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  1. Article ; Online: Atmospheric temperature and humidity demonstrated strong correlation with productivity in tropical moist deciduous forests

    Behera, Soumit Kumar / Behera, Mukunda Dev / Tuli, Rakesh / Barik, Saroj K.

    Environ Monit Assess. 2023 Jan., v. 195, no. 1 p.69-69

    2023  

    Abstract: Tropical forests sequester six times higher carbon than that released by humans annually into the atmosphere. These biodiversity-rich tropical forests have high net primary productivity (NPP), which differs among constituent plant communities. Tropical ... ...

    Abstract Tropical forests sequester six times higher carbon than that released by humans annually into the atmosphere. These biodiversity-rich tropical forests have high net primary productivity (NPP), which differs among constituent plant communities. Tropical moist deciduous forests occupy 179,335 km² of India’s geographical area and constitute 44% of the country’s total protected area (PA) forests. The productivity of these forests has neither been estimated specifically nor precisely. We measured the annual NPP of three predominant distinct community types, viz., mixed (DM), sal (SM), and teak (TP), in a tropical moist deciduous forest in northern India. The NPP was estimated from tree biomass data collected from nine long-term ecological research (LTER) plots of 1 ha each representing the above three community types. The estimated annual NPP were 10.28, 6.25, and 9.79 Mg ha⁻¹ year⁻¹ in DM; 8.93, 7.09, and 10.59 Mg ha⁻¹ year⁻¹ in SM; and 14.57, 7.14, and 13.56 Mg ha⁻¹ year⁻¹ in TP for the years 2010, 2011, and 2012, respectively. The NPP was correlated with tree density, height and DBH, species richness, diversity, microclimatic and edaphic variables, and leaf area index (LAI) using principal component analysis (PCA) and generalized linear modeling (GLM). Air temperature and humidity were strongly related to NPP in all the community types, while “complementarity” and “selection effects” contributed to the NPP in both the sal and mixed forest communities with equal importance, and the NPP in teak plantation ould point to “dominance effect.”
    Keywords Tectona grandis ; air temperature ; biomass ; carbon ; conservation areas ; deciduous forests ; humidity ; leaf area index ; microclimate ; mixed forests ; net primary productivity ; principal component analysis ; species richness ; trees ; India
    Language English
    Dates of publication 2023-01
    Size p. 69.
    Publishing place Springer International Publishing
    Document type Article ; Online
    ZDB-ID 782621-7
    ISSN 1573-2959 ; 0167-6369
    ISSN (online) 1573-2959
    ISSN 0167-6369
    DOI 10.1007/s10661-022-10668-7
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Epigenetic malleability at core promoter initiates tobacco PR-1a expression post salicylic acid treatment

    Lodhi, Niraj / Singh, Mala / Srivastava, Rakesh / Sawant, Samir V. / Tuli, Rakesh

    Mol Biol Rep. 2023 Jan., v. 50, no. 1 p.417-431

    2023  

    Abstract: BACKGROUND: Tobacco’s PR-1a gene is induced by pathogen attack or exogenous application of salicylic acid (SA). Nucleosome mapping and chromatin immunoprecipitation assay were used to delineate the histone modifications on the PR-1a promoter. However, ... ...

    Abstract BACKGROUND: Tobacco’s PR-1a gene is induced by pathogen attack or exogenous application of salicylic acid (SA). Nucleosome mapping and chromatin immunoprecipitation assay were used to delineate the histone modifications on the PR-1a promoter. However, the epigenetic modifications of the inducible promoter of the PR-1a gene are not fully understood yet. METHODS AND RESULTS: Southern approach was used to scan the promoter of PR-1a to identify presence of nucleosomes, ChIP assays were performed using anti-histones antibodies of repressive chromatin by di- methylated at H3K9 and H4K20 or active chromatin by acetylated H3K9/14 and H4K16 to find epigenetic malleability of nucleosome over core promoter in uninduced or induced state post SA treatment. Class I and II mammalian histone deacetylase (HDAC) inhibitor TSA treatment was used to enhance the expression of PR-1a by facilitating the histone acetylation post SA treatment. Here, we report correlated consequences of the epigenetic modifications correspond to disassembly of the nucleosome (spans from − 102 to + 55 bp, masks TATA and transcription initiation) and repressor complex from core promoter, eventually initiates the transcription of PR-1a gene post SA treatment. While active chromatin marks di and trimethylation of H3K4, acetylation of H3K9 and H4K16 are increased which are associated to the transcription initiation of PR-1a following SA treatment. However, in uninduced state constitutive expression of a negative regulator (SNI1) of AtPR1, suppresses AtPR1 expression by six-fold in Arabidopsis thaliana. Further, we report 50-to-1000-fold increased expression of AtPR1 in uninduced lsd1 mutant plants, up to threefold increased expression of AtPR1 in uninduced histone acetyl transferases (HATs) mutant plants, SNI1 dependent negative regulation of AtPR1, all together our results suggest that inactive state of PR-1a is indeed maintained by a repressive complex. CONCLUSION: The study aimed to reveal the mechanism of transcription initiation of tobacco PR-1a gene in presence or absence of SA. This is the first study that reports nucleosome and repressor complex over core promoter region maintains the inactivation of gene in uninduced state, and upon induction disassembling of both initiates the downstream gene activation process.
    Keywords Arabidopsis thaliana ; acetylation ; acid treatment ; chromatin immunoprecipitation ; epigenetics ; gene activation ; gene expression ; genes ; histone acetyltransferase ; histone deacetylase ; histones ; mammals ; methylation ; mutants ; nucleosomes ; pathogens ; promoter regions ; salicylic acid ; tobacco ; transcription initiation
    Language English
    Dates of publication 2023-01
    Size p. 417-431.
    Publishing place Springer Netherlands
    Document type Article ; Online
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-022-08074-w
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Atmospheric temperature and humidity demonstrated strong correlation with productivity in tropical moist deciduous forests.

    Behera, Soumit Kumar / Behera, Mukunda Dev / Tuli, Rakesh / Barik, Saroj K

    Environmental monitoring and assessment

    2022  Volume 195, Issue 1, Page(s) 69

    Abstract: Tropical forests sequester six times higher carbon than that released by humans annually into the atmosphere. These biodiversity-rich tropical forests have high net primary productivity (NPP), which differs among constituent plant communities. Tropical ... ...

    Abstract Tropical forests sequester six times higher carbon than that released by humans annually into the atmosphere. These biodiversity-rich tropical forests have high net primary productivity (NPP), which differs among constituent plant communities. Tropical moist deciduous forests occupy 179,335 km
    MeSH term(s) Humans ; Tropical Climate ; Temperature ; Humidity ; Environmental Monitoring ; Forests ; Trees ; Biomass
    Language English
    Publishing date 2022-11-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 782621-7
    ISSN 1573-2959 ; 0167-6369
    ISSN (online) 1573-2959
    ISSN 0167-6369
    DOI 10.1007/s10661-022-10668-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size

    Pathak, Ashish K. / Singh, Sudhir P. / Sharma, Ritika / Nath, Vishal / Tuli, Rakesh

    3 Biotech. 2022 Feb., v. 12, no. 2

    2022  

    Abstract: Litchi is a sub-tropical fruit crop with genotypes that bear fruits with variable seed size. Small seed size is a desirable trait in litchi, as it improves consumers’ preference and facilitates fruit processing. Seed specific transcriptome analysis was ... ...

    Abstract Litchi is a sub-tropical fruit crop with genotypes that bear fruits with variable seed size. Small seed size is a desirable trait in litchi, as it improves consumers’ preference and facilitates fruit processing. Seed specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to identify the genes associated with seed development. The transcriptomic sequence data from seeds at mid-development stages (16–28 days after anthesis) were de-novo assembled into 1,39,608 Trinity transcripts. Out of these, 6325 transcripts expressed differentially between the two contrasting genotypes. Several putative genes for salicylic acid, jasmonic acid and brassinosteriod pathways were down-regulated in seeds of the small-seeded litchi. The putative regulators of seed maturation and seed storage were down-regulated in the small-seeded genotype. Embryogenesis, cell expansion, seed size and stress related Trinity transcripts exhibited differential expression. Further studies on gene characterization will reveal the early regulators of seed size in litchi.
    Keywords Litchi ; embryogenesis ; flowering ; fruits ; gene expression regulation ; genes ; genotype ; jasmonic acid ; salicylic acid ; seed maturation ; seed size ; seed storage ; transcriptomics
    Language English
    Dates of publication 2022-02
    Size p. 47.
    Publishing place Springer International Publishing
    Document type Article
    ZDB-ID 2600522-0
    ISSN 2190-5738 ; 2190-572X
    ISSN (online) 2190-5738
    ISSN 2190-572X
    DOI 10.1007/s13205-021-03098-8
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size.

    Pathak, Ashish K / Singh, Sudhir P / Sharma, Ritika / Nath, Vishal / Tuli, Rakesh

    3 Biotech

    2022  Volume 12, Issue 2, Page(s) 47

    Abstract: Litchi is a sub-tropical fruit crop with genotypes that bear fruits with variable seed size. Small seed size is a desirable trait in litchi, as it improves consumers' preference and facilitates fruit processing. Seed specific transcriptome analysis was ... ...

    Abstract Litchi is a sub-tropical fruit crop with genotypes that bear fruits with variable seed size. Small seed size is a desirable trait in litchi, as it improves consumers' preference and facilitates fruit processing. Seed specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to identify the genes associated with seed development. The transcriptomic sequence data from seeds at mid-development stages (16-28 days after anthesis) were de-novo assembled into 1,39,608 Trinity transcripts. Out of these, 6325 transcripts expressed differentially between the two contrasting genotypes. Several putative genes for salicylic acid, jasmonic acid and brassinosteriod pathways were down-regulated in seeds of the small-seeded litchi. The putative regulators of seed maturation and seed storage were down-regulated in the small-seeded genotype. Embryogenesis, cell expansion, seed size and stress related Trinity transcripts exhibited differential expression. Further studies on gene characterization will reveal the early regulators of seed size in litchi.
    Supplementary information: The online version contains supplementary material available at 10.1007/s13205-021-03098-8.
    Language English
    Publishing date 2022-01-22
    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/s13205-021-03098-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Epigenetic malleability at core promoter initiates tobacco PR-1a expression post salicylic acid treatment.

    Lodhi, Niraj / Singh, Mala / Srivastava, Rakesh / Sawant, Samir V / Tuli, Rakesh

    Molecular biology reports

    2022  Volume 50, Issue 1, Page(s) 417–431

    Abstract: Background: Tobacco's PR-1a gene is induced by pathogen attack or exogenous application of salicylic acid (SA). Nucleosome mapping and chromatin immunoprecipitation assay were used to delineate the histone modifications on the PR-1a promoter. However, ... ...

    Abstract Background: Tobacco's PR-1a gene is induced by pathogen attack or exogenous application of salicylic acid (SA). Nucleosome mapping and chromatin immunoprecipitation assay were used to delineate the histone modifications on the PR-1a promoter. However, the epigenetic modifications of the inducible promoter of the PR-1a gene are not fully understood yet.
    Methods and results: Southern approach was used to scan the promoter of PR-1a to identify presence of nucleosomes, ChIP assays were performed using anti-histones antibodies of repressive chromatin by di- methylated at H3K9 and H4K20 or active chromatin by acetylated H3K9/14 and H4K16 to find epigenetic malleability of nucleosome over core promoter in uninduced or induced state post SA treatment. Class I and II mammalian histone deacetylase (HDAC) inhibitor TSA treatment was used to enhance the expression of PR-1a by facilitating the histone acetylation post SA treatment. Here, we report correlated consequences of the epigenetic modifications correspond to disassembly of the nucleosome (spans from - 102 to + 55 bp, masks TATA and transcription initiation) and repressor complex from core promoter, eventually initiates the transcription of PR-1a gene post SA treatment. While active chromatin marks di and trimethylation of H3K4, acetylation of H3K9 and H4K16 are increased which are associated to the transcription initiation of PR-1a following SA treatment. However, in uninduced state constitutive expression of a negative regulator (SNI1) of AtPR1, suppresses AtPR1 expression by six-fold in Arabidopsis thaliana. Further, we report 50-to-1000-fold increased expression of AtPR1 in uninduced lsd1 mutant plants, up to threefold increased expression of AtPR1 in uninduced histone acetyl transferases (HATs) mutant plants, SNI1 dependent negative regulation of AtPR1, all together our results suggest that inactive state of PR-1a is indeed maintained by a repressive complex.
    Conclusion: The study aimed to reveal the mechanism of transcription initiation of tobacco PR-1a gene in presence or absence of SA. This is the first study that reports nucleosome and repressor complex over core promoter region maintains the inactivation of gene in uninduced state, and upon induction disassembling of both initiates the downstream gene activation process.
    MeSH term(s) Animals ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Salicylic Acid/pharmacology ; Salicylic Acid/metabolism ; Nicotiana/genetics ; Nicotiana/metabolism ; Promoter Regions, Genetic/genetics ; Chromatin/metabolism ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Epigenesis, Genetic ; Acetylation ; Mammals/metabolism ; Nuclear Proteins/genetics ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism
    Chemical Substances Nucleosomes ; Salicylic Acid (O414PZ4LPZ) ; Chromatin ; SNI1 protein, Arabidopsis ; Nuclear Proteins ; Arabidopsis Proteins
    Language English
    Publishing date 2022-11-06
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-022-08074-w
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  7. Article: Corrigendum: Pathway Editing Targets for Thiamine Biofortification in Rice Grains.

    Minhas, Anu P / Tuli, Rakesh / Puri, Sanjeev

    Frontiers in plant science

    2019  Volume 9, Page(s) 1813

    Abstract: This corrects the article DOI: 10.3389/fpls.2018.00975.]. ...

    Abstract [This corrects the article DOI: 10.3389/fpls.2018.00975.].
    Language English
    Publishing date 2019-01-21
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2018.01813
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  8. Article: A bidirectional promoter from Papaya leaf crumple virus functions in both monocot and dicot plants

    Alok, Anshu / Tiwari, Siddharth / Tuli, Rakesh

    Physiological and molecular plant pathology. 2019 Dec., v. 108

    2019  

    Abstract: The intergenic region of Papaya leaf crumple virus (PaLCrV) transcribes the complementary (C) and virion (V) strand promoters, expressing the C1-C4 and V1-V2 genes respectively in opposite directions. Activities of the bidirectional promoter of PaLCrV in ...

    Abstract The intergenic region of Papaya leaf crumple virus (PaLCrV) transcribes the complementary (C) and virion (V) strand promoters, expressing the C1-C4 and V1-V2 genes respectively in opposite directions. Activities of the bidirectional promoter of PaLCrV in the C and V directions were compared with the 35S promoter of Cauliflower mosaic virus (CaMV35S), using β-glucuronidase (uidA) as the reporter gene. The resulting promoter constructs were named as pC, pV, and p35S respectively, and transformed into Arabidopsis thaliana, wheat and rice. GUS activity in leaf, stem, root, and flower of Arabidopsis, and the calli of wheat and rice was estimated using histochemical staining, fluorometric assay, and real-time PCR. The expression study showed that the transcription from pC was 12–13 folds higher than that from p35S in root and leaf of Arabidopsis. It expressed at a higher level in root, stem, leaf, flower, and silique of Arabidopsis, and in the callus of wheat and rice, as compared to p35S. The pV also expressed in both monocots and dicots, though the activity was lower as compared to p35S in all the cases. Hence, the C promoter of PaLCrV is a good candidate for high-level expression of transgenes in a wide variety of tissues in dicot and monocot plants.
    Keywords Arabidopsis thaliana ; Cauliflower mosaic virus ; Liliopsida ; callus ; flowers ; fluorometry ; intergenic DNA ; leaves ; papayas ; plant pathology ; promoter regions ; quantitative polymerase chain reaction ; reporter genes ; rice ; siliques ; transgenes ; virion ; viruses ; wheat
    Language English
    Dates of publication 2019-12
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 742470-x
    ISSN 0885-5765
    ISSN 0885-5765
    DOI 10.1016/j.pmpp.2019.101423
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Predicting the growth and trend of COVID-19 pandemic using machine learning and cloud computing.

    Tuli, Shreshth / Tuli, Shikhar / Tuli, Rakesh / Gill, Sukhpal Singh

    Internet of things (Amsterdam, Netherlands)

    2020  Volume 11, Page(s) 100222

    Abstract: The outbreak of COVID-19 Coronavirus, namely SARS-CoV-2, has created a calamitous situation throughout the world. The cumulative incidence of COVID-19 is rapidly increasing day by day. Machine Learning (ML) and Cloud Computing can be deployed very ... ...

    Abstract The outbreak of COVID-19 Coronavirus, namely SARS-CoV-2, has created a calamitous situation throughout the world. The cumulative incidence of COVID-19 is rapidly increasing day by day. Machine Learning (ML) and Cloud Computing can be deployed very effectively to track the disease, predict growth of the epidemic and design strategies and policies to manage its spread. This study applies an improved mathematical model to analyse and predict the growth of the epidemic. An ML-based improved model has been applied to predict the potential threat of COVID-19 in countries worldwide. We show that using iterative weighting for fitting Generalized Inverse Weibull distribution, a better fit can be obtained to develop a prediction framework. This has been deployed on a cloud computing platform for more accurate and real-time prediction of the growth behavior of the epidemic. A data driven approach with higher accuracy as here can be very useful for a proactive response from the government and citizens. Finally, we propose a set of research opportunities and setup grounds for further practical applications.
    Language English
    Publishing date 2020-05-12
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2542-6605
    ISSN (online) 2542-6605
    DOI 10.1016/j.iot.2020.100222
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  10. Article: Pathway Editing Targets for Thiamine Biofortification in Rice Grains.

    Minhas, Anu P / Tuli, Rakesh / Puri, Sanjeev

    Frontiers in plant science

    2018  Volume 9, Page(s) 975

    Abstract: Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has ...

    Abstract Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as
    Language English
    Publishing date 2018-07-10
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2018.00975
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