Biology subjects

Srivastava, I.

Publications and source records attributed to Srivastava, I..

12 recordsLinked to original sources

bioRxiv2026

Anatomically Programmable and Optically Tunable 3D-Bioprinted Tumor-Mimicking Phantoms for Quantitative Nanofluorophore Benchmarking

Surgical resection remains a primary treatment for solid tumors, with fluorescence-guided surgery offering improved intraoperative visualization and precision. However, conventional murine models provide limited control over anatomical and optical variables critical to evaluating fluorescent imaging agents. Here, we developed 3D-bioprinted, anatomically tailored and optically tunable tumor-mimicking phantoms (TMPs) as a reproducible platform for quantitative nanofluorophore evaluation under tissue-relevant surgical conditions. These TMPs recreate subcutaneous, epithelial, and intraperitoneal tumor presentations while enabling controlled variation of lesion geometry, spatial distribution, tissue pigmentation, cellular composition, and nanofluorophore concentration. Semiconducting polymer nanofluorophores (SPNs) with distinct emission profiles were incorporated as model imaging agents and evaluated using an in vivo imaging system (IVIS). The engineered phantoms enabled quantitative assessment of wavelength-dependent fluorescence, lesion visualization and delineation across diverse geometries and tissue backgrounds, multiplexed imaging of spatially distinct lesions, and simulation of fluorescence-guided tumor resection. Constructs incorporating GFP-expressing cancer cells further demonstrated simultaneous visualization of cellular and nanoprobe-derived fluorescence. Collectively, these findings establish anatomically programmable TMPs as a versatile, reproducible framework for benchmarking fluorescent imaging agents, systematically interrogating anatomical and optical determinants of imaging performance, and advancing fluorescence-guided surgical strategies before in vivo evaluation and clinical translation.

bioengineering↗

bioRxiv2026

Biomineralized Surface-Enhanced Raman Scattering Nanotags Encode Biomolecular Identity into Machine Learning-Resolvable Plasmonic Fingerprints

Surface-enhanced Raman scattering (SERS) nanotags provide highly sensitive platforms for in vitro diagnostics but often require complex, disease-specific customization that limits clinical translation. Biomineralization, in which biomolecules mediate inorganic material synthesis, offers a versatile yet underexplored strategy for generating functional SERS nanotags. Here, we demonstrate that biomolecule-directed biomineralization of gold nanoparticles (AuNPs) using amino acids and exosomes generates distinct nano-bio interfacial architectures that encode biomolecular identity into machine learning-resolvable SERS fingerprints through modulation of plasmonic coupling and Raman reporter organization. As a proof-of-concept system, amino acid-biomineralized AuNPs were synthesized using biomolecules with diverse physicochemical properties, including differences in size, polarity, and charge. The resulting nanotags were characterized using UV-Vis spectroscopy, SERS, fluorescence spectroscopy, dynamic light scattering (DLS), and transmission electron microscopy (TEM). Random forest and support vector machine (SVM) models successfully differentiated amino acid-dependent SERS signatures with near-perfect classification performance. Extending this approach to a biologically complex preclinical cancer model, exosome-biomineralized AuNP nanotags were generated using exosomes derived from clinically relevant pediatric patient-derived osteosarcoma and neuroblastoma tumors. Distinct exosome-dependent spectral fingerprints enabled SVM classification with 93.9% accuracy, while Shapley Additive exPlanations (SHAP) and t-distributed stochastic neighbor embedding (t-SNE) analyses identified diagnostically relevant spectral regions and visualized clustering between tumor classes. Collectively, this work establishes biomineralization as a strategy for transforming complex biomolecular and cellular information into computationally resolvable optical fingerprints, enabling scalable and label-free diagnostic classification of patient-derived biomolecular samples.

bioengineering↗

bioRxiv2026

Modular Albumin-Chaperoned NIR-II Nanofluorophores Enables Pan-Ovarian Cancer Imaging Across Multiscale Tumor Models

Ovarian cancer remains the most lethal gynecological malignancy, primarily due to late-stage diagnosis and the challenges of achieving complete cytoreduction. While fluorescence image-guided surgery (FIGS) offers intraoperative visualization, current clinical agents are limited by insufficient brightness, rapid photobleaching, and poor molecular selectivity, particularly in the near-infrared window. Here, we report the rational modular design of ultrabright NIR-II semiconducting polymer (SP) nanofluorophores for high-fidelity ovarian cancer imaging. By nanoconfining of a representative hydrophobic SP within a functional albumin matrix induces a "chaperone" effect that suppresses aggregation-induced quenching and shifts emission in the NIR-II window (1000-1250 nm). This platform integrates a dual-receptor targeting strategy, leveraging intrinsic albumin-receptor interactions (GP60 and SPARC) alongside folate receptor alpha (FR) functionalization. This synergistic approach enables pan-ovarian cancer imaging by ensuring high-affinity binding across diverse tumor phenotypes, regardless of heterogeneous receptor expression. Across a multiscale validation framework, the nanofluorophores demonstrate efficient receptor-mediated endocytosis in 2D cultures and deep interstitial penetration in 3D tumor spheroids. Furthermore, microfluidic tumor-on-chip models incorporating endothelial-like fenestrations confirm controlled extravasation and targeting under physiological shear stress. 3D bioprinted tumor phantoms and ex vivo porcine ovary tissues further confirm that BSA-FA@SP2 provides superior lesion delineation and signal-to-background ratios compared to indocyanine green, a clinical standard. Importantly, the nanofluorophores exhibit excellent hemocompatibility, with minimal hemolysis and negligible complement activation, indicating a non-immunogenic, stealth profile. Collectively, this work establishes albumin-shielded NIR-II nanofluorophores as a robust platform for precision intraoperative pan-ovarian imaging and advances the translational potential of nanotechnology-enabled surgical oncology.

bioengineering↗

bioRxiv2026

Architecture-Dependent Stability, Cellular Uptake, and Redox Modulation of Poly(p-Coumaric Acid) Hybrid Nanoparticles for Ovarian Carcinoma Intervention

The clinical efficacy of fluorescence-guided surgery (FGS) is often compromised by the poor photostability and biologically inert nature of conventional contrast agents such as Indocyanine Green (ICG). While nanocarriers can enhance dye stability, they often function primarily as passive delivery vehicles, requiring additive complexity to achieve therapeutic effects. Here, we report a structure-guided approach to develop self-theranostic hybrid nanoparticles where the polycondensation kinetics of the polymer core, poly(p-coumaric acid) (PCA), serve as a critical design parameter governing nanoparticle assembly and downstream optical and biological performance. By systematically varying the reaction duration, we synthesized PCA variants with distinct polymer growth profiles that influence nanoparticle morphology, ICG encapsulation, and fluorescence stability. The optimized PCA1.5h formulation significantly improved the stability of encapsulated ICG, maintaining robust NIR-I fluorescence under storage and surgical illumination conditions. Beyond acting as a structural scaffold, the PCA matrix retained intrinsic redox-modulating activity, leading to increased reactive oxygen species (ROS) signal generation and reduced viability in multiple ovarian cancer cells. The imaging performance of these nanoparticles was further evaluated using 3D bioprinted intraperitoneal tumor phantoms designed to simulate key optical and spatial features relevant to fluorescence-guided imaging. This work establishes reaction-time-dependent PCA growth profiles as an important formulation parameter for integrating imaging performance and intrinsic biological activity within a simplified hybrid nanomaterial platform. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/717943v3_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@6eab63org.highwire.dtl.DTLVardef@1b6220borg.highwire.dtl.DTLVardef@75010dorg.highwire.dtl.DTLVardef@1982be7_HPS_FORMAT_FIGEXP M_FIG TOC C_FIG

bioengineering↗

bioRxiv2025

Ultrabright NIR-II Nanoprobes for Ex Vivo Bioimaging: Protein Nanoengineering Meets Molecular Engineering

Near-infrared (NIR) fluorescence imaging is a powerful, non-invasive tool for cancer diagnosis, enabling real-time, high-resolution visualization of biological systems. While most probes target the first NIR window (NIR-I, 750-950 nm), recent advances focus on the second window (NIR-II, 1000-1700 nm), which offers deeper tissue penetration and reduced interferences from scattering and autofluorescence. However, many current NIR-II nanoprobes show suboptimal brightness and limited validations in more human-centric models. Here, we present an orthogonal strategy combining molecular engineering, by modulating the amount and position of thiophene moieties in semiconducting polymers (SPs), with protein nanoengineering to develop ultrabright NIR-II imaging probes optimized for ex vivo bioimaging in large animal models. The molecular tuning amplifies the NIR-II fluorescence brightness while screening endogenous proteins as encapsulating matrices to improve colloidal stability and enable active targeting. Molecular docking identified bovine serum albumin as the effective candidate, and the resulting protein-complexed nanoprobes were characterized for size, colloidal stability under physiological conditions, and optical performances. Imaging performances were evaluated using tumor-mimicking phantoms in porcine lungs, simulating cancer surgery, and injected at clinically relevant concentrations into ovine brains and porcine ovaries for microvascular visualization and tissue discrimination, respectively. In all scenarios, our protein-complexed nanoprobes outperformed the FDA-approved clinical dye indocyanine green in signal-to-background ratios. Initial in vitro assays confirmed their hemocompatibility, biocompatibility, and cellular uptake in ovarian adenocarcinoma cells. This integrated approach offers a promising platform for developing next-generation ultrabright NIR-II nanoprobes with improved brightness and stability, advancing the potential for image-guided surgery and future clinical translation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/665782v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@c8a20org.highwire.dtl.DTLVardef@1403bedorg.highwire.dtl.DTLVardef@1e474corg.highwire.dtl.DTLVardef@1daed69_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

3D Tumor-Mimicking Phantom Models for Assessing NIR I/II Nanoparticles in Fluorescence-Guided Surgical Interventions

Fluorescence image-guided surgery (FIGS) offers high spatial resolution and real-time feedback but is limited by shallow tissue penetration and autofluorescence from current clinically approved fluorophores. The near-infrared (NIR) spectrum, specifically the NIR-I (700-900 nm) and NIR-II (950-1700 nm), addresses these limitations with deeper tissue penetration and improved signal-to-noise ratios. However, biological barriers and suboptimal optical performance under surgical conditions have hindered the clinical translation of NIR-I/II nanoprobes. In vivo mouse models have shown promise, but these models do not replicate the complex optical scenarios encountered during real-world surgeries. Existing tissue-mimicking phantoms used to evaluate NIR-I/II imaging systems are useful but fall short when assessing nanoprobes in surgical environments. These phantoms often fail to replicate the tumor microenvironment, limiting their predictive assessment. To overcome these challenges, we propose developing tumor-mimicking phantom models (TMPs) that integrate key tumor features, such as tunable tumor cell densities, in vivo-like nanoparticle concentrations, biologically relevant factors (pH, enzymes), replicate light absorption components (hemoglobin), and light scattering components (intralipid). These TMPs enable more clinically relevant assessments of NIR-I/II nanoprobes, including optical tissue penetration profiling, tumor margin delineation, and ex vivo thoracic surgery on porcine lungs. The components of TMPs can be further modulated to closely match the optical profiles of in vivo and ex vivo tumors. Additionally, 3D bioprinting technology facilitates a high-throughput platform for screening nanoprobes under realistic conditions. This approach will identify high-performing NIR-I/II probes with superior surgical utility, bridging the gap between preclinical findings and clinical applications, and ensuring results extend beyond traditional in vivo mouse studies. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=46 SRC="FIGDIR/small/636085v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@12b283aorg.highwire.dtl.DTLVardef@5e2dc7org.highwire.dtl.DTLVardef@10f6c36org.highwire.dtl.DTLVardef@189590d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Near-Infrared Afterglow Luminescence Amplification via Albumin Complexation of Semiconducting Polymer Nanoparticles for Surgical Navigation in Ex Vivo Porcine Models

Afterglow imaging, leveraging persistent luminescence following light cessation, has emerged as a promising modality for surgical interventions. However, the scarcity of efficient near-infrared (NIR) responsive afterglow materials, along with their inherently low brightness and lack of cyclic modulation in afterglow emission, has impeded their widespread adoption. Addressing these challenges requires a strategic repurposing of afterglow materials that improve on such limitations. Here, we have developed an afterglow probe, composed of bovine serum albumin (BSA) coated with an afterglow material, a semiconducting polymer dye (PFODBT/SP1), called BSA@SP1 demonstrating a substantial amplification of the afterglow luminescence ([~]3-fold) compared to polymer-lipid coated PFODBT (DSPE-PEG@SP1) under same experimental conditions. This enhancement is believed to be attributed to the electron-rich matrix provided by BSA that immobilizes SP1 and enhances the generation of 1O2 radicals, which improves the afterglow luminescence brightness. Through molecule docking, physicochemical characterization, and optical assessments, we highlight BSA@SP1s superior afterglow properties, cyclic afterglow behavior, long-term colloidal stability, and biocompatibility. Furthermore, we demonstrate superior tissue permeation profiling of afterglow signals of BSA@SP1s compared to fluorescence signals using ex vivo tumor-mimicking phantoms and various porcine tissue types (skin, muscle, and fat). Expanding on this, to showcase BSA@SP1s potential in image-guided surgeries, we implanted tumor-mimicking phantoms within porcine lungs and conducted direct comparisons between fluorescence and afterglow-guided interventions to illustrate the latters superiority. Overall, our study introduces a promising strategy for enhancing current afterglow materials through protein complexation, resulting in both ultrahigh signal-to-background ratios and cyclic afterglow signals.

bioengineering↗

bioRxiv2024

Projection-Targeted Photopharmacology Reveals Distinct Anxiolytic Roles for Presynaptic mGluR2 in Prefrontal- and Insula-Amygdala Synapses

Dissecting how membrane receptors regulate neural circuit function is critical for deciphering basic principles of neuromodulation and mechanisms of therapeutic drug action. Classical pharmacological and genetic approaches are not well-equipped to untangle the roles of specific receptor populations, especially in long-range projections which coordinate communication between brain regions. Here we use viral tracing, electrophysiological, optogenetic, and photopharmacological approaches to determine how presynaptic metabotropic glutamate receptor 2 (mGluR2) activation in the basolateral amygdala (BLA) alters anxiety-related behavior. We find that mGluR2-expressing neurons from the ventromedial prefrontal cortex (vmPFC) and posterior insular cortex (pIC) preferentially target distinct cell types and subregions of the BLA to regulate different forms of avoidant behavior. Using projection-specific photopharmacological activation, we find that mGluR2-mediated presynaptic inhibition of vmPFC-BLA, but not pIC-BLA, connections can produce long-lasting decreases in spatial avoidance. In contrast, presynaptic inhibition of pIC-BLA connections decreased social avoidance, novelty-induced hypophagia, and increased exploratory behavior without impairing working memory, establishing this projection as a novel target for the treatment of anxiety disorders. Overall, this work reveals new aspects of BLA neuromodulation with therapeutic implications while establishing a powerful approach for optical mapping of drug action via photopharmacology. Highlights- Basolateral amygdala is a key site for anxiolytic action of mGluR2 agonism - BLA receives dense Grm2+ inputs from ventromedial prefrontal cortex and posterior insular cortex - Photoactivation of mGluR2 has distinct anxiolytic effects in vmPFC-BLA and pIC-BLA synapses - Grm2+ vmPFC and pIC projections target medial and lateral BLA subregions, respectively

neuroscience↗

bioRxiv2023

A novel mouse model of cerebral adrenoleukodystrophy highlights NLRP3 activity in lesion pathogenesis

ObjectiveWe sought to create and characterize a mouse model of the inflammatory, cerebral demyelinating phenotype of X-linked adrenoleukodystrophy (ALD) that would facilitate the study of disease pathogenesis and therapy development. We also sought to cross-validate potential therapeutic targets such as fibrin, oxidative stress, and the NLRP3 inflammasome, in post-mortem human and murine brain tissues. BackgroundALD is caused by mutations in the gene ABCD1 encoding a peroxisomal transporter. More than half of males with an ABCD1 mutation develop the cerebral phenotype (cALD). Incomplete penetrance and absence of a genotype-phenotype correlation imply a role for environmental triggers. Mechanistic studies have been limited by the absence of a cALD phenotype in the Abcd1-null mouse. MethodsWe generated a cALD phenotype in 8-week-old, male Abcd1-null mice by deploying a two-hit method that combines cuprizone (CPZ) and experimental autoimmune encephalomyelitis (EAE) models. We employed in vivo MRI and post-mortem immunohistochemistry to evaluate myelin loss, astrogliosis, blood-brain barrier (BBB) disruption, immune cell infiltration, fibrin deposition, oxidative stress, and Nlrp3 inflammasome activation in mice. We used bead-based immunoassay and immunohistochemistry to evaluate IL-18 in CSF and post-mortem human cALD brain tissue. ResultsMRI studies revealed T2 hyperintensities and post-gadolinium enhancement in the medial corpus callosum of cALD mice, similar to human cALD lesions. Both human and mouse cALD lesions shared common histologic features of myelin phagocytosis, myelin loss, abundant microglial activation, T and B-cell infiltration, and astrogliosis. Compared to wild-type controls, Abcd1-null mice had more severe cerebral inflammation, demyelination, fibrin deposition, oxidative stress, and IL-18 activation. IL-18 immunoreactivity co-localized with macrophages/microglia in the perivascular region of both human and mouse brain tissue. InterpretationThis novel mouse model of cALD suggests loss of Abcd1 function predisposes to more severe cerebral inflammation, oxidative stress, fibrin deposition, and Nlrp3 pathway activation, which parallels the findings seen in humans with cALD. We expect this model to enable long-sought investigations into cALD mechanisms and accelerate development of candidate therapies for lesion prevention, cessation, and remyelination. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/564025v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1fbfebforg.highwire.dtl.DTLVardef@111e1e8org.highwire.dtl.DTLVardef@10647eborg.highwire.dtl.DTLVardef@15b9af4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Synaptic plasticity via receptor tyrosine kinase / G protein-coupled receptor crosstalk

Cellular signaling involves a large repertoire of membrane receptors operating in overlapping spatiotemporal regimes and targeting many common intracellular effectors. However, both the molecular mechanisms and physiological roles of crosstalk between receptors, especially those from different superfamilies, are poorly understood. We find that the receptor tyrosine kinase (RTK), TrkB, and the G protein-coupled receptor (GPCR), metabotropic glutamate receptor 5 (mGluR5), together mediate a novel form of hippocampal synaptic plasticity in response to brain-derived neurotrophic factor (BDNF). Activated TrkB enhances constitutive mGluR5 activity to initiate a mode-switch that drives BDNF-dependent sustained, oscillatory Ca2+ signaling and enhanced MAP kinase activation. This crosstalk is mediated, in part, by synergy between G{beta}{gamma}, released by TrkB, and Gq-GTP, released by mGluR5, to enable a previously unidentified form of physiologically relevant RTK/GPCR crosstalk.

cell biology↗

bioRxiv2022

Impaired glutamate reuptake induces synaptic mistuning in rat hippocampal slices, that can be counteracted by ketamine

Mistuning of synaptic transmission has been proposed to underlie many psychiatric disorders, with decreased reuptake of the excitatory neurotransmitter glutamate as one contributing factor. Synaptic tuning occurs through several diverging and converging forms of plasticity. By recording evoked field postsynaptic potentials in the CA1 area in hippocampal slices, we found that inhibiting glutamate transporters using DL-TBOA causes retuning of synaptic transmission, resulting in a new steady state with reduced synaptic strength and a lower threshold for inducing long-term synaptic potentiation (LTP). Moreover, we also found reduced threshold for LTP in a rat model of depression that has decreased levels of glutamate transporters. Most importantly, we found that the antidepressant ketamine counteracts the effects of increased glutamate on the various steps involved in synaptic retuning. We therefore propose that ketamines mechanism of action as an antidepressant is to restore adequate synaptic tuning.

neuroscience↗

bioRxiv2019

Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

Transcription of heterochromatic genes residing within the constitutive heterochromatin is paradoxical to the tenets of the epigenetic code. Drosophila melanogaster heterochromatic genes serve as an excellent model system to understand the mechanisms of their transcriptional regulation. Recent developments in chromatin conformation techniques have revealed that genome organization regulates the transcriptional outputs. Thus, using 5C-seq in S2 cells, we present a detailed characterization of the hierarchical genome organization of Drosophila pericentromeric heterochromatin and its contribution to heterochromatic gene expression. We show that pericentromeric TAD borders are enriched in nuclear Matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs which indicates their transcriptional co-regulation. To elucidate how heterochromatic factors, influence the expression of heterochromatic genes, we performed 5C-seq in the HP1a or Su(var)3-9 depleted cells. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. Subset of active heterochromatic genes have been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Interestingly, the knock-down of dMES-4 (H3K36 methyltransferase), downregulates expression of the heterochromatic genes. This indicates that the local chromatin interactions and the combination of heterochromatic factors (HP1a or H3K9me3) along with the H3K36me3 is crucial to drive the expression of heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, can bind to both H3K9me3 or HP1a and facilitate the heterochromatic gene expression by regulating the H3K36me3 levels. Therefore, our findings provide mechanistic insights into the interplay of genome organization and chromatin factors at the pericentromeric heterochromatin that regulates Drosophila melanogaster heterochromatic gene expression.

genomics↗