Biology subjects

Pushpavanam, K.

Publications and source records attributed to Pushpavanam, K..

5 recordsLinked to original sources

bioRxiv2026

From Generation to Discrimination: Vision Foundation Models for Synthetic SEM Image Detection

In materials science, the integrity of scanning electron microscopy (SEM) images is paramount for quality control and validation of research outcomes. However, the introduction of sophisticated generative artificial intelligence, particularly Generative Adversarial Networks (GANs), has introduced a novel vulnerability: the potential for highly realistic, artificially synthesized SEM images to be used fraudulently in scientific literature. To address this challenge, we present a deep learning-based framework capable of distinguishing between authentic SEM images and those synthesized by Generative Adversarial Networks (GANs). Using FastGAN and StyleGAN2-ADA, two state-of-the-art GAN models, we generated synthetic SEM datasets to complement real imaging data. We fine-tuned a pre-trained Contrastive Language-Image Pre-training (CLIP) Vision Transformer (ViT-L-14) for binary classification. By unfreezing the final transformer blocks and appending a custom classification head, the model effectively captures the subtle, high-level artifacts inherent in GAN-generated upsampling. This work highlights the potential of deep learning to safeguard scientific imaging workflows and provides an important step toward detecting and mitigating image forgeries in materials science publications.

bioengineering↗

bioRxiv2026

Bacterial Swarming-Guided Biomineralization Enables Pattern Formation in Engineered Living Materials

Engineered living materials (ELMs) harness the adaptive and self-replicating capabilities of biological systems to create functional materials for sensing, catalysis, and biomineralization. While most ELM strategies rely on static microbial assemblies, the role of bacterial motility in structuring living materials remains unexplored. Here, for the first time, we demonstrate how swarming motility in Escherichia coli MG1655 can be induced to guide spatio-temporally organized calcium phosphate mineralization. The mineralized calcium phosphate is characterized by scanning electron microscopy and elemental analysis. By systematically varying phosphate sources and their concentrations in calcium-rich media, we observe the emergence of regularly spaced concentric mineralized patterns. The previously undocumented observation of the concentric patterns was rationalized through a continuum model that captures the spatiotemporal coupling between swarm expansion and mineral deposition. The model shows that this coupling can generate recurrent front arrest and restart, leading to concentric ring formation. Finally, we show that altering the phosphate species results in distinct mineral morphologies. Together, this work establishes a novel framework for integrating bacterial swarming with biomineralization, enabling dynamic and programmable pattern formation in ELMs.

bioengineering↗

bioRxiv2026

Recombinant Photo-tagging Enables Fluorescent Labelling of Biomolecules and Visualization of Liquid-Liquid Phase Separation

Liquid-liquid phase separation (LLPS) of biomolecules has emerged as a fundamental principle governing biological systems. A key aspect to understand LLPS is the ability to visualize these coacervates, which requires labelling strategies. Fluorescent labelling of biomolecules remains one of the widely adopted techniques involving either small-molecule chemical conjugation or recombinant expression alongside a fluorescent protein. These small-molecule fluorophores are typically employed in excess, which further necessitates additional downstream processing steps, including separation of the conjugated molecules from the unreacted fluorophores. On the other hand, recombinantly appended fluorescent protein affects the functioning of the labelled biomolecule owing to its large size. There is still a need to develop a labelling technique with small molecular weight fluorophores that is also genetically encodable. We previously discovered that the C-terminal peptide fragment (CTPF) released during photo-exposure of a green-to-red photoconvertible fluorescent protein (PhoCl1) displayed red fluorescence. Notably, this chromophore displays broad excitation and emission wavelength profiles, rendering it robust under multiple excitation wavelengths. We leverage this phenomenon to achieve post-expression fluorescent labelling by genetically fusing PhoCl1 to the target peptide or protein to be labelled (TPTL). We successfully demonstrated this approach of conferring fluorescence to silica binding peptide, riboflavin kinase enzyme, TEV protease, Lanthanide Binding Peptide and maltose binding protein, all of which exhibited red fluorescence upon photocleavage. Finally, we demonstrate the applicability of this probe to visualize LLPS of CTPF tagged elastin-like polypeptide in the presence of polymeric crowder. We anticipate that this strategy for inducing red fluorescence in non-fluorescent biomolecules via a photocleavable protein will open new avenues for minimally perturbative fluorescent labelling.

bioengineering↗

bioRxiv2026

Spontaneous Phase Separation Enables Rapid, Polymerization-Free Fabrication of Dissolvable Hydrogels

Hydrogels are cross-linked polymeric networks with wide applications in drug delivery, tissue engineering, biosensing, and environmental remediation. These hydrogels additionally host living cells, small molecules and biological propagules, which further expand the applications of these materials. However, most if not all fabrication methods require covalent modifications. In this work, for the first time, we demonstrate that polymer mixtures can access an additional material state beyond the conventionally described homogeneous and two-phase regimes. By deliberately selecting polymers with a known propensity to phase separate and formulating compositions far from the binodal boundary, the system transitions directly into a mechanically stable hydrogel. We demonstrate this technique using a model system of poly (ethylene glycol) (PEG) and dextran (DEX). We have systematically characterized the hydrogels through FTIR, MALDI-TOF to discern the molecular compositions of the hydrogels. We also modulate the optical transparency of these hydrogels by varying the molecular weight of the polymers. These experimental findings are supplemented with coarse grained (CG) simulation insights to investigate the mechanistic origins of phase separation propensity with varying molecular weights of dextran. We utilized coexisting densities in the two phases using CG simulations to predict the role of dextran molecular weight on the partitioning of PEG and DEX in the two phases. Finally, we exploit the fabricated hydrogels ability to encapsulate live cells, antibiotics and plant seeds. We anticipate that this ATPS-based fabrication technique will provides a scalable, crosslinker-free route to multifunctional hydrogels enabling advanced applications in drug delivery and responsive materials.

bioengineering↗

bioRxiv2023

Fluorogenesis: Inducing Fluorescence in a Non-Fluorescent Protein Through Photoinduced Chromophore Transfer of a Genetically Encoded Chromophore

Fluorescent proteins, while essential for bioimaging, are limited to visualizing cellular localization without offering additional functionality. We report for the first time a strategy to expand the chemical, structural, and functional diversity of fluorescent proteins by harnessing light to induce red fluorescence in a previously non-fluorescent protein. We accomplish this by inducing the transfer of the genetically encoded chromophore from a photocleavable protein (PhoCl1) to a non-fluorescent kinase (MjRibK) inducing red fluorescence in the latter. We have employed analytical and spectroscopic techniques to validate the presence of red fluorescence in MjRibK. Furthermore, molecular dynamics simulations were carried out to investigate the amino acid residues of MjRibK involved in the generation of red fluorescence. Finally, we demonstrate the ability of the red fluorescent MjRibK to operate as a cyclable high-temperature sensor. We anticipate that this light-induced chromophore transfer strategy will open new possibilities for developing multifunctional genetically encoded fluorescent sensors.

biochemistry↗