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  1. Book ; Online ; E-Book: Role of plant growth promoting microorganisms in sustainable agriculture and nanotechnology

    Kumar, Ajay / Singh, Amit Kishore / Choudhary, Krishna Kumar

    2019  

    Author's details edited by Ajay Kumar, Amit Kishore Singh, Krishna Kumar Choudhary
    Keywords Microorganisms ; Sustainable agriculture ; Nanotechnology
    Subject code 579
    Language English
    Size 1 Online-Ressource (300 Seiten)
    Publisher Elsevier
    Publishing place Duxford ; Cambridge, MA ; Kidlington
    Publishing country Great Britain
    Document type Book ; Online ; E-Book
    Note Includes bibliographical references and index
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT020143792
    ISBN 978-0-12-817005-2 ; 9780128170045 ; 0-12-817005-0 ; 0128170042
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book ; Online ; E-Book: Climate change and agricultural ecosystems

    Choudhary, Krishna Kumar / Kumar, Ajay / Singh, Amit Kishore

    current challenges and adaptation

    2019  

    Author's details edited by Krishna Kumar Choudhary, Ajay Kumar, Amit Kishore Singh
    Keywords Crops and climate ; Agriculture/Environmental aspects
    Language English
    Size 1 Online-Ressource (xviii, 467 Seiten), Illustrationen
    Publisher Woodhead Publishing
    Publishing place Oxford
    Publishing country Great Britain
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT020069909
    ISBN 978-0-128-17522-4 ; 9780128164839 ; 0-128-17522-2 ; 0128164832
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article ; Online: Revisiting the role of phenylpropanoids in plant defense against UV-B stress

    Singh, Pooja / Singh, Amantika / Choudhary, Krishna Kumar

    Plant Stress. 2023 Mar., v. 7 p.100143-

    2023  

    Abstract: Ultraviolet-B (UV-B) radiation from the past few decades has been widely studied due to the substantial depletion of the stratospheric ozone (O₃) layer, causing morphological, physiological, cytological, and biochemical alterations in plants. As a potent ...

    Abstract Ultraviolet-B (UV-B) radiation from the past few decades has been widely studied due to the substantial depletion of the stratospheric ozone (O₃) layer, causing morphological, physiological, cytological, and biochemical alterations in plants. As a potent abiotic stress factor, enhanced reactive oxygen species (ROS) generation has been flagged as a key factor under UV-B stress. UV-B adversely affects plant growth and development. Plants have evolved defense strategies under UV-B stress to counteract these detrimental effects. The most common protective response is an accumulation of secondary metabolites. These provide photoprotection by acting as UV-B absorbing compounds through quenching ROS and reactive nitrogen species (RNS).UV-B-induced metabolites share a common origin in the phenylpropanoid biosynthetic pathway. These phenylpropanoids induced via UV Resistance Locus 8 (UVR8) signaling are transcriptionally regulated by MYB transcription factors (TFₛ) and are efficiently transported to different cellular and membrane-limited compartments. The accumulation of metabolites like flavonoids, anthocyanins, lignins and tannins in plants marks the importance of its metabolism in UV-B tolerance mechanism. Plant species responded differently to increased UV-B exposure in terms of phenylpropanoid concentration. Apart from UV-B screening agents, these are also potent ROS scavengers due to their structural composition and less reactive nature. The dynamic balance between ROS accumulation under UV-B stress and its metabolism via phenylpropanoids holds the key to the stress tolerance attributes of a plant. The present review focuses on the UV-B-induced secondary metabolites in plants, their biosynthesis, and defense strategies that will help in the elucidation of medicinally important bioactive compounds as well as in the development of UV-B tolerant plants.
    Keywords abiotic stress ; anthocyanins ; biochemical pathways ; biosynthesis ; growth and development ; lignin ; ozone ; phenylpropanoids ; plant growth ; plant stress ; radiation resistance ; reactive nitrogen species ; reactive oxygen species ; resistance genes ; secondary metabolites ; stratosphere ; stress tolerance ; transcription (genetics) ; ultraviolet radiation ; Abiotic stresses ; UV-B ; ROS ; Antioxidative defense
    Language English
    Dates of publication 2023-03
    Publishing place Elsevier B.V.
    Document type Article ; Online
    Note Use and reproduction
    ISSN 2667-064X
    DOI 10.1016/j.stress.2023.100143
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Introducing R as a smart version of calculators enables beginners to explore it on their own.

    Choudhary, Krishna / Pico, Alexander R

    F1000Research

    2021  Volume 10, Page(s) 859

    Abstract: Rapid technological advances in the past decades have enabled molecular biologists to generate large-scale and complex data with affordable resource investments, or obtain such data from public repositories. Yet, many graduate students, postdoctoral ... ...

    Abstract Rapid technological advances in the past decades have enabled molecular biologists to generate large-scale and complex data with affordable resource investments, or obtain such data from public repositories. Yet, many graduate students, postdoctoral scholars, and senior researchers in the biosciences find themselves ill-equipped to analyze large-scale data. Global surveys have revealed that active researchers prefer short training workshops to fill their skill gaps. In this article, we focus on the challenge of delivering a short data analysis workshop to absolute beginners in computer programming. We propose that introducing R or other programming languages for data analysis as smart versions of calculators can help lower the communication barrier with absolute beginners. We describe this comparison with a few analogies and hope that other instructors will find them useful. We utilized these in our four-hour long training workshops involving participatory live coding, which we delivered in person and via videoconferencing. Anecdotal evidence suggests that our exposition made R programming seem easy and enabled beginners to explore it on their own.
    MeSH term(s) Humans ; Programming Languages ; Research Personnel ; Students
    Language English
    Publishing date 2021-08-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.54685.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Spontaneous persistent activity and inactivity in vivo reveals differential cortico-entorhinal functional connectivity.

    Choudhary, Krishna / Berberich, Sven / Hahn, Thomas T G / McFarland, James M / Mehta, Mayank R

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3542

    Abstract: Understanding the functional connectivity between brain regions and its emergent dynamics is a central challenge. Here we present a theory-experiment hybrid approach involving iteration between a minimal computational model and in vivo ... ...

    Abstract Understanding the functional connectivity between brain regions and its emergent dynamics is a central challenge. Here we present a theory-experiment hybrid approach involving iteration between a minimal computational model and in vivo electrophysiological measurements. Our model not only predicted spontaneous persistent activity (SPA) during Up-Down-State oscillations, but also inactivity (SPI), which has never been reported. These were confirmed in vivo in the membrane potential of neurons, especially from layer 3 of the medial and lateral entorhinal cortices. The data was then used to constrain two free parameters, yielding a unique, experimentally determined model for each neuron. Analytic and computational analysis of the model generated a dozen quantitative predictions about network dynamics, which were all confirmed in vivo to high accuracy. Our technique predicted functional connectivity; e. g. the recurrent excitation is stronger in the medial than lateral entorhinal cortex. This too was confirmed with connectomics data. This technique uncovers how differential cortico-entorhinal dialogue generates SPA and SPI, which could form an energetically efficient working-memory substrate and influence the consolidation of memories during sleep. More broadly, our procedure can reveal the functional connectivity of large networks and a theory of their emergent dynamics.
    MeSH term(s) Entorhinal Cortex/physiology ; Animals ; Neurons/physiology ; Models, Neurological ; Male ; Connectome ; Nerve Net/physiology ; Membrane Potentials/physiology ; Neural Pathways/physiology ; Computer Simulation ; Mice
    Language English
    Publishing date 2024-05-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47617-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Urn models for stochastic gene expression yield intuitive insights into the probability distributions of single-cell mRNA and protein counts.

    Choudhary, Krishna / Narang, Atul

    Physical biology

    2020  Volume 17, Issue 6, Page(s) 66001

    Abstract: Fitting the probability mass functions from analytical solutions of stochastic models of gene expression to the single-cell count distributions of mRNA and protein molecules can yield valuable insights into mechanisms underlying gene expression. ... ...

    Abstract Fitting the probability mass functions from analytical solutions of stochastic models of gene expression to the single-cell count distributions of mRNA and protein molecules can yield valuable insights into mechanisms underlying gene expression. Solutions of chemical master equations are available for various kinetic schemes but, even for the basic ON-OFF genetic switch, they take complex forms with generating functions given as hypergeometric functions. Interpretation of gene expression dynamics in terms of bursts is not consistent with the complete range of parameters for these functions. Physical insights into the probability mass functions are essential to ensure proper interpretations but are lacking for models considering genetic switches. To fill this gap, we develop urn models for stochastic gene expression. We sample RNA polymerases or ribosomes from a master urn, which represents the cytosol, and assign them to recipient urns of two or more colors, which represent time intervals in which no switching occurs. Colors of the recipient urns represent sub-systems of the promoter states, and the assignments to urns of a specific color represent gene expression. We use elementary principles of discrete probability theory to solve a range of kinetic models without feedback, including the Peccoud-Ycart model, the Shahrezaei-Swain model, and models with an arbitrary number of promoter states. In the last case, we obtain a novel result for the protein distribution. For activated genes, we show that transcriptional lapses, which are events of gene inactivation for short time intervals separated by long active intervals, quantify the transcriptional dynamics better than bursts. We show that the intuition gained from our urn models may also be useful in understanding existing solutions for models with feedback. We contrast our models with urn models for related distributions, discuss a generalization of the Delaporte distribution for single-cell data analysis, and highlight the limitations of our models.
    MeSH term(s) Gene Expression ; Kinetics ; Models, Genetic ; Promoter Regions, Genetic ; Proteins/metabolism ; RNA, Messenger/metabolism ; Single-Cell Analysis ; Stochastic Processes
    Chemical Substances Proteins ; RNA, Messenger
    Language English
    Publishing date 2020-09-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2133216-2
    ISSN 1478-3975 ; 1478-3967
    ISSN (online) 1478-3975
    ISSN 1478-3967
    DOI 10.1088/1478-3975/aba50f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Trends of adult height in India from 1998 to 2015: Evidence from the National Family and Health Survey.

    Choudhary, Krishna Kumar / Das, Sayan / Ghodajkar, Prachinkumar

    PloS one

    2021  Volume 16, Issue 9, Page(s) e0255676

    Abstract: Aim: The aim of the study is to investigate the trends in adult height between two consecutive surveys of NHFS and explore differences across variables such as gender, wealth, social groups etc.: Methods: We used the NFHS-II (1998-99), NFHS-III (2005- ...

    Abstract Aim: The aim of the study is to investigate the trends in adult height between two consecutive surveys of NHFS and explore differences across variables such as gender, wealth, social groups etc.
    Methods: We used the NFHS-II (1998-99), NFHS-III (2005-2006) and NFHS-IV (2015-16) (all three for women and last two for men) data to examine the trends in average height. Comparison was done between the two age strata of 15-25 and 26-50 years, across both male and female, to assess the trends.
    Results: Between NFHS-III and NFHS-IV, the average height of women in the age group of 15-25 showed a decline by 0.12 cm [95% CI, -0.24 to 0.00, p-0.051] while in the 26-50 years age strata it demonstrated significant improvement in the mean height by 0.13 cm [95% CI, 0.02 to 0.023, p-0.015]. However, Between NFHS III and IV, the average height of women in the poorest wealth index category registered a significant decline [-0.57cm, 95% CI, -076 to -0.37, p-0.000]. Between NFHS III and IV, the average height of Scheduled Tribe (ST) women in the age group of 15-25 years also exhibited a significant decline by 0.42 cm, [95% CI, -0.73 to -0.12, p-0.007]. Among men, between the two surveys, both the age groups of 15-25 years and 26-50 years showed significant decline in average height: 1.10 cm [95% CI, -1.31 to -.099 cm, p-0.00] and 0.86 cm [95% CI, -1.03 to -0.69, p-0.000], respectively.
    Conclusion: In the context of an overall increase in average heights worldwide the decline in average height of adults in India is alarming and demands an urgent enquiry. The argument for different standards of height for Indian population as different genetic group needs further scrutiny. However, the trends from India clearly underline the need to examine the non-genetic factors also to understand the interplay of genetic, nutritional and other social and environmental determinants on height.
    MeSH term(s) Adolescent ; Adult ; Body Height ; Environment ; Female ; Growth Disorders/epidemiology ; Health Surveys ; Humans ; India/epidemiology ; Male ; Middle Aged ; Nutritional Status ; Socioeconomic Factors ; Young Adult
    Language English
    Publishing date 2021-09-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0255676
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Analytical Expressions and Physics for Single-Cell mRNA Distributions of the lac Operon of E. coli.

    Choudhary, Krishna / Narang, Atul

    Biophysical journal

    2019  Volume 117, Issue 3, Page(s) 572–586

    Abstract: Mechanistic models of stochastic gene expression are of considerable interest, but their complexity often precludes tractable analytical expressions for messenger RNA (mRNA) and protein distributions. The lac operon of Escherichia coli is a model system ... ...

    Abstract Mechanistic models of stochastic gene expression are of considerable interest, but their complexity often precludes tractable analytical expressions for messenger RNA (mRNA) and protein distributions. The lac operon of Escherichia coli is a model system with regulatory elements such as multiple operators and DNA looping that are shared by many operons. Although this system is complex, intuition suggests that fast DNA looping may simplify it by causing the repressor-bound states of the operon to equilibrate rapidly, thus ensuring that the subsequent dynamics are governed by slow transitions between the repressor-free and the equilibrated repressor-bound states. Here, we show that this intuition is correct by applying singular perturbation theory to a mechanistic model of lac transcription with the scaled time constant of DNA looping as the perturbation parameter. We find that at steady state, the repressor-bound states satisfy detailed balance and are dominated by the looped states; moreover, the interaction between the repressor-free and the equilibrated repressor-bound states is described by an extension of the Peccoud-Ycart two-state model in which both (repressor-free and repressor-bound) states support transcription. The solution of this extended two-state model reveals that the steady-state mRNA distribution is a mixture of the Poisson and negative hypergeometric distributions, which reflects mRNAs obtained by transcription from the repressor-bound and repressor-free states. Finally, we show that the physics revealed by perturbation theory makes it easy to derive the extended two-state model equations for complex regulatory architectures.
    MeSH term(s) Escherichia coli/genetics ; Gene Expression Regulation, Bacterial ; Lac Operon/genetics ; Models, Genetic ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Single-Cell Analysis
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2019-07-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2019.06.029
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Coping Strategies with Stress and Anxiety of Tri-Pillar of the Education System in COVID-19 Pandemic Period

    Rawat, Narinder Singh / Choudhary, Krishna Chandra

    SSRN Electronic Journal ; ISSN 1556-5068

    2020  

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    DOI 10.2139/ssrn.3596912
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Assessment of Fatty Acid Profile and Seed Mineral Nutrients of Two Soybean (Glycine max L.) Cultivars Under Elevated Ultraviolet-B: Role of ROS, Pigments and Antioxidants.

    Choudhary, Krishna Kumar / Agrawal, Shashi Bhushan

    Photochemistry and photobiology

    2016  Volume 92, Issue 1, Page(s) 134–143

    Abstract: Current scenarios under global climate change envisage a considerable increase in ultraviolet B (UV-B) radiation in near future which may affect the productivity and yield quality of major agricultural crops. Present investigation was conducted to ... ...

    Abstract Current scenarios under global climate change envisage a considerable increase in ultraviolet B (UV-B) radiation in near future which may affect the productivity and yield quality of major agricultural crops. Present investigation was conducted to examine various defense strategies adopted against elevated UV-B (ambient + 7.2 kJ m-(2) day-(1) ) and their impact on seed nutrients, content and quality of oil including fatty acid profile of two soybean cultivars (JS-335 and PS-1042). Elevated UV-B (eUV-B) exposure leads toward higher unsaturation of fatty acids and changes in other oil quality parameters (acid, iodine and saponification value) indicated that eUV-B favored the synthesis of long-chain fatty acids with fewer carboxylic acid groups, making the oil rancid, with undesirable flavor and low nutritional value. The effect was more severe in JS-335 as compared to PS-1042. Negative effects were also seen on nutrients of soybean seeds. Adverse effects resulted due to insufficient quenching of ROS (superoxide radical and hydrogen peroxide) by the defense system and thus unable to overcome the imposed oxidative stress. Credit of better performance by PS-1042 against eUV-B may be given to the adoption of efficient defense strategies like higher wax deposition, increase in lignin and flavonoids (quercetin and kaempferol) contents.
    Language English
    Publishing date 2016-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 123540-0
    ISSN 1751-1097 ; 0031-8655
    ISSN (online) 1751-1097
    ISSN 0031-8655
    DOI 10.1111/php.12544
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