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Article ; Online: Understanding the Target Search by Multiple Transcription Factors on Nucleosomal DNA.

Kumar Mishra, Sujeet / Bhattacherjee, Arnab

Chemphyschem : a European journal of chemical physics and physical chemistry

2023 Volume 24, Issue 8, Page(s) e202200644

Abstract: The association of multiple Transcription Factors (TFs) in the cis-regulatory region is imperative for developmental changes in eukaryotes. The underlying process is exceedingly complex, and it is not at all clear what orchestrates the overall search ... ...

Abstract	The association of multiple Transcription Factors (TFs) in the cis-regulatory region is imperative for developmental changes in eukaryotes. The underlying process is exceedingly complex, and it is not at all clear what orchestrates the overall search process by multiple TFs. In this study, by developing a theoretical model based on a discrete-state stochastic approach, we investigated the target search mechanism of multiple TFs on nucleosomal DNA. Experimental kinetic rate constants of different TFs are taken as input to estimate the Mean-First-Passage time to recognize the binding motifs by two TFs on a dynamic nucleosome model. The theory systematically analyzes when the TFs search their binding motifs hierarchically and when simultaneously by proceeding via the formation of a protein-protein complex. Our results, validated by extensive Monte Carlo simulations, elucidate the molecular basis of the complex target search phenomenon of multiple TFs on nucleosomal DNA.
MeSH term(s)	Transcription Factors/genetics ; Transcription Factors/metabolism ; Nucleosomes ; DNA/chemistry ; Protein Binding ; Kinetics ; Binding Sites
Chemical Substances	Transcription Factors ; Nucleosomes ; DNA (9007-49-2)
Language	English
Publishing date	2023-02-15
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2025223-7
ISSN	1439-7641 ; 1439-4235
ISSN (online)	1439-7641
ISSN	1439-4235
DOI	10.1002/cphc.202200644
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The role of nucleotide opening dynamics in facilitated target search by DNA-repair proteins.

Mishra, Sujeet Kumar / Sangeeta / Heermann, Dieter W / Bhattacherjee, Arnab

Biochimica et biophysica acta. Gene regulatory mechanisms

2024 Volume 1867, Issue 2, Page(s) 195026

Abstract: Preserving the genomic integrity stands a fundamental necessity, primarily achieved by the DNA repair proteins through their continuous patrolling on the DNA in search of lesions. However, comprehending how even a single base-pair lesion can be swiftly ... ...

Abstract	Preserving the genomic integrity stands a fundamental necessity, primarily achieved by the DNA repair proteins through their continuous patrolling on the DNA in search of lesions. However, comprehending how even a single base-pair lesion can be swiftly and specifically recognized amidst millions of base-pair sites remains a formidable challenge. In this study, we employ extensive molecular dynamics simulations using an appropriately tuned model of both protein and DNA to probe the underlying molecular principles. Our findings reveal that the dynamics of a non-canonical base generate an entropic signal that guides the one-dimensional search of a repair protein, thereby facilitating the recognition of the lesion site. The width of the funnel perfectly aligns with the one-dimensional diffusion length of DNA-binding proteins. The generic mechanism provides a physical basis for rapid recognition and specificity of DNA damage sensing and recognition.
Language	English
Publishing date	2024-04-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2918786-2
ISSN	1876-4320 ; 1874-9399
ISSN (online)	1876-4320
ISSN	1874-9399
DOI	10.1016/j.bbagrm.2024.195026
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Article ; Online: How Do Nucleosome Dynamics Regulate Protein Search on DNA?

Mishra, Sujeet Kumar / Bhattacherjee, Arnab

The journal of physical chemistry. B

2023 Volume 127, Issue 25, Page(s) 5702–5717

Abstract: Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein-DNA complexes comprising octameric histone core proteins and ∼150 base pairs of DNA. In addition to acting as a DNA compaction vehicle, the dynamics of nucleosomes regulate ... ...

Abstract	Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein-DNA complexes comprising octameric histone core proteins and ∼150 base pairs of DNA. In addition to acting as a DNA compaction vehicle, the dynamics of nucleosomes regulate the DNA site accessibility for the nonhistone proteins, thereby controlling regulatory processes involved in determining the cell identity and cell fate. Here, we propose an analytical framework to analyze the role of nucleosome dynamics on the target search process of transcription factors through a simple discrete-state stochastic description of the search process. By considering the experimentally determined kinetic rates associated with protein and nucleosome dynamics as the only inputs, we estimate the target search time of a protein via first-passage probability calculations separately during nucleosome breathing and sliding dynamics. Although both the nucleosome dynamics permit transient access to the DNA sites that are otherwise occluded by the histone proteins, our result suggests substantial differences between the protein search mechanism on a nucleosome performing breathing and sliding dynamics. Furthermore, we identify the molecular factors that influence the search efficiency and demonstrate how these factors together portray a highly dynamic landscape of gene regulation. Our analytical results are validated using extensive Monte Carlo simulations.
MeSH term(s)	Nucleosomes ; Histones/metabolism ; DNA/metabolism ; Transcription Factors/genetics
Chemical Substances	Nucleosomes ; Histones ; DNA (9007-49-2) ; Transcription Factors
Language	English
Publishing date	2023-06-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c01278
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Article: Awareness and Attitude of Dental Practitioners on Impact of Music Therapy on Patients Anxiety Level during Various Types of Dental Treatments.

Mitra, Mayukh / Panda, Abikshyeet / Kumar, Harish / Mishra, Pallavi / Adhikary, Tamanna / Bhattacharyya, Arnab

Journal of pharmacy & bioallied sciences

2023 Volume 15, Issue Suppl 1, Page(s) S524–S528

Abstract: Music therapy plays an important role in reducing the anxiety of patients during various procedures of dental treatments. Dental practitioners should also be aware of the employment of music therapy on patients before various dental treatments to reduce ... ...

Abstract	Music therapy plays an important role in reducing the anxiety of patients during various procedures of dental treatments. Dental practitioners should also be aware of the employment of music therapy on patients before various dental treatments to reduce dental anxiety and the feasibility of its implementation in regular dental practice. A questionnaire study was conducted regarding the awareness and attitude of dental practitioners on the impact of music therapy on dental patients, to which 305 participants responded. A comparison was made between the Undergraduates, Postgraduates, Faculties, Interns, and Private practitioners. They were also asked about the drawbacks associated with music therapy. There was a level of agreement amongst participants regarding the awareness of music therapy. But there was a statistically significant difference (
Language	English
Publishing date	2023-07-05
Publishing country	India
Document type	Journal Article
ZDB-ID	2573569-X
ISSN	0975-7406 ; 0976-4879
ISSN (online)	0975-7406
ISSN	0976-4879
DOI	10.4103/jpbs.jpbs_533_22
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Article: Cancer Stem Cells in Head and Neck Squamous Cell Carcinoma.

Kumar, Harish A / Desai, Anupama / Mohiddin, Gouse / Mishra, Pallavi / Bhattacharyya, Arnab / Nishat, Roquaiya

Journal of pharmacy & bioallied sciences

2023 Volume 15, Issue Suppl 2, Page(s) S826–S830

Abstract: Cancer stem cells (CSCs) are a small sub-population of cells within a tumor mass proficient of tumor initiation and progression. Distinguishing features possessed by CSCs encompass self-renewal, regeneration and capacity to differentiate. These cells are ...

Abstract	Cancer stem cells (CSCs) are a small sub-population of cells within a tumor mass proficient of tumor initiation and progression. Distinguishing features possessed by CSCs encompass self-renewal, regeneration and capacity to differentiate. These cells are attributed to the phenomenon of aggression, recurrence and metastasis in neoplasms. Due to their cancer initiating and contributing features, a proper understanding of these CSCs and its microenvironment would aid in better understanding of cancer and designing better targeted therapeutic strategies for improved clinical outcome, thus improving the prognosis. This article dispenses a narrative review of CSCs in the context of head and neck carcinoma under the sub headings of overview of cancer stem cells, methods of isolation of these cells, putative CSC markers of head and neck cancer, signaling pathways used by these cells and their therapeutic implications.
Language	English
Publishing date	2023-07-11
Publishing country	India
Document type	Journal Article ; Review
ZDB-ID	2573569-X
ISSN	0975-7406 ; 0976-4879
ISSN (online)	0975-7406
ISSN	0976-4879
DOI	10.4103/jpbs.jpbs_81_23
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Article ; Online: Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.

Mondal, Anupam / Mishra, Sujeet Kumar / Bhattacherjee, Arnab

Biophysical journal

2022 Volume 121, Issue 23, Page(s) 4526–4542

Abstract: Critical lineage commitment events are staged by multiple transcription factors (TFs) binding to their cognate motifs, often positioned at nucleosome-enriched regions of chromatin. The underlying mechanism remains elusive due to difficulty in ... ...

Abstract	Critical lineage commitment events are staged by multiple transcription factors (TFs) binding to their cognate motifs, often positioned at nucleosome-enriched regions of chromatin. The underlying mechanism remains elusive due to difficulty in disentangling the heterogeneity in chromatin states. Using a novel coarse-grained model and molecular dynamics simulations, here we probe the association of Sox2 and Oct4 proteins that show clustered binding at the entry-exit region of a nucleosome. The model captures the conformational heterogeneity of nucleosome breathing dynamics that features repeated wrap-unwrap transitions of a DNA segment from one end of the nucleosome. During the dynamics, DNA forms bulges that diffuse stochastically and may regulate the target search dynamics of a protein by nonspecifically interacting with it. The overall search kinetics of the TF pair follows a "dissociation-compensated-association" mechanism, where Oct4 binding is facilitated by the association of Sox2. The cooperativity stems from a change in entropy caused by an alteration in the nucleosome dynamics upon TF binding. The binding pattern is consistent with a live-cell single-particle tracking experiment, suggesting the mechanism observed for clustered binding of a TF pair, which is a hallmark of cis-regulatory elements, has broader implications in understanding gene regulation in a complex chromatin environment.
MeSH term(s)	Nucleosomes ; DNA
Chemical Substances	Nucleosomes ; DNA (9007-49-2)
Language	English
Publishing date	2022-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.10.039
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Article ; Online: Awareness and attitude of dental practitioners on impact of music therapy on patients anxiety level during various types of dental treatments

Mayukh Mitra / Abikshyeet Panda / Harish Kumar / Pallavi Mishra / Tamanna Adhikary / Arnab Bhattacharyya

Journal of Pharmacy and Bioallied Sciences, Vol 15, Iss 5, Pp 524-

2023 Volume 528

Abstract	Music therapy plays an important role in reducing the anxiety of patients during various procedures of dental treatments. Dental practitioners should also be aware of the employment of music therapy on patients before various dental treatments to reduce dental anxiety and the feasibility of its implementation in regular dental practice. A questionnaire study was conducted regarding the awareness and attitude of dental practitioners on the impact of music therapy on dental patients, to which 305 participants responded. A comparison was made between the Undergraduates, Postgraduates, Faculties, Interns, and Private practitioners. They were also asked about the drawbacks associated with music therapy. There was a level of agreement amongst participants regarding the awareness of music therapy. But there was a statistically significant difference (p = 0.011) noted across groups. The majority of the participants agreed that it could be incorporated into a regular dental practice as a stress management procedure.
Keywords	anxiety ; dental treatment ; music therapy ; patients ; questionnaire ; Pharmacy and materia medica ; RS1-441 ; Analytical chemistry ; QD71-142
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Legal Question-Answering in the Indian Context

Nigam, Shubham Kumar / Mishra, Shubham Kumar / Mishra, Ayush Kumar / Shallum, Noel / Bhattacharya, Arnab

Efficacy, Challenges, and Potential of Modern AI Models

2023

Abstract: Legal QA platforms bear the promise to metamorphose the manner in which legal experts engage with jurisprudential documents. In this exposition, we embark on a comparative exploration of contemporary AI frameworks, gauging their adeptness in catering to ... ...

Abstract	Legal QA platforms bear the promise to metamorphose the manner in which legal experts engage with jurisprudential documents. In this exposition, we embark on a comparative exploration of contemporary AI frameworks, gauging their adeptness in catering to the unique demands of the Indian legal milieu, with a keen emphasis on Indian Legal Question Answering (AILQA). Our discourse zeroes in on an array of retrieval and QA mechanisms, positioning the OpenAI GPT model as a reference point. The findings underscore the proficiency of prevailing AILQA paradigms in decoding natural language prompts and churning out precise responses. The ambit of this study is tethered to the Indian criminal legal landscape, distinguished by its intricate nature and associated logistical constraints. To ensure a holistic evaluation, we juxtapose empirical metrics with insights garnered from seasoned legal practitioners, thereby painting a comprehensive picture of AI's potential and challenges within the realm of Indian legal QA.
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence
Subject code	340
Publishing date	2023-09-26
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Kinetic origin of nucleosome invasion by pioneer transcription factors.

Mondal, Anupam / Mishra, Sujeet Kumar / Bhattacherjee, Arnab

Biophysical journal

2021 Volume 120, Issue 23, Page(s) 5219–5230

Abstract: Recently, a cryo-electron microscopy study has captured different stages of nucleosome breathing dynamics that show partial unwrapping of DNA from histone core to permit transient access to the DNA sites by transcription factors. In practice, however, ... ...

Abstract	Recently, a cryo-electron microscopy study has captured different stages of nucleosome breathing dynamics that show partial unwrapping of DNA from histone core to permit transient access to the DNA sites by transcription factors. In practice, however, only a subset of transcription factors named pioneer factors can invade nucleosomes and bind to specific DNA sites to trigger essential DNA metabolic processes. We propose a discrete-state stochastic model that considers the interplay of nucleosome breathing and protein dynamics explicitly and estimate the mean time to search the target DNA sites. It is found that the molecular principle governing the search process on nucleosome is very different compared to that on naked DNA. The pioneer factors minimize their search times on nucleosomal DNA by compensating their nucleosome association rates by dissociation rates. A fine balance between the two presents a tradeoff between their nuclear mobility and error associated with the search process.
MeSH term(s)	Cryoelectron Microscopy ; DNA/genetics ; Histones ; Nucleosomes ; Transcription Factors/metabolism
Chemical Substances	Histones ; Nucleosomes ; Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2021-10-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.10.039
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Article ; Online: Analysing the distribution of SARS-CoV-2 infections in schools: integrating model predictions with real world observations

Mukherjee, Arnab / Mishra, Sharmistha / Kumar Murty, Vijaya / Chaudhuri, Swetaprovo

bioRxiv

Abstract: School closures were used as strategies to mitigate transmission in the COVID-19 pandemic. Understanding the nature of SARS-CoV-2 outbreaks and the distribution of infections in classrooms could help inform targeted or `precision9 preventive measures and ...

Abstract	School closures were used as strategies to mitigate transmission in the COVID-19 pandemic. Understanding the nature of SARS-CoV-2 outbreaks and the distribution of infections in classrooms could help inform targeted or `precision9 preventive measures and outbreak management in schools, in response to future pandemics. In this work, we derive an analytical model of Probability Density Function (PDF) of SARS-CoV-2 secondary infections and compare the model with infection data from all public schools in Ontario, Canada between September-December, 2021. The model accounts for major sources of variability in airborne transmission like viral load and dose-response (i.e., the human body9s response to pathogen exposure), air change rate, room dimension, and classroom occupancy. Comparisons between reported cases and the modeled PDF demonstrated the intrinsic overdispersed nature of the real-world and modeled distributions, but uncovered deviations stemming from an assumption of homogeneous spread within a classroom. The inclusion of near-field transmission effects resolved the discrepancy with improved quantitative agreement between the data and modeled distributions. This study provides a practical tool for predicting the size of outbreaks from one index infection, in closed spaces such as schools, and could be applied to inform more focused mitigation measures.
Keywords	covid19
Language	English
Publishing date	2023-12-21
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.12.21.572736
Database	COVID19

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