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  1. Article ; Online: Diversity of SARS-CoV-2 isolates driven by pressure and health index.

    Singh, R K Sanayaima / Malik, Md Zubbair / Singh, R K Brojen

    Epidemiology and infection

    2021  Volume 149, Page(s) e38

    Abstract: One of the main concerns about the fast spreading coronavirus disease 2019 (Covid-19) pandemic is how to intervene. We analysed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) isolates data using the multifractal approach and found a rich in ...

    Abstract One of the main concerns about the fast spreading coronavirus disease 2019 (Covid-19) pandemic is how to intervene. We analysed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) isolates data using the multifractal approach and found a rich in viral genome diversity, which could be one of the root causes of the fast Covid-19 pandemic and is strongly affected by pressure and health index of the hosts inhabited regions. The calculated mutation rate (mr) is observed to be maximum at a particular pressure, beyond which mr maintains diversity. Hurst exponent and fractal dimension are found to be optimal at a critical pressure (Pm), whereas, for P > Pm and P < Pm, we found rich genome diversity relating to complicated genome organisation and virulence of the virus. The values of these complexity measurement parameters are found to be increased linearly with health index values.
    MeSH term(s) COVID-19/virology ; Genome, Viral/genetics ; Humans ; Mutation Rate ; SARS-CoV-2/genetics
    Language English
    Publishing date 2021-02-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 632982-2
    ISSN 1469-4409 ; 0950-2688
    ISSN (online) 1469-4409
    ISSN 0950-2688
    DOI 10.1017/S0950268821000248
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Complexity in SARS-CoV-2 genome data: Price theory of mutant isolates

    Mandal, Saurav / Singh, R.K. Sanayaima / Sharma, Saurabh Kumar / Malik, Md. Zubbair / Singh, R.K. Brojen

    bioRxiv

    Abstract: SARS-CoV-2 is a highly virulent and deadly RNA virus causing the Covid-19 pandemic and several deaths across the world. The pandemic is so fast that any concrete theory of sudden widespread of this disease is still not known. In this work, we studied and ...

    Abstract SARS-CoV-2 is a highly virulent and deadly RNA virus causing the Covid-19 pandemic and several deaths across the world. The pandemic is so fast that any concrete theory of sudden widespread of this disease is still not known. In this work, we studied and analyzed a large number of publicly available SARS-CoV-2 genomes across the world using the multifractal approach. The mutation events in the isolates obey the Markov process and exhibit very high mutational rates, which occur in six specific genes and highest in orf1ab gene, leading to virulent nature. f (α) analysis indicated that the isolates are highly asymmetric (left-skewed), revealing the richness of complexity and dominance by large fluctuations in genome structure organization. The values of Hq and Dq are found to be significantly large, showing heterogeneous genome structure self-organization, strong positive correlation in organizing the isolates, and quite sensitive to fluctuations in and around it. We then present multiple-isolates hosts-virus interaction models, and derived Price equation for the model. The phase plane analysis of the model showed asymptotic stability type bifurcation. The competition among the mutant isolates drives the trade-off of the dominant mutant isolates, otherwise confined to the present hosts.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.05.04.077511
    Database COVID19

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  3. Article ; Online: Complexity in SARS-CoV-2 genome data: Price theory of mutant isolates

    Mandal, Saurav / Singh, R.K. Sanayaima / Sharma, Saurabh Kumar / Malik, Md. Zubbair / Singh, R.K. Brojen

    bioRxiv

    Abstract: SARS-CoV-2 is a highly virulent and deadly RNA virus causing the Covid-19 pandemic and several deaths across the world. The pandemic is so fast that any concrete theory of sudden widespread of this disease is still not known. In this work, we studied and ...

    Abstract SARS-CoV-2 is a highly virulent and deadly RNA virus causing the Covid-19 pandemic and several deaths across the world. The pandemic is so fast that any concrete theory of sudden widespread of this disease is still not known. In this work, we studied and analyzed a large number of publicly available SARS-CoV-2 genomes across the world using the multifractal approach. The mutation events in the isolates obey the Markov process and exhibit very high mutational rates, which occur in six specific genes and highest in orf1ab gene, leading to virulent nature. f(alpha) analysis indicated that the isolates are highly asymmetric (left-skewed), revealing the richness of complexity and dominance by large fluctuations in genome structure organization. The values of Hq and Dq are found to be significantly large, showing heterogeneous genome structure self-organization, strong positive correlation in organizing the isolates, and quite sensitive to fluctuations in and around it. We then present multiple-isolates hosts-virus interaction models, and derived Price equation for the model. The phase plane analysis of the model showed asymptotic stability type bifurcation. The competition among the mutant isolates drives the trade-off of the dominant mutant isolates, otherwise confined to the present hosts.
    Keywords covid19
    Language English
    Publishing date 2020-05-04
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.05.04.077511
    Database COVID19

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  4. Article: Phenotypic and molecular studies for genetic stability assessment of cryopreserved banana meristems derived from field and in vitro explant sources

    Agrawal, Anuradha / Sanayaima, Rajkumari / Singh, Rakesh / Tandon, Rajesh / Verma, Smriti / Tyagi, R. K

    In vitro cellular & developmental biology. 2014 June, v. 50, no. 3

    2014  

    Abstract: Explants used for cryopreservation of banana (Musa L. spp.) are mainly sourced from tissue culture. Here, we demonstrate the successful use of sucker meristems (SM) obtained from field-raised plants for cryopreservation of Indian Musa ABB cv. ‘Karpura ... ...

    Abstract Explants used for cryopreservation of banana (Musa L. spp.) are mainly sourced from tissue culture. Here, we demonstrate the successful use of sucker meristems (SM) obtained from field-raised plants for cryopreservation of Indian Musa ABB cv. ‘Karpura Chakkarakeli’. In addition, the genetic stability of plants recovered from cryopreserved and regenerated meristems after hardening and transfer to field conditions was studied using 11 phenotypic (biometric) characters and 21 simple sequence repeat (SSR) markers. The regenerative potential of cryopreserved SM was compared with two types of routinely employed explants of banana germplasm: in vitro-raised single-shoot meristems (IVM) and proliferating meristems (PM). The regeneration frequency of SM was high (60.0 ± 11.5%) and statistically comparable to PM (68.3 ± 4.4%) and IVM (55.6 ± 11.1%) after using the droplet vitrification cryopreservation technique. The total time required for cryopreserving plants from SM (∼2� mo) was substantially less than that for PM (14� mo) and IVM (8� mo). The SSR profiles of plants recovered from cryopreserved PM, IVM, and SM and compared with control plants had a similarity coefficient of 0.92. Data on phenotypic traits revealed that cryopreserved plants were statistically comparable to the mother plants raised from suckers for all important growth and yield parameters. This study broadens the possibilities to cryopreserve Musa germplasm, by applying the droplet vitrification method to a new type of explant, the SM. The results presented in this paper show that Musa meristems can be effectively cryopreserved for storage and regeneration of true-to-type plants.
    Keywords Musa ; bananas ; cryopreservation ; genetic stability ; germplasm ; meristems ; microsatellite repeats ; tissue culture ; vitrification
    Language English
    Dates of publication 2014-06
    Size p. 345-356.
    Publishing place Springer-Verlag
    Document type Article
    ISSN 1054-5476
    DOI 10.1007/s11627-014-9606-4
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Phenotypic and molecular studies for genetic stability assessment of cryopreserved banana meristems derived from field and in vitro explant sources

    Agrawal, Anuradha / Sanayaima, Rajkumari / Singh, Rakesh / Tandon, Rajesh / Verma, Smriti / Tyagi, R. K.

    In vitro cellular & developmental biology: plant

    Volume v. 50,, Issue no. 3

    Abstract: Explants used for cryopreservation of banana (Musa L. spp.) are mainly sourced from tissue culture. Here, we demonstrate the successful use of sucker meristems (SM) obtained from field-raised plants for cryopreservation of Indian Musa ABB cv. ‘Karpura ... ...

    Abstract Explants used for cryopreservation of banana (Musa L. spp.) are mainly sourced from tissue culture. Here, we demonstrate the successful use of sucker meristems (SM) obtained from field-raised plants for cryopreservation of Indian Musa ABB cv. ‘Karpura Chakkarakeli’. In addition, the genetic stability of plants recovered from cryopreserved and regenerated meristems after hardening and transfer to field conditions was studied using 11 phenotypic (biometric) characters and 21 simple sequence repeat (SSR) markers. The regenerative potential of cryopreserved SM was compared with two types of routinely employed explants of banana germplasm: in vitro-raised single-shoot meristems (IVM) and proliferating meristems (PM). The regeneration frequency of SM was high (60.0 ± 11.5%) and statistically comparable to PM (68.3 ± 4.4%) and IVM (55.6 ± 11.1%) after using the droplet vitrification cryopreservation technique. The total time required for cryopreserving plants from SM (∼2� mo) was substantially less than that for PM (14� mo) and IVM (8� mo). The SSR profiles of plants recovered from cryopreserved PM, IVM, and SM and compared with control plants had a similarity coefficient of 0.92. Data on phenotypic traits revealed that cryopreserved plants were statistically comparable to the mother plants raised from suckers for all important growth and yield parameters. This study broadens the possibilities to cryopreserve Musa germplasm, by applying the droplet vitrification method to a new type of explant, the SM. The results presented in this paper show that Musa meristems can be effectively cryopreserved for storage and regeneration of true-to-type plants.
    Keywords Musa ; cryopreservation ; bananas ; vitrification ; meristems ; germplasm ; microsatellite repeats ; genetic stability ; tissue culture
    Language English
    Document type Article
    ISSN 1054-5476
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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