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Article ; Online: Pathway-resolved decomposition demonstrates correlation and noise dependencies of redundant information processing in recurrent feed-forward topologies.

Biswas, Ayan

2022 Volume 105, Issue 3-1, Page(s) 34406

Abstract: In a biochemical assay that converts fan-in networks into feed-forward loops (FFLs), we show that the inter-regulator redundant information about the output gene product can be decomposed into finer components, mediated by the constituent pathways. ... ...

Abstract	In a biochemical assay that converts fan-in networks into feed-forward loops (FFLs), we show that the inter-regulator redundant information about the output gene product can be decomposed into finer components, mediated by the constituent pathways. Variance-based information within the linear noise regime facilitates quantifying these submodular redundancies. Contrary to the conventional wisdom on information decomposition, we report that information redundancy depends nontrivially on inter-regulator correlation. For the type-1 coherent (C1) and incoherent (I1) FFLs, the direct regulatory path-mediated redundancy is certainly correlation independent. However, components induced by the indirect regulatory path and interpathway interference are correlation dependent in (non)linear fashion. The trade-off between information redundancy and similarly decomposable extrinsic noise from input to output node has been demonstrated for the pathways and full motifs. Our analyses suggest that the interpathway cross redundancy positively and negatively influences the superposition of elementary redundancies in the C1- and I1-FFLs, respectively. Their corresponding total extrinsic noise is produced by the weighted sum and difference of the pathway-specific components. We find that the I1-FFL is able to manufacture more varied redundancy and extrinsic noise responses compared to the C1-FFL. Underlying the differing characteristics of the composite metrics across FFL variants, there exist uniformly behaving pathway-dependent elements. The decomposition framework has been meticulously explored in biologically rational parametric realizations through analytical estimates and stochastic simulations.
Language	English
Publishing date	2022-04-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.105.034406
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Multivariate information processing characterizes fitness of a cascaded gene-transcription machinery.

Biswas, Ayan

Chaos (Woodbury, N.Y.)

2019 Volume 29, Issue 6, Page(s) 63108

Abstract: We report that a genetic two-step activation cascade processes diverse flavors of information, e.g., synergy, redundancy, and unique information. Our computations measuring reduction in Shannon entropies and reduction in variances produce differently ... ...

Abstract	We report that a genetic two-step activation cascade processes diverse flavors of information, e.g., synergy, redundancy, and unique information. Our computations measuring reduction in Shannon entropies and reduction in variances produce differently behaving absolute magnitudes of these informational flavors. We find that similarity can be brought in if these terms are evaluated in fractions with respect to corresponding total information. Each of the input signal and final gene-product is found to generate common or redundant information fractions (mostly) to predict each other, whereas they also complement one another to harness synergistic information fraction, predicting the intermediate biochemical species. For an optimally growing signal to maintain fixed steady-state abundance of activated downstream gene-products, the interaction information fractions for this cascade module shift from net-redundancy to information-independence.
MeSH term(s)	Electronic Data Processing ; Genetic Fitness ; HeLa Cells ; Humans ; Markov Chains ; Multivariate Analysis ; Signal-To-Noise Ratio ; Transcription, Genetic
Language	English
Publishing date	2019-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1472677-4
ISSN	1089-7682 ; 1054-1500
ISSN (online)	1089-7682
ISSN	1054-1500
DOI	10.1063/1.5092447
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Article: In silico characterization of five novel disease-resistance proteins in

Dhiman, Vedikaa / Biswas, Soham / Shekhawat, Rajveer Singh / Sadhukhan, Ayan / Yadav, Pankaj

3 Biotech

2024 Volume 14, Issue 2, Page(s) 48

Abstract: In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by : Supplementary information: The online version contains supplementary material ... ...

Abstract	In the current study, gene network analysis revealed five novel disease-resistance proteins against bacterial leaf blight (BB) and rice blast (RB) diseases caused by Supplementary information: The online version contains supplementary material available at 10.1007/s13205-023-03893-5.
Language	English
Publishing date	2024-01-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-023-03893-5
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Article ; Online: Electrochemistry-enabled residue-specific modification of peptides and proteins.

Bandyopadhyay, Ayan / Biswas, Pranay / Kundu, Sudipta K / Sarkar, Rajib

Organic & biomolecular chemistry

2024 Volume 22, Issue 6, Page(s) 1085–1101

Abstract: Selective chemical reactions at precise amino acid residues of peptides and proteins have become an exploding field of research in the last few decades. With the emerging utility of bioconjugated peptides and proteins as drug leads and therapeutic agents, ...

Abstract	Selective chemical reactions at precise amino acid residues of peptides and proteins have become an exploding field of research in the last few decades. With the emerging utility of bioconjugated peptides and proteins as drug leads and therapeutic agents, the design of smart protocols to modulate and conjugate biomolecules has become necessary. During this modification, the most important concern of biochemists is to keep intact the structural integrity of the biomolecules. Hence, a soft and selective biocompatible reaction environment is necessary. Electrochemistry, a mild and elegant tunable reaction platform to synthesize complex molecules while avoiding harsh and toxic chemicals, can provide such a reaction condition. However, this strategy is yet to be fully exploited in the field of selective modification of polypeptides. With this possibility, the use of electrochemistry as a reaction toolbox in peptide and protein chemistry is flourishing day by day. Unfortunately, there is no suitable review article summarizing the residue-specific modification of biomolecules. The present review provides a comprehensive summary of the latest manifested electrochemical approaches for the modulation of five redox-active amino acid residues, namely cysteine, tyrosine, tryptophan, histidine and methionine, found in peptides and proteins. The article also highlights the incredible potential of electrochemistry for the regio- as well as chemoselective bioconjugation strategy of biomolecules.
MeSH term(s)	Electrochemistry ; Proteins/chemistry ; Peptides/chemistry ; Amino Acids ; Methionine/chemistry
Chemical Substances	Proteins ; Peptides ; Amino Acids ; Methionine (AE28F7PNPL)
Language	English
Publishing date	2024-02-07
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/d3ob01857a
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Article ; Online: Synthesis, antimicrobial, anticancer evaluation and molecular docking with Bax and MDM2 of dibromosterculic acid.

Bose, Rahul / Paul, Ayan / Dutta, Rajashree / Hazra, Anjan / Pramanik, Arindam / Mandal Biswas, Suparna

Natural product research

2023 , Page(s) 1–8

Abstract: Dibromosterculic acid [8-(1,2-dibromo-2-octylcyclopropyl)-octanoic acid], a new synthetic derivative was prepared by bromination of sterculic acid. This synthetic derivative showed strong fungicidal activity against two pathogenic fungal species ... ...

Abstract	Dibromosterculic acid [8-(1,2-dibromo-2-octylcyclopropyl)-octanoic acid], a new synthetic derivative was prepared by bromination of sterculic acid. This synthetic derivative showed strong fungicidal activity against two pathogenic fungal species namely
Language	English
Publishing date	2023-12-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2185747-7
ISSN	1478-6427 ; 1478-6419
ISSN (online)	1478-6427
ISSN	1478-6419
DOI	10.1080/14786419.2023.2294107
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Article ; Online: Extrinsic noise of the target gene governs abundance pattern of feed-forward loop motifs.

Momin, Md Sorique Aziz / Biswas, Ayan

Physical review. E

2020 Volume 101, Issue 5-1, Page(s) 52411

Abstract: Feed-forward loop (FFL) is found to be a recurrent structure in bacterial and yeast gene transcription regulatory networks. In a generic FFL, transcription factor (TF) S regulates production of another TF X while both of these TFs regulate production of ... ...

Abstract	Feed-forward loop (FFL) is found to be a recurrent structure in bacterial and yeast gene transcription regulatory networks. In a generic FFL, transcription factor (TF) S regulates production of another TF X while both of these TFs regulate production of final gene-product Y. Depending upon the regulatory programs (activation or repression), FFLs are grouped into two broad classes: coherent (C) and incoherent (I), each class containing four distinct types (C1-C4 and I1-I4). These FFL types are experimentally observed to occur with varied frequencies, C1 and I1 being the abundant ones. Here we present a stochastic framework singling out the absolute value of the normalized covariance of X and Y to be the determining factor behind the abundance of FFLs while considering differential promoter activities of X and Y. Our theoretical construct employs two possible signal integration mechanisms (additive and multiplicative) to synthesize Y while steady-state population level of S remains fixed or becomes tunable reflecting two possible environmental signaling scenarios. Our model categorically points out that abundant FFLs exhibit higher amount of the designated metric which has a biophysical connotation of extrinsic noise for the target gene Y. Our predictions emanating from an overarching analytical expression utilizing biologically plausible parametric conditions are substantiated by stochastic simulation.
MeSH term(s)	Analysis of Variance ; Feedback, Physiological ; Gene Regulatory Networks ; Models, Genetic ; Transcription, Genetic
Language	English
Publishing date	2020-06-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.101.052411
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Book ; Online: Design of a Low-Power High-Gain Bio-Medical Operational Amplifier in 65nm Technology using gm/ID Methodology

Biswas, Ayan / Dhabal, Supriya / Venkateswaran, Palaniandavar

2023

Abstract: Operational Amplifiers (Op-Amps) play a crucial role in the field of biomedical engineering, as they enable signal amplification and processing in various medical devices. With the increasing demand for portable and low-power biomedical devices, ... ...

Abstract	Operational Amplifiers (Op-Amps) play a crucial role in the field of biomedical engineering, as they enable signal amplification and processing in various medical devices. With the increasing demand for portable and low-power biomedical devices, designing Op-Amps specifically tailored for such applications is essential. In response to this need, a low-power high-gain Op-Amp designed for biomedical applications using TSMC 65nm technology has been proposed. This Op-Amp incorporates a two-stage miller compensated topology, which is well-known for its superior performance in gain, gain bandwidth product and power consumption. The proposed Op-Amp contributes to the field of biomedical engineering by offering a tailored solution that enhances signal processing capabilities, enables accurate data acquisition, and improves overall efficiency in healthcare systems. The design methodology and simulation results presented in this paper provide insights into the performance and potential impact of the Op-Amp in advancing biomedical devices and systems.
Keywords	Computer Science - Hardware Architecture ; Electrical Engineering and Systems Science - Systems and Control
Subject code	621
Publishing date	2023-09-09
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: SwinDocSegmenter

Banerjee, Ayan / Biswas, Sanket / Lladós, Josep / Pal, Umapada

An End-to-End Unified Domain Adaptive Transformer for Document Instance Segmentation

2023

Abstract: Instance-level segmentation of documents consists in assigning a class-aware and instance-aware label to each pixel of the image. It is a key step in document parsing for their understanding. In this paper, we present a unified transformer encoder- ... ...

Abstract	Instance-level segmentation of documents consists in assigning a class-aware and instance-aware label to each pixel of the image. It is a key step in document parsing for their understanding. In this paper, we present a unified transformer encoder-decoder architecture for en-to-end instance segmentation of complex layouts in document images. The method adapts a contrastive training with a mixed query selection for anchor initialization in the decoder. Later on, it performs a dot product between the obtained query embeddings and the pixel embedding map (coming from the encoder) for semantic reasoning. Extensive experimentation on competitive benchmarks like PubLayNet, PRIMA, Historical Japanese (HJ), and TableBank demonstrate that our model with SwinL backbone achieves better segmentation performance than the existing state-of-the-art approaches with the average precision of \textbf{93.72}, \textbf{54.39}, \textbf{84.65} and \textbf{98.04} respectively under one billion parameters. The code is made publicly available at: \href{https://github.com/ayanban011/SwinDocSegmenter}{github.com/ayanban011/SwinDocSegmenter} Comment: Accepted to ICDAR 2023 (San Jose, California)
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning
Subject code	006
Publishing date	2023-05-08
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mechano-regulation by clathrin pit-formation and passive cholesterol-dependent tubules during de-adhesion.

Mandal, Tithi / Biswas, Arikta / Ghosh, Tanmoy / Manikandan, Sreekanth / Kundu, Avijit / Banerjee, Ayan / Mitra, Dhrubaditya / Sinha, Bidisha

Cellular and molecular life sciences : CMLS

2024 Volume 81, Issue 1, Page(s) 43

Abstract: Adherent cells ensure membrane homeostasis during de-adhesion by various mechanisms, including endocytosis. Although mechano-chemical feedbacks involved in this process have been studied, the step-by-step build-up and resolution of the mechanical changes ...

Abstract	Adherent cells ensure membrane homeostasis during de-adhesion by various mechanisms, including endocytosis. Although mechano-chemical feedbacks involved in this process have been studied, the step-by-step build-up and resolution of the mechanical changes by endocytosis are poorly understood. To investigate this, we studied the de-adhesion of HeLa cells using a combination of interference reflection microscopy, optical trapping and fluorescence experiments. We found that de-adhesion enhanced membrane height fluctuations of the basal membrane in the presence of an intact cortex. A reduction in the tether force was also noted at the apical side. However, membrane fluctuations reveal phases of an initial drop in effective tension followed by saturation. The area fractions of early (Rab5-labelled) and recycling (Rab4-labelled) endosomes, as well as transferrin-labelled pits close to the basal plasma membrane, also transiently increased. On blocking dynamin-dependent scission of endocytic pits, the regulation of fluctuations was not blocked, but knocking down AP2-dependent pit formation stopped the tension recovery. Interestingly, the regulation could not be suppressed by ATP or cholesterol depletion individually but was arrested by depleting both. The data strongly supports Clathrin and AP2-dependent pit-formation to be central to the reduction in fluctuations confirmed by super-resolution microscopy. Furthermore, we propose that cholesterol-dependent pits spontaneously regulate tension under ATP-depleted conditions.
MeSH term(s)	Humans ; Clathrin/metabolism ; Coated Pits, Cell-Membrane/metabolism ; HeLa Cells ; Endocytosis/physiology ; Cholesterol/metabolism ; Adenosine Triphosphate/metabolism ; Cell Membrane/metabolism
Chemical Substances	Clathrin ; Cholesterol (97C5T2UQ7J) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2024-01-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-023-05072-4
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Article ; Online: Environmental bisphenol A disrupts methylation of steroidogenic genes in the ovary of Paradise threadfin Polynemus paradiseus via abnormal DNA methylation: Implications for human exposure and health risk assessment.

Kundu, Sourav / Ray, Archisman / Das Gupta, Subhadeep / Biswas, Ayan / Roy, Shreya / Kumar Tiwari, Nitish / Kumar, V Santhana / Das, Basanta Kumar

Chemosphere

2024 Volume 351, Page(s) 141236

Abstract: Bisphenol A, endocrine-disrupting chemicals (EDCs) impacting disease development via epigenetic modifications, is crucial in transcriptional regulation. However, ecotoxicology's limited exploration of epigenetics prompted our study's objective: examining ...

Abstract	Bisphenol A, endocrine-disrupting chemicals (EDCs) impacting disease development via epigenetic modifications, is crucial in transcriptional regulation. However, ecotoxicology's limited exploration of epigenetics prompted our study's objective: examining the extended exposure of riverine Bisphenol A (BPA), a potent EDC, on DNA methylation during female paradise threadfin (Polynemus paradiseus) reproductive maturation. Assessing BPA contamination in riverine water, we collected fish samples from two locations with distinct contamination levels. In the highly contaminated region (Hc), we observed elevated DNA methylation in aromatase (7.5-fold), 20β-HSD (3-fold), and FSHR (2-fold) genes. Hormone receptor investigation highlighted an escalating connection between transcriptional hyper-methylation and contamination levels. Additionally, our study revealed a positive correlation between oocyte growth and global DNA methylation, suggesting BPA's potential to modify DNA methylation in female paradise threadfins. This effect likely occurs through changes in hormone receptor expression, persisting throughout oocyte maturation. Notably, our research, the first of its kind in estuarine areas, confirmed BPA contamination in paradise threadfins, raising concerns about potential health risks for humans.
MeSH term(s)	Animals ; Humans ; Female ; DNA Methylation ; Ovary ; Benzhydryl Compounds/metabolism ; Endocrine Disruptors/metabolism ; Fishes ; Hormones/metabolism ; Risk Assessment ; Phenols
Chemical Substances	bisphenol A (MLT3645I99) ; Benzhydryl Compounds ; Endocrine Disruptors ; Hormones ; Phenols
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2024.141236
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