Biology subjects

Kaushik, K.

Publications and source records attributed to Kaushik, K..

8 recordsLinked to original sources

bioRxiv2024

Super Resolved Structural Imaging of Mitochondrial Network using Orange Emissive Carbon Nanodot as Fluorescent Probe

Super-resolution microscopy (SRM), coupled with appropriate bright and photostable fluorescent probes, has revolutionized the ability to study organelle dynamics with unprecedented spatial and temporal resolution. An increasing trend of designing nanomaterial probes that has unprecedented advantages over the organic molecular probes has become the frontier in SRM based imaging of subcellular organelles. Herein, we report the development of orange-emissive fluorescent carbon nanodots (CNDs) via a one-pot synthesis that has excellent capabilities to target mitochondria. Spectroscopic analysis confirms the presence of guanidine on the surface of CNDs, thus facilitating its ability to selectively target mitochondria. The CNDs were highly capable for the super resolution radial fluctuation (SRRF) imaging of mitochondrial network and the morphology. The synthesized CNDs exhibited excellent photoluminescent properties along with high biocompatibility and non-toxicity, which could be used for their application in mitochondria-based imaging modalities.

biochemistry↗

bioRxiv2024

Carbon nanodots as a red emissive fluorescent probe for the super-resolution microscopy of DNA dynamics during paclitaxel treatment

Paclitaxel is a commonly used frontline chemotherapeutic drug for cancer treatment. It is known to be functional by arresting the microtubule disassembly during mitosis. Recently, a non-mitotic pathway has been evolving and thus contemplating the mitotic mechanism. Here, using super-resolution microscopy (SRM), we directly visualized the nuclear dynamics and unveiled the mechanism of paclitaxel treatment. A new class of non-toxic, biocompatible and highly fluorescent carbon nanodots (CNDs) were used as a fluorescent probe that were highly capable to directly stain the nuclear DNA, capture the SRM imaging of chromosome and the chromatin structures. Apart from SRM imaging of chromosomes during all stages of normal mitotic cell division, CNDs successfully visualized the formation of lagging, mis-segregated and bridging chromosomes which leads to the multi-micronucleus formation upon paclitaxel treatment. A detailed chromatin remodelling analysis suggested that heterochromatin played an important role in the formation of condensed multi-micronucleus, ultimately leading to cell death. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/620846v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1d5bb12org.highwire.dtl.DTLVardef@ecd313org.highwire.dtl.DTLVardef@15bb3corg.highwire.dtl.DTLVardef@b79273_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Autism and Intellectual Disability-Associated MYT1L Mutation Alters Human Cortical Interneuron Differentiation, Maturation, and Physiology

MYT1L is a neuronal transcription factor highly expressed in the developing and adult brain. While pathogenic MYT1L mutation causes neurodevelopmental disorders, these have not been characterized in human models of neurodevelopment. Here, we defined the consequences of pathogenic MYT1L mutation in human pluripotent stem cell-derived cortical interneurons. During differentiation, mutation reduced MYT1L expression and increased progenitor cell cycle exit and neuronal differentiation and synapse-related gene expression, morphological complexity, and synaptic puncta formation. Conversely, interneuron maturation was compromised, while variant neurons exhibited altered sodium and potassium channel activity and reduced function in electrophysiological analyses. CRISPRi-based knockdown similarly impaired interneuron differentiation and maturation, supporting loss of function-based effects. We further defined MYT1L genome-wide occupancy in interneurons and related this to the transcriptomic dysregulation resulting from MYT1L mutation, to identify direct targets that could mediate these phenotypic consequences. Together, this work delineates contributors to the etiology of neurodevelopmental disorders resulting from MYT1L mutation.

developmental biology↗

bioRxiv2023

Talk To A Scientist: A Framework for a Webinar-Based Science Outreach Platform for Children

Given their future roles as citizens and decision makers, science outreach focused on children is important and relevant. We describe a scientist-led outreach platform (Talk To A Scientist), that uses a webinar-based approach to discuss a range of science topics with children (6-16 years). Based in India and led by two working scientists, Talk To A Scientist has been running for nearly 3 years, with a large and diverse reach across school students. In addition to webinars, the platform regularly hosts archived video content and weekly science activities, along with occasional summer family quizzes and age-specific webinars. We outline the framework used to build Talk To A Scientist, and discuss key considerations and challenges in the development and expansion of the program. We believe that the Talk To A Scientist outreach model focused on children can serve as a guideline for the implementation of similar platforms across diverse settings, and is amenable to a range of modifications to enhance engagement, sustain interest, and tailor outreach to specific groups.

scientific communication and education↗

bioRxiv2022

Targeting the Search: An Upgraded Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies (B-AMP v2.0) with a Focus on Biofilm Protein Targets

Bacterial biofilms, often as multispecies communities, are recalcitrant to conventional antibiotics, making the treatment of biofilm infections a challenge. There is a push towards developing novel anti-biofilm approaches, such as antimicrobial peptides (AMPs), with activity against specific biofilm targets. In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases. The biofilm targets can be searched for using the name of the source organism, and function and type of protein, and results include designated Target IDs (unique to B-AMP v2.0), UniProt IDs, 3D predicted protein structures, PDBQT files, pre-defined protein function, and relevant scientific literature. To present an example of the combined applicability of both, the AMP and biofilm target libraries in the repository, we present two case studies. In the first case study, we expand an in silico pipeline to evaluate AMPs against a single biofilm target in the multidrug resistant, bacterial pathogen Corynebacterium striatum, using 3D protein-peptide docking models from previous work and Molecular Dynamics simulations ([~]1.18 {micro}s). In the second case study, we build an in silico pipeline to identify candidate AMPs (using AMPs with both anti-Gram positive and anti-Gram negative activity) against two biofilm targets with a common functional classification in Pseudomonas aeruginosa and Staphylococcus aureus, widely-encountered bacterial co-pathogens. With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.

bioinformatics↗

bioRxiv2021

AMPing up the search: An in silico approach to identifying Antimicrobial Peptides (AMPs) with potential anti-biofilm activity

Antibiotic resistance is a public health threat, and the rise of multidrug-resistant bacteria, including those that form protective biofilms, further compounds this challenge. Antimicrobial peptides (AMPs) have been recognized for their anti-infective properties, including their ability to target processes important for biofilm formation. However, given the vast array of natural and synthetic AMPs, determining potential candidates for anti-biofilm testing is a significant challenge. In this study, we present an in silico approach, based on open-source tools, to identify AMPs with potential anti-biofilm activity. This approach is developed using the sortase-pilin machinery, important for adhesion and biofilm formation, of the multidrug-resistant, biofilm-forming pathogen C. striatum as the target. Using homology modeling, we modeled the structure of the C. striatum sortase C protein, resembling the semi-open lid conformation adopted during pilus biogenesis. Next, we developed a structural library of 5544 natural and synthetic AMPs from sequences in the DRAMP database. From this library, AMPs with known anti-Gram positive activity were filtered, and 100 select AMPs were evaluated for their ability to interact with the sortase C protein using in-silico molecular docking. Based on interacting residues and docking scores, we built a preference scale to categorize candidate AMPs in order of priority for future in vitro and in vivo biofilm studies. The considerations and challenges of our approach, and the resources developed, which includes a search-enabled repository of predicted AMP structures and protein-peptide interaction models relevant to biofilm studies (B-AMP), can be leveraged for similar investigations across other biofilm targets and biofilm-forming pathogens.

bioinformatics↗

bioRxiv2018

Evidence that recurrent Group A streptococcus tonsillitis is animmunosusceptibility disease involving antibody deficiency and aberrant Tfh cells

One Sentence SummaryRecurrent tonsillitis is a multifactorial disease associated with an aberrant tonsillar germinal center response to Group A Streptococcus.\n\nABSTRACTRecurrent Group A Streptococcus (GAS) tonsillitis (RT) is a common indication for pediatric tonsillectomy. Strep throat is highly prevalent among children; yet, it is unknown why some children develop RT. To gain insights into this classic childhood disease, we performed phenotypic, genotypic, and functional studies on pediatric GAS RT and non-RT tonsils. We observed significantly smaller germinal centers in GAS RT tonsils, and underrepresentation of GAS-specific germinal center follicular helper (GC Tfh) CD4+ T cells. RT children exhibited reduced antibody responses to GAS virulence factor SpeA. Risk and protective HLA Class II alleles for RT were identified. Finally, SpeA induced granzyme B+ GC Tfh cells in RT tonsils that had capacity to kill B cells. Together, these observations suggest that RT susceptibility can occur due to genetic differences that can result in aberrant GC Tfh cells and poor antibody responses to GAS SpeA.

immunology↗

bioRxiv2018

Increased production of the extracellular polysaccharide Psl can give a growth advantage to Pseudomonas aeruginosa in low-iron conditions

In infections, biofilm formation is associated with a number of fitness advantages, such as resistance to antibiotics and to clearance by the immune system. Biofilm formation has also been linked to fitness advantages in environments other than in vivo infections; primarily, biofilms are thought to help constituent organisms evade predation and to promote intercellular signaling. The opportunistic human pathogen Pseudomonas aeruginosa forms biofilm infections in lungs, wounds, and on implants and medical devices. However, the tendency toward biofilm formation originated in this bacteriums native environment, primarily plants and soil. Such environments are polymicrobial and often resource-limited. Other researchers have recently shown that the P. aeruginosa extracellular polysaccharide Psl can bind iron. For the lab strain PA01, Psl is also the dominant adhesive and cohesive \"glue\" holding together multicellular aggregates and biofilms. Here, we perform quantitative time-lapse confocal microscopy and image analysis of early biofilm growth by PA01. We find that aggregates of P. aeruginosa have a growth advantage over single cells of P. aeruginosa in the presence of Staphylococcus aureus in low-iron environments. Our results suggest the growth advantage of aggregates is linked to their high Psl content and to the production of an active factor by S. aureus. We posit that the ability of Psl to promote iron acquisition may have been linked to the evolutionary development of the strong biofilm-forming tendencies of P. aeruginosa.

microbiology↗