdar biofilm formation and associated extracellular matrix architecture in ciprofloxacin-resistant isolates at subinhibitory concentrations, suggesting that ciprofloxacin modulates biofilm-associated pathways beyond its canonical bactericidal targets. Together, our findings establish the rdar morphotype as a clinically relevant biofilm phenotype in uropathogenic E. coli and reveal an antibiofilm activity of ciprofloxacin that is uncoupled from antibiotic resistance. These results underscore the importance of considering antibiotic-mediated modulation of biofilm behavior when interpreting treatment responses and designing strategies to combat persistent urinary tract infections.

microbiology↗

bioRxiv2026

If the shoe fits? -- technical nuances of plasma proteomic workflows in clinical and preclinical contexts

The push for new clinical biomarkers has seen rapid innovation in biofluid analysis, particularly for plasma. For mass-spectrometry (MS)-based analysis, achieving depth and quantitative accuracy whilst ensuring throughput continues to shape plasma methods development. Numerous workflows have emerged that mitigate high-abundance suppression and expand dynamic range, especially when paired with next-generation MS instrumentation. Yet systematic evaluations that also consider biological variables (e.g., biofluid type, species) and technical parameters (e.g., MS methods) are limited. Here, we benchmarked eight sample-preparation workflows spanning neat approaches (SP3, STrap), depletion (perchloric acid, PerCA), and corona-enrichment strategies (MagNet HILIC/SAX, Enrich-iST, ProteoNano). We compared their performance across human plasma, human serum, and rat plasma, analysing all samples on an Orbitrap Astral (Thermo) using two plasma-optimised data-independent acquisition (DIA) methods: one discovery-maximised and one throughput-maximised. We identified 2,726 human and 3,767 rat proteins across workflows and methods, including [~]1,000 from neat plasma. Increasing throughput incurred a [~]20-30% reduction in depth, depending on workflow and species. EV-enrichment produced the deepest proteomes but with distinct compositions relative to neat, depleted, and secreted-protein-enriched samples, revealing a unique sub-proteome niche. Several workflows also performed markedly better in rat plasma, supporting improved sensitivity for preclinical analyses. Enrichment or depletion dramatically reshaped the balance of tissue-and cell-specific proteins detectable in plasma, suggesting that workflow choice should be guided by the organs, immune targets, or inflammatory signals most relevant to the study. In this vein, statistical analysis of differentially abundant proteins showed that >90% of detected proteins were significantly altered between workflows, with the largest numbers arising from the corona-enrichment strategies, underscoring how strongly workflow choice shapes the downstream proteome. Taken together, these findings emphasise a rapidly expanding plasma methodological landscape, where the most effective workflow is the one most precisely tailored to a cohorts biology.

systems biology↗

bioRxiv2026

The essential function of the apical polar ring during the blood stage of Plasmodium falciparum

The apical polar ring (APR) is a defining cytoskeletal structure in apicomplexan parasites, critical for parasite morphology and host cell invasion. However, its molecular composition and function remain elusive in Plasmodium falciparum. Here, we identify and characterize PfAPR1 as an APR-resident protein. Conditional knockout of PfAPR1 reveals its essential role in asexual replication. Using iterative ultrastructure expansion microscopy (iU-ExM), we show that PfAPR1 predominantly localizes to the basal APR ring. Loss of PfAPR1 causes defects in daughter cell segmentation and subpellicular microtubules organization, while IMC formation and apical polarity are largely preserved. PfAPR1-KO parasites contact host red blood cells but fail to form a tight junction, resulting in a complete block in invasion. Using PfAPR1 as molecular bait, we identify additional APR proteins and delineate APR biogenesis with U-ExM. These findings define the molecular architecture and function of the APR in P. falciparum, highlighting it as a promising antimalarial target.

microbiology↗

bioRxiv2025

Sexual dimorphism in the complete connectome of the Drosophila male central nervous system

Sex differences in behaviour exist across all animals, typically under strong genetic regulation. In Drosophila, fruitless/doublesex transcription factors can identify dimorphic neurons but their organisation into functional circuits remains unclear. We present the connectome of the entire Drosophila male central nervous system. This contains 166,691 neurons spanning the brain and nerve cord, fully proofread and annotated including fruitless/doublesex expression and 11,691 types. We provide the first comprehensive comparison between male and female brain connectomes to synaptic resolution, finding 7,205 isomorphic, 114 dimorphic, 262 male-specific and 69 female-specific types. This resource enables analysis of full sensory-to-motor circuits underlying complex behaviours and the impact of dimorphic elements. Sex-specific/dimorphic neurons are concentrated in higher brain centres while the sensory and motor periphery are largely isomorphic. Within higher centres, male-specific connections are organised into hotspots defined by male-specific neurons or arbours. Numerous circuit switches reroute sensory information to form antagonistic circuits controlling opposing behaviours.

neuroscience↗

bioRxiv2025

Depletion of a neural cell adhesion molecule disrupts both epithelial and germ layer identity in sea anemone embryos

Assembly of cells into epithelial layers marks the early steps of tissue organization and embryonic development in most animals. Although several conserved proteins are known to be essential for epithelialization in bilaterians, it is unclear whether these are sufficient to drive epithelial organization in all metazoans. Using proteomics and knockdown approaches in embryos of the early-branching sea anemone Nematostella vectensis, we identified the neural cell adhesion molecule NCAM2 to be essential for organization of the primary epithelial layer. NCAM2 belongs to the immunoglobulin family of cell adhesion molecules with roles in inter-cellular adhesion and signaling. In this work, we show that NCAM2 is enriched at the apical cell junctions and is required for Nematostella epithelial cell identity. Importantly, embryos depleted for NCAM2 fail to gastrulate. Both whole-embryo germ layer patterning and tissue changes required for gastrulation are impaired. Together, our data show that in Nematostella NCAM2 is required for both epithelial and germ layer organization.

developmental biology↗

bioRxiv2025

Cell cycle dysregulation contributes to neurodegeneration in humanneurons from ALS/FTD-related C9orf72 repeat expansion carriers.

The C9orf72 hexanucleotide repeat expansion GGGGCC (G4C2) cause the most common genetic forms of ALS and frontotemporal dementia, affecting thousands of patients worldwide with uniformly fatal outcomes. C9orf72 ALS/FTD patients lack targeted treatments because druggable molecular vulnerabilities remain unidentified. Using iPSC-derived motor neurons from C9orf72 carriers and age-matched controls, we performed comprehensive cell cycle analysis, drug screening, and single-nucleus RNA sequencing validation in human brain tissue. C9orf72 neurons exhibit age-dependent cell cycle reentry with increased S-phase cells, elevated cyclin and CDK expression, and aberrant cell cycle gene signatures confirmed in patient brain excitatory neurons. Mechanistically, arginine-containing dipeptide repeat proteins (poly-GR, poly-PR) drive this cell cycle activation through CDK4/6 pathway stimulation, while C9orf72 loss-of-function alone shows no effect. Critically, the FDA-approved CDK4/6 inhibitor palbociclib normalizes cell cycle progression, reduces S-phase entry, and rescues neuronal survival with significant reduction in motor neuron death. Single-nucleus RNA-sequencing analyses from C9orf72 patient cortex reveals cell cycle-activated neuronal subclusters. Copy number variation, gene ontology and pathways analyses revealed alterations in DNA repair pathways, cell cycle regulation and cell cycle transition, validating our in vitro findings. These results identify cell cycle dysregulation as a therapeutic target in C9orf72 ALS/FTD with clinical translation potential using existing therapeutics.

neuroscience↗

bioRxiv2024

Phytochemicals from Daucus carota have therapeutic potential against Triple-Negative Breast Cancer PDK1 and PLK1.

Triple-negative breast cancer (TNBC) is a deadly form of breast cancer that lacks estrogen, progesterone, and HER2 receptors. The development of drugs for TNBC has been challenging due to the lack of specific therapeutic targets. However, recent studies have shown that targeting the ATP active of the PDK-1 and PLK-1 proteins could be potential drug targets for TNBC treatment. New medications for TNBC have considerable adverse effects, highlighting the need for more targeted and effective therapies. In this study, we employed various computational approaches, including molecular docking, molecular dynamics (MD) simulations, pharmacokinetic studies, binding free energy calculations, principal component analysis (PCA), and alanine scanning analysis, to identify bioactive compounds from Daucus carota-extracted natural compounds that can bind to these ATP-binding sites and inhibit the activity of PDK1 and PLK1. Our study revealed that eight compounds showed reasonably good docking scores, binding free energies, and ADMET properties against the PDK1 and PLK1 enzymes. Astragalin and scolimoside showed substantial binding affinity and persistent interactions in the pocket region of the two proteins. Further MD simulation studies for 150 ns also suggested that the compounds were stably bound in the active site with very minor fluctuations. We believe that the identified hits for PDK1 and PLK1 from Daucus carota will be effective against TNBC in performing the biological assays.

bioinformatics↗

bioRxiv2023

Optimized Mass Spectrometry Detection of Thyroid Hormones and Polar Metabolites in Rodent Cerebrospinal Fluid

BackgroundThyroid hormones (TH) are required for brain development and function. Cerebrospinal fluid (CSF), which bathes the brain and spinal cord, contains TH as free or transthyretin (TTR)-bound. Tight thyroid hormone level regulation in the central nervous system is essential for developmental gene expression that governs neurogenesis, myelination, and synaptogenesis. This integrated function of TH highlights the importance of developing precise and reliable methods for assessing TH levels in CSF. Methods: we report an optimized LC-MS based method to measure thyroid hormones in rodent CSF and serum, applicable to both fresh and frozen samples. Results: We find distinct differences in CSF thyroid hormone in pregnant dams vs. non-pregnant adults and in embryonic vs. adult CSF. Further, targeted LC-MS metabolic profiling uncovers distinct central carbon metabolism in the CSF of these populations. Conclusions: TH detection and metabolite profiling of related metabolic pathways open new avenues of rigorous research into CSF thyroid hormone and will inform future studies on metabolic alterations in CSF during normal development.

neuroscience↗

bioRxiv2023

In situ architecture of Opa1-dependent mitochondrial cristae remodeling

Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). The mechanisms for how Opa1 influences cristae shape have remained unclear due to lack of native three-dimensional views of cristae. We perform in situ cryo-electron tomography of cryo-focused ion beam milled mouse embryonic fibroblasts with defined Opa1 states to understand how each form of Opa1 influences cristae architecture. In our tomograms, we observe a variety of cristae shapes with distinct trends dependent on s-Opa1:l-Opa1 balance. Increased l-Opa1 levels promote cristae stacking and elongated mitochondria while increased s-Opa1 levels correlated with irregular cristae packing and round mitochondria shape. Functional assays indicate a role for l-Opa1 in wild-type apoptotic and calcium handling responses, and compromised respiratory function under Opa1 imbalance. In summary, we provide three-dimensional visualization of cristae architecture to reveal relationships between mitochondrial ultrastructure and cellular function dependent on Opa1-mediated membrane remodeling. HighlightsO_LIIn situ ultrastructural characterization of mitochondrial cristae with different forms of Opa1. C_LIO_LIMitochondria with predominantly l-Opa1 show crista stacking, longer cristae, reduced globular cristae and an absence of tubular cristae. C_LIO_LIMitochondria with mostly s-Opa1 showed irregular cristae packing with wider cristae junctions and narrower cristae. C_LIO_LIl-Opa1 expressing cells with WT-like cristae junction properties, show wild-type apoptotic response and calcium handling. C_LIO_LIImbalance in Opa1 processing show compromised respiratory function and an increase in amorphous cristae. C_LI

biophysics↗

bioRxiv2022

MAM-STAT3-induced upregulation of mitochondrial Ca+2 causes immunosenescence in patients with type A mandibuloacral dysplasia

Homozygous lamina/c p.R527C mutations result in severe mandibuloacral dysplasia (MAD) and progeroid syndrome, but the underlying molecular pathology remains unknown. Here, we report on three patients with MAD, all displaying severe systemic inflammaging and characterized the major molecular pathways involved in the manifestation of this disease. Analysis of induced pluripotent stem cell (IPSC)-derived mesenchymal stem cells (MAD-iMSCs) obtained from the patients revealed that increased mitochondrial Ca+2 loading was the root cause of lost mitochondrial membrane potential, abnormal fission/fusion and fragmentation, which then participated in inflammaging by inducing the inflammasome. These alterations in Ca+2 homeostasis were mediated by signal transducer and activator of transcription 3 (STAT3), which is located on the mitochondrial associated membrane (MAM). STAT3 function could be rescued by treatment with clinically-approved IL-6 blockers, or by correction of R527C mutations. In addition, extracellular vesicles (EVs) obtained from MAD-iMSCs displayed reduced immunomodulatory function, being unable to rescue bleomycin-induced lung fibrosis and triggering mitochondrial dysfunction, senescence, and fibrosis in healthy cells. Our results provide new insights into the pathology of complex lamin-associated MAD with systemic immunosenescence, and suggest that targeting defective mitochondrial Ca+2 homeostasis may represent a promising novel therapy for this condition.

cell biology↗

bioRxiv2022

Biodiversity effects on seedling biomass growth are modulated by light environment across functional groups

O_LITree biodiversity has the potential to ensure consistency in the functioning of forest ecosystems, not just over space, but over long-timescales by maintaining composition through recruitment. However, for continued buffering in the face of global environmental change, the sensitivity of biodiversity-ecosystem functioning relationships to heterogeneous environments needs to be understood. C_LIO_LISeedling recruitment in carbon-rich tropical forests is a result of biotic and abiotic drivers but their combined outcomes at the community-level remain poorly understood. Although biodiversity in seedling communities can potentially increase their growth and biomass accumulation, abiotic drivers like light can alter this effect through divergent effects on constituent species and functional groups. In forests with high baseline heterogeneity in microclimates, these processes can enhance or constrain regeneration. C_LIO_LIWe tested the effects and interactions between species richness and canopy cover on the growth of seedling communities consisting of tropical broad-leaved evergreen and deciduous forest species using a fully crossed manipulated experiment in the Andaman Islands, India and compared these with field observations from a long-term forest plot in the same landscape. C_LIO_LIWe show that in the critical seedling establishment phase, species richness and light increase community biomass independently. Accounting for variation across species, individual species on average accumulated more biomass in communities with both higher light and higher diversity. C_LIO_LIWe also show that overyielding in species rich communities fits expectations from a model of complementarity with non-random overyielding than selection or spatial insurance effects. C_LIO_LISynthesis Taken together, our results show that the potential for biodiversity to increase ecosystem functioning in seedling communities is modulated by light. Further understanding on the interaction of biodiversity with multiple abiotic drivers and their effect on regeneration dynamics is crucial for predicting future ecosystem functioning. C_LI

ecology↗

bioRxiv2021

A Chimeric Peptide Inhibits Red Blood Cell Invasion by Plasmodium falciparum with Hundredfold Increased Efficacy

Inhibition of tight junction formation between two malaria parasite proteins, apical membrane antigen 1 and rhoptry neck protein 2, crucial for red blood cell invasion, prevents the disease progression. In this work, we have utilized a unique approach to design a chimeric peptide, prepared by fusion of the best features of two peptide inhibitors, that has displayed parasite growth inhibition, in-vitro, with nanomolar IC50, which is hundredfold better than any of its parent peptides. Further, to gain structural insights, we computationally modeled the hybrid peptide on its receptor.

biochemistry↗

bioRxiv2020

Ramifications of the diverse mRNA patterns in Acanthamoeba royreba

Free-living amoebae are distributed worldwide and can be found in a variety of environments. While most Acanthamoebae have been isolated from soil and water, A. royreba and A. culbertsoni were isolated from mammalian cell cultures. A. royrebas isolation from placental and tumoral tissue, its unusual ability to grow in mammalian cell culture media at 35{degrees}C, and the presence of a primitive centriole, prompted us to investigate the potential for mammalian information in A. royreba. While some soil amoeba contain small amounts of fungal and bacterial information, presumably from the microbes they phagocytosed, the informational content of A. royreba, in some instances, was very different with > 70% of the mRNA being non-amoebic. Here we show that the proteins and mRNA content associated with A. royreba are extremely diverse and represent multiple Kingdoms, Orders, Phyla, and Genera from around the globe. The information in A. royreba, such as placental proteins from numerous mammals, the preponderance of non-amoebic mRNA, and its ability to tolerate harsh environments including Megarad irradiation, leads to a discussion regarding the possible role of this amoebae as an immunological gatekeeper protecting fetal or malignant tissue from destruction and its potential as a vehicle for panspermia.

cell biology↗

bioRxiv2019

Individual and concurrent effects of drought and chilling stresses on morpho-physiological characteristics and oxidative metabolism of maize cultivars

Maize belongs to tropical environment and is extremely sensitive to drought and chilling stress, particularly at early developmental stages. The present study investigated the individual and combine effects of drought (15% PEG-Solution) and chilling stress (15{degrees}C/12{degrees}C) on the morpho-physiological growth, osmolyte accumulation, production and regulations of reactive oxygen species (ROS) and the activities of antioxidants in two maize hybrids i.e., XD889 and XD319 and two inbred cultivars i.e., Yu13 and Yu37. Individual and combined drought and chilling stresses stimulated the production of O2{square}, H2O2, OH{square} and enhanced malondialdehyde (MDA) contents which led to reduced photosynthetic pigments and morphological growth. Drought, chilling and drought + chilling stress conditions induced the compatible osmolytes, ROS detoxifying proteins and antioxidants to counterbalanced the oxidative damage. It was found that the concurrent occurrence of drought + chilling stress was more lethal for maize seedling growth than the drought and chilling individual stresses. However, the performance of hybrid maize cultivars (XD889 and XD319) was better than the inbred maize cultivars (Yu13 and Yu37). For improving tolerance to individual and concurrent drought and chilling stress in maize, future research focus should be on developing genetically engineer plants that have the ability to generate specific response against sub-optimal temperature and water deficit conditions.

plant biology↗

bioRxiv2018

Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins

Post-translational modifications of the RNA polymerase II C-terminal domain (CTD) coordinate the transcription cycle. Crosstalk between different modifications is poorly understood. Here, we show how acetylation of lysine residues at position 7 of characteristic heptad repeats (K7ac)--only found in higher eukaryotes--regulates phosphorylation of serines at position 5 (S5p), a conserved mark of polymerases initiating transcription. We identified the regulator of pre-mRNA domain-containing (RPRD) proteins as reader proteins of K7ac. K7ac enhanced CTD peptide binding to the CTD-interacting domain (CID) of RPRD1A and RPRD1B proteins in isothermal calorimetry and molecular modeling experiments. Deacetylase inhibitors increased K7ac- and decreased S5-phosphorylated polymerases, consistent with acetylation-dependent S5 dephosphorylation by an RPRD-associated S5 phosphatase. Consistent with this model, RPRD1B knockdown increased S5p, but enhanced K7ac, indicating RPRD proteins recruit K7 deacetylases, including HDAC1. We also report auto-regulatory crosstalk between K7ac and S5p via RPRD proteins and their interactions with acetyl- and phospho-eraser proteins.

molecular biology↗