Biology subjects

Arora, D.

Publications and source records attributed to Arora, D..

7 recordsLinked to original sources

bioRxiv2025

Multi-site Assessment of Methods for Cell Preservation Upstream of Single Cell RNA Sequencing

Single cell RNA sequencing (scRNA-seq) is a revolutionary technique to identify cell types and their molecular phenotype in heterogeneous biological specimens. ScRNA-seq typically requires fresh, high quality single cell suspensions that are processed immediately to preserve their molecular profiles. This presents a challenge for samples with long preparation times and prevents collection at remote sites lacking the required instrumentation for sample processing. Recently, several commercial assays have been released that enable sample preservation at the time of collection either via fixation or cryopreservation, allowing for sample processing to occur months after the initial collection. The Association of Biomolecular Research Facilities (ABRF) DNA Sequencing (DSRG) and Genomics Bioinformatics (GBiRG) Research Groups have undertaken a cross-platform, multi-site study to assess the performance and reproducibility of three platforms: a) 10x Genomics FLEX, b) Parse Bioscience Evercode WT v2 and c) Honeycomb Bio HIVE. Total leukocytes were isolated from a single healthy individual using the EasySep RBC depletion reagent. Cells were then characterized by collecting a 21-color flow cytometry dataset for reference and the remaining material was used for scRNA-seq procedures where different sites then processed either the fixed or cryopreserved cells for each method. We evaluated performance of each method across traditional scRNA-seq quality control metrics and analysis applications, including gene/transcript detection sensitivity, cell type discovery and annotation, and differential expression. We demonstrate that data from the methods tested can be effectively integrated and produce concordant results with regard to cell type annotation and relative abundance, though we observe platform-specific differences in the expression of a subset of genes. Preservation-based methods also show better retention of fragile granulocyte populations compared with fresh samples processed using the 10x 3 workflow. The improvements to preservation methods are changing the way research is conducted and our thorough investigation into the performance of each method provides a valuable resource to help scientists determine the most appropriate single cell preservation workflow given their sample collection logistics and laboratory infrastructure constraints.

genomics↗

bioRxiv2025

Human Attitudes Toward Insects and Spiders: Exploring the Paradoxes of Ecological Value and Discomfort

Insects, with over a million species, are important to ecosystems, contributing to pollination, nutrient cycling, and pest control, yet public perceptions often lean negative due to fear, disgust, or cultural influences. The study explores human attitudes toward insects via a 17-question Google Forms survey, finding consistent perceptions across demographics, except for education level, which impacts ecological awareness and tolerance. A notable exception was the belief that all insects are harmful, which varied significantly by age, and gender differences in handling dangerous insects. Principal Component Analysis identified three key dimensions--environmental awareness, demographic influences, and emotional responses-- explaining 38% of the variance. The findings highlight paradoxes in public views, such as recognizing insects ecological value while expressing discomfort with their presence. Education emerges as a critical factor in fostering positive attitudes, suggesting targeted campaigns could bridge knowledge gaps and promote coexistence with these essential creatures.

scientific communication and education↗

bioRxiv2025

A contextualised protein language model reveals the functional syntax of bacterial evolution

Bacteria have evolved a vast diversity of functions and behaviours that are currently incompletely understood and poorly predicted from DNA sequence alone. To understand the syntax of bacterial evolution and discover genome-to-phenotype relationships, we curated over 1.3 million genomes spanning bacterial phylogenetic space, represented each as an ordered sequence of proteins, and used these sequences to train a transformer-based, contextualised protein language model, Bacformer. By pretraining on genome-wide evolutionary patterns, Bacformer captures the compositional and positional relationships of proteins and thereby provides a whole-genome framework for linking genomic organisation and content to measurable bacterial traits. We demonstrate the ability of Bacformer to accurately predict protein-protein interactions; uncover operon structure, which we validated experimentally; infer important phenotypic traits, including antimicrobial resistance, while revealing likely causal genes; and design template synthetic proteomes with desirable properties. Thus, Bacformer establishes a genomic foundation model that reveals the evolutionary rules governing bacterial gene organisation, function, and phenotype, opening a route to systematic whole-genome engineering.

microbiology↗

bioRxiv2025

Multi-Omics Analysis of Heat Stress-Induced Memory in Arabidopsis

In their natural environment, plants experience temperature fluctuations, including intensified heat waves driven by climate change, which pose significant threats to their productivity. To adapt, plants have evolved diverse mechanisms to withstand heat stress (HS), minimizing potential damage and ensuring survival. One such adaptation is acquired thermotolerance (AT), where prior exposure to HS primes plants to withstand subsequent severe HS. AT can persist for several days and involves a recovery period during which plants establish heat stress memory (HSM), reorganize cellular processes, and strengthen stress resilience. The molecular mechanisms underlying HSM remain the subject of active investigation. In this study, we employ a high-throughput comparative multi-omics approach to unravel the transcriptome, metabolome, and proteome of Arabidopsis thaliana seedlings during distinct intervals of the HSM phase. Our findings provide insights into the intricacies of HS recovery and the memory process. Notably, distinct temporal responses emerge at both the transcriptional and protein levels during the early and late recovery phases. Transcripts associated with HSM are upregulated during the early HS recovery phase, indicating a rapid response crucial for initial memory formation, while corresponding protein levels remain elevated throughout the recovery period, supporting memory consolidation. Additionally, metabolite profiles reveal distinctive patterns across the HS memory phase. This marks the first detailed multi-omic analysis of the HSM phase in Arabidopsis seedlings, providing insights into the multifaceted nature of this complex process. These comprehensive datasets hold promise in elucidating regulators of HS resilience, thereby enhancing efforts in breeding HS-tolerant crops

plant biology↗

bioRxiv2024

Single-Cell Transcriptomics Unveils Skin Cell Specific Antifungal Immune Responses and IL-1Ra- IL-1R Immune Evasion Strategies of Emerging Fungal Pathogen Candida auris

Candida auris is an emerging multidrug-resistant fungal pathogen that preferentially colonizes and persists in skin tissue, yet the host immune factors that regulate the skin colonization of C. auris in vivo are unknown. In this study, we employed unbiased single-cell transcriptomics of murine skin infected with C. auris to understand the cell type-specific immune response to C. auris. C. auris skin infection results in the accumulation of immune cells such as neutrophils, inflammatory monocytes, macrophages, dendritic cells, T cells, and NK cells at the site of infection. We identified fibroblasts as a major non-immune cell accumulated in the C. auris infected skin tissue. The comprehensive single-cell profiling revealed the transcriptomic signatures in cytokines, chemokines, host receptors (TLRs, C-type lectin receptors, NOD receptors), antimicrobial peptides, and immune signaling pathways in individual immune and non-immune cells during C. auris skin infection. Our analysis revealed that C. auris infection upregulates the expression of the IL-1RN gene (encoding IL-1R antagonist protein) in different cell types. We found IL-1Ra produced by macrophages during C. auris skin infection decreases the killing activity of neutrophils. Furthermore, C. auris uses a unique cell wall mannan outer layer to evade IL-1R-signaling mediated host defense. Collectively, our single-cell RNA seq profiling identified the transcriptomic signatures in immune and non-immune cells during C. auris skin infection. Our results demonstrate the IL-1Ra and IL-1R-mediated immune evasion mechanisms employed by C. auris to persist in the skin. These results enhance our understanding of host defense and immune evasion mechanisms during C. auris skin infection and identify potential targets for novel antifungal therapeutics.

microbiology↗

bioRxiv2022

Mapping the adaptor protein complex interaction network in Arabidopsis identifies P34 as a common stability regulator

Adaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargos and coated vesicle accessory proteins. Since in plants endocytic and post-Golgi trafficking intersect at the trans-Golgi network, unique mechanisms for sorting cargos of overlapping vesicular routes are anticipated. The plant AP complexes are part of the sorting machinery, but despite some functional information, their cargoes, accessory proteins, and regulation remain largely unknown. Here, by means of various proteomics approaches, we generated the overall interactome of the five AP and the TPLATE complexes in Arabidopsis thaliana. The interactome converged on a number of hub proteins, including the thus far unknown adaptin binding-like protein, designated P34. P34 interacted with the clathrin-associated AP complexes, controlled their stability and, subsequently, influenced clathrin-mediated endocytosis and various post-Golgi trafficking routes. Altogether, the AP interactome network offers substantial resources for further discoveries of unknown endomembrane trafficking regulators in plant cells.

plant biology↗

bioRxiv2019

Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems

Proximity-dependent biotin labelling (PDL) uses a promiscuous biotin ligase (PBL) or a peroxidase fused to a protein of interest. This enables covalent biotin labelling of proteins and allows subsequent capture and identification of interacting and neighbouring proteins without the need for the protein complex to remain intact. To date, only few papers report on the use of PDL in plants. Here we present the results of a systematic study applying a variety of PDL approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols which combine Mass Spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as test-case. We further benchmark the efficiency of various PBLs in comparison with one-step affinity purification approaches. We identified both known as well as novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both non-biotinylated as well as biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to infer structural information of protein complexes.

plant biology↗