Biology subjects

Balakrishnan, P.

Publications and source records attributed to Balakrishnan, P..

6 recordsLinked to original sources

bioRxiv2026

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↗

bioRxiv2026

Genomic Evolution of SARS-CoV-2 Delta Variants Pre- and Post-Omicron Emergence using Alignment-free Machine Learning models

The SARS-CoV-2 Delta variant (B.1.617.2), initially classified as a variant of concern due to its enhanced transmissibility and vaccine-escape mutations, underwent further genomic changes following the emergence of the Omicron variant (B.1.1.529). This study investigates the genomic differences in Delta variant spike gene sequences collected before and after the emergence of Omicron. A total of 190 sequences were analyzed using an alignment-free approach incorporating k-mer-based feature extraction and machine learning models, including convolutional neural networks (CNN), K-means clustering, and random forest classification. The random forest model achieved 93% accuracy, with significant F1 scores, effectively distinguishing the two Delta variant groups. Comparative analysis revealed 157 persistent mutations and four vanished mutations in the post-Omicron group. Cluster analysis showed notable shifts, indicating stable yet evolving genomic patterns over time. The study demonstrates the advantage of alignment-free methods in detecting subtle sequence variations that alignment-based approaches may overlook. These findings enhance our understanding of SARS-CoV-2 evolution and provide a framework for identifying key genomic signatures relevant to public health. The methodology and insights gained offer potential applications in variant surveillance, vaccine design, and viral evolutionary studies, supporting preparedness for future SARS-CoV-2 variant emergence.

genomics↗

bioRxiv2025

What's next for Indian Ornithology? 101 key research questions

India has a rich history of ornithology, and bird research in this field has expanded considerably in recent decades, spurred by a growing number of birdwatchers and ornithologists. Despite this progress, critical gaps remain. This paper highlights key areas where further research is needed and identifies pressing questions that will shape Indian ornithology in the coming years. Drawing from diverse inputs, we present a curated list of 101 research questions spanning across the various disciplines in ornithology - Natural History, Physiology and Disease Ecology, Behaviour, Population and Community Ecology, Habitat Ecology, Macroecology and Biogeography, Population Genetics and Evolution, Applied/Economic Ornithology and Conservation. The list was compiled through a multi-stage process, starting with a public open call for questions, followed by review and curation by a smaller panel of subject specialists. Each question was independently scored by a panel of experts based on three criteria: generality, novelty, and relevance. To account for variation in scoring styles, scores were normalised using Z-scores. The top 101 research questions were then selected based on these standardised scores. Each question is accompanied by an annotation that describes the significance of the question, and highlights opportunities to address it. While our list of research questions highlights significant research priorities, it is not intended to be exhaustive. Rather, it reflects the perspectives of those involved in its curation, who deemed these questions particularly relevant and impactful towards advancing Indian ornithology. We expect these questions to spark new project ideas among students, researchers, and citizen scientists, while guiding funders, managers, and policymakers toward priority research areas.

ecology↗

bioRxiv2024

Diversity and abundance of tree microhabitats in the tropical forests of southern Western Ghats, India

Tree microhabitats (TMHs) are proven tools for assessing and monitoring diversity. These structures on trees are potential indicators of biota, but there is a huge gap in TMH-related knowledge from the tropical regions, the cradles of biodiversity. Thus, an inventory was made to document the TMHs in the tropical forests of southern Western Ghats, India. In evergreen forests, 3,637 TMH host and 450 cavity host trees were identified from the 6,363 trees sampled. The density of TMHs was 972.57{+/-}341.25 ha-1 and cavity density was 63.13{+/-}11.91 ha-1. In moist deciduous forests, out of 1,545 trees sampled, 1,108 hosted TMHs and 212 trees hosted cavities. The density of TMHs was 493.67{+/-}133.28 ha-1 and cavity density was 42.00{+/-}15.01 ha-1. TMHs were categorised into nine categories and 33 sub-categories. The TMH and cavity occurrences were significantly influenced by species richness, stand density, basal area, diameter and height of trees, and density of healthy, unhealthy and dead trees. Dominant and codominant individuals hosted more TMHs and cavities in the deciduous stands while in evergreen, intermediate and overtopped trees had more TMHs and intermediate and codominant had more cavities. In both the habitats the important species of the habitat were also major hosts for TMHs and cavities. HighlightsO_LIPrimary inventory of diversity of TMHs and their host trees in tropical forests C_LIO_LITMH and cavity occurrences are significantly influenced by stand characteristics C_LIO_LIKey species in the habitats also form major hosts for TMHs and cavities C_LIO_LIDominant and codominant individuals host more TMHs and cavities in deciduous stands C_LIO_LIIntermediate and overtopped trees host more TMHs, intermediate and codominant host more cavities in evergreen C_LI

ecology↗

bioRxiv2022

Identification of chemo-sensory genes from antennae of female banana pseudostem weevil, Odoiporous longicollis by transcriptomics approach

In the present study, the female O. longicollis antennal transcriptome was constructed by Illumina Hiseq 2500 sequencing, with the aim of discovering olfaction-related genes. Totally 12, 411 unigenes were identified from the transcriptome assembly and the putative genes functions were annotated using gene ontology tools. We identified 46 putative chemosensory unigenes likely essential for insect olfaction including 19 odorant binding proteins, 3 Niemann-Pick type C (NPC) protein, 6 odorant receptors, 15 ionotropic receptors, and 3 sensory neuron membrane proteins. The key function of these chemosensory genes in the antennae are discussed. Phylogenetic analysis of NPC revealed that the identified proteins had a close relationship with Coleopterans than other insects. This is the first ever report on identification of olfactory genes from O. longicollis which may provide new leads for control of this major pest.

molecular biology↗

bioRxiv2021

The evolution of regulatory elements in the emerging promoter variant strains of HIV-1

In a multicentric, observational, investigator-blinded, and longitudinal clinical study of 764 ART-naive subjects, we identified nine different promoter-variant strains of HIV-1 subtype C (HIV-1C) emerging in the Indian population, with some of these variants being reported for the first time. Unlike several previous studies, our work here focuses on the evolving viral regulatory elements, not coding sequences. The emerging viral strains contain additional copies of the existing transcription factor binding sites (TFBS), including TCF-1/LEF-1, RBEIII, AP-1, and NF-{kappa}B, created by sequence duplication. The additional TFBS are genetically diverse and may blur the distinction between the modulatory region of the promoter and the viral enhancer. In a follow-up analysis, we found trends, but not significant associations between any specific variant promoter and prognostic markers, probably because the emerging viral strains might not have established mono infections yet. Illumina sequencing of four clinical samples containing a co-infection indicated the domination of one strain over the other and establishing a stable ratio with the second strain at the follow-up time-points. Since a single promoter regulates viral gene expression and constitutes the master regulatory circuit with Tat, the acquisition of additional and variant copies of the TFBS may significantly impact viral latency and latent reservoir characteristics. Further studies are urgently warranted to understand how the diverse TFBS profiles of the viral promoter may modulate the characteristics of the latent reservoir, especially following the initiation of antiretroviral therapy. Significance StatementA unique conglomeration of TFBS enables the HIV-1 promoter to accomplish two diametrically opposite functions - transcriptional activation and transcriptional silencing. The various phases of viral latency -establishment, maintenance, and reversal -collectively determine the replication fitness of individual viral strains. A profound variation in the TFBS composition of the viral promoter may significantly alter the viral latency properties and the latent reservoir characteristics. Although the duplication of certain TFBS remains a quality unique to HIV-1C, the high-level genetic recombination of HIV-1 may promote the transfer of such molecular properties to the other HIV-1 subtypes. The emergence of several promoter-variant viral strains may make the task of a functional cure more challenging in HIV-1C.

microbiology↗