Biology subjects

Sharma, L. K.

Publications and source records attributed to Sharma, L. K..

10 recordsLinked to original sources

bioRxiv2026

Searching for a New Home or Rare Dispersal? Habitat Suitability and Landscape Connectivity of the Tibetan Brown Bear across the Indian Cold Deserts and the Tibetan Plateau

Understanding habitat suitability and landscape connectivity is essential for conserving wide-ranging carnivores in climate-sensitive high-altitude mountain ecosystems. The first occurrence record of the Tibetan brown bear (Ursus arctos pruinosus) from the Changthang region of Ladakh, India, has raised questions about whether this individual represents an isolated dispersal event or reflects functional connectivity with source populations on the Tibetan Plateau. To evaluate potential habitat suitability and transboundary connectivity, we compiled species occurrence records and associated environmental predictors and developed an ensemble species distribution model using biomod2. We then assessed landscape connectivity using circuit theory implemented in Circuitscape to identify potential ecological corridors. Our models indicate that approximately 1,011,818 km{superscript 2} (21.34%) of the combined Ladakh (India) and the Tibetan Plateau landscape is currently suitable for the species, of which only [~]207,000 km{superscript 2} represents highly suitable habitat. Annual precipitation, precipitation of the wettest month, and precipitation of the warmest quarter were the most influential predictors of habitat suitability. Connectivity analysis identified potential corridors linking the eastern Changthang region of Ladakh with suitable habitat on the Tibetan Plateau, suggesting plausible transboundary ecological connectivity. These results indicate that the recent record from Changthang is more likely driven by landscape-scale functional connectivity than by an isolated dispersal event. Although the mapped corridors represent probable connectivity pathways rather than confirmed movement routes, this study provides the first spatially explicit assessment of habitat suitability and potential transboundary connectivity for the Tibetan brown bear across the Ladakh and Tibetan Plateau landscape.

ecology↗

bioRxiv2025

Integrative Single-Cell RNA and ATAC Sequencing Reveals the Impact of Chronic Cigarette Smoking on Lung Epithelial Responses to Influenza and Hyperoxia

Cigarette smoke (CS) is a significant risk factor for developing acute respiratory distress syndrome (ARDS), but the cellular and molecular mechanisms linking smoking to ARDS susceptibility remain unclear. Our goal was to improve our understanding of these mechanisms. To address this, we established a mouse model comparing long-term CS exposure to non-smoking controls, examining responses to influenza infection and hyperoxia-induced lung injury. The mice were divided into six groups (n=1 per group): control (CON), cigarette smoke (CS), hyperoxia (HYP), influenza infection (FLU), cigarette smoke plus hyperoxia (CS+HYP), and cigarette smoke plus influenza infection (CS+FLU). Single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) were performed on lung tissues. Quality control analysis using Seurat (v5.1.0) and Signac (v1.13.1) retained 78,402 cells from scRNA-seq and 84,144 cells from scATAC-seq, with 32,305 matched cells identified across both datasets. Differential gene expression analysis revealed significant smoking-associated alterations in cellular responses to influenza infection and hyperoxia exposure. Pathway enrichment indicated heightened immune responses, inflammatory signaling, and cellular survival pathways in smoking-exposed animals. Integration of scRNA-seq and scATAC-seq identified key transcription factors (TFs), including those involved in immune regulation, tissue repair, and chromatin remodeling mediating these responses. Overall, this study underscores the role of chronic cigarette smoke exposure in exacerbating pathways critical to ARDS pathogenesis, providing potential targets for therapeutic intervention.

bioinformatics↗

bioRxiv2023

Beyond Traditional Methods: Innovative Integration of LISS IV and Sentinel 2A Imagery for Unparalleled Insight into Himalayan Ibex Habitat Suitability

Despite advancements in remote sensing, satellite imagery is underutilized in conservation research. Multispectral data from various sensors have great potential for mapping landscapes, but distinct spectral and spatial resolution capabilities are crucial for accurately classifying wildlife habitats. Our study aimed to develop a technique for precisely discerning habitat categories for the Himalayan Ibex (Capra sibirica) using different satellite imagery. To address both spectral and spatial challenges, we utilized LISS IV and Sentinel 2A data and integrated the LISS IV data with Sentinel 2A data along with their corresponding geometric information. Employing multiple supervised classification algorithms, we found the Random Forest (RF) algorithm to outperform others. The integrated (LISS IV-Sentinel 2A) classified image achieved the highest accuracy, with an overall accuracy of 86.17% and a Kappa coefficient of 0.84. To map the suitable habitat of the Ibex, we conducted ensemble modeling using the Land Cover Land Use (LCLU) of all three image types (LISS IV, Sentinel 2A, Integrated) and other predictors such as topographical, soil type, vegetation, and water radiometric indices. The integrated model provided the most accurate prediction of suitable habitat for the Ibex, surpassing the other two LCLU classes derived from individual images. The Soil Adjusted Vegetation Index (SAVI) and elevation were identified as crucial factors in identifying suitable habitats These findings hold valuable implications for the development of effective conservation strategies, as accurate classification schemes enable the identification of vital landscape elements. By precisely classifying LULC satellite images and identifying crucial habitats for the Ibex, this pilot study provides a new and valuable strategy for conservation planning. It enhances our ability to preserve and protect the habitat of wildlife species in the mountain ecosystem of the Himalayas.

ecology↗

bioRxiv2021

Understanding distribution and occupancy of Himalayan Monal in Uttarkashi district, Uttarakhand

The Himalayan Monal is a conservation priority species in its entire distribution range. Its population is declining in many areas due to various anthropogenic threats. The information on species distribution and its abundance is lacking in many areas which are vital for conservation and management planning. Hence, through the present study, we have assessed the abundance and occupancy of Himalayan monal in Uttarkashi district (Uttarakhand). We used camera traps and conventional sign surveys for documenting the species during 2018-2019. We installed a total of 69 camera traps (2819 trap nights) and surveyed 54 trails (650 km) which represents entire habitat and topographic variability of the landscape. The occupancy and detection probability was modelled using the habitat variables. The top model showed that occupancy probability of Himalayan monal was positively influenced by the slope ({beta} =27.52 {+/-}16.25) and negatively influenced by Reserve Forest (RF) ({beta}= -8.14 SE {+/-} 4.99). The observed naive occupancy of Himalayan Monal was 0.69 in the study area, which was slightly lower than the estimated occupancy. However, in the null model, the site occupancy estimated was found to be 0.82{+/-}0.08 and with detection probability 0.23{+/-}0.03. The overall abundance of monal was estimated about 171.58 {+/-}10.2 in the study area with an average density of 0.62/ km2. The activity pattern analysis indicates that monal remains very active between 6.00 hrs -12.00 hrs and relatively less active during mid-day when humans are most active 11.30 hrs-16.30 hrs. The present study is a first attempt to estimate occupancy and abundance using camera traps as well as sign survey for the species primarily from non-Protected Area (PA). We found that Himalayan monal is abundant outside the PAs, which is a good indication for its long-term viability and also identified areas for conservation and management prioritization in Uttarkashi.

ecology↗

bioRxiv2020

New insights on species divergence in red panda

With the recent classification of red panda into two phylogenetic species, we propose Siang river as a potential boundary for species divergence between the Himalayan red panda (Ailurus fulgens) and the Chinese red panda (Ailurus styani). Bayesian based phylogeny and MJ network splited all the sequences into two distinct clusters in accordance to the origin of the samples collected from the east and west side of the Siang river. The clade 1, that represented Himalayan red panda, was formed by inclusion of samples originated from the north West Bengal, Sikkim, and central Arunachal Pradesh and South Tibet. While, clade 2 represented Chinese red panda by inclusion of the samples originated from Dibang valley of eastern Arunachal Pradesh, India and Southwest China. We suggest being associated with diverse habitats, threats and transboundary distribution, both species of red panda require regional as well as multilateral cooperation for making species survival plan.

evolutionary biology↗

bioRxiv2020

Fine-scale landscape genetics unveiling contemporary asymmetric movement of red panda (Ailurus fulgens) in Kangchenjunga landscape, India

Wildlife management in rapid changing landscapes requires critical planning through cross cutting networks, and understanding of landscape features, often affected by the anthropogenic activities. The present study demonstrates fine-scale spatial patterns of genetic variation and contemporary gene flow of red panda (Ailurus fulgens) populations with respect to landscape connectivity in Kangchenjunga Landscape (KL), India. The study found about 1309.54 Km2 area suitable for red panda in KL-India, of which 62.21% area fell under the Protected Area network. We identified 24 unique individuals from 234 feces collected at nine microsatellite loci. The spatially explicit and non-explicit Bayesian clustering algorithms evident to exhibit population structuring and supported red panda populations to exist in meta-population frame work. In concurrence to the habitat suitability and landscape connectivity models, gene flow results supported a contemporary asymmetric movement of red panda by connecting KL- India in a crescent arc. We demonstrate the structural-operational connectivity of corridors in KL-India that facilitated red panda movement in the past. We also seek for cooperation in Nepal, Bhutan and China to aid in preparing for a comprehensive monitoring plan for the long-term conservation and management of red panda in trans-boundary landscapes.

genetics↗

bioRxiv2020

New insights of zoogeographical distribution of Himalayan goral (Naemorhedus goral) from Indian Himalayan Region

In the present study, we explored the intraspecific genetic variation and phylogeographic relationship among all the reported species in the genus Naemorhedus distributed in a wide range of habitats. The Bayesian based phylogeny demonstrated that Himalayan goral, is a highly diverged species from the other reported species of gorals. We claim the presence of two valid sub-species of Himalayan goral, i.e. N. g. bedfordi and N. g. goral, distributed in the western and central Himalaya, respectively. The comparative analysis with the inclusion of data available from different ranges, suggests the presence of plausibly six species of gorals across the distribution with a few valid subspecies. Further, we report that N. griseus is a valid species and not the synonyms of N. goral considering the observed discrepancy in the available sequences. We recommend all the sub-species present at distant locations may be considered as Evolutionary Significant Units (ESUs) and, therefore, appeal to provide them special attention for long term conservation and management.

genetics↗

bioRxiv2020

Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples

The ongoing spread of pandemic coronavirus disease (COVID-19) is caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). In the lack of specific drugs or vaccines for SARS-CoV-2, demands rapid diagnosis and management are crucial for controlling the outbreak in the community. Here we report the development of the first rapid-colorimetric assay capable of detecting SARS-CoV-2 in the human nasopharyngeal RNA sample in less than 30 minutes. We utilized a nanomaterial-based optical sensing platform to detect RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2, where the formation of oligo probe-target hybrid led to salt-induced aggregation and changes in gold-colloid color from pink to blue in visible range. Accordingly, we found a change in colloid color from pink to blue in assay containing nasopharyngeal RNA sample from the subject with clinically diagnosed COVID-19. The colloid retained pink color when the test includes samples from COVID-19 negative subjects or human papillomavirus (HPV) infected women. The results were validated using nasopharangeal RNA samples from suspected COVID-19 subjects (n=136). Using RT-PCR as gold standard, the assay was found to have 85.29% sensitivity and 94.12% specificity. The optimized method has detection limit as little as 0.5 ng of SARS-CoV-2 RNA. Overall, the developed assay rapidly detects SARS-CoV-2 RNA in clinical samples in a cost-effective manner and would be useful in pandemic management by facilitating mass screening.

microbiology↗

bioRxiv2020

How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography

SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.

genomics↗

bioRxiv2020

Designing a multi-epitope peptide-based vaccine against SARS-CoV-2

COVID-19 pandemic has resulted so far 14,395,16 confirmed cases with 85,711 deaths from the 212 countries, or territories. Due to multifacet issues and challenges in implementation of the safety & preventive measures, inconsistent coordination between societies-governments and most importanly lack of specific vaccine to SARS-CoV-2, the spread of Wuhan originated virus is still uprising after taking a heavy toll on human life. In the present study, we mapped several immunogenic epitopes (B-cell, T-cell, and IFN-gamma) over the entire structural proteins of SARS-CoV-2 and by applying various computational and immunoinformatics approaches, we designed a multi-epitope peptide based vaccine that predicted high immunogenic response in the largest proportion of worlds human population. To ensure high expression of the recombinant vaccine in E. coli, codon optimization and in-silico cloning were also carried out. The designed vaccine with high molecular affinity to TLR3 and TLR4, was found capable to initiate effective innate and adaptive immune response. The immune simulation also suggested uprising high levels of both B-cell and T-cell mediated immunity which on subsequent exposure cleared antigen from the system. The proposed vaccine found promising by yielding desired results and hence, should be tested by practical experimentations for its functioning and efficacy to neutralize SARS-CoV-2.

bioinformatics↗