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  1. Article ; Online: Geminiviral C4/AC4 proteins: An emerging component of the viral arsenal against plant defence.

    Kumar, Rohit / Dasgupta, Indranil

    Virology

    2023  Volume 579, Page(s) 156–168

    Abstract: Virus infection triggers a plethora of defence reactions in plants to incapacitate the intruder. Viruses, in turn, have added additional functions to their genes so that they acquire capabilities to neutralize the above defence reactions. In plant- ... ...

    Abstract Virus infection triggers a plethora of defence reactions in plants to incapacitate the intruder. Viruses, in turn, have added additional functions to their genes so that they acquire capabilities to neutralize the above defence reactions. In plant-infecting viruses, the family Geminiviridae comprises members, majority of whom encode 6-8 genes in their small single-stranded DNA genomes. Of the above genes, one which shows the most variability in its amino acid sequence is the C4/AC4. Recent studies have uncovered evidence, which point towards a wide repertoire of functions performed by C4/AC4 revealing its role as a major player in suppressing plant defence. This review summarizes the various plant defence mechanisms against viruses and highlights how C4/AC4 has evolved to counter most of them.
    MeSH term(s) Viral Proteins/genetics ; Viral Proteins/metabolism ; RNA Interference ; Genes, Viral ; Geminiviridae/genetics ; Plant Diseases ; Begomovirus/genetics
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2023-01-10
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2023.01.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Ethical Oversight of Direct-to-Consumer Neurotechnologies: The FDA, the FTC, or Self-Regulation?

    Dasgupta, Ishan

    AJOB neuroscience

    2019  Volume 10, Issue 4, Page(s) 200–201

    MeSH term(s) Morals ; United States ; United States Food and Drug Administration
    Language English
    Publishing date 2019-10-22
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2576262-X
    ISSN 2150-7759 ; 2150-7740
    ISSN (online) 2150-7759
    ISSN 2150-7740
    DOI 10.1080/21507740.2019.1665133
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  3. Article ; Online: Rational Use of Immunosuppressive Corticosteroids in Liver-Directed Adeno-Associated Virus Gene Therapy Studies.

    Dasgupta, Ishani / Keeler, Allison M

    Human gene therapy

    2022  Volume 33, Issue 3-4, Page(s) 116–118

    MeSH term(s) Adrenal Cortex Hormones/therapeutic use ; Dependovirus/genetics ; Genetic Therapy ; Genetic Vectors/genetics ; Genetic Vectors/therapeutic use ; Liver
    Chemical Substances Adrenal Cortex Hormones
    Language English
    Publishing date 2022-03-08
    Publishing country United States
    Document type News
    ZDB-ID 1028152-6
    ISSN 1557-7422 ; 1043-0342
    ISSN (online) 1557-7422
    ISSN 1043-0342
    DOI 10.1089/hum.2022.29199.ida
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    Zs.A 2988: Show issues Location:
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  4. Article ; Online: Principles and practice of virus induced gene silencing for functional genomics in plants.

    Jagram, Neelam / Dasgupta, Indranil

    Virus genes

    2022  Volume 59, Issue 2, Page(s) 173–187

    Abstract: Virus induced gene silencing (VIGS) has, of late, emerged as an important tool for transient silencing of genes in plants. This is now being increasingly used to determine functions of novel genes in a wide variety of plants, many of which are important ... ...

    Abstract Virus induced gene silencing (VIGS) has, of late, emerged as an important tool for transient silencing of genes in plants. This is now being increasingly used to determine functions of novel genes in a wide variety of plants, many of which are important crops yielding food and fiber or are sources of products having pharmaceutical uses. The technology for VIGS comprises the development of vectors derived from viruses, choosing the optimal orientation and size of the gene to be targeted and adopting the most suitable method of inoculation. This review gives a brief overview of the main aspects of VIGS technology as is being practiced. It also discusses the challenges the technology faces and the possible way ahead to improve its robustness, so that the technology finds wider applications.
    MeSH term(s) Gene Silencing ; Genetic Vectors ; Plants/genetics ; RNA Interference ; Genomics ; Plant Viruses/genetics
    Language English
    Publishing date 2022-10-20
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 639496-6
    ISSN 1572-994X ; 0920-8569
    ISSN (online) 1572-994X
    ISSN 0920-8569
    DOI 10.1007/s11262-022-01941-5
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  5. Article ; Online: Characterization of the functional domains of nuclear shuttle protein (NSP) of Indian cassava mosaic virus using green fluorescent protein as reporter.

    Patil, Basavaprabhu L / Dasgupta, Indranil

    Virus genes

    2022  Volume 58, Issue 4, Page(s) 308–318

    Abstract: Indian cassava mosaic virus (ICMV), responsible for the cassava mosaic disease in India, harbours two circular genomic components, DNA-A and DNA-B; the former being responsible for the encapsidation and replication and the latter for intra- and inter- ... ...

    Abstract Indian cassava mosaic virus (ICMV), responsible for the cassava mosaic disease in India, harbours two circular genomic components, DNA-A and DNA-B; the former being responsible for the encapsidation and replication and the latter for intra- and inter-cellular movement of the viral DNA. Two proteins, encoded by DNA-B, the movement protein (MP) and the nuclear shuttle protein (NSP), act in concert on the newly replicated viral DNA to move it from the nucleus to the cell periphery. To map the functional domains of NSP, the intra-cellular localization of its full-length protein and deletion derivatives was studied in the epidermal cells of detached leaves of the laboratory host plant, Nicotiana benthamiana, where the target proteins were transiently expressed as GFP fusions. This analysis revealed domains for nuclear localization at the N-terminus, as well as for localization towards the cell periphery both at the C-terminus and center of the NSP.
    MeSH term(s) Begomovirus/genetics ; DNA, Viral ; Green Fluorescent Proteins/genetics ; Nuclear Proteins ; Nicotiana/genetics
    Chemical Substances DNA, Viral ; Nuclear Proteins ; Green Fluorescent Proteins (147336-22-9)
    Language English
    Publishing date 2022-05-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639496-6
    ISSN 1572-994X ; 0920-8569
    ISSN (online) 1572-994X
    ISSN 0920-8569
    DOI 10.1007/s11262-022-01909-5
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  6. Article ; Online: Silencing suppressor protein PRT of rice tungro bacilliform virus interacts with the plant RNA silencing-related protein SGS3.

    Naresh, Madhvi / Purkayastha, Arunima / Dasgupta, Indranil

    Virology

    2023  Volume 581, Page(s) 71–80

    Abstract: Background: Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved ... ...

    Abstract Background: Rice tungro bacilliform virus (RTBV) is a double stranded DNA containing virus which causes the devastating tungro disease of rice in association with an RNA virus, rice tungro spherical virus. RNA silencing is an evolutionarily conserved antiviral defence pathway in plants as well as in several classes of higher organisms. Many viruses, in turn, encode proteins which are termed Viral Suppressor of RNA Silencing (VSR) because they downregulate or suppress RNA silencing.
    Results: Using an RNA silencing suppressor assay we show that RTBV protease (PRT) acts as a mild VSR. A truncated version of PRT gene abolished the silencing suppression activity. We also show in planta interaction of PRT with the SGS3 protein of Solanum tuberosum and Arabidopsis thaliana using bimolecular fluorescence complementation assay (BIFC). Transient expression of PRT in Nicotiana benthamiana caused an increased accumulation of the begomovirus Sri Lankan cassava mosaic virus (SLCMV) DNA-A, which indicated a virulence function imparted on an unrelated virus.
    Conclusion: The finding supports the idea that PRT acts as suppressor of RNA silencing and this action may be mediated by its interaction with SGS3.
    MeSH term(s) RNA Interference ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Tungrovirus/genetics ; Peptide Hydrolases/metabolism ; Arabidopsis ; Endopeptidases/genetics ; Plant Diseases ; Oryza ; Arabidopsis Proteins/genetics
    Chemical Substances Plant Proteins ; Peptide Hydrolases (EC 3.4.-) ; Endopeptidases (EC 3.4.-) ; SGS3 protein, Arabidopsis ; Arabidopsis Proteins
    Language English
    Publishing date 2023-03-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2023.02.013
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  7. Article ; Online: Chunking as a rational solution to the speed-accuracy trade-off in a serial reaction time task.

    Wu, Shuchen / Éltető, Noémi / Dasgupta, Ishita / Schulz, Eric

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 7680

    Abstract: When exposed to perceptual and motor sequences, people are able to gradually identify patterns within and form a compact internal description of the sequence. One proposal of how sequences can be compressed is people's ability to form chunks. We study ... ...

    Abstract When exposed to perceptual and motor sequences, people are able to gradually identify patterns within and form a compact internal description of the sequence. One proposal of how sequences can be compressed is people's ability to form chunks. We study people's chunking behavior in a serial reaction time task. We relate chunk representation with sequence statistics and task demands, and propose a rational model of chunking that rearranges and concatenates its representation to jointly optimize for accuracy and speed. Our model predicts that participants should chunk more if chunks are indeed part of the generative model underlying a task and should, on average, learn longer chunks when optimizing for speed than optimizing for accuracy. We test these predictions in two experiments. In the first experiment, participants learn sequences with underlying chunks. In the second experiment, participants were instructed to act either as fast or as accurately as possible. The results of both experiments confirmed our model's predictions. Taken together, these results shed new light on the benefits of chunking and pave the way for future studies on step-wise representation learning in structured domains.
    MeSH term(s) Humans ; Reaction Time ; Learning ; Memory
    Language English
    Publishing date 2023-05-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-31500-3
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  8. Article ; Online: P4 protein of an Indian isolate of rice tungro bacilliform virus modulates gene silencing.

    Naresh, Madhvi / Purkayastha, Arunima / Dasgupta, Indranil

    Virus genes

    2023  Volume 60, Issue 1, Page(s) 55–64

    Abstract: Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro ... ...

    Abstract Plant hosts and their viral pathogens are engaged in a constant cycle of defense and counter-defense as part of a molecular arms race, principal among them being the plant RNAi defense and the viral RNAi suppressor counter-defense. Rice tungro bacilliform virus (RTBV), member of the family Caulimoviridae, genus Tungrovirus, species Tungrovirus oryzae, infects rice in South- and Southeast Asia and causes severe symptoms of stunting, yellow-orange discoloration and twisting of leaf tips. To better understand the possible counter-defensive roles of RTBV against the host RNAi defense system, we explored the ability of the P4 protein of an Indian isolate of RTBV to act as a possible modulator of RNAi. Using a transient silencing and silencing suppression assay in Nicotiana benthamiana, we show that P4 not only displays an RNAi suppressor function, but also potentially enhances RNAi. The results also suggests that the N-terminal 168 amino acid residues of P4 are sufficient to maintain RNAi suppressor activity. Taken together with the earlier reports this work strengthens the view that the P4 protein carries out RNAi suppressor and a potential RNAi enhancer function.
    MeSH term(s) Tungrovirus/genetics ; Gene Silencing ; RNA Interference ; Oryza/genetics ; Plant Diseases/genetics
    Language English
    Publishing date 2023-12-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639496-6
    ISSN 1572-994X ; 0920-8569
    ISSN (online) 1572-994X
    ISSN 0920-8569
    DOI 10.1007/s11262-023-02039-2
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  9. Article ; Online: Spin-orbit effects in pentavalent iridates: models and materials.

    Bhowal, Sayantika / Dasgupta, Indra

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

    2021  Volume 33, Issue 45

    Abstract: Spin-orbit effects in heavy ... ...

    Abstract Spin-orbit effects in heavy 5
    Language English
    Publishing date 2021-08-27
    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/ac1aed
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  10. Article ; Online: Recent Advances in miRNA Delivery Systems.

    Dasgupta, Ishani / Chatterjee, Anushila

    Methods and protocols

    2021  Volume 4, Issue 1

    Abstract: MicroRNAs (miRNAs) represent a family of short non-coding regulatory RNA molecules that are produced in a tissue and time-specific manner to orchestrate gene expression post-transcription. MiRNAs hybridize to target mRNA(s) to induce translation ... ...

    Abstract MicroRNAs (miRNAs) represent a family of short non-coding regulatory RNA molecules that are produced in a tissue and time-specific manner to orchestrate gene expression post-transcription. MiRNAs hybridize to target mRNA(s) to induce translation repression or mRNA degradation. Functional studies have demonstrated that miRNAs are engaged in virtually every physiological process and, consequently, miRNA dysregulations have been linked to multiple human pathologies. Thus, miRNA mimics and anti-miRNAs that restore miRNA expression or downregulate aberrantly expressed miRNAs, respectively, are highly sought-after therapeutic strategies for effective manipulation of miRNA levels. In this regard, carrier vehicles that facilitate proficient and safe delivery of miRNA-based therapeutics are fundamental to the clinical success of these pharmaceuticals. Here, we highlight the strengths and weaknesses of current state-of-the-art viral and non-viral miRNA delivery systems and provide perspective on how these tools can be exploited to improve the outcomes of miRNA-based therapeutics.
    Language English
    Publishing date 2021-01-20
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2409-9279
    ISSN (online) 2409-9279
    DOI 10.3390/mps4010010
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