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Biology subjects

Raman, S.

Publications and source records attributed to Raman, S..

At least 19 recordsLinked to original sources

Hollow homes: Roost selection and role of roost morphometrics in the cavity-roosting Bamboo Bat (Genus Tylonycteris) from the Western Ghats, southern India

Bat species occupy diverse day-roosting habitats, ranging from rock-based to plant-based substrates. Depending on the properties of roosting substrates and the ability of bats to adapt to them, roosts can be stable or ephemeral over time. Bamboo bats (genus Tylonycteris) occupy bamboo cavities and possess adaptations such as a flattened skull, thickened thumb pads and modified soles of the feet, making them specialised for roosting within often ephemeral bamboo internodes. The Western Ghats host a bamboo bat species that has traditionally been considered a subspecies of Southeast Asia's Tylonycteris pachypus. However, its precise taxonomic status is unresolved, and recent analyses suggest this population could be a potential new species. Nevertheless, their roosting ecology and the role of bamboo properties in occupancy remain unexplored. By comparing properties of used and unused cavities by the bamboo bats in the Western Ghats, we investigated how physical roost characteristics are associated with cavity occupancy and how the roost properties and space available differed between solitary and non-solitary roosts. We found that only the area of the cavity mouth was associated with occupancy, and all tested properties, including roost volume, were similar for solitary and non-solitary roosts. Our findings are similar to patterns reported from other Tylonycteris species, but these findings contribute to the comparative understanding of bamboo bat roost selection across the tropics. It also opens up future avenues to investigate the understudied ecological continuum in the Indian tropics that involves bats, bamboo, pest insects, cavity-dwelling taxa and bamboo harvesters in further detail.

ecology↗

Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma

The genomic landscape of osteosarcoma, the most common bone cancer worldwide, is among the most structurally complex of all human malignancies. The identification of recurrent and functionally consequential patterns has thus remained a challenge. Across 236 whole-genome sequencing osteosarcoma samples, we uncovered five genomic hotspots of clustered structural variation collectively altered in 58% of tumors. Four were associated with amplification of oncogenes ( MYC , CCND3 , CCNE1 , CDK4) , while the fifth mapped largely upstream of TP53 . Hotspot events showed coordinated patterns of co-occurrence and mutual exclusivity with each other and with tumor suppressor alterations, suggesting genomic context-specific selection. We found localized transcriptional dysregulation at hotspot event loci, and single cells harboring these events converged on a neural crest-like program, linking these structural alterations to a less differentiated cell state. These events were also detectable non-invasively through liquid biopsies and displayed ongoing structural evolution throughout disease progression, a finding with potential clinical utility. Our results provide novel insight into how complex rearrangements shape oncogenesis in osteosarcoma, with broader relevance to other cancers characterized by complex genomes.

cancer biology↗

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↗

Metastatic Osteosarcoma is Characterized by Loss of Osteoblastic Lineage Fidelity

Osteosarcoma (OS) is a rare and aggressive bone cancer with limited therapeutic progress in several decades. To characterize the transcriptional diversity of malignant cell states in OS, we analyzed single-nucleus RNA sequencing data from 24 tumors, including both primary and metastatic lesions. We identified a canonical osteoblastic cell state that predominated in primary tumor cells, but was dampened in metastases. Integrating tumor data with data from embryonic skeletal development and an experimental osteoblast differentiation model revealed that metastatic OS cells resemble poorly specified mesenchyme enriched for non-osseous programs. Clonal populations in metastatic samples acquired mesenchymal cell states distinct from paired primary tumors. Similar cell state shifts were evident in post-treatment primary tumors relative to paired pre-treatment samples. Our results suggest that localized post-treatment and metastatic OS malignant cells lose osteoblastic lineage fidelity, which may represent a unifying axis of disease evolution and reveal new therapeutic vulnerabilities.

Cancer Biology↗

Systematic mapping of chromatin dysregulation driven by viral transcriptional regulators at scale

Viral transcriptional regulators (vTRs) reprogram host cell transcriptional and epigenetic networks to promote infection, persistence, and oncogenic transformation. Despite their broad essentiality to viral pathogenesis, thousands of putative vTRs remain functionally uncharacterized. Here we apply PROD-ATAC, a pooled single-cell epigenomic screening platform, to map chromatin accessibility dysregulation induced by over 100 vTRs in a single assay. Our screen identified dozens of vTRs which directly and indirectly remodel chromatin, including variants with no previously reported epigenetic activity. Comparative analyses revealed that unrelated vTRs frequently opened chromatin regions associated with the same host transcription factor networks, including the NF-{kappa}B, AP-1, p53, and Sp1/KLF families. Integration of chromatin accessibility and transcriptomic datasets highlighted that epigenetic perturbations often coincide with downstream gene expression changes. By adapting PROD-ATAC to incorporate small-molecule perturbations, we demonstrate that targeted inhibition of host features (including the MAPK signaling cascade) can illuminate host dependencies for vTR-induced epigenomic dysregulation. These results establish a scalable framework for discovering virus-host chromatin interactions and suggest that epigenetic manipulation of host regulatory networks is a widespread and conserved function of many diverse vTRs.

genomics↗

In silico investigation of alternative splicing of microexons in human peripheral tissues

Microexons are highly conserved fragments of exons ranging from 3 to 51 nucleotides (nts), representing a precise but poorly understood layer of post-transcriptional regulation outside the central nervous system. While their role in neuronal development is well documented, their behavior in peripheral tissues remains largely uncharacterized. In this study, we utilized VAST-TOOLS to perform a comprehensive meta-analysis of alternative microexon splicing across independent transcriptomic datasets spanning hepatic, pulmonary, renal, and colonic tissues. By comparing the diseased and wild-type (WT) profiles, we identified a robust set of differentially spliced microexons (DSMs) unique to each disease. Our findings suggest that microexon dysregulation in the liver, lung, kidney and colon may not be a primary driver of specific diseases, but rather a signature of a broader collapse in cellular splicing homeostasis. We propose that this phenomenon of differential splicing, particularly within critical hub proteins, fundamentally compromises protein interaction networks, thereby priming the cell for the diverse phenotypic failures observed across chronic disease states.

genomics↗

Transcriptional control of neuronal maintenance by SOX2 during inner ear innervation

The cochlear sensory epithelium and the spiral ganglion neurons it supports arise from a common pool of otic progenitors, yet the neurons remain dependent on the epithelium for guidance and survival long after the two lineages diverge. How that dependency is sustained as the progenitor pool generates increasingly restricted cell types is unknown. Here we show that SOX2 maintains this regulatory continuity. Deletion of Sox2 from the cochlear epithelium after cochlear neurogenesis does not affect neuroblast generation, delamination and proliferation; however, peripheral axons failed to reach the epithelium and neurons were progressively lost, identifying a non-cell-autonomous requirement for epithelial SOX2. Transcriptomic profiling revealed a SOX2-dependent epithelial programme enriched for neurotrophic and axon-guidance genes, including Ntf3 and Bdnf. In cochlear organoids, acute Sox2 deletion reduced H3K27ac at regulatory elements while H3K4me1 remained stable, consistent with SOX2 maintaining the activity of previously marked enhancers. Ntf3 and Bdnf exemplified distinct regulatory trajectories. At Ntf3, SOX2 occupied an enhancer whose activity depended on Sox2, whereas at Bdnf it occupied promoter-proximal elements in progenitors before ATOH1 engaged these and a hair-cell-active distal enhancer. Thus, SOX2 links sensory fate specification to epithelial-neuronal communication. More generally, our findings suggest that regulatory competence can persist through lineage restriction, while changing transcription-factor inputs partition its output among descendants to coordinate their development.

developmental biology↗

Viral transcriptional regulators extensively rewire host pathways through diverse mechanisms

Viral transcriptional regulators (vTRs) reprogram host gene regulatory networks to promote replication, persistence, and immune evasion. Despite the identification of hundreds of vTRs in human viruses, how they rewire host pathways remains unclear. Here, we systematically profiled 95 vTRs from diverse human viruses across multiple functional assays. vTRs perturb immune, cell proliferation/death, and signaling pathways through various mechanisms; some bind DNA directly, others cooperate or antagonize human transcription factors (hTFs), and some remodel chromatin. vTRs can act as activators or repressors and recruit similar but not identical repertoires of proteins as hTFs. These findings reveal vTRs as versatile transcriptional modulators that converge on conserved host "pressure points" while diversifying across pathways to promote viral replication and persistence. Notably, many vTR dysregulate genes within autoimmune, neurological, and cardiovascular risk loci, revealing mechanistic links to disease. Together, we provide a comprehensive resource for understanding and targeting viral control of human transcription.

genomics↗

Mapping unsolved lipidomes accelerates lipid discovery in major bacterial pathogens

Unlike gene-first approaches to understanding bacterial pathogenesis, molecule-forward discovery can uncover unexpected chemical diversity. Here, new lipidomic analytical methods and quality metrics defined the large scope of unknown lipids in the worlds deadliest pathogen, Mycobacterium tuberculosis (Mtb). This map allowed rapid discovery of Mtb lysyldiacylglycerol linked to the biosynthetic gene lysX, which controls in vivo infection outcomes in moth larvae, mice, guinea pigs, and here, zebrafish. A broader search for orthologous lysyltransferase domains identified the Staphylococcus aureus virulence gene mprF, where the same lipoamino acid was shown to be a previously unknown biosynthetic product. Thus, lipidomic mapping showed that the cell envelope composition of well-studied bacterial pathogens remains substantially unsolved and offers a new way to generate lists of discoverable lipids to accelerate molecular discovery.

microbiology↗

Mapping Structural Constraints and Adaptive Potential in a Capsule-Degrading Phage Tailspike Protein

Bacteriophage tailspike proteins (TSPs) degrade bacterial capsules to enable infection, yet the molecular determinants of their function and host range remain unclear. We applied deep mutational scanning (DMS) to the endosialidase TSP of Escherichia coli K1 phage K1F, generating 22,365 single-amino-acid variants using an enhanced ORACLE phage engineering platform. Functional scores revealed the TSP is structurally fragile yet harbors pockets of adaptive flexibility. Mutations within the {beta}-propeller active site uncovered residues accommodating longer sialic acid chains than captured by structural studies, while the {beta}-helix stalk emerged as an adaptive "tuning knob" modulating processivity and specificity. Comparative selections across K1 strains identified discrimination hotspots in {beta}-barrel loops and distal residues outside canonical binding sites, implicating capsule modifications and O-antigen presence as key modulators of host range. By resolving how specific mutations modulate function and host range, this study offers a roadmap for designing phages that overcome capsule-based defenses in pathogenic bacteria.

biochemistry↗

Multiscale 3D whole joint cellular and molecular mapping dissects the relationship between structure and pain

Understanding musculoskeletal joints from a 3D multiscale perspective, from molecular to anatomical levels, is essential for resolving the confounding relationships between structure and pain, elucidating the intricate mechanisms regulating joint health and diseases, and developing new treatment strategies. Here, we introduce a musculoskeletal joint immunostaining and clearing (MUSIC) method specifically designed to overcome key challenges of immunostaining and optical clearing of intact joints. Coupled with large-field light sheet microscopy, our approach enables 3D high-resolution, microscale neurovascular mapping within the context of whole-joint anatomy without the need for image coregistration across various joints, including temporomandibular joints, knees, and spines, and multiple species, including mouse, rat, and pig. Our findings reveal 3D heterogeneous distributions of neurovascular networks and previously uncharacterized neurovascular pathways within joints. Using the proteoglycan 4 knockout (Prg4-/-) mouse model of joint degeneration, we identified significant alterations in joint-wide neurovascular architecture, highlighting neurovascular changes along degenerative processes. Furthermore, in a traumatic joint injury mouse model, we observed long-lasting pain behavior and a time-course 3D neurovascular remodeling preceding detectable joint morphological change, bridging microscale alterations with potential pain mechanisms. This platform offers a powerful tool for multiscale 3D analysis, enabling new insights into joint pathophysiology and intricate interplay among joint tissues.

bioengineering↗

Force patterning drives cell flows and 3D spatial order in auditory epithelia

During development, coordinated cell behavior drives the morphogenesis of epithelia into intricate structures essential for their physiological functions. How this coordination is achieved in epithelia composed of multiple cell types remains unclear. We study development of the avian auditory epithelium comprising sensory hair cells (HCs) and non-sensory supporting cells (SCs). Initially, HCs and SCs are arranged into mosaics by Notch-Delta signaling. During development, HCs partially extrude from the epithelium, establish a ten-fold gradient in apical surface area across the tissue, and intercalate with SCs to form near-hexagonal order. Using a combination of experiments and a 3D-vertex model, we show that an increase of contractility at the apical junctions between SCs compared to those between HCs and SCs drives spatial order within the epithelial plane and along the apical-basal axis. A faster increase of HC apical area at one end of the epithelium than the other leads to opposite fluxes of HCs and SCs and establishes the observed gradients in apical surface area and density of HCs along the auditory epithelium while maintaining a uniform degree of hexagonal order throughout. Our findings reveal that patterned junctional contractility can spatially coordinate cell behavior across both the plane and depth of a mixed epithelium, providing a general mechanism for generating complex three-dimensional tissue architectures during organogenesis.

developmental biology↗

Multiobjective learning and design of bacteriophage specificity

To better understand and design proteins, it is crucial to consider the multifunctional landscapes on which all proteins exist. Proteins are often optimized for single functions during design and engineering, without considering the countless other functionalities that may contribute to or interfere with the intended outcome. In this work, we apply deep learning to understand and design the multifunctional host-targeting landscape of the T7 bacteriophage receptor binding protein for enhanced infectivity, pre-defined specificity, and high generality in virulence toward unseen strains. We compare several different model architectures and design approaches and experimentally characterize designed phages optimized for 26 diverse tasks. We demonstrate that with multiobjective machine learning, it is possible to design complex specificities at success rates that can enable low-throughput validation of predicted hits. Our results show that the targeting capabilities of T7 are highly plastic, with opposite specificities often separated by only a few mutations. This level of tunability underscores how models trained on multifunctional data can uncover key principles of phage biology and specificity. The same modeling framework can be applied to guide the multiobjective design of other proteins or mutable biological systems, offering a general strategy for navigating multifunctional landscapes.

synthetic biology↗

High-throughput discovery of transmembrane helix dimers from human single-pass membrane proteins with TOXGREEN sort-seq

The oligomerization of the transmembrane helices of single-pass membrane proteins is crucial to biological function and its misregulation can lead to many diseases. The study of transmembrane helix oligomerization is facilitated by the availability of genetic reporter assays, which are essential tools for understanding the organization and biology of single-pass systems. In particular, reporter assays are crucial for mapping the oligomerization interfaces of transmembrane helices through scanning mutagenesis but their application is limited by the need to clone and measure each construct individually. Here, we present "TOXGREEN sort-seq", a high-throughput version of the TOXGREEN assay that enables the direct measurement of transmembrane helix oligomerization in large libraries using fluorescence-activated cell sorting and next-generation sequencing. We show that TOXGREEN sort-seq is robust and reproduce the direct measurements of individual constructs with good accuracy and sensitivity. The method produced high-quality mutational profiles from a library of 17,400 constructs designed to probe the interface of 100 potential GASright dimers predicted from sequences of human single-pass membrane proteins. We report the validated structural model of twelve dimers involved in a variety of biological functions, including immune response (interleukin-22 receptor subunit alpha-1, butyrophilin-like protein 3, hepatitis A virus cellular receptor 2), transport (transferrin receptor protein 1), and cell-surface signaling and proliferation (syndecan-3; semaphorins 5A, 6B and 6D). Remarkably, all three semaphorins in the dataset formed strong dimers and produced mutational profiles consistent with the computational structure. These findings open the possibility that dimerization may be relevant to these proteins activity and provide a validated interface for assessing their biological role.

biophysics↗

Energetic and structural control of polyspecificity in a multidrug transporter

Multidrug efflux pumps are dynamic molecular machines that drive antibiotic resistance by harnessing ion gradients to export chemically diverse substrates. Despite their clinical importance, the molecular principles underlying multidrug promiscuity and energy efficiency remain poorly understood. Using multiparametric deep mutational scanning across eight substrates and two energy conditions, we deconvolute the contributions of substrate recognition, energetic coupling, and protein stability, providing an integrated, high-resolution view of multidrug transport. We find that substrate specificity arises from a distributed network of residues extending beyond the binding site, with mutations that reshape binding, coupling, conformational flexibility, and membrane interactions. Further, we apply a pH-based selection scheme to measure the effect of mutation on pH-dependent transport efficiency. By integrating these data, we reveal a fundamental relationship between efficiency and promiscuity: highly efficient variants exhibit broad substrate profiles, while inefficient variants are narrower. These findings establish a direct link between energy coupling and polyspecificity, uncovering the biochemical logic underlying multidrug transport.

biochemistry↗

IMPORTANT: Advanced Pollen Classification of Indian Medicinal Plants through SEM and Computer Vision

Pollen grains of plant species have unique morphological characteristics. The variability in shape, size, and microscopic pollen surface features can be efficiently used to determine the plant species to which they belong. This approach can be instrumental in regions with rich biodiversity in plant species, specifically in medicinal plant. The creation of a pollen dataset for these species using SEM images and a computer vision application can be beneficial for their identification. We have developed a robust approach utilizing scanning electron microscopy (SEM) to generate high-resolution pollen images from 28 plant species of medicinal importance and employed computer vision techniques for accurate segmentation and classification based on diverse morphological features. In this study, a dataset comprising 269 images for segmentation and 5842 images was used for classification across 28 classes. In addition, we have created a globally accessible database named IMPORTANT (Indian Medicinal Plants Pollen Images Dataset for Research, Training, and Analysis of Neural Networks) to facilitate easy retrieval and sharing of pollen images. This study can effectively identify medicinal plant species by utilizing the microscopic features of pollen SEM images through the IMPORTANT database. Since the pollen of even closely related species vary in their morphological characteristics, this approach can efficiently determine the closely related species with accuracy and precision.

plant biology↗

Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts

Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries for systematically assessing gene essentiality in bacteriophages. Using PhageMaP, we generate gene essentiality maps across hundreds of genes in the model phage T7 and the non-model phage Bas63, on diverse hosts. These maps provide fundamental insights into genome organization, gene function, and host-specific conditional essentiality. By applying PhageMaP to a collection of anti-phage defense systems, we uncover phage genes that either inhibit or activate eight defenses and offer novel mechanistic hypotheses. Furthermore, we engineer synthetic phages with enhanced infectivity by modular transfer of a PhageMaP-discovered defense inhibitor from Bas63 to T7. PhageMaP is generalizable, as it leverages homologous recombination, a universal cellular process, for locus-specific barcoding. This versatile tool advances bacteriophage functional genomics and accelerates rational phage design for therapy.

microbiology↗

Mechanical coupling of compartments drives polarity and patterning of mouse auditory epithelium

Morphogenetic information arises from a combination of genetically encoded cellular properties and emergent cellular behaviours. The spatio-temporal implementation of this information is critical to ensure robust, reproducible tissue shapes, yet the principles underlying its organisation remain unknown. We investigated this principle using the mouse auditory epithelium, the organ of Corti (OC). OC consists of a sensory domain, which transduces sound through polar mechanosensory hair cells (HC), part of a mosaic with supporting cells (SC). On either side of the sensory domain are non-sensory domains. These domains undergo cellular rearrangements, which, together, lead to a spiral cochlea that contains planar polarised HCs. This makes the mammalian cochlea a compelling system to understand coordination across spatial scales. Using genetic and ex-vivo approaches, we found patterning of OC into sensory and non-sensory domains is associated with a combinatorial expression of adhesion molecules, which underpins OC into spatially defined compartments, enabling planar cell polarity (PCP) cues to regulate compartment-specific organisation. Through compartment-specific knockouts of the PCP protein, Vangl2, we find evidence of compartment coupling, a non-linear influence on the organisation within one compartment when cellular organisation is disrupted in another. In the OC, compartment coupling originates from vinculin-dependent junctional mechanics, coordinating cellular dynamics across spatial scales. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/613243v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@11d31c1org.highwire.dtl.DTLVardef@1ad85dcorg.highwire.dtl.DTLVardef@12f4a0corg.highwire.dtl.DTLVardef@1a663ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗