Biology subjects

Sharma, R. K.

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

11 recordsLinked to original sources

bioRxiv2026

Snow leopard-mediated apparent competition between wild ungulates and domestic livestock in the Trans-Himalaya

Across High Asia, snow leopards Panthera uncia share habitats with pastoralists and consume both wild and domestic herbivores. Increasing wild prey is vital for predator conservation, but its effect on livestock depredation is unclear: it could decrease depredation through apparent facilitation or increase it through apparent competition. We investigated this association using a 13-year time series dataset from Upper Spiti Landscape in the Indian Trans-Himalaya. Long-term data on elusive carnivores are rare, making this time series especially valuable for testing predator-mediated interactions. We found higher wild ungulate density was accompanied by significantly greater depredation of free-ranging livestock, and this association remained positive after bootstrapping to account for uncertainty in density estimates. These results suggest snow leopard-mediated apparent competition between wild and domestic herbivores. We recommend conservation efforts that increase wild prey must also integrate effective livestock protection and support strategies to enhance coexistence between predators, prey and pastoralists.

ecology↗

bioRxiv2025

Computational Stabilization of the Human VH Germline Repertoire to Enable Conditional Multi-Specific Therapeutic Development

Protein-based biologic therapies, particularly antibody-like therapeutics, have emerged as a major modality to treat nearly all chronic and infectious diseases. Antagonists have dominated the first wave of antibody and antibody-like biologics, whereas agonism has generally been challenging due to systemic activation leading to issues with therapeutic index and problems with pleiotropic activity. Additionally, agonists that use native proteins such as cytokines can be challenging to produce at scale given these proteins evolved to act locally and are not designed for large scale manufacturing. To address these challenges, we generated a biologics platform comprised of stabilized human VH domains (VH-Select) which encompass the entire human germline repertoire with the goal of building multispecific biologics denoted Tentacles that use avidity-based binding to achieve conditional activity directed to specific cell types or tissues. Stabilizing disulfides and point mutations were identified computationally with Rosetta, evaluated in vitro, and combined into designs with 3-5 amino acid substitutions for each of the seven germline families (VH1-VH7). Computational design was also employed to reduce dimerization from both VL and homotypic VH-VH interactions. Optimization of specific sequences improved expression by greater than 600-fold and thermostability by more than 20{degrees}C. Each of the germline variants were screened for low HLA class II binding and incorporated into a library which demonstrated significant improvements in cellular protein production, thereby increasing sequence diversity for screening campaigns. These VH-Select scaffolds are useful for the discovery of novel binders used to build multispecific Tentacles designed for cis-interactions that achieve cell- and tissue-specific activation. As an example of the utility of the platform, we generated a set of Tentacles that use VH-Select binders to conditionally agonize IL2R{gamma}{beta} and 41BB on PD1+, LAG3+, or CD8+ T cells. These Tentacles demonstrate promising manufacturability, antibody-like exposure in vivo, and strong anti-tumor activity in a humanized tumor model. Overall, we believe the incorporation of VH-Select binders into multispecific Tentacles has the potential to create a host of conditionally active biologics to treat various chronic and acute diseases.

bioengineering↗

bioRxiv2025

Environmental DNA Metabarcoding Effectively Detects Invasive Species, Pests, and Community Changes in Taiwan Rice Fields

Rice fields represent man-made semi-aquatic wetlands primed for invasive pests. Monitoring rice field biodiversity using conventional methods, however, is time-consuming and laborious. Environmental DNA (eDNA) methods can provide a fast and effective means to monitor rice field communities and inform management decisions. Our study provides proof-of-concept of rice field eDNA biodiversity assessments, with a focus on native and non-native pests across cultivation phases. We collected eDNA samples from locations in southern Taiwan during planting and harvesting, employing eDNA metabarcoding (COI) to detect diverse taxonomic groups. We assigned 77 ASVs across all sites to animal taxa, 34 of which were identified to species. Overall, 18 species were designated as native or non-native (83.3% and 16.6%, respectively), including three major rice pests, Chilo suppressalis (native), Coptotermes formosanus (native), and Pomacea canaliculata (non-native). Cultivation status affected overall diversity, with higher species richness during planting compared to harvesting. No significant differences were observed between native and non-native taxa between cultivation phases. Altogether, we detected a complex environment across trophic levels comprised of both native and non-native agricultural pests using limited sampling effort, demonstrating eDNA analysis as an efficient biomonitoring approach in rice agroecosystems with direct applications for pest, invasive species, and vector surveillance within Taiwan.

ecology↗

bioRxiv2025

M6A reader protein YTHDF3 regulates cardiomyocyte death and atrophy by modulating the alternative splicing program

BackgroundThe functional impact of m6A modifications on RNA is governed by reader proteins that read the m6A marks and process the RNA accordingly. Recent studies have highlighted the importance of m6A reader proteins in the heart. However, the function of a reader protein Ythdf3 in the heart remains completely unknown. ObjectiveWe aim to uncover the function of Ythdf3 in the hearts. Methods& ResultsHere, we show that Ythdf3 is indispensable for the heart, and its knockdown leads to cardiac cachexia evident by cardiomyocyte atrophy, death, and less dense myofibrils visualized by electron microscopy. We also found downregulation of Ythdf3 in response to doxorubicin, and its overexpression rescues doxorubicin-induced cardiomyocyte atrophy and death. Contrary to primarily cytoplasmic localization, we found that Ythdf3 localizes in the cardiomyocyte nucleus. Furthermore, using co-immunoprecipitation coupled with LC-MS/MS, we show that Ythdf3 interacts with splicing proteins like DDX5 and HNRNPU and regulates alternative splicing in the heart. Mechanistically, we found that Ythdf3 regulates the splicing of CaMKII{delta}, and its knockdown leads to an increase in CaMKII{delta}A and CaMKII{delta}C isoforms while a decrease in CaMKII{delta}9 isoform. ConclusionCollectively, Ythdf3 knockdown in the adult heart leads to cardiac cachexia due to the alteration of the splicing program.

cell biology↗

bioRxiv2024

Harnessing Environmental DNA (eDNA) to Explore Frugivorous Interactions: A Case Study in Papaya (Carica papaya) and Pineapple (Ananas comosus)

Plant-animal interactions (PAIs) are critical in ecosystem function, mediating energy flow and species interactions. Traditional methods of tracking PAIs, such as morphological identification and camera trapping, are limited in speed and scalability, posing challenges for comprehensive biodiversity monitoring. Recently, environmental DNA (eDNA) metabarcoding has emerged as a promising technique for detecting species interactions non-destructively. This pilot study explores the application of eDNA metabarcoding to investigate interactions involving partially consumed and intact fruits of Carica papaya and Ananas comosus. eDNA metabarcoding were performed from of 36 partially consumed and 6 intact fruit samples. Metabarcoding of mitochondrial COI gene fragments revealed a diverse range of taxa, with Arthropoda, particularly insects, being the most abundant. Results indicated significant differences in taxonomic composition between pineapple and papaya samples, where both the fruit hold some unique as well as shared taxa. Furthermore, the diversity also differed between consumed and intact fruits, suggesting that partially consumed fruits serve as rich eDNA sources, capturing interactions with various frugivores and decomposers. Signal from various organisms detected through eDNA metabarcoding from consumed and damaged fruits allowed us to capture a wide array of taxa, revealing insights into species composition and ecological relationships. The unique ASVs associated with each fruit type suggest that certain taxa may showing preferences based on fruit characteristics such as sugar content, texture, or chemical profile. Present work highlighted the importance of eDNA based methods in unraveling the taxonomic composition of fruit-associated plant-animal interactions. This method needs limited taxonomic expertise, less labors, fast and effective, which can be implemented in monitoring ecological and economical species interactions.

ecology↗

bioRxiv2024

Sca-1 expression depicts pro-inflammatory murine neutrophils under steady state and pathological conditions

Neutrophils play a crucial role in various pathophysiological conditions, yet targeting them for therapeutic intervention has been discouraged due to the associated risk of infections. Thus, identification of neutrophil subsets and their involvement in inflammatory conditions is warranted for targeted therapeutic strategies. This study, through screening of surface proteins on neutrophils isolated from different tissue microenvironments, identified a distinct neutrophil subset, CD11b+Ly6G+Sca1+ neutrophils, expressing Stem cell antigen-1 (Sca-1). Interestingly, these Sca1pos neutrophils were more abundant in the liver than BM, blood, and lungs. Further analysis revealed that Sca1pos neutrophils are mature and activated with enhanced effector functions, including superoxide generation, phagocytosis, degranulation, and NETosis. Tracing studies demonstrated ageing-independent characteristics of Sca1pos neutrophils. Remarkably, Sca1pos pro-inflammatory neutrophils promote T cell proliferation through ROS, while inhibition of Sca-1 restores T cell proliferation and ROS generation. Intriguingly, inflammatory as well as metabolic cues induce the transition of conventional neutrophils (Sca1neg) to Sca1pos neutrophils and differentiation of progenitors (granulocyte monocyte progenitors, GMPs) into Sca1pos neutrophils. Furthermore, in vivo models of acute inflammation, peritonitis, and chronic inflammatory condition, non-alcoholic steatohepatitis (NASH), exhibit an increase of Sca1pos neutrophils at inflammatory sites, while the pharmacological approach using NAC specifically mitigates the expansion of these pro-inflammatory neutrophils. Collectively, our findings unveil a novel subset of Sca1pos neutrophils with implications for inflammation. Significance StatementNeutrophilic inflammation remains the leading driver in infectious and inflammatory diseases. Targeting neutrophil populations remained un-recommended due to hampering the immunological functions of neutrophils. The heterogeneity of neutrophils provides the perspective to target altered neutrophil subsets, but subtle changes defining neutrophil subsets make it complex and ambiguous. Our study identified abundant expression of Sca1on distinct neutrophils under steady state and inflammation. Thus, we reported previously undefined Sca1pos pro-inflammatory neutrophil subsets and elucidated their regulation. This study further established their involvement in acute and chronic inflammatory conditions. This understanding may further pave the way toward targeting specific neutrophil subsets in pathologies characterized by neutrophilic inflammation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/613221v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@62f3eaorg.highwire.dtl.DTLVardef@7baed3org.highwire.dtl.DTLVardef@12da63org.highwire.dtl.DTLVardef@1bfcce9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICD11b+Ly6G+Sca1+ neutrophil subset identified with <1% presence in BM and >40% frequency in the liver. C_LIO_LIThese neutrophils are mature and activated, demonstrating enhanced effector functions. C_LIO_LISca1pos neutrophils promote T cell proliferation and display pro-inflammatory characteristics. C_LIO_LIConventional Sca1neg neutrophils transition into Sca1pos neutrophils in response to inflammatory signals, while progenitors undergo differentiation. C_LIO_LIBoth acute and chronic inflammatory models show the expansion of CD11b+Ly6G+Sca1+ neutrophils. C_LI

immunology↗

bioRxiv2024

The unseen invaders: tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P. maculata (Golden Apple Snails) across Taiwan

The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations from 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion in Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.

ecology↗

bioRxiv2023

Musashi-2 causes cardiac hypertrophy and heart failure by inducing mitochondrial dysfunction through destabilizing Cluh and Smyd1 mRNA

Regulation of RNA stability and translation by RNA-binding proteins (RBPs) is a crucial process altering gene expression. Musashi family of RBPs comprising Msi1 and Msi2 are known to control RNA stability and translation. However, despite the presence of MSI2 in the heart, its function remains entirely unknown. Here, we aim to explore the cardiac functions of MSI2. We confirmed the presence of MSI2 in the adult mouse, rat heart, and neonatal rat cardiomyocytes. Furthermore, Msi2 was significantly enriched in the hearts cardiomyocyte fraction. Next, using RNA-seq data and isoform-specific PCR primers, we identified, Msi2 isoforms 1, 4, and 5 and two novel putative isoforms labeled as Msi2 isoforms 6 and 7 to be expressed in the heart. Overexpression of Msi2 isoforms led to cardiac hypertrophy in cultured cardiomyocytes. Additionally, Msi2 was also found to be significantly increased in a pressure-overload model of cardiac hypertrophy. To validate the hypertrophic effects, we selected isoforms 4 and 7 due to their unique alternative splicing patterns. AAV9-mediated overexpression of Msi2 isoforms 4 and 7 in murine hearts led to cardiac hypertrophy, dilation, heart failure, and eventually early death, confirming a pathological function for Msi2. Using global proteomics, gene ontology, transmission electron microscopy, and transmembrane potential measurement assays increased MSI2 was found to cause mitochondrial dysfunction in the heart. Mechanistically, we identified Cluh and Smyd1 as direct downstream targets of Msi2. Overexpression of Cluh or Smyd1 inhibited Msi2-induced hypertrophy and mitochondrial dysfunction in cardiomyocytes. Collectively, we show that Msi2 induces hypertrophy, mitochondrial dysfunction, and heart failure.

cell biology↗

bioRxiv2023

Aurora kinase A/AURKA interacts with the mitochondrial ATP synthase to regulate energy metabolism and cell death

Cancer cells often hijack metabolic pathways to obtain the energy required to sustain their proliferation. Understanding the molecular mechanisms underlying cancer cell metabolism is key to fine-tune the metabolic preference of specific tumors, and potentially offer new therapeutic strategies. Here, we show that the pharmacological inhibition of mitochondrial Complex V delays the cell cycle by arresting breast cancer cell models in the G0/G1 phase. Under these conditions, the abundance of the multifunctional protein Aurora kinase A/AURKA is specifically lowered. We then demonstrate that AURKA directly interacts with the mitochondrial Complex V core subunits ATP5F1A and ATP5F1B. Altering the AURKA/ATPF1A/ATPF1B nexus is sufficient to trigger G0/G1 arrest, and this is accompanied by decreased glycolysis and mitochondrial respiration rates. Last, we discover that the roles of the AURKA/ATPF1A/ATPF1B nexus depend on the specific metabolic propensity of triple-negative breast cancer cell lines, where they correlate with cell fate. On one hand, the nexus induces G0/G1 arrest in cells relying on oxidative phosphorylation as the main source of energy. On the other hand, it allows to bypass cell cycle arrest and it triggers cell death in cells with a glycolytic metabolism. Altogether, we provide evidence that AURKA and mitochondrial Complex V subunits cooperate to maintain cell metabolism in breast cancer cells. Our work paves the way to novel anti-cancer therapies targeting the AURKA/ATPF1A/ATPF1B nexus to lower cancer cell metabolism and proliferation.

cell biology↗

bioRxiv2020

Spatial variation in population-density of snow leopards in a multiple use landscape in Spiti Valley, Trans-Himalaya

The endangered snow leopard Panthera uncia occurs in human use landscapes in the mountains of South and Central Asia. Conservationists generally agree that snow leopards must be conserved through a land-sharing approach, rather than land-sparing in the form of strictly protected areas. Effective conservation through land-sharing requires a good understanding of how snow leopards respond to human use of the landscape. Snow leopard density is expected to show spatial variation within a landscape because of variation in the intensity of human use and the quality of habitat. However, snow leopards have been difficult to enumerate and monitor. Variation in the density of snow leopards remains undocumented, and the impact of human use on their populations is poorly understood. We examined spatial variation in snow leopard density in Spiti Valley, an important snow leopard landscape in India, via spatially explicit capture recapture analysis of camera trap data. We camera trapped an area encompassing a minimum convex polygon of 953 km2. We estimated an overall density of 0.49 (95% CI: 0.39-0.73) adult snow leopards per 100 km2. Using AIC, our best model showed the density of snow leopards to depend on wild prey density, movement about activity centres to depend on altitude, and the expected number of encounters at the activity centre to depend on topography. Models that also used livestock biomass as a density covariate ranked second, but the effect of livestock was weak. Our results highlight the importance of maintaining high density pockets of wild prey populations in multiple use landscapes to enhance snow leopard conservation.

ecology↗

bioRxiv2020

Protective efficacy of calcium phosphate nanoparticle adsorbed bivalent subunit vaccine of Pasteurella multocida against homologous challenge in mice

Swine pasteurellosis, caused by Pasteurella multocida capsular types A and D, causes heavy economic loss to the pig farmers. The vaccine presently used is abacterin of Pasteurella multocida capsular type B that is proven to be effective against bovine pasteurellosis. However, its efficacy against swine pasteurellosis is questionable. The present study was carried out to evaluate the efficacy of calcium phosphate nanoparticle adjuvanted bivalent subunit vaccine prepared from Pasteurella multocida capsular types A and D along with a monovalent subunit vaccine prepared from Pasteurella multocida capsular type B in mice. The Alum precipitated bacterin vaccine was used as the control. The bivalent subunit vaccine comprising the immune components of both the capsular types showed significantly higher IgG response than either of the other two vaccines. Both the calcium phosphate nanoparticle adjuvanted vaccines could elicit 100% protection in mice against homologous challenges but the aluminum hydroxide adjuvanted bacterin vaccine could not elicit significant protection. Based on this preliminary work, it was concluded that the bivalent subunit vaccine would be a better option for immunization of swine against swine pasteurellosis. IMPORTANCE OF THE WORKThe swine pasteurellosis is an important economic disease affecting the pig population in the North-eastern part of India that contributes the major pig population. The disease is caused by Serotype A and D of Pasteurella multocida. At present the inactivated vaccine is used that is actually developed against P52 strain of serotype B:2 of Pasteurella multocida, which is mainly involved in haemorrhagic septicaemia (or bovine pasteurellosis) that affects the cattle, buffaloe, sheep and goat. As a result, the present vaccine does not give sufficient protection in pigs but gives significant protection in cattle, buffaloe, sheep and goat. Hence, there is a need of development of vaccine that can address specifically swine pasteurellosis by targeting serotype A and D of Pasteurella multocida.

microbiology↗