Biology subjects

Sarma, K.

Publications and source records attributed to Sarma, K..

11 recordsLinked to original sources

bioRxiv2026

Socially regulated genes are spatially hyperconnected to enhancers in the ant brain

Caste identity in Harpegnathos saltator ants remains plastic beyond development and throughout adulthood. Adult Harpegnathos workers can become dominant reproductives, known as "gamergates," through a social caste transition that involves extensive transcriptional and cellular remodeling of the brain. To gain insight into the epigenetic regulation of this process, we generated comprehensive, caste-specific epigenomic atlases of the Harpegnathos brain, including chromatin accessibility, histone modifications, and 3D genome architecture. Using these data we refined the genome assembly, annotated enhancers, and linked them to target genes. We then identified candidate 3D-architectural factors, many of which were specifically upregulated in gamergate brains. Promoters of genes upregulated during the worker-gamergate transition formed an unusually high number of 3D chromatin contacts with their regulatory regions, and most of these contacts were already present in workers. We propose that the pre-existing hyper-connectivity of socially regulated genes is essential to adult brain plasticity and behavioral reprogramming.

genomics↗

bioRxiv2025

Gastruloid patterning reflects division of labor among biased stem cell clones

Division of labor, whereby individuals specialize in complementary roles to collectively achieve beneficial outcomes, is a recurring phenomenon in economics, ecology, and microbiology. In development, individual cells specialize, but this specialization is thought to arise from instruction by external signaling cues upon otherwise interchangeable progenitors. It is unclear if progenitors exhibit some degree of specialization, and if so, whether that specialization is optimized for developmental outcomes. Using fluorescence-based lineage tracing in combination with spatial transcriptomics, we show that, in the gastruloid model of early development, individual stem cell clones harbored reproducible spatial propensities for anterior or posterior fates that result in a spontaneous division of labor during axial organization. Gastruloids derived from pure clones generated elongated structures less frequently than a polyclonal population, but mixing clones allowed clones to follow their inherent propensity, restoring proper axial elongation. Spatial transcriptomics reveals that pure clones show disrupted gene expression with inappropriate coexpression of anterior and posterior markers, while clone combinations restore proper spatial organization. We further show that propensities are globally utilized: a clone with a particular propensity can adopt different fates depending on what is more optimal for development as a whole. Perturbations to key developmental signaling pathways disrupted this sorting and profiling revealed molecular characteristics of propensity. Proper developmental outcomes may thus emerge from the coordinated action of intrinsically biased clonal populations.

developmental biology↗

bioRxiv2025

Pooled scanning of protein variants identifies novel RNA-binding mutants

Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying separation-of-function mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein for its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein-RNA interactions.

biochemistry↗

bioRxiv2025

Innate Immune Memory is Stimulus Specific

Innate immune memory (also termed trained immunity) is defined in part by its ability to cross-protect against heterologous pathogens, and can be generated by many different stimuli, suggesting a "universal" trained state. However, different stimuli could form distinct memories, leading to stimulus-specific trained responses. Here, we use primary human monocyte-derived macrophages to demonstrate phenotypic and epigenetic stimulus specificity of innate immune memory six days after initial exposure. Quantification of cytokine production with single-molecule RNA imaging demonstrates stimulus-specific patterns of response to restimulation at the single cell level. Differential licensing of inflammatory transcription factors is associated with encoding of specificities in chromatin. Trained cells show stronger responses to secondary stimuli that are more similar to the initial stimulus they experienced, suggesting a functional role for these stimulus-specific memories. Rather than activating a universal training state, our findings demonstrate that different stimuli impart specific memories that generate distinct training phenotypes in macrophages.

immunology↗

bioRxiv2024

AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance

Cellular responses to environmental stimuli are typically thought to be governed by genetically encoded programs. We demonstrate that melanoma cells can form and maintain cellular memories during the acquisition of therapy resistance that exhibit characteristics of cellular learning and are dependent on the transcription factor AP-1. We show that cells exposed to a low dose of therapy adapt to become resistant to a high dose, demonstrating that resistance was not purely selective. The application of therapy itself results in the encoding of transient gene expression into cellular memory and that this encoding occurs for both transiently induced and probabilistically arising expression. Chromatin accessibility showed concomitant persistence. A two-color AP-1 reporter system showed that these memories are encoded in cis, constituting an example of activating cis epigenetics. Our findings establish the formation and maintenance of cellular memories as a critical aspect of gene regulation during the development of therapy resistance.

systems biology↗

bioRxiv2023

Predicting Suitable Habitats Of Critically Endangered Chinese Pangolin In Assam, India

Chinese pangolin is a least known species in terms of its ecology and population status in India. The present study of Chinese pangolin in Kaziranga-Karbi-Anglong landscape aimed to gather information on species distribution and population status and also an account of threats of the species was investigated. A total of 24 occurrence points were collected from all over Assam and used to get a predictive potential distribution map for the species via Maxent and Random Forest models. To understand the knowledge level of the local people, a total of 13 villages in the north east boundary of North Karbi Anglong Wildlife Sactuary have been surveyed and 160 respondents were interviewed. The AUC values for the two models namely Maxent (0.736) and Random Forest (0.87) were different. Out of the six environmental parameters chosen, the altitude clarified the maximum variation in the model (62 %) followed by the seasonal temperature (bio4; 19.6 %) in the Maxent model. At the same time, these two variables were also found to be of greater significance in the Random Forest model. The species has been least seen by most of the respondents in the last 10 years (43.7%). Most of the respondent of age class 18-24 years never saw a pangolin (82.5%) in the area which depict the population decline of the spcies. Scales were the most used body parts for traditional medicine (58.8%) especially for exceesive saliva secretion in children. The resultant potential habitat in the predictive distribution map in Assam needs to be confirmed with ground verification and accordingly inclusion in the priority conservation zone for Chinese pangolin in Assam should be done.

ecology↗

bioRxiv2021

Development Of Novel Multiplex PCR For Rapid Diagnosis Of Coinfected Hemo-Parasites In Cattle

A novel, rapid and specific multiplex polymerase chain reaction has been developed for the diagnosis of hemo-parasitic infection in bovine blood by three of the most common hemo-parasites. The reported method relied on the detection of the three different bovine hemoparasites isolated from red blood cells (RBCs) of cattle by conventional Giemsa stained blood smear (GSBS) and confirmed by multiplex PCR. The designed multiplex primer sets can amplify 205, 313 and 422 bp fragments of apocytochrome b, sporozoite and macroschizont 2 (spm2) and 16S rRNA gene for Babesia bigemina, Theileria annulata and Anaplasma marginale, respectively. This multiplex PCR was sensitive with the ability to detect the presence of 150 ng of genomic DNA. The primers used in this multiplex PCR also showed highly specific amplification of specific gene fragments of each respective parasite DNA without the presence of non-specific and non-target PCR products. This multiplex PCR system was used to diagnose GSBS confirmed blood samples (N=12) found infected or co-infected with hemoparasites. A comparison of the two detection methods revealed that 58.33% of specimens showed concordant diagnoses with both techniques. The specificity, positive predictive value and kappa coefficient of agreement was highest for diagnosis of B. bigemina and lowest for A. marginale. The overall Kappa coefficient for diagnosis based on GSBS for multiple pathogen compared to multiplex PCR was 0.56 slightly behind the threshold of 0.6 of agreement. Therefore, confirmation should always be made based on PCR to rule out false positive due to differences in subjective observations, stain particles and false negative due to low level of parasitaemia. The simplicity and rapidity of this specific multiplex PCR method make it suitable for large-scale epidemiological studies and for follow-up of drug treatments.

molecular biology↗

bioRxiv2021

BisMapR: a strand-specific, nuclease-based method for genome-wide R-loop detection

R-loops are three stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation as seen in some neurodevelopmental diseases and cancers and is associated with compromised genome stability. Genome-wide profiling of R-loops in normal cells and their comparison in disease states can help identify precise locations of pathogenic R-loops and advance efforts to attenuate deviant R-loops while preserving biologically important ones. Toward this, we have developed an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce high-resolution, genome-wide R-loop profiles that retain strand information. Furthermore, BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. We applied BisMapR to reveal discrete R-loop behavior at gene promoters and enhancers. We show that gene promoters exhibiting antisense transcription form R-loops in both directions. and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. Thus, BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression.

genomics↗

bioRxiv2020

Image-based patch selection for deep learning to improve automated Gleason grading in histopathological slides

Automated Gleason grading can be a valuable tool for physicians when assessing risk and planning treatment for prostate cancer patients. Semantic segmentation provides pixel-wise Gleason predictions across an entire slide, which can be more informative than classification of pre-selected homogeneous regions. Deep learning methods can automatically learn visual semantics to accomplish this task, but training models on whole slides is impractical due to large image sizes and scarcity of fully annotated data. Patch-based methods can alleviate these problems, and have been shown to produce significant results in histopathology segmentation. However, the irregular contours of biopsies on slides makes performance highly dependent on patch selection. In the traditional grid-based strategy, many patches lie on biopsy boundaries, reducing segmentation accuracy due to a reduction in contextual information. In this paper, we propose an automatic patch selection process based on image features. This algorithm segments the biopsy and aligns patches based on the tissue contour to maximize the amount of contextual information in each patch. This method was used to generate patches for a fully convolutional network to segment high grade, low grade, and benign tissue from a set of 59 histopathological slides, and results were compared against manual physician labels. We show that using our image-based patch selection algorithm results in a significant improvement in segmentation accuracy over the traditional grid-based approach. Our results suggest that informed patch selection can be a valuable addition to an automated histopathological analysis pipeline.

bioengineering↗

bioRxiv2020

Red Panda: A novel method for detecting variants in single-cell RNA sequencing

Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at identifying single nucleotide variations or micro (1-50bp) insertions and deletions in single-cell RNA sequencing (scRNA-seq) data. Generating high-quality variant data is vital to the study of the aforementioned diseases, among others. In this study, we report the design and implementation of Red Panda, a novel method to accurately identify variants in scRNA-seq data. Variants were called on scRNA-seq data from human articular chondrocytes, mouse embryonic fibroblasts (MEFs), and simulated data stemming from the MEF alignments. Red Panda had the highest Positive Predictive Value at 45.0%, while other tools--FreeBayes, GATK HaplotypeCaller, GATK UnifiedGenotyper, Monovar, and Platypus--ranged from 5.8%-41.53%. From the simulated data, Red Panda had the highest sensitivity at 72.44%. We show that our method provides a novel and improved mechanism to identify variants in scRNA-seq as compared to currently-existing software. AvailabilitySource code freely available under the MIT License at https://github.com/adambioi/red_panda, and is supported on Linux

bioinformatics↗

bioRxiv2018

Mapping native R-loops genome-wide using a targeted nuclease approach

R-loops are three-stranded DNA:RNA hybrids that are pervasive in the eukaryotic and prokaryotic genomes and have been implicated in a variety of nuclear processes, including transcription, replication, DNA repair, and chromosome segregation. While R-loops may have physiological roles, the formation of stable, aberrant R-loops has been observed in disease, particularly neurological disorders and cancer. Despite the importance of these structures, methods to assess their distribution in the genome invariably rely on affinity purification, which requires large amounts of input material, is plagued by high level of noise, and is poorly suited to capture dynamic and unstable R-loops. Here, we present a new method that leverages the affinity of RNase H for DNA:RNA hybrids to target micrococcal nuclease to genomic sites that contain R-loops, which are subsequently cleaved, released, and sequenced. Our R-loop mapping method, MapR, is as specific as existing techniques, less prone to recover non-specific repetitive sequences, and more sensitive, allowing for genome-wide coverage with low input material and read numbers, in a fraction of the time.

molecular biology↗