Arnab Barua
A Layman' and a seeker' who is doing a journey towards the known and unknown truth of 'Life', who wants to understand the beautiful relations between Theoretical Physics, mathematics and Biology............
Topics : (a) Statistical mechanics of biological systems:
Identification of cell decision-making principles:
Single cell decision-making has been a major focus of biology. However, in multicellular systems, the regulation of single cell decisions and their impact on the total system behaviour are far from being well understood. We view cell decision-making as a communication between the cell and its microenvironment. Cells can be viewed as signalling processing units, which receive signals and process them via interconnected pathways. The result of this information processing is the decision of cells for their fate, phenotype and generally speaking their future state. We regard information as an organizing principle for the spatio-temporal evolution of multi-cellular biological systems. Using multi-scale modeling, we try to delineate the design principles of cell decision-making. In particularly, we focus on specific cell fate determination mechanisms such as Notch-Delta signalling, in developmental systems, retina, collective cell migration etc. .
Publications:
(1) Cell decision-making through the lens of Bayesian learning;
A. Barua, H. Hatzikirou
Entropy 2023, 25(4), 609;
https://doi.org/10.3390/e25040609
A. A. Pujar, A. Barua, D. Singh, U. Roy, M. K. Jolly and H. Hatzikirou
Biorxiv 2021;
https://doi.org/10.1101/2021.11.16.468748
(3) Close to optimal cell sensing ensures the robustness of tissue differentiation process: the avian photoreceptor mosaic case;
A. Barua, A. Beygi, H. Hatzikirou
Entropy 2021, 23(7), 867;
https://doi.org/10.3390/e23070867
(4) Entropy-driven cell decision-making predicts "fluid-to-solid" transition in multicellular systems;
A. Barua, S. Syga, P. Mascheroni, N. Kavallaris, M. Meyer-Hermann, A. Deutsch, H. Hatzikirou
New Journal of Physics, Volume 22, December 2020; https://iopscience.iop.org/article/10.1088/1367-2630/abcb2e
(5) A least microenvironmental uncertainty principle (LEUP) as a generative model of collective cell migration mechanisms;
A. Barua, J. M. N. Sedeño, M. Meyer-Hermann, H. Hatzikirou
Scientific Reports , 22371, 2020;
https://www.nature.com/articles/s41598-020-79119-y
(b) Systems Biology:
Mathematical Modelling of Metabolites for various kinds of flours:
Food supplementation with a fiber mix of guar gum and chickpea flour represents a promising approach to reduce the risk of type 2 diabetes mellitus (T2DM) by attenuating postprandial glycemia. To investigate the effects on postprandial metabolic fluxes of glucose-derived metabolites in response to this fiber mix, a randomized, cross-over study was designed. 12 healthy, male subjects consumed three different flatbreads either supplemented with 2% or 4% guar gum and 15% chickpea flour each or without supplementation (control) and the flatbreads were enriched with ~2% of 13C-labeled wheat flour. Blood was collected at 16 intervals over a period of 360 minutes after bread intake and plasma samples were analyzed by GC-MS based metabolite profiling combined with stable isotope-assisted metabolomics. Although metabolite levels of the downstream metabolites of glucose, specifically lactate and alanine, were not altered in response to the fiber mix, supplementation of 4% guar gum was shown to significantly delay and reduce the exogenous formation of these metabolites. Metabolic modeling and computation of appearance rates revealed that the effects induced by the fiber mix were strongest for glucose and attenuated downstream of glucose. Further investigations to explore the potential of fiber mix supplementation to counteract the development of metabolic diseases are warranted.
Publication(s):
(1) Fibre mix addition of guar gum to wheat-based flatbread delays the appearance of glucose and its downstream metabolites in plasma
L. Schlicker , H. M. Boers , C-A. Dudek , G. Zhao , A. Barua , J-P. Trezzi , M. Meyer-Hermann, D. M. Jacobs and K. Hiller
Metabolites 2019, 9(5), 91;
https://doi.org/10.3390/metabo9050091
(c)Animal Behaviour and Camouflage strategy:
Influence of Arsenic in Camouflage Strategy of Common River Prawn:
Camouflage is an interesting adaptation (for survivability) by organisms in terms of different aggregation or fusion of colourations. Understanding these camouflage strategies in the presence of arsenic on transparent/semi-transparent species is pretty challenging. Previously, several researchers have demonstrated that colouration or pigmentation strategy in an organism is a strategy to merge with the environment to escape from predatory threats. Our study was done on a semi-transparent freshwater prawn species which exhibits a strategy of pigment droplets on its exoskeleton. Unlike previous studies, our findings robustly indicate the fact that pigment droplets are not the only reason for colouration. The pigment droplets rather regulate the darkness of the exoskeleton. However, the transparency of the abdominal muscles additionally plays a crucial role in creating a background of the pigment droplets. The transparency muscles allow light to pass through the abdomen, thus creating a semi-transparent appearance. The degree of semi-transparency is also regulated by the intensity of light. The abdomen and the pigment droplets on the exoskeleton cumulatively as well as contrastingly maintain the transparency and the colour quotient of the prawns. In our study, we have majorly concentrated on the abdominal region of the prawns as it appears to be the key semi-transparent feature of the organism. This research is directed to an ecotoxicological aspect where we showed that arsenic in chronic non-lethal concentration, can notably alter the colouration pattern in this prawn model within a short period of time. Finally, we have used an image processing algorithm to assess the alteration of colouration in this organism.
Publication(s):
(1) Understanding the Role of Arsenic in Camouflage Strategy: A Study with Common River Prawn
M. Bose , K. Jas, A. Barua, and C. Munshi
Preprints (2022), 2022030027;
