Biology subjects

Zaidi, A.

Publications and source records attributed to Zaidi, A..

11 recordsLinked to original sources

bioRxiv2026

Iron as a critical determinant for survival, oxidative stress, and infectivity of Leishmania parasites

Iron is an essential for all living organisms, including humans, and is present in RBCs & other iron-binding proteins that play crucial roles in oxygen transport, DNA synthesis & electron transport. Similarly, iron also plays a critical role in parasite biology. The unicellular Leishmania parasites scavenge essential iron inside host macrophages. We investigated the impact of iron on parasite growth, apoptosis, oxidative stress, and the expression of proteins involved in ROS, thiol metabolism, Fe-S clusters, and infectivity in macrophages. Our findings revealed that optimum iron concentrations promote parasite proliferation, whereas higher levels induce toxicity, leading to DNA fragmentation and caspase-like activity. Iron supplementation enhances parasite tolerance to oxidative stress by decreasing intracellular ROS and increasing total intracellular thiol content in a concentration-dependent manner. However, iron depletion increases ROS levels and decreases total thiol content in a concentration-dependent manner, which disrupts redox homeostasis. To support our finding, we further exposed these treated parasites to menadione, which supports that iron-supplemented cells can better survive under oxidative stress than the depleted cells. Furthermore, extra iron availability increases the expression of key metabolic proteins, Fe-S clusters (Nbp35, Frataxin, IScU) and thiol metabolism (TryS, TryR, CS, SAT, cTXN, cTXNPx), while under iron-depleted conditions these proteins were downregulated except frataxin. In vitro infectivity demonstrated that iron supplementation enhances parasite infectivity, while iron depletion impairs percentage infectivity. Our study demonstrates the roles of iron in the survival, redox regulation, and virulence of L. donovani, which can correlate with the role of cellular iron homeostasis in VL pathogenesis.

microbiology↗

bioRxiv2025

Organoid Pharmacotyping of Pancreatic Cancer Enables Functional Precision Oncology and Drug Repurposing

PurposePancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with limited benefit from current cytotoxic regimens and poor predictive value of genomics alone. Patient-derived organoids (PDOs) represent a promising platform for functional precision oncology, yet systematic pharmacotyping of genomically annotated PDAC PDOs remains sparse. Experimental DesignWe established a clinically annotated panel of ten treatment-naive PDAC PDOs spanning well-, moderately-, and poorly differentiated tumors. PDOs were evaluated for morphologic and genomic fidelity and screened against 1,813 clinically relevant small molecules in a high-throughput 384-well format. Drug sensitivities were quantified at the compound and drug-family levels and integrated with histologic grade, pathway-level mutational profiles, and available clinical treatment information. ResultsPDOs preserved hallmark tumor features, including glandular organization and subclonal mutational architecture. Pharmacotyping revealed both shared and subtype-specific vulnerabilities. Classical (well/moderately differentiated) PDOs showed enriched mutations in DNA repair, mitotic spindle, and chromatin-regulatory pathways and were preferentially sensitive to topoisomerase inhibitors, microtubule poisons, and HDAC inhibitors. In contrast, basal (poorly differentiated) PDOs displayed coordinated defects in mitochondrial function, vesicle trafficking, and ubiquitin-mediated proteostasis, at the pathway level, that conferred a previously unrecognized vulnerability to cardiac glycosides. Sensitivities to standard PDAC agents were heterogeneous across models, underscoring the limited predictive value of genotype alone and the need for functional drug testing. ConclusionsThis integrated genomic and pharmacologic analysis demonstrates that PDO pharmacotyping identifies biologically grounded, actionable vulnerabilities in PDAC, including novel therapeutic opportunities in basal, chemo-resistant tumors. These findings support PDO-guided functional profiling as a clinically relevant platform for refining drug selection and expanding treatment options for patients with PDAC. SignificancePDAC is dominated by chemoresistance and lacks reliable genomic predictors of therapy response. By integrating high-throughput drug screening with mutation-informed pathway analysis in patient-derived organoids, we identify differentiation-linked therapeutic liabilities, including a previously unrecognized vulnerability to cardiac glycosides in basal PDAC. These results highlight PDO pharmacotyping as a powerful functional complement to genomics for guiding treatment selection in pancreatic cancer.

cancer biology↗

bioRxiv2025

Gangliosides Modulate the Secretion of Extracellular Vesicles and Their Misfolded Protein Cargo

Gangliosides are glycosphingolipids that play an integral role in cell signaling and provide neuroprotection. While present on extracellular vesicles (EVs) - key mediators of intercellular communication - their role in EV biogenesis remains unclear. Here, we identify gangliosides, both endogenously synthesized and exogenously administered, as key modulators of EV biogenesis, with the specific composition of their glycan headgroup and the presence or absence of sialic acid and N-acetyl-D-galactosamine residues dictating whether they promote or inhibit EV biogenesis. We show that GM1 and other complex gangliosides enhance EV secretion, while disruption of ganglioside synthesis impairs it. GM1 supplementation restores EV secretion in Huntingtons disease (HD) fibroblasts and HD cell models that have lower than normal levels of gangliosides, and in cells with a genetic block of ganglioside synthesis that models rare early-onset neurodegenerative diseases. Notably, GM1 also enhances EV-mediated secretion of pathogenic misfolded proteins, including mutant huntingtin (mHTT), -synuclein and tau, reducing intracellular burden and providing mechanistic insight into the mHTT-lowering effects of GM1 treatments in HD models. Our findings shed light on the neuroprotective roles of gangliosides and highlight their potential for therapeutic exploitation in misfolded protein disorders.

cell biology↗

bioRxiv2025

Discovery, characterization, and application of chromosomal integration sites in the hyperthermophilic crenarchaeon Sulfolobus islandicus

Sulfolobus islandicus, an emerging crenarchaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has considerably limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs (crRNAs) targeting eight chromosomal integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. By leveraging the endogenous CRISPR-Cas systems, we integrated the reporter gene lacS into these sites and validated heterologous gene expression through a {beta}-galactosidase reporter assay, which revealed significant positional effects on expression levels. As a proof of concept, we utilized these characterized sites to genetically manipulate lipid ether composition by overexpressing GDGT (glycerol dibiphytanyl glycerol tetraether) ring synthase B (GrsB) in S. islandicus, a key enzyme in GDGT biosynthesis. This study expands the genetic toolbox for S. islandicus and highlights a concept that could be widely applicable to other Sulfolobales, advancing their potential as robust platforms for archaeal synthetic biology and industrial biotechnology.

synthetic biology↗

bioRxiv2024

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

Mitochondria play a key role in energy production and cellular metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we exploited Variational Autoencoder (VAE), an unsupervised deep learning framework, to design novel mitochondrial targeting sequences (MTSs). In silico analysis revealed that a high fraction of generated peptides are functional and possess features important for mitochondrial targeting. Additionally, we devised a sampling scheme to indirectly address biases arising from the differences in mitochondrial protein import machinery and characterized artificial MTSs in four eukaryotic organisms. These sequences displayed significant diversity, sharing less than 60% sequence identity with MTSs in the UniProt database. Moreover, we trained a separate VAE and employed latent space interpolation to design dual targeting sequences capable of targeting both mitochondria and chloroplasts, shedding light on their evolutionary origins. As a proof-of-concept, we demonstrate the application of these artificial MTSs in increasing titers of 3-hydroxypropionic acid through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Overall, our work not only demonstrates the potential of generative artificial intelligence in designing novel, functional mitochondrial targeting sequences but also highlights their utility in engineering mitochondria for both fundamental research and practical applications in biology.

synthetic biology↗

bioRxiv2024

Silver Armor Against Bacteria: A Battle of Antimicrobial Effectiveness

For many farmers, there is a need to improve crop resistance to pathogenic organisms. Floridas climate and hurricane-prone location promotes the spread of many crop pathogens making management difficult and expensive. Therefore, this study evaluates using a Do-It-Yourself, DIY, method to produce colloidal silver solutions that may be used as effective inhibitors of bacteria growth. The efficacy was compared across gram-negative and gram-positive bacteria species. Production of colloidal silver used an electric current from eight 9-volt batteries wired in series. The starting silver was a jewelry chain, approx. 98% silver, suspended in a container of distilled water. Treatment effects were compared to a commercially available silver solution (10K, ppm) as the positive control via the Kirby-Baur method. Each petri dish was divided into four quadrants, into which each had a treated cellulose square impregnated with a treatment solution. Treatments were: T1-10K ppm AgNp; T-2-5ppm AgNp, T3-3ppm AgNp; and positive control T4-blank water control. The dimensions of Zones of Clearance (ZOC) and the bacterial growth surrounding treated squares were analyzed. The experiment was replicated four times. Data analysis conducted using one-way ANOVA with post hoc separation of means using the T test and Tukeys HSD. The positive control solution was the most effective bactericide across all species, followed by Treatment-2 (5-ppm treatment), which caused ZOC in gram-negative species. Treatment-3, the 3ppm, did not significantly affect bacterial suppression, while activity at 5ppm suggests that simple home-based, DIY systems can produce low cost, bactericidal nano-silver solutions. In this experiment the bacterium that tested that is also beneficial to plants, R. rubrum, showed an increased tolerance to all silver treatments. Improving homemade, DIY, systems may provide low-cost treatment solutions against some bacteria species important to backyard agriculturists.

plant biology↗

bioRxiv2024

Microglia/macrophage-specific deletion of TLR-4 protects against neural effects of diet-induced obesity

Obesity is associated with numerous adverse neural effects, including reduced neurogenesis, cognitive impairment, and increased risks for developing Alzheimers disease (AD) and vascular dementia. Obesity is also characterized by chronic, low-grade inflammation that is implicated in mediating negative consequences body-wide. Toll-like receptor 4 (TLR4) signaling from peripheral macrophages is implicated as an essential regulator of the systemic inflammatory effects of obesity. In the brain, obesity drives chronic neuroinflammation that involves microglial activation, however the contributions of microglia-derived TLR4 signaling to the consequences of obesity are poorly understood. To investigate this issue, we first generated mice that carry an inducible, microglia/macrophage-specific deletion of TLR4 that yields long-term TLR4 knockout only in brain indicating microglial specificity. Next, we analyzed the effects of microglial TLR4 deletion on systemic and neural effects of a 16-week of exposure to control versus obesogenic high-fat diets. In male mice, TLR4 deletion generally yielded limited effects on diet-induced systemic metabolic dysfunction but significantly reduced neuroinflammation and impairments in neurogenesis and cognitive performance. In female mice maintained on obesogenic diet, TLR4 deletion partially protected against weight gain, adiposity, and metabolic impairments. Compared to males, females showed milder diet-induced neural consequences, against which TLR4 deletion was protective. Collectively, these findings demonstrate a central role of microglial TLR4 signaling in mediating the neural effects of obesogenic diet and highlight sexual dimorphic responses to both diet and TLR4.

neuroscience↗

bioRxiv2023

Ischaemic Preconditioning attenuates Chronic Renal Damage following Ischaemia Reperfusion Injury

Acute Kidney Injury (AKI) is a common cause of Chronic Kidney Disease (CKD). The leading cause of AKI worldwide is Ischaemia Reperfusion Injury (IRI), seen most commonly in the clinical setting as a result of sepsis-driven hypotension. We are increasingly recognising, however, that AKI and CKD are one closely associated continuum of disease, rather than distinct entities. Ischaemic Preconditioning (IPC) is a strategy aimed at reducing the deleterious effects of IRI. This study demonstrates an efficacious model of kidney IRI, and the protective influence of IPC in attenuating renal injury/fibrosis. A rat model of bilateral kidney IRI was used: Male Lewis rats (n=84) were assigned to IRI, sham or IPC. In IRI, renal pedicles were clamped for 45 minutes. IPC groups underwent pulsatile IPC prior to IRI. Kidneys were retrieved at 24-hours, 48-hours, 7-days, 14-days and 28-days, and assessed histologically. IRI led to marked histological damage and renal fibrosis development by 28 days. Histological injury scores and degree of fibrosis were significantly increased following IRI and attenuated with IPC. IPC resulted in a 66% reduction in renal fibrosis at 28 days (p<0.001). IRI also led to a significant increase in serum creatinine acutely, which was attenuated by IPC (p<0.0001). Interestingly at 14-days, there was limited histological damage and differentiation between IRI and IPC kidneys was difficult. IPC can protect from both acute and chronic kidney damage. 14-days post IRI represents a transitional phase, which maybe a timepoint for commitment to either fibrosis or recovery, and hence offers potential for therapeutic intervention.

pathology↗

bioRxiv2023

Naive Huntington's disease microglia mount a normal response to inflammatory stimuli but display impaired development of innate immune tolerance that can be counteracted by ganglioside GM1

Chronic activation and dysfunction of microglia have been implicated in the pathogenesis and progression of many neurodegenerative disorders, including Huntingtons Disease (HD). HD is a genetic condition caused by a mutation that affects the folding and function of huntingtin (HTT). Signs of microglia activation have been observed in HD patients even before the onset of symptoms. It is unclear, however, whether pro-inflammatory microglia activation in HD results from cell-autonomous expression of mutant HTT or is the response of microglia to a diseased brain environment, or both. In this study, we used primary microglia isolated from HD knock-in mice (Q140) and wild-type (Q7) mice to investigate their response to inflammatory conditions in vitro in the absence of confounding effects arising from brain pathology. We show that naive Q140 microglia do not undergo spontaneous pro-inflammatory activation and respond to inflammatory triggers, including stimulation of TLR4 and TLR2 and exposure to necrotic cells, with similar kinetics of pro-inflammatory gene expression as wild-type microglia. Upon termination of the inflammatory insult, the transcription of pro-inflammatory cytokines is tapered off in Q140 and wild-type microglia with similar kinetics. However, the ability of Q140 microglia to develop tolerance in response to repeated inflammatory stimulations is partially impaired, potentially contributing to the establishment of chronic neuroinflammation in HD. We further show that ganglioside GM1, a glycosphingolipid with anti-inflammatory effects in wild-type microglia, not only decreases the production of pro-inflammatory cytokines and nitric oxide in activated Q140 microglia, but also dramatically dampen microglia response to re-stimulation with LPS in an experimental model of tolerance. These effects are independent from the expression of interleukin 1 receptor associated kinase 3 (Irak-3), a strong modulator of LPS signaling involved in the development of innate immune tolerance and previously shown to be upregulated by immune cell treatment with gangliosides. Altogether, our data suggest that external triggers are required for HD microglia activation, but a cell-autonomous dysfunction that affects the ability of HD microglia to acquire tolerance might contribute to the establishment of neuroinflammation in HD. Administration of GM1 might be beneficial to attenuate chronic microglia activation and neuroinflammation.

neuroscience↗

bioRxiv2022

Sugar sensation and mechanosensation in the egg-laying preference shift of Drosophila suzukii

The agricultural pest Drosophila suzukii differs from most other Drosophila species in that it lays eggs in ripe, rather than overripe, fruit. Previously we showed that changes in bitter taste sensation accompanied this adaptation (Dweck et al., 2021). Here we show that D. suzukii has also undergone a variety of changes in sweet taste sensation. D. suzukii has a weaker preference than D. melanogaster for laying eggs on substrates containing all three primary fruit sugars: sucrose, fructose, and glucose. Major subsets of D. suzukii taste sensilla have lost electrophysiological responses to sugars. Expression of several key sugar receptor genes is reduced in the taste organs of D. suzukii. By contrast, certain mechanosensory channel genes, including nompC, are expressed at higher levels in the taste organs of D. suzukii, which has a higher preference for stiff substrates. Finally, we find that D. suzukii responds differently from D. melanogaster to combinations of sweet and mechanosensory cues. Thus, the two species differ in sweet sensation, mechanosensation, and their integration, which are all likely to contribute to the differences in their egg-laying preferences in nature.

neuroscience↗

bioRxiv2017

A population phylogenetic view of mitochondrial heteroplasmy

The mitochondrion has recently emerged as an active player in a myriad of cellular processes. Additionally, it was recently shown that more than 200 diseases are known to be linked to variants in mitochondrial DNA or in nuclear genes interacting with mitochondria. This has reinvigorated interest in its biology and population genetics. Mitochondrial heteroplasmy, or genotypic variation of mitochondria within an individual, is now understood to be common in humans and important in human health. However, it is still not possible to make quantitative predictions about the inheritance of heteroplasmy and its proliferation within the body, partly due to the lack of an appropriate model. Here, we present a population-genetic framework for modeling mitochondrial heteroplasmy as a process that occurs on an ontogenetic phylogeny, with genetic drift and mutation changing heteroplasmy frequencies during the various developmental processes represented in the phylogeny. Using this framework, we develop a Bayesian inference method for inferring rates of mitochondrial genetic drift and mutation at different stages of human life. Applying the method to previously published heteroplasmy frequency data, we demonstrate a severe effective germline bottleneck comprised of the cumulative genetic drift occurring between the divergence of germline and somatic cells in the mother and the separation of germ layers in the offspring. Additionally, we find that the two somatic tissues we analyze here undergo tissue-specific bottlenecks during embryogenesis, less severe than the effective germline bottleneck, and that these somatic tissues experience little additional genetic drift during adulthood. We conclude with a discussion of possible extensions of the ontogenetic phylogeny framework and its possible applications to other ontogenetic processes in addition to mitochondrial heteroplasmy.

genomics↗