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  1. Artikel ; Online: Gene Silencing via RNA Interference in Cryptococcus.

    Bose, Indrani

    Methods in molecular biology (Clifton, N.J.)

    2024  Band 2775, Seite(n) 91–106

    Abstract: RNA interference (RNAi) is a molecular biology technique for silencing specific eukaryotic genes without altering the DNA sequence in the genome. The silencing effect occurs because of decreased levels of mRNA that then result in decreased protein levels ...

    Abstract RNA interference (RNAi) is a molecular biology technique for silencing specific eukaryotic genes without altering the DNA sequence in the genome. The silencing effect occurs because of decreased levels of mRNA that then result in decreased protein levels for the gene. The specificity of the silencing is dependent upon the presence of sequence-specific double-stranded RNA (dsRNA) that activates the cellular RNAi machinery. This chapter describes the process of silencing a specific target gene in Cryptococcus using a dual promoter vector. The plasmid, pIBB103, was designed with two convergent GAL7 promoters flanking a ura5 fragment that acts as a reporter for efficient RNAi. The target gene fragment is inserted between the promoters to be transcribed from both directions leading to the production of dsRNA in cells that activate the RNAi pathway.
    Mesh-Begriff(e) RNA Interference ; Promoter Regions, Genetic ; Cryptococcus/genetics ; RNA, Double-Stranded/genetics ; RNA, Double-Stranded/metabolism ; Genetic Vectors/genetics ; Plasmids/genetics ; Gene Silencing
    Sprache Englisch
    Erscheinungsdatum 2024-05-17
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3722-7_7
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Tipping the Balance: A Criticality Perspective.

    Bose, Indrani

    Entropy (Basel, Switzerland)

    2022  Band 24, Heft 3

    Abstract: Cell populations are often characterised by phenotypic heterogeneity in the form of two distinct subpopulations. We consider a model of tumour cells consisting of two subpopulations: non-cancer promoting (NCP) and cancer-promoting (CP). Under steady ... ...

    Abstract Cell populations are often characterised by phenotypic heterogeneity in the form of two distinct subpopulations. We consider a model of tumour cells consisting of two subpopulations: non-cancer promoting (NCP) and cancer-promoting (CP). Under steady state conditions, the model has similarities with a well-known model of population genetics which exhibits a purely noise-induced transition from unimodality to bimodality at a critical value of the noise intensity σ2. The noise is associated with the parameter
    Sprache Englisch
    Erscheinungsdatum 2022-03-14
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e24030405
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  3. Artikel ; Online: Emergent phenomena in living systems:A statistical mechanical perspective.

    Bose, Indrani

    Journal of biosciences

    2022  Band 47

    Abstract: A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature of the key ... ...

    Abstract A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature of the key processes like gene expression and cell differentiation give rise to fluctuations (noise) at the levels of the biomolecules, and this combined with nonlinear interactions gives rise to a number of emergent phenomena. In this review, we describe and discuss some of these phenomena which have the character of phase transitions in physical systems. We specifically focus on noise-induced transitions in a stochastic model of gene expression and in a population genetics model which have no analogs when the dynamics are solely deterministic in nature. Some of these transitions exhibit critical-point phenomena belonging to the mean-field Ising universality class of equilibrium phase transitions. A number of other examples, ranging from biofilms to homeostasis in adult tissues, are also discussed, which exhibit behaviour similar to critical phenomena in equilibrium and nonequilbrium phase transitions. The examples illustrate how the subject of statistical mechanics provides a bridge between theoretical models and experimental observations.
    Mesh-Begriff(e) Cell Differentiation ; Stochastic Processes
    Sprache Englisch
    Erscheinungsdatum 2022-09-09
    Erscheinungsland India
    Dokumenttyp Journal Article ; Review
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
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  4. Buch ; Online: Emergent phenomena in living systems

    Bose, Indrani

    a statistical mechanical perspective

    2023  

    Abstract: A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature of the key ... ...

    Abstract A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature of the key processes like gene expression and cell differentiation give rise to fluctuations (noise) in the levels of the biomolecules and this combined with nonlinear interactions give rise to a number of emergent phenomena. In this review, we describe and discuss some of these phenomena which have the character of phase transitions in physical systems. We specifically focus on noise-induced transitions in a stochastic model of gene expression and in a population genetics model which have no analogs when the dynamics are solely deterministic in nature. Some of these transitions exhibit critical-point phenomena belonging to the mean-field Ising universality class of equilibrium phase transitions. A number of other examples, ranging from biofilms to homeostasis in adult tissues, are also discussed which exhibit behavior similar to critical phenomena in equilibrium and nonequilbrium phase transitions. The examples illustrate how the subject of statistical mechanics provides a bridge between theoretical models and experimental observations.

    Comment: 29 pages, 4 figures
    Schlagwörter Condensed Matter - Statistical Mechanics ; Physics - Biological Physics ; Quantitative Biology - Quantitative Methods
    Thema/Rubrik (Code) 612
    Erscheinungsdatum 2023-08-31
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Buch ; Online: Growth, Poverty Trap and Escape

    Bose, Indrani

    2023  

    Abstract: The well-known Solow growth model is the workhorse model of the theory of economic growth, which studies capital accumulation in a model economy as a function of time with capital stock, labour and technology efiiciency as the basic ingredients. The ... ...

    Abstract The well-known Solow growth model is the workhorse model of the theory of economic growth, which studies capital accumulation in a model economy as a function of time with capital stock, labour and technology efiiciency as the basic ingredients. The capital is assumed to be in the form of manufacturing equipments and materials. Two important parameters of the model are: the saving fraction $s$ of the output of a production function and the technology efficiency parameter $A$, appearing in the production function. The saved fraction of the output is fully invested in the generation of new capital and the rest is consumed. The capital stock also depreciates as a function of time due to the wearing out of old capital and the increase in the size of the labour population. We propose a stochastic Solow growth model assuming the saving fraction to be a sigmoidal function of the per capita capital $k_p$. We derive analytically the steady state probability distribution $P(k_p)$ and demonstrate the existence of a poverty trap, of central concern in development economics. In a parameter regime, $P(k_p)$ is bimodal with the twin peaks corresponding to states of poverty and well-being respectively. The associated potential landscape has two valleys with fluctuation-driven transitions between them. The mean exit times from the valleys are computed and one finds that the escape from a poverty trap is more favourable at higher values of $A$. We identify a critical value of $A_c$ below (above) which the state of poverty (well-being) dominates and propose two early signatures of the regime shift occurring at $A_c$. The economic model, with conceptual foundation in nonlinear dynamics and statistical mechanics, share universal features with dynamical models from diverse disciplines like ecology and cell biology.
    Schlagwörter Physics - Physics and Society ; Quantitative Finance - General Finance
    Thema/Rubrik (Code) 612
    Erscheinungsdatum 2023-10-13
    Erscheinungsland us
    Dokumenttyp Buch ; Online
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  6. Artikel: Emergent phenomena in living systems: A statistical mechanical perspective

    Bose, Indrani

    Journal of biosciences. 2022 June, v. 47, no. 2

    2022  

    Abstract: A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature of the key ... ...

    Abstract A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature of the key processes like gene expression and cell differentiation give rise to fluctuations (noise) at the levels of the biomolecules, and this combined with nonlinear interactions gives rise to a number of emergent phenomena. In this review, we describe and discuss some of these phenomena which have the character of phase transitions in physical systems. We specifically focus on noise-induced transitions in a stochastic model of gene expression and in a population genetics model which have no analogs when the dynamics are solely deterministic in nature. Some of these transitions exhibit critical-point phenomena belonging to the mean-field Ising universality class of equilibrium phase transitions. A number of other examples, ranging from biofilms to homeostasis in adult tissues, are also discussed, which exhibit behaviour similar to critical phenomena in equilibrium and nonequilbrium phase transitions. The examples illustrate how the subject of statistical mechanics provides a bridge between theoretical models and experimental observations.
    Schlagwörter adults ; biochemical compounds ; biofilm ; cell differentiation ; gene expression ; homeostasis ; mechanics ; population genetics ; stochastic processes
    Sprache Englisch
    Erscheinungsverlauf 2022-06
    Umfang p. 22.
    Erscheinungsort Springer India
    Dokumenttyp Artikel
    Anmerkung Review
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
    DOI 10.1007/s12038-021-00247-2
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    Z 5290: Hefte anzeigen

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  7. Artikel ; Online: Molecular Pathogenesis of Nipah Virus.

    Talukdar, Pratik / Dutta, Debankita / Ghosh, Elija / Bose, Indrani / Bhattacharjee, Sourish

    Applied biochemistry and biotechnology

    2023  Band 195, Heft 4, Seite(n) 2451–2462

    Abstract: Viral diseases are causing mayhem throughout the world. One of the zoonotic viruses that have emerged as a potent threat to community health in the past few decades is Nipah virus. Nipah viral sickness is a zoonotic disease whose main carrier is bat. ... ...

    Abstract Viral diseases are causing mayhem throughout the world. One of the zoonotic viruses that have emerged as a potent threat to community health in the past few decades is Nipah virus. Nipah viral sickness is a zoonotic disease whose main carrier is bat. This disease is caused by Nipah virus (NiV). It belongs to the henipavirous group and of the family paramyxoviridae. Predominantly Pteropus spp. is the carrier of this virus. It was first reported from the Kampung Sungai Nipah town of Malaysia in 1998. Human-to-human transmission can also occur. Several repeated outbreaks were reported from South and Southeast Asia in the recent past. In humans, the disease is responsible for rapid development of acute illness, which can result in severe respiratory illness and serious encephalitis. Therefore, this calls for an urgent need for health authorities to conduct clinical trials to establish possible treatment regimens to prevent any further outbreaks.
    Mesh-Begriff(e) Animals ; Humans ; Nipah Virus/genetics ; Henipavirus Infections/epidemiology ; Henipavirus Infections/prevention & control ; Zoonoses/epidemiology ; Zoonoses/prevention & control ; Disease Outbreaks ; Chiroptera
    Sprache Englisch
    Erscheinungsdatum 2023-01-19
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review
    ZDB-ID 392344-7
    ISSN 1559-0291 ; 0273-2289
    ISSN (online) 1559-0291
    ISSN 0273-2289
    DOI 10.1007/s12010-022-04300-0
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  8. Artikel ; Online: Molecular Pathogenesis of Nipah Virus

    Talukdar, Pratik / Dutta, Debankita / Ghosh, Elija / Bose, Indrani / Bhattacharjee, Sourish

    Appl Biochem Biotechnol. 2023 Apr., v. 195, no. 4 p.2451-2462

    2023  

    Abstract: Viral diseases are causing mayhem throughout the world. One of the zoonotic viruses that have emerged as a potent threat to community health in the past few decades is Nipah virus. Nipah viral sickness is a zoonotic disease whose main carrier is bat. ... ...

    Abstract Viral diseases are causing mayhem throughout the world. One of the zoonotic viruses that have emerged as a potent threat to community health in the past few decades is Nipah virus. Nipah viral sickness is a zoonotic disease whose main carrier is bat. This disease is caused by Nipah virus (NiV). It belongs to the henipavirous group and of the family paramyxoviridae. Predominantly Pteropus spp. is the carrier of this virus. It was first reported from the Kampung Sungai Nipah town of Malaysia in 1998. Human-to-human transmission can also occur. Several repeated outbreaks were reported from South and Southeast Asia in the recent past. In humans, the disease is responsible for rapid development of acute illness, which can result in severe respiratory illness and serious encephalitis. Therefore, this calls for an urgent need for health authorities to conduct clinical trials to establish possible treatment regimens to prevent any further outbreaks.
    Schlagwörter Nipah henipavirus ; Pteropus ; community health ; encephalitis ; pathogenesis ; respiratory tract diseases ; viruses ; zoonoses ; Malaysia
    Sprache Englisch
    Erscheinungsverlauf 2023-04
    Umfang p. 2451-2462.
    Erscheinungsort Springer US
    Dokumenttyp Artikel ; Online
    Anmerkung Review
    ZDB-ID 392344-7
    ISSN 0273-2289
    ISSN 0273-2289
    DOI 10.1007/s12010-022-04300-0
    Datenquelle NAL Katalog (AGRICOLA)

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  9. Artikel ; Online: Criticality in cell differentiation.

    Bose, Indrani / Pal, Mainak

    Journal of biosciences

    2017  Band 42, Heft 4, Seite(n) 683–693

    Abstract: Cell differentiation is an important process in living organisms. Differentiation is mostly based on binary decisions with the progenitor cells choosing between two specific lineages. The differentiation dynamics have both deterministic and stochastic ... ...

    Abstract Cell differentiation is an important process in living organisms. Differentiation is mostly based on binary decisions with the progenitor cells choosing between two specific lineages. The differentiation dynamics have both deterministic and stochastic components. Several theoretical studies suggest that cell differentiation is a bifurcation phenomenon, well-known in dynamical systems theory. The bifurcation point has the character of a critical point with the system dynamics exhibiting specific features in its vicinity. These include the critical slowing down, rising variance and lag-1 autocorrelation function, strong correlations between the fluctuations of key variables and non-Gaussianity in the distribution of fluctuations. Recent experimental studies provide considerable support to the idea of criticality in cell differentiation and in other biological processes like the development of the fruit fly embryo. In this review, an elementary introduction is given to the concept of criticality in cell differentiation. The correspondence between the signatures of criticality and experimental observations on blood cell differentiation in mice is further highlighted.
    Mesh-Begriff(e) Animals ; Cell Differentiation/genetics ; Cell Lineage/genetics ; Drosophila melanogaster/cytology ; Drosophila melanogaster/growth & development ; Drosophila melanogaster/metabolism ; Gene Regulatory Networks ; Humans ; Mice ; Models, Genetic ; Models, Statistical ; Stem Cells/cytology ; Stem Cells/metabolism ; Stochastic Processes ; Systems Theory
    Sprache Englisch
    Erscheinungsdatum 2017-12-29
    Erscheinungsland India
    Dokumenttyp Journal Article ; Review
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
    DOI 10.1007/s12038-017-9721-6
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  10. Buch ; Online: Bifurcation and Criticality

    Bose, Indrani / Ghosh, Sayantari

    2019  

    Abstract: Equilibrium and nonequilibrium systems exhibit power-law singularities close to their critical and bifurcation points respectively. A recent study has shown that biochemical nonequilibrium models with positive feedback belong to the universality class of ...

    Abstract Equilibrium and nonequilibrium systems exhibit power-law singularities close to their critical and bifurcation points respectively. A recent study has shown that biochemical nonequilibrium models with positive feedback belong to the universality class of the mean-field Ising model. Through a mapping between the two systems, effective thermodynamic quantities like temperature, magnetic field and order parameter can be expressed in terms of biochemical parameters. In this paper, we demonstrate the equivalence using a simple deterministic approach. As an illustration we consider a model of population dynamics exhibiting the Allee effect for which we determine the exact phase diagram. We further consider a two-variable model of positive feedback, the genetic toggle, and discuss the conditions under which the model belongs to the mean-field Ising universality class. In the biochemical models, the supercritical pitchfork bifurcation point serves as the critical point. The dynamical behaviour predicted by the two models is in qualitative agreement with experimental observations and opens up the possibility of exploring critical point phenomena in laboratory populations and synthetic biological circuits.

    Comment: 13 Pages, 5 Figures
    Schlagwörter Quantitative Biology - Quantitative Methods ; Condensed Matter - Statistical Mechanics ; Nonlinear Sciences - Adaptation and Self-Organizing Systems
    Thema/Rubrik (Code) 612
    Erscheinungsdatum 2019-06-03
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    Dokumenttyp Buch ; Online
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