Biology subjects

Kaushik, M.

Publications and source records attributed to Kaushik, M..

7 recordsLinked to original sources

bioRxiv2026

Beyond the Axenic Culture Filtrate Secretome: BONCAT and conventional proteomics together reveal the Infection-associated secreted protein repertoire of Acinetobacter baumannii in the human lung Epithelial cell line A549

Acinetobacter baumannii (Ab) is an important opportunistic pathogen responsible for pneumonia, bloodstream infections, and sepsis. Although several virulence determinants have been characterized, the bacterial secreted protein repertoire associated with host cell infection remains incompletely understood. Conventional proteomic analyses of axenic cultures provide valuable information but cannot distinguish proteins synthesized before infection from those produced during host pathogen interactions. This study combined bioorthogonal noncanonical amino acid tagging (BONCAT) with conventional proteomics to characterize the infection associated Ab secreted protein repertoire recovered from human lung epithelial A549 cells. To achieve pathogen selective metabolic labelling, an Ab clinical isolate that had caused neonatal sepsis (Ab7) was engineered to express a methionyl tRNA synthetase variant, MetRSNLL (L10N, Y258L, H299L), capable of incorporating azidonorleucine (ANL) into newly synthesised bacterial proteins. Labelling conditions were optimized using methionine biosynthesis inhibitory amino acids, which reduced endogenous methionine availability without appreciably affecting bacterial growth. Efficient ANL incorporation was confirmed by flow cytometry, confocal microscopy, biotin streptavidin assays, and in gel fluorescence. Metabolic labelling also remained compatible with bacterial intracellular survival. Sequential labelling with azidohomoalanine (AHA) before infection and ANL during A549 infection enabled the temporal assignment of bacterial protein synthesis. Subsequent SDS PAGE fractionation and LC MS/MS identified 152 infection-associated proteins, including 23 containing experimentally detected amino acid analogue modifications. Among these, 13 were AHA only, nine were ANL only, and one contained both analogues. Notably, 117 proteins were not detected in either axenic reference proteome. The infection associated fraction exhibited enrichment of predicted signal peptide containing and outer membrane proteins, while functional annotation identified enrichment of bacterial secretion system components among infection-only proteins. These findings demonstrate the complementary strengths of BONCAT and conventional proteomics: BONCAT provides evidence of bacterial protein synthesis during infection, whereas conventional proteomics expands detection beyond proteins containing identifiable analogue modified peptides. Although extracellular recovery does not establish active secretion, the combined approach reveals a host associated bacterial protein repertoire extending beyond axenic observations. This framework supports future investigations into bacterial adaptation, host pathogen interactions, and the prioritization of candidate diagnostic biomarkers, subject to functional characterization and clinical validation. The study establishes a methodological foundation for investigating infection-associated protein synthesis and release in complex host pathogen environments.

microbiology↗

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↗

bioRxiv2025

The effect of above-ground vegetation on soil microbiome in urban green spaces: A systematic evidence map

Soil microbiome in urban areas is continuously shaped by urbanization and associated processes like native plant species removal, type of vegetation (native and exotic), soil physicochemical properties and anthropogenic activities, and the introduction of invasive plants, etc. Subsequently, above-ground vegetation is shaped by the soil microbiome. However, such information is hardly included while selecting plant species for greening efforts or plantations within green spaces. This could be due to a lack of studies connecting above-ground vegetation and soil microbial communities. In particular, the number of studies investigating soil microbiota and its effects on aboveground vegetation are gaining traction only recently. Existing studies vary in research questions, methodologies, urban green spaces explored, microbial community aspects, and soil characteristics examined. In this study, we are conducting a systematic evidence mapping to consolidate this research and identify global trends and gaps. We focus on the effect of above-ground vegetation on the soil microbiome in urban green spaces. Using an exhaustive search string, we retrieved 598 papers in total from two databases (Web of Science and SCOPUS) and one search engine (Google Scholar). By focusing on these relationships, we provide insights for planning and maintaining urban green spaces. This evidence mapping contributes to the scientific understanding of urban green spaces and offers practical guidance for rapidly urbanizing countries, emphasizing the integration of soil microbial communities in designing and restoring urban green spaces across different geographical locations.

ecology↗

bioRxiv2024

State of India's Birds 2023: A framework to leverage semi-structured citizen science for bird conservation

Birds and their habitats are threatened with extinction around the world. Regional assessments of the State of Birds are a vital means to prioritize data-driven conservation action by informing national and global policy. Such evaluations have traditionally relied on data derived from extensive, long-term, systematic surveys that require significant resources, limiting their feasibility to a few regions in the world. In the absence of such structured long-term datasets, semi-structured datasets have recently emerged as a promising alternative in other regions around the world. Semi-structured data are generated and uploaded by birdwatchers to citizen science platforms like eBird. Such data contain inherent biases because birdwatchers are not required to adhere to a fixed protocol. An evaluation of the status of birds from semi-structured data is therefore a difficult task that requires careful curation of data and the use of robust statistical methods to reduce errors and biases. In this paper, we present a methodology that was developed for this purpose, and was applied to produce the comprehensive State of Indias Birds (SoIB) 2023 report. SoIB 2023 assessed the status of 942 bird species in India by evaluating each species based on three metrics: 1) long-term change: change in abundance between the year 2022 and the year-interval pre-2000; 2) current annual trend: mean annual change in abundance from 2015 to 2022; and 3) distribution range size. We found evidence that 204 species have declined in the long term, and 142 species are currently declining. We present and discuss important insights about Indias birds that can guide research and conservation action in the region. We hope that the detailed methodology described here can act as a blueprint to produce State of Birds assessments from semi-structured citizen science datasets and springboard conservation action in many other regions where structured data is lacking but strong communities of birders exist. Open Research StatementThe primary data are already publicly available on eBird (Sullivan et al. 2014), and other data are already published in a GitHub repository (stateofindiasbirds 2024).

ecology↗

bioRxiv2021

Disentangling the effects of past logging and ongoing cryptic anthropogenic disturbance on vegetation structure and composition in Himalayan Foothills, India

Most tropical forests have undergone commercial logging. Even where logging has ceased, subsistence harvest of forest resources often persists especially in South-East Asia. Understanding of impacts of frequent forest resources extraction in areas recovering from past selective logging would be essential for designing the appropriate management interventions. We studied the impacts of current chronic anthropogenic disturbances (hereafter CAD) and past selective logging on vegetation structure, diversity, and regeneration, and the invasion of a non-native shrub, Lantana camara, in three major forest types in the Himalayan foothills, India. We analyzed field data on intensity of CAD and vegetation variables, collected from 269 stratified random plots, using ordination and generalized linear (mixed) modeling approaches. Our results, based on 2758 adult trees of 54 species, showed that forest types differed in disturbance regimes depending on protection level and availability of fodder tree species. Intensity of CAD depended on proximity to settlements (for livestock related disturbances). Whereas selective logging, including firewood collection, was associated with land protection status. Selective logging reduced the extent of mature forest but facilitated regeneration, thereby promoting secondary forest features such as tree density and canopy cover. In contrast, the interaction between lopping and selective logging was negatively associated with regeneration. Past logging facilitated L. camara invasion in Dry and Hill forests but not in Moist forest. Finally, while selective logging marginally enhanced tree diversity, CAD reduced native shrub diversity. Our study demonstrates that selective logging followed by CAD arrest forest recovery, as evident from the suppression of mature forest elements, loss of shrub biomass, reduced regeneration rate, and facilitation of invasive species. To abate these impacts, alternative livelihood/subsistence options that sustain forests and local communities should be explored. Additionally, CAD management should be site-specific as local ecological contexts modify their impacts on forests.

ecology↗

bioRxiv2020

Habitat patch size and tree species richness shape the bird community in urban green spaces of rapidly urbanizing region of India.

Rapid urbanization and associated biodiversity loss is rampant globally but especially a cause of concern for developing countries. However, numerous studies investigating the role of urban green spaces have established their key role in conserving larger suites of species in urban area. Yet our knowledge is lopsided due to lag in research in developing countries. We examined how landscape and local scale features of urban green spaces influence bird species richness, density, fine-foraging guild richness and composition during breeding and non-breeding season. This is the first study of this nature in one the Himalayan states of India. We quantified landscape level variables in the 250m buffer around 18 urban green spaces. We sampled vegetation and bird community during breeding and non-breeding season through 52 intensive sampling point spread across 18 urban green spaces. Size of the urban green space at landscape level and tree richness at the local scale emerged as important predictor variables influencing bird species richness, density and richness of imperiled insectivorous guild across seasons. Urban green spaces within education institutions and offices experiencing much less management supported higher bird richness and density whereas city parks were the most species poor. Community composition was affected more strongly by built-up cover and barren area in the matrix and also by tree species richness within urban green spaces. City planners should focus on establishing larger city parks during design stage whereas biodiversity potential of the existing urban green spaces could be enhanced by selecting native tree and shrub species to increase overall habitat complexity.

ecology↗

bioRxiv2020

Discovery of tREP-18, a novel class of tRNA encoded peptide with potent leishmanicidal activity

In the post genomic era, tRNA-derived fragments have emerged as a new class of non-coding gene regulators, those play crucial roles both at the transcriptional and translational levels, in different cellular biogenesis. However, none of the studies has ever asked whether tRNAs can also be translated into peptides with any biological significance. Thus, we present a novel hypothesis which suggested that; design and synthesis of tRNA-derived peptides from prokaryotic genome can be exploited for developing unique chemotherapeutics against neglected tropical diseases, like Visceral leishmaniasis (VL) and its aggressive form known as post kalazar dermal leishmaniasis (PKDL). To achieve this aim, we have used a novel system biology-based strategy, which involved; i) mining of unique tRNAs from E. coli genome and their translation into peptide in silico, ii) designing of theoretical 3D models to evaluate their stability, iii) prediction of their biological activity by screening against anti-parasitic database to filter the lead peptide. Based on this strategy, a unique tRNA-derived peptide (tREP-18) was selected, chemically synthesized, and used in vitro for elucidating its therapeutic significance against L. donovani, a causative agent of VL and PKDL. Our findings demonstrated that, tREP-18 can impose high level toxicity to L. donovani promastigotes, by disrupting the ultrastructural cellular architect, destabilizing the mitochondrial membrane potential ({Delta}{Psi}m), thus leading to drastic reduction in cell viability and proliferation. It also imparted high level of toxicity to BS12 a clinical isolate of PKDL. Conceivably, we for the first time reports a novel tRNA-derived peptide "tREP18" with excellent anti-leishmanial property, which can be further utilized for developing it as antileishmanial drug. One Sentence SummaryHere we report a novel first-in-class tRNA encoded peptide and its super anti-leishmanial characteristics.

synthetic biology↗