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Article ; Online: The photodynamic approach to the molecular-level origin of metal-guided photochromism and ultrafast absorption spectroscopy.

Bar, Nandagopal / Chowdhury, Pranesh / Kanti Das, Gourab

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

2024 Volume 312, Page(s) 124031

Abstract: Metal-guided photochromic material (photochromic complex) is one of the latest versions of photo-responsive materials due to their smart behaviour and promising real-world applications. The present work explores the molecular-level origin of metal-guided ...

Abstract	Metal-guided photochromic material (photochromic complex) is one of the latest versions of photo-responsive materials due to their smart behaviour and promising real-world applications. The present work explores the molecular-level origin of metal-guided photochromism using a photodynamic approach and ultrafast absorption spectroscopy, to address all existing lacunas. Here, rhodamine B (RhB) dye containing the Schiff base zinc complex is considered a representative photochromic complex for both theoretical treatment and experimental observations. Detailed theoretical studies, including geometry optimization, frontier molecular orbital (FMO) analysis, transition state (TS) identification, and natural bond orbital (NBO) analysis, along with spectral studies, are employed to investigate the photodynamic equilibrium (enol-form keto-form). This equilibrium is regulated by the interplay of intrinsic factors (push-pull effect) and extrinsic factors (such as UV-light, the phenolic-OH group, metal ions, and solvents). The potential energy surface (PES) of the photo-conversion (enol →enol→keto→ meta-stable keto) is evaluated. While, the PES of the reversion (meta-stable keto →enol) is constructed based on the studies of thermo-reversion and photo-reversion. Finally, the theoretical findings related to the photodynamic equilibrium are validated by direct experimental evidence obtained through femtosecond transient absorption (fs-TA) spectroscopy.
Language	English
Publishing date	2024-02-13
Publishing country	England
Document type	Journal Article
ZDB-ID	210413-1
ISSN	1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
ISSN (online)	1873-3557
ISSN	0370-8322 ; 0584-8539 ; 1386-1425
DOI	10.1016/j.saa.2024.124031
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Article ; Online: Mechanistic insight highlights the key steps and significance of metal in Ir(III)-catalysed C-H activated chromones generation.

Pal, Poulami / Das, Gourab Kanti

Organic & biomolecular chemistry

2022

Abstract: A mild C-H activation reaction catalysed by an Ir(III)-complex to generate chromones from salicylaldehydes at room temperature has been studied theoretically to explore the reaction mechanism. The DFT study reveals that the key point of the catalytic ... ...

Abstract	A mild C-H activation reaction catalysed by an Ir(III)-complex to generate chromones from salicylaldehydes at room temperature has been studied theoretically to explore the reaction mechanism. The DFT study reveals that the key point of the catalytic cycle is cyclometallation, more precisely it is in the C-H metallation step where the significance of the metal becomes obvious. The favourable pathway includes several steps, namely, coordination of the substrate with the metal catalyst, O-H metallation, C-H metallation, denitrogenation, migration insertion, proton transfer, and demetallation. On removal of one pivalic acid, the metal is activated and the C-H metallation proceeds
Language	English
Publishing date	2022-11-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/d2ob01785g
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Correction: A biomass-derived dual crosslinked DNA-nanoparticle hydrogel for visible light-induced photodynamic bacterial inactivation.

Das, Gourab / Nayak, Suman / Kotness, Dinesh Kumar / Das, Prolay

Soft matter

2024 Volume 20, Issue 2, Page(s) 449

Abstract: Correction for 'A biomass-derived dual crosslinked DNA-nanoparticle hydrogel for visible light-induced photodynamic bacterial inactivation' by Gourab ... ...

Abstract	Correction for 'A biomass-derived dual crosslinked DNA-nanoparticle hydrogel for visible light-induced photodynamic bacterial inactivation' by Gourab Das
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Published Erratum
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d3sm90175k
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Article: Scrub Typhus Presenting as Bilateral Sixth Nerve Palsy.

Bhattacharjee, Sukriti / Debbarma, Bibhu / Debbarma, Rajesh K / Das, Gourab

Cureus

2024 Volume 16, Issue 3, Page(s) e56692

Abstract: Scrub typhus, a tropical rickettsial infection, can have various neurological manifestations. Here, we present the case of an otherwise healthy 19-year-old female who presented to the emergency department with fever, headache, and diplopia. On ... ...

Abstract	Scrub typhus, a tropical rickettsial infection, can have various neurological manifestations. Here, we present the case of an otherwise healthy 19-year-old female who presented to the emergency department with fever, headache, and diplopia. On examination, she was found to have bilateral sixth nerve palsy and bilateral papilledema. Initial unenhanced CT of the brain and CT venogram were unremarkable. The cerebrospinal fluid study was normal. Later, bloodwork revealed high titers of
Language	English
Publishing date	2024-03-22
Publishing country	United States
Document type	Case Reports
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.56692
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Article ; Online: LncRTPred: Predicting RNA-RNA mode of interaction mediated by lncRNA.

Das, Gourab / Das, Troyee / Parida, Sibun / Ghosh, Zhumur

IUBMB life

2023 Volume 76, Issue 1, Page(s) 53–68

Abstract: Long non-coding RNAs (lncRNAs) play a significant role in various biological processes. Hence, it is utmost important to elucidate their functions in order to understand the molecular mechanism of a complex biological system. This versatile RNA molecule ... ...

Abstract	Long non-coding RNAs (lncRNAs) play a significant role in various biological processes. Hence, it is utmost important to elucidate their functions in order to understand the molecular mechanism of a complex biological system. This versatile RNA molecule has diverse modes of interaction, one of which constitutes lncRNA-mRNA interaction. Hence, identifying its target mRNA is essential to understand the function of an lncRNA explicitly. Existing lncRNA target prediction tools mainly adopt thermodynamics approach. Large execution time and inability to perform real-time prediction limit their usage. Further, lack of negative training dataset has been a hindrance in the path of developing machine learning (ML) based lncRNA target prediction tools. In this work, we have developed a ML-based lncRNA-mRNA target prediction model- 'LncRTPred'. Here we have addressed the existing problems by generating reliable negative dataset and creating robust ML models. We have identified the non-interacting lncRNA and mRNAs from the unlabelled dataset using BLAT. It is further filtered to get a reliable set of outliers. LncRTPred provides a cumulative_model_score as the final output against each query. In terms of prediction accuracy, LncRTPred outperforms other popular target prediction protocols like LncTar. Further, we have tested its performance against experimentally validated disease-specific lncRNA-mRNA interactions. Overall, performance of LncRTPred is heavily dependent on the size of the training dataset, which is highly reflected by the difference in its performance for human and mouse species. Its performance for human species shows better as compared to that for mouse when applied on an unknown data due to smaller size of the training dataset in case of mouse compared to that of human. Availability of increased number of lncRNA-mRNA interaction data for mouse will improve the performance of LncRTPred in future. Both webserver and standalone versions of LncRTPred are available. Web server link: http://bicresources.jcbose.ac.in/zhumur/lncrtpred/index.html. Github Link: https://github.com/zglabDIB/LncRTPred.
MeSH term(s)	Humans ; Animals ; Mice ; RNA, Long Noncoding/genetics ; RNA, Messenger/genetics ; Computational Biology/methods
Chemical Substances	RNA, Long Noncoding ; RNA, Messenger
Language	English
Publishing date	2023-08-22
Publishing country	England
Document type	Journal Article
ZDB-ID	1492141-8
ISSN	1521-6551 ; 1521-6543
ISSN (online)	1521-6551
ISSN	1521-6543
DOI	10.1002/iub.2778
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Article ; Online: MicroRNA mediated gene regulatory circuits leads to machine learning based preliminary detection of acute myeloid leukemia.

Sarkar, Arijita / Das, Troyee / Das, Gourab / Ghosh, Zhumur

Computational biology and chemistry

2023 Volume 104, Page(s) 107859

Abstract: Acute Myeloid Leukemia (AML) can be detected based on morphology, cytochemistry, immunological markers, and cytogenetics. MicroRNAs (miRNAs) influence key biological pathways in multiple haematological malignancies including AML. In this work, we have ... ...

Abstract	Acute Myeloid Leukemia (AML) can be detected based on morphology, cytochemistry, immunological markers, and cytogenetics. MicroRNAs (miRNAs) influence key biological pathways in multiple haematological malignancies including AML. In this work, we have analysed the miRNome and the transcriptome of normal and AML samples and have identified the significant set of miRNA-target mRNA pairs present within AML- Peripheral Blood and AML- Bone Marrow samples from both tissue and cell lines. The miRNA target genes are further filtered based on their functional significance in AML system. These filtered genes constitute the set of selected miRNA target features, which have been finally used for developing machine learning based prediction tool, 'TbAMLPred' for preliminary detection of AML. This model implements both unsupervised clustering and supervised classification algorithms that would increase the reliability of prediction. Our results show that the selected miRNA target-based features can separate the control and disease samples linearly. Overall, we put forward 'TbAMLPred' for a non-invasive mode of preliminary AML diagnosis in future. Github link for accessing TbAMLPred: https://github.com/zglabDIB/TbAMLPred.
MeSH term(s)	Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Reproducibility of Results ; Leukemia, Myeloid, Acute/diagnosis ; Leukemia, Myeloid, Acute/genetics ; Cell Line ; Gene Regulatory Networks/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2023-03-31
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2023.107859
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Article ; Online: Insights into colistin-mediated fluorescence labelling of bacterial LPS.

Mandal, Saurodeep / Patra, Dipanwita / Mandal, Sukhendu / Das, Gourab Kanti / Sahoo, Prithidipa

RSC advances

2024 Volume 14, Issue 4, Page(s) 2770–2777

Abstract: Gram-negative bacterial infections are becoming untreatable due to their ability to mutate, and the gradual development of their resistance to the available antimicrobials. In recent times colistin, a drug of last resort, started losing its efficacy ... ...

Abstract	Gram-negative bacterial infections are becoming untreatable due to their ability to mutate, and the gradual development of their resistance to the available antimicrobials. In recent times colistin, a drug of last resort, started losing its efficacy towards multidrug-resistant bacterial infections. Colistin targets bacterial endotoxin lipopolysaccharides (LPS) and destabilises the cytoplasmic membrane by disrupting the outer LPS membrane. In this study, we have tried to label the bacterial LPS, the main constituent of the cytoplasmic membrane of bacterial cells, to try to understand the interaction mechanism of LPS with colistin. The chemosensor, naphthaldehyde appended furfural (NAF) that selectively recognises colistin can label LPS, by showing its fluorescence signals. The computationally derived three-dimensional structure of LPS has been introduced to speculate on the possible binding mode of colistin with LPS, and this was also thoroughly studied with the help of quantum mechanics and molecular dynamics energy minimisation. Fluorescence microscopy and FE-SEM microscopic studies were also used to observe the change in the structural morphology of colistin-sensitive and resistant
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d3ra07107c
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Article ; Online: TarpiD, a database of putative and validated targets of piRNAs.

Gupta, Pooja / Das, Gourab / Chattopadhyay, Trisha / Ghosh, Zhumur / Mallick, Bibekanand

Molecular omics

2023 Volume 19, Issue 9, Page(s) 706–713

Abstract: Piwi-interacting RNAs (piRNAs) are a novel class of 18-36 nts long small non-coding single-stranded RNAs that play crucial roles in a wide array of critical biological activities besides maintaining genome integrity by transposon silencing. piRNAs ... ...

Abstract	Piwi-interacting RNAs (piRNAs) are a novel class of 18-36 nts long small non-coding single-stranded RNAs that play crucial roles in a wide array of critical biological activities besides maintaining genome integrity by transposon silencing. piRNAs influence biological processes and pathways by regulating gene expression at transcriptional and post-transcriptional level. Studies have reported that piRNAs silence various endogenous genes post-transcriptionally by binding to respective mRNAs through interaction with the PIWI proteins. Several thousands of piRNAs have been discovered in animals, but their functions remain largely undiscovered owing to a lack of proper guiding principles of piRNA targeting or diversity in targeting patterns amongst piRNAs from the same or different species. Identification of piRNA targets is essential for deciphering their functions. There are a few tools and databases on piRNAs, but there are no systematic and exclusive repositories to obtain information on target genes regulated by piRNAs and other related information. Hence, we developed a user-friendly database named TarpiD (Targets of piRNA Database) that offers comprehensive information on piRNA and its targets, including their expression, methodologies (high-throughput or low-throughput) for target identification/validation, cells/tissue types, diseases, target gene regulation types, target binding regions, and key functions driven by piRNAs through target gene interactions. The contents of TarpiD are curated from the published literature and enable users to search and download the targets of a particular piRNA or the piRNAs that target a specific gene for use in their research. This database harbours 28 682 entries of piRNA-target interactions supported by 15 methodologies reported in hundreds of cell types/tissues from 9 species. TarpiD will be a valuable resource for a better understanding of the functions and gene-regulatory mechanisms mediated by piRNAs. TarpiD is freely accessible for academic use at https://tarpid.nitrkl.ac.in/tarpid_db/.
MeSH term(s)	Animals ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Piwi-Interacting RNA ; Gene Expression Regulation ; Proteins/metabolism
Chemical Substances	RNA, Small Interfering ; Piwi-Interacting RNA ; Proteins
Language	English
Publishing date	2023-10-30
Publishing country	England
Document type	Journal Article
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/d3mo00098b
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Article ; Online: A biomass-derived dual crosslinked DNA-nanoparticle hydrogel for visible light-induced photodynamic bacterial inactivation.

Das, Gourab / Nayak, Suman / Kotness, Dinesh Kumar / Das, Prolay

Soft matter

2023 Volume 19, Issue 48, Page(s) 9511–9519

Abstract: Sustainability in developing novel nanomaterials (NPs) from biomass sources is a challenging proposition mainly due to the difficulty of infusing or retaining desired chemical functionalities in the biomass substrate. In this study, we demonstrate the ... ...

Abstract	Sustainability in developing novel nanomaterials (NPs) from biomass sources is a challenging proposition mainly due to the difficulty of infusing or retaining desired chemical functionalities in the biomass substrate. In this study, we demonstrate the synthesis of DNA-nanoparticles (DNA-NP) from onion genomic DNA as a plant biomass source through controlled hydrothermal pyrolysis to retain functional groups in the NPs for predictable downstream chemical transformations. A dual crosslinking scheme was introduced that involves the DNA-NP to form a hydrogel. Chemical crosslinking was achieved through the formation of a Schiff base between the -CHO groups of glutaraldehyde and the amine functionality present on the DNA-NP surface as well as in the nucleobases of the dangling DNA strands of DNA-NP. Simultaneous physical entanglement was attained through hybridization-mediated self-assembly of the dangling DNA strands of the DNA-NP with untransformed onion genomic DNA. As a corollary of the dual crosslinking, the resulting hydrogel not only displayed remarkable mechanical strength but also showed self-healing properties. The ability of the DNA-NP to generate reactive oxygen species (ROS) with visible light irradiation is translated to the hydrogel, making the system potent for biofilm destruction. The high loading efficiency of the model drug ampicillin sodium (Amp) in the hydrogel was achieved which was released in four days. This hints towards the application of the hydrogel through combination antibiotic-antibacterial photodynamic treatment (APDT) as demonstrated here with both Gram-positive and Gram-negative bacteria.
MeSH term(s)	Hydrogels/chemistry ; Anti-Bacterial Agents/chemistry ; Biomass ; Gram-Negative Bacteria ; Gram-Positive Bacteria ; Nanoparticles/chemistry ; DNA ; Light
Chemical Substances	Hydrogels ; Anti-Bacterial Agents ; DNA (9007-49-2)
Language	English
Publishing date	2023-12-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2191476-X
ISSN	1744-6848 ; 1744-683X
ISSN (online)	1744-6848
ISSN	1744-683X
DOI	10.1039/d3sm01400b
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Article ; Online: Acetic Acid-Catalyzed Regioselective C(sp

Mane, Kishor D / Mukherjee, Anirban / Das, Gourab Kanti / Suryavanshi, Gurunath

The Journal of organic chemistry

2022 Volume 87, Issue 8, Page(s) 5097–5112

Abstract: An atom economical and environmentally benign protocol has been developed for the regioselective C( ... ...

Abstract	An atom economical and environmentally benign protocol has been developed for the regioselective C(sp
Language	English
Publishing date	2022-03-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/acs.joc.1c03019
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