Biology subjects

Nadeem, A.

Publications and source records attributed to Nadeem, A..

10 recordsLinked to original sources

bioRxiv2026

DNA Sequence-Programmed Protein Coronas Determine Intracellular Fate and Proteostatic Stress of Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) show promise for optical biosensing, imaging, and drug delivery, but turning them into safe, precision nanomedicine tools requires understanding how nanotube surface chemistry dictates recognition and processing by cells. Like other nanomaterials, carbon nanotubes acquire a biomolecular corona on contact with biological fluids, and corona identity is increasingly recognized as central to sensor performance and drug delivery efficacy. However, whether corona identity also governs the intracellular fate of carbon nanotubes remains largely unknown. Here, we show that the single-stranded DNA wrapping of (6,5)-enriched single-walled carbon nanotubes reprograms their protein corona, intracellular trafficking, and macrophage response. By profiling (AT)15, (GT)15, and (CT)15 wrapped SWCNTs, we show that the wrapping sequence programs both the protein corona and the resulting proteostatic stress on macrophages. Photoluminescence imaging and confocal Raman measurements reported that (AT)15 is internalized the most yet leaves the proteome and nanotube structure largely undisturbed, whereas (CT)15, taken up the least, undergoes the most aggressive intracellular degradation and drives the highest oxidative and proteostatic stress. Corona proteomics indicated that all three tested nanotubes form coronas with distinct functional identities that are responsible for divergent intracellular routes. Time-resolved intracellular proteomics combined with functional assays resolved how the host cell reorganizes its biomolecular complexity over time, including oxidative outputs, aside from a sequence-independent core response involving particle engagement, phagosomal sorting, and lysosomal processing. These findings provide mechanistic insight into nanomaterial-cell interactions and the wrapping sequence as a tunable, nucleotide-level design handle for controlling the intracellular fate of carbon nanomaterials, with potential implications for safe and effective nanomedicine platforms.

bioengineering↗

bioRxiv2026

Structure-affinity correlations and separable optical activity in carbon nanotube protein coronas

Biomolecular corona on nanoparticle surfaces enriches low-abundance proteins and compresses the dynamic range of the plasma proteome. Single-walled carbon nanotubes are particularly attractive because their surface chemistry is highly tunable, and their near-infrared fluorescence directly reports corona modulation. However, how surface chemistry shapes the corona and how the corona relates to the fluorescence response remain unclear. We profiled protein enrichment patterns and the resulting fluorescence in a library of 25 chemically modified carbon nanotubes by quantitative proteomics and near-infrared fluorescence spectroscopy. We found that polymer and quantum-defect chemistry orthogonally modulate corona composition and dispersion forces are the dominant, universal driver of protein-nanotube binding. Proteomics and fluorescence correlation analyses indicate that enrichment and fluorescence response are partially decoupled. A subset of corona proteins stays optically silent, but where responses occur, enriched proteins respond at lower, physiologically relevant ranges than depleted ones. Our findings inform design principles for carbon nanomaterial-based sensors and biomarker discovery platforms.

biochemistry↗

bioRxiv2026

Object Speed Perception during Self-Motion in Depth

During sideways movement of an observer, optic flow parsing - in which an objects speed in the world is extracted from all the other visual movement present in the scene, self-generated and otherwise - has been shown to be incomplete, leading to biases in speed perception, particularly when object and observer are moving in opposite directions. Here, we assess how judgements about the speed of objects moving in depth (judged relative to the world) towards or away from an observer (6 m/s) are affected by simultaneous movement of the observer either in the same or opposite direction as the object. In a virtual reality display, participants (n = 25) viewed a sphere simulated as moving in a corridor either while they were stationary or during visually simulated self-motion in the same or opposite direction as the object. They judged the spheres movement relative to the world by comparing its motion to a probe sphere that travelled laterally across the corridor in front of them. In a second experiment (n = 28) participants performed the same task but during faster self-motion (10 m/s). The second cohort also judged the direction in which the object was perceived to move during the same combinations of self and object speeds. Object speed was overestimated when the object travelled in the direction opposite to the observer compared to how objects motion was judged when the observer was stationary. However, object speed was also overestimated during self-motion in the same direction as the object where participants were also much more likely to misjudge the direction of motion of the object. Precision of judgements was lower when self-motion was simulated than it was for stationary observers. A simple arithmetic model of flow parsing fails to capture these results satisfactorily, suggesting that different mechanisms may be at play when the observer travels in the same direction as a moving object and is vulnerable to misperceiving its direction of travel.

animal behavior and cognition↗

bioRxiv2026

NheABC is a pH-dependent cytotoxin that contributes to the virulence of Bacillus cereus

Bacillus cereus is a Gram-positive bacterium widely distributed in food, soil, and plants. It is a spore-forming, facultative anaerobic bacterium known as a food-borne opportunistic human pathogen responsible for causing gastrointestinal and non-gastrointestinal infections, including wound-associated infections. In the present study, we report that among single-component, bi-component, and tripartite alpha pore-forming toxin (-PFT) producing bacteria, the tripartite NheABC toxin produced by B. cereus induced the maximum cell death in infected epithelial cells. Similar to its effects in 2D monolayers, NheABC exhibited potent cell toxicity in 3D spheroids and intestinal organoids, targeting their cell membrane and mitochondria. Moreover, using erythrocytes as a model system, we found that the cytolytic activity of NheABC is pH-dependent, and was markedly reduced at acidic pH (5.5). The pH-dependent biological activity of NheABC was further confirmed by a liposome leakage assay. Importantly, NheABC enhanced the colonization of B. cereus in a non-gastrointestinal murine wound infection model. Overall, our study highlights the role of pH in regulating NheABC-mediated cytotoxicity in mammalian cells, which may lead to the development of novel therapeutic strategies for managing B. cereus gastrointestinal and non-gastrointestinal infections.

microbiology↗

bioRxiv2025

Mechanisms involved in the lipid membrane tubulation activity of the pH-responsive MakA protein from Vibrio cholerae

Bacterial pore-forming toxins (PFTs) are key virulence factors that disrupt host cell membranes. The Vibrio cholerae cytotoxin MakA, a member of the ClyA structural family of -PFTs, exhibits a unique, pH-dependent ability to induce lipid membrane tubulation. This study elucidates the molecular mechanisms underlying this process. We identify the N-terminal histidine residue (His30) of MakA as a critical pH sensor that is indispensable for membrane tubulation but not required for membrane binding and cell lysis. Substitution of His30 with lysine, MakAH30K , abrogated tubulation without affecting membrane insertion, instead triggering aberrant membrane fusion events. Circular dichroism spectroscopy analysis revealed that the MakAH30K substitution attenuates the robust -helical transition observed in wild-type MakA upon lipid membrane binding, providing a molecular explanation for its functional defect. Furthermore, we established that membrane cholesterol contributes to MakA-induced tubulation of lipid membranes, as its absence or mutation of a putative cholesterol-binding motif MakAI236D&I237D abolishes both membrane association and tubule formation. A key implication of our work is the mechanistic uncoupling of membrane tubulation from cytolysis, revealing that MakA can perturb membranes via distinct pathways. These findings define a sophisticated activation mechanism where His30 protonation in the acidic host environment and specific cholesterol binding synergistically drive the conformational change necessary for helical oligomerization and membrane tubulation. We discuss our findings from the viewpoint of possible convergent evolution, where bacterial PFTs like MakA partly may mimic ancient membrane remodelers involved in membrane repair pathways, such as ESCRT-III, but for bacterial fitness in host interactions and pathogenesis. Moreover, the present study provides a foundation for possible development of therapeutic strategies aimed at inhibiting these critical interactions.

biochemistry↗

bioRxiv2025

Enhancing Optical Properties and Stability of DNA-Functionalized Carbon Nanotubes with Cryoprotectant Mediated Lyophilization

The long-term optical performance and stability of single-walled carbon nanotubes (SWCNTs) functionalized with single-stranded DNA are critical for their application in near-infrared (NIR) fluorescence biological sensing and imaging. However, the aggregation of such DNA-SWCNTs during storage presents a significant challenge. Here, we explored the use of lyophilization combined with various cryoprotectants to enhance the long-term stability and reconstitution of DNA-SWCNTs at room temperature. Five conventionally used cryoprotectants, including glucose, sucrose, mannitol, polyethylene glycol (PEG), and polyvinyl alcohol (PVA), were evaluated for their ability to maintain desired optical properties and prevent aggregation of SWCNTs through the process of lyophilization and reconstitution. Our results indicated that glucose and PEG, particularly in an 80:20 ratio by weight, provided the best performance, preserving NIR fluorescence and ensuring consistent reconstitution without significant aggregation. Further, in vitro studies using murine macrophages demonstrated that lyophilized SWCNTs with glucose-PEG protectants and then held at room temperature before subsequent reconstitution maintained stable intracellular optical performance, supporting their potential for long-term storage, ease of transport, and use in biomedical applications. These findings suggest that the optimized lyophilization protocol with specific cryoprotectant combinations can significantly improve the shelf life and reproducibility of SWCNT-based sensors, paving the way for their broader application in biological and clinical settings.

bioengineering↗

bioRxiv2024

Machine Learning Assisted Spectral Fingerprinting for Immune Cell Phenotyping

Spectral fingerprinting has emerged as a powerful tool, adept at identifying chemical compounds and deciphering complex interactions within cells and engineered nanomaterials. Using near-infrared (NIR) fluorescence spectral fingerprinting coupled with machine learning techniques, we uncover complex interactions between DNA-functionalized single-walled carbon nanotubes (DNA-SWCNTs) and live macrophage cells, enabling in situ phenotype discrimination. Through the use of Raman microscopy, we showcase statistically higher DNA-SWCNT uptake and a significantly lower defect ratio in M1 macrophages as compared to M2 and naive phenotypes. NIR fluorescence data also indicate that distinctive intra-endosomal environments of these cell types give rise to significant differences in many optical features such as emission peak intensities, center wavelengths, and peak intensity ratios. Such features serve as distinctive markers for identifying different macrophage phenotypes. We further use a support vector machine (SVM) model trained on SWCNT fluorescence data to identify M1 and M2 macrophages, achieving an impressive accuracy of > 95%. Finally, we observe that the stability of DNA-SWCNT complexes, influenced by DNA sequence length, is a crucial consideration for applications such as cell phenotyping or mapping intra-endosomal microenvironments using AI techniques. Our findings suggest that shorter DNA-sequences like GT6 give rise to more improved model accuracy (> 87%) due to increased active interactions of SWCNTs with biomolecules in the endosomal microenvironment. Implications of this research extend to the development of nanomaterial-based platforms for cellular identification, holding promise for potential applications in real time monitoring of in vivo cellular differentiation. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/583608v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@11e2c60org.highwire.dtl.DTLVardef@1f3553forg.highwire.dtl.DTLVardef@61dcb9org.highwire.dtl.DTLVardef@e216b4_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Protein-lipid interaction at low pH induces oligomerisation of the MakA cytotoxin from Vibrio cholerae

Many pathogenic bacteria produce protein toxins that target and perturb host cell membranes. The secreted -pore-forming toxins (-PFTs) cause membrane damage via pore formation. This study demonstrates a remarkable, hitherto unknown mechanism by an -PFT protein from Vibrio cholerae. As part of the MakA/B/E tripartite toxin, MakA is involved in membrane pore formation similar to other -PFTs. In contrast, MakA protein alone induces tube-like structures in the acidic lysosomal host cell compartment. In vitro studies unravel the dynamics of tubular growth, which occur in a pH-, lipid- and concentration-dependent manner. A 3.7-[A] cryo-electron microscopy structure of MakA filaments reveals a unique protein-lipid superstructure. In its active -PFT conformation, MakA embeds its transmembrane helices into a thin annular lipid bilayer and spirals around a central cavity. Our study provides molecular insights into a novel tubulation mechanism of an -PFT protein, revealing a new mode of action by a secreted bacterial toxin.

cell biology↗

bioRxiv2021

A tripartite cytolytic toxin formed by Vibrio cholerae proteins with flagellum-facilitated secretion

The protein MakA was discovered as a motility-associated secreted toxin from Vibrio cholerae, Here, we show that MakA is part of a gene cluster encoding four additional proteins: MakB, MakC, MakD and MakE. The MakA, MakB and MakE proteins were readily detected in culture supernatants of wild type V. cholerae whereas secretion was very much reduced from a flagellum deficient mutant. Crystal structures of MakA, MakB and MakE revealed structural relationship to a superfamily of bacterial pore-forming proteins. Cloning and expression of MakA/B/E in Escherichia coli resulted in toxicity of the bacteria towards Caenorhabditis elegans used as a predatory organism model. None of these Mak proteins alone or in pairwise combinations were cytolytic but an equimolar mixture of MakA, MakB and MakE acted as a tripartite cytolytic toxin in vitro causing lysis of erythrocytes and cytotoxicity on cultured human colon carcinoma cells. Formation of oligomeric complexes on liposomes was observed by electron microscopy. Oligomer interaction with membranes was initiated by MakA membrane binding followed by MakB and MakE joining in formation of a pore structure. A predicted membrane insertion domain of MakA was shown by site-directed mutagenesis to be essential for toxicity towards C. elegans. Bioinformatic analyses revealed that the makCDBAE gene cluster is present as a novel genomic island in the vast majority of sequenced genomes of V. cholerae and the fish pathogen V. anguillarum. We suggest that the hitherto unrecognized cytolytic MakA/B/E toxin can contribute to Vibrionaceae fitness and virulence potential in different host environments and organisms. Significance StatementVibrio cholerae, responsible for outbreaks and pandemics of cholera disease, is a highly motile organism by virtue of a single flagellum. We describe that the flagellum facilitates the secretion of three V. cholerae proteins encoded by a hitherto unrecognized novel genomic island. The proteins MakA/B/E can form a tripartite cytolytic toxin that lyses erythrocytes and is cytotoxic to cultured human cells. A structural basis for the Mak protein cytolytic activity was obtained by X-ray crystallography. Flagellum-facilitated secretion, remarkably ensuring spatially co-ordinated delivery of Mak proteins, revealed a new role for the V. cholerae flagellum considered of particular significance for the bacterial environmental persistence. Our findings will pave the way for the development of new diagnostics and therapeutic strategies against pathogenic Vibrionaceae.

biochemistry↗

bioRxiv2020

The Vibrio cholerae cytotoxin MakA induces noncanonical autophagy resulting in the spatial inhibition of canonical autophagy

Autophagy plays an essential role in the defence against many microbial pathogens as a regulator of both innate and adaptive immunity. Among some pathogens, sophisticated mechanisms have evolved that promote their ability to evade or subvert host autophagy. Here, we describe a novel mechanism of autophagy subversion mediated by the recently discovered Vibrio cholerae cytotoxin, MakA. pH-dependent endocytosis of MakA by host cells resulted in the formation of a cholesterol-rich endolysosomal membrane aggregate in the perinuclear region. Aggregate formation induced the noncanonical autophagy pathway driving unconventional LC3 lipidation on endolysosomal membranes. Subsequent sequestration of the ATG12-ATG5-ATG16L1 E3-like enzyme complex required for LC3 lipidation at the membranous aggregate resulted in an inhibition of both canonical autophagy and autophagy-related processes including the unconventional secretion of IL-1β. These findings identify a novel mechanism of host autophagy subversion and immune modulation employed by V. cholerae during bacterial infection.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗