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Article: Newcastle Disease in Backyard Poultry Rearing in the Northeastern States of India: Challenges and Control Strategies.

Puro, Kekunguu / Sen, Arnab

2022 Volume 9, Page(s) 799813

Language	English
Publishing date	2022-04-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2022.799813
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Article: Niche adaptation of Frankia do not drastically influence their metabolic profiling

Sarkar, Indrani / Sen, Arnab

Journal of forest research. 2022 Mar. 04, v. 27, no. 2

2022

Abstract: Metabolic-profiling (metabolomics/metabonomics) is a measurement strategy among biological systems for low-molecular-weight metabolites and their corresponding intermediates acting as dynamic physiological, pathophysiological and developmental stimuli. ... ...

Abstract	Metabolic-profiling (metabolomics/metabonomics) is a measurement strategy among biological systems for low-molecular-weight metabolites and their corresponding intermediates acting as dynamic physiological, pathophysiological and developmental stimuli. Information regarding the metabolomics of Frankia is elusive. In this study, we analyzed 48 Frankia whole-genome sequences. Kyoto Encyclopedia of Genes and Genomes (KEGG) database and KEGG Automatic Annotation Server (KAAS) were used for the prediction and functional annotation of genes associated with diverse metabolic pathways. Comprehensive codon and amino-acid usage analyses along with tRNA adaptation index and dN/dS-based evolutionary inquest were performed. We have used the Database-of-Essential-Genes (DEG) server to predict the essentiality of the metabolic pathway-related-genes. We found a strong effect of compositional constraints on the metabolic pathway genes of Frankia. The evolutionary analysis revealed the conserved nature of the studied genes. Since the metabolic pathway-related genes were found to be housekeeping genes, they are conserved and less evolved. This was further validated with a dN/dS value of less than 1. Moreover, the number of synonymous changes was more than non-synonymous changes so that the amino acid sequence remains identical. The cluster of orthologs (COG) analysis revealed “metabolism” as the main functional category of the studied gene set. The core metabolic pathway-related genes among considered Frankia strains accumulated 115 genes. This study for the first time reveals the genomic characteristics of the metabolic pathway-related genes among Frankia. From all the analysis, we could hypothesize that in spite of their host specificity and differential taxonomical distribution, Frankia maintain a core metabolic proficiency among them.
Keywords	Frankia ; amino acid sequences ; amino acids ; biochemical pathways ; databases ; forests ; genomics ; host specificity ; metabolites ; metabolomics ; prediction ; research
Language	English
Dates of publication	2022-0304
Size	p. 100-105.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2104467-3
ISSN	1610-7403 ; 1341-6979
ISSN (online)	1610-7403
ISSN	1341-6979
DOI	10.1080/13416979.2022.2028707
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Weak Universality Induced by Q=±2e Charges at the Deconfinement Transition of a (2+1)-Dimensional U(1) Lattice Gauge Theory.

Sau, Indrajit / Sen, Arnab / Banerjee, Debasish

Physical review letters

2023 Volume 130, Issue 7, Page(s) 71901

Abstract: Matter-free lattice gauge theories (LGTs) provide an ideal setting to understand confinement to deconfinement transitions at finite temperatures, which is typically due to the spontaneous breakdown (at large temperatures) of the center symmetry ... ...

Abstract	Matter-free lattice gauge theories (LGTs) provide an ideal setting to understand confinement to deconfinement transitions at finite temperatures, which is typically due to the spontaneous breakdown (at large temperatures) of the center symmetry associated with the gauge group. Close to the transition, the relevant degrees of freedom (Polyakov loop) transform under these center symmetries, and the effective theory depends on only the Polyakov loop and its fluctuations. As shown first by Svetitsky and Yaffe, and subsequently verified numerically, for the U(1) LGT in (2+1) dimensions, the transition is in the 2D XY universality class, while for the Z_{2} LGT, it is in the 2D Ising universality class. We extend this classic scenario by adding higher charged matter fields and show that the critical exponents γ and ν can change continuously as a coupling is varied, while their ratio is fixed to the 2D Ising value. While such weak universality is well known for spin models, we demonstrate this for LGTs for the first time. Using an efficient cluster algorithm, we show that the finite temperature phase transition of the U(1) quantum link LGT in the spin S=1/2 representation is in the 2D XY universality class, as expected. On the addition of Q=±2e charges distributed thermally, we demonstrate the occurrence of weak universality.
Language	English
Publishing date	2023-03-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.130.071901
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Article ; Online: Quantum Scars from Zero Modes in an Abelian Lattice Gauge Theory on Ladders.

Banerjee, Debasish / Sen, Arnab

Physical review letters

2021 Volume 126, Issue 22, Page(s) 220601

Abstract: We consider the spectrum of a U(1) quantum link model where gauge fields are realized as S=1/2 spins and demonstrate a new mechanism for generating quantum many-body scars (high-energy eigenstates that violate the eigenstate thermalization hypothesis) in ...

Abstract	We consider the spectrum of a U(1) quantum link model where gauge fields are realized as S=1/2 spins and demonstrate a new mechanism for generating quantum many-body scars (high-energy eigenstates that violate the eigenstate thermalization hypothesis) in a constrained Hilbert space. Many-body dynamics with local constraints has attracted much attention due to the recent discovery of nonergodic behavior in quantum simulators based on Rydberg atoms. Lattice gauge theories provide natural examples of constrained systems since physical states must be gauge invariant. In our case, the Hamiltonian H=O_{kin}+λO_{pot}, where O_{pot} (O_{kin}) is diagonal (off-diagonal) in the electric flux basis, contains exact midspectrum zero modes at λ=0 whose number grows exponentially with system size. This massive degeneracy is lifted at any nonzero λ but some special linear combinations that simultaneously diagonalize O_{kin} and O_{pot} survive as quantum many-body scars, suggesting an "order-by-disorder" mechanism in the Hilbert space. We give evidence for such scars and show their dynamical consequences on two-leg ladders with up to 56 spins, which may be tested using available proposals of quantum simulators. Results on wider ladders point towards their presence in two dimensions as well.
Language	English
Publishing date	2021-06-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.126.220601
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Article ; Online: An overview of

Gtari, Maher / Beauchemin, Nicholas J / Sarker, Indrani / Sen, Arnab / Ghodhbane-Gtari, Faten / Tisa, Louis S

Applied and environmental microbiology

2024 , Page(s) e0028824

Abstract: In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the : Importance: ... ...

Abstract	In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Importance: While
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/aem.00288-24
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Article ; Online: Neem and Turmeric in the management of Covid Associated Mucormycosis (CAM) derived through network pharmacology.

Datta, Sutapa / Sarkar, Indrani / Sen, Gargi / Sen, Arnab

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 8, Page(s) 3281–3294

Abstract: Mucormycosis or 'Black Fungus' has been known to target immunocompromised individuals even before the emergence of COVID-19. Nevertheless, the present circumstances provide the best opening for Covid Associated Mucormycosis (CAM), as the global pandemic ... ...

Abstract	Mucormycosis or 'Black Fungus' has been known to target immunocompromised individuals even before the emergence of COVID-19. Nevertheless, the present circumstances provide the best opening for Covid Associated Mucormycosis (CAM), as the global pandemic is engulfing a large part of human population making them immunocompromised. This drastic increase in Mucormycosis infections has to be addressed as early as possible. There is a growing tendency of relying upon herbal drugs that have minimal side effects and does not compromise our immune system. Recently, the concept of network pharmacology has grabbed the attention of modern science, especially advanced medical sciences. This is a new discipline that can use computational power to systematically catalogue the molecular interactions between botanical formulations and the human body. In this study, Neem and Turmeric was considered as the target plants and an attempt was made to reveal various aspects through which phytocompounds derived from them may effectively manage CAM menace. We have taken a step-by-step approach for identifying the target proteins and ligands associated with Mucormycosis treatment. Functional network analysis and Molecular docking approaches were applied to validate our findings. Quercetin derived from both Neem and Turmeric was found to be one of the main phytocompounds working against Mucormycosis. Along with that, Caffeic acid, Curcumin, Kaempferol, Tetrahydrocurcumin and Myricetin also play a pivotal role in fighting against Black-Fungus. A thorough analysis of our result suggested a triple-front attack on the fungal pathogens and the approaches are necrosis inhibition, iron chelation and immuno-boosting.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Mucormycosis/drug therapy ; Curcuma ; Network Pharmacology ; Molecular Docking Simulation ; COVID-19
Language	English
Publishing date	2022-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2048077
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Article ; Online: In silico

Sarkar, Indrani / Sen, Arnab

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 8, Page(s) 3706–3710

Abstract: The ongoing outbreak of Coronavirus disease 2019 (COVID-19) is a matter of great concern. Although the mortality rate caused by this virus is less than that of SARS and MERS, it is showing higher efficacy in terms of human-to-human transmission. Several ... ...

Abstract	The ongoing outbreak of Coronavirus disease 2019 (COVID-19) is a matter of great concern. Although the mortality rate caused by this virus is less than that of SARS and MERS, it is showing higher efficacy in terms of human-to-human transmission. Several strategies have been taken by scientists and researchers worldwide to combat this virus. Numerous phytochemicals and synthesized chemicals are under incessant inspection to obtain a potent anti-covid drug. Since, till now no precise therapy is available for covid patients, researchers are trying to categorize all possible anti-covid substances. Repurposing of drugs and combined drug therapy are becoming popular in treating such viral diseases. In this study, we are proposing the repurposing of three chemicals
MeSH term(s)	COVID-19/drug therapy ; Common Cold ; Dexamethasone/pharmacology ; Dextromethorphan ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Prednisolone/pharmacology ; Protease Inhibitors ; SARS-CoV-2
Chemical Substances	Protease Inhibitors ; Dextromethorphan (7355X3ROTS) ; Dexamethasone (7S5I7G3JQL) ; Prednisolone (9PHQ9Y1OLM) ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2020-11-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1850528
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Article ; Online: In-silico

Lala, Mousikha / Bhattacharjee, Soumita / Ghosh, Chandra / Sen, Arnab / Sarkar, Indrani

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 8, Page(s) 3511–3523

Abstract: One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however, the specific causes remain unclear. Despite numerous papers that have been flooded in different scientific journals clear clinical picture of COVID-19 ... ...

Abstract	One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however, the specific causes remain unclear. Despite numerous papers that have been flooded in different scientific journals clear clinical picture of COVID-19 aftermath persists to remain fuzzy. The survivors of severe COVID-19infection having defeated the virus are just the starting of an uncharted recovery path. Currently, there is no drug available that is safe to consume to combat this pandemic. However, researchers still struggling to find specific therapeutic solutions. The present study employed an
MeSH term(s)	Citrus/chemistry ; Humans ; COVID-19/complications ; Phytochemicals/chemistry ; Phytochemicals/therapeutic use ; Post-Acute COVID-19 Syndrome/drug therapy ; Molecular Docking Simulation ; Plant Extracts/chemistry ; Drug Development ; Cyclooxygenase 2/chemistry ; Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors ; Receptors, N-Methyl-D-Aspartate/chemistry ; Protein Binding ; Vascular Cell Adhesion Molecule-1/antagonists & inhibitors ; Cyclooxygenase 2 Inhibitors/chemistry ; Limonene/chemistry ; Limonene/pharmacology
Chemical Substances	Phytochemicals ; Plant Extracts ; Cyclooxygenase 2 (EC 1.14.99.1) ; Receptors, N-Methyl-D-Aspartate ; Vascular Cell Adhesion Molecule-1 ; Cyclooxygenase 2 Inhibitors ; Limonene (9MC3I34447)
Language	English
Publishing date	2022-03-17
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2051744
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Article: Whole genome sequencing of

Chhettri, Saroja / Sevigny, Joseph / Pesce, Céline / Sarkar, Indrani / Thomas, W Kelley / Nouioui, Imen / Sen, Gargi / Tisa, Louis S / Sen, Arnab

Journal of genomics

2024 Volume 12, Page(s) 6–13

Abstract: ... ...

Abstract	Streptomyces
Language	English
Publishing date	2024-01-01
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2692697-0
ISSN	1839-9940
ISSN	1839-9940
DOI	10.7150/jgen.87156
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Article ; Online: Analytic approaches to periodically driven closed quantum systems: methods and applications.

Sen, Arnab / Sen, Diptiman / Sengupta, K

Journal of physics. Condensed matter : an Institute of Physics journal

2021 Volume 33, Issue 44

Abstract: We present a brief overview of some of the analytic perturbative techniques for the computation of the Floquet Hamiltonian for a periodically driven, or Floquet, quantum many-body system. The key technical points about each of the methods discussed are ... ...

Abstract	We present a brief overview of some of the analytic perturbative techniques for the computation of the Floquet Hamiltonian for a periodically driven, or Floquet, quantum many-body system. The key technical points about each of the methods discussed are presented in a pedagogical manner. They are followed by a brief account of some chosen phenomena where these methods have provided useful insights. We provide an extensive discussion of the Floquet-Magnus (FM) expansion, the adiabatic-impulse approximation, and the Floquet perturbation theory. This is followed by a relatively short discourse on the rotating wave approximation, a FM resummation technique and the Hamiltonian flow method. We also provide a discussion of some open problems which may possibly be addressed using these methods.
Language	English
Publishing date	2021-08-24
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1472968-4
ISSN	1361-648X ; 0953-8984
ISSN (online)	1361-648X
ISSN	0953-8984
DOI	10.1088/1361-648X/ac1b61
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