Theory in Biosciences最新文献

{"title":"Correction to: The biological Maxwell's demons: exploring ideas about the information processing in biological systems.","authors":"Eduardo Mizraji","doi":"10.1007/s12064-021-00356-4","DOIUrl":"https://doi.org/10.1007/s12064-021-00356-4","url":null,"abstract":"","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8568851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39437759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Information transmission in a two-step cascade: interplay of activation and repression.","authors":"Tuhin Subhra Roy,&nbsp;Mintu Nandi,&nbsp;Ayan Biswas,&nbsp;Pinaki Chaudhury,&nbsp;Suman K Banik","doi":"10.1007/s12064-021-00357-3","DOIUrl":"https://doi.org/10.1007/s12064-021-00357-3","url":null,"abstract":"<p><p>We present an information-theoretic formalism to study signal transduction in four architectural variants of a model two-step cascade with increasing input population. Our results categorize these four types into two classes depending upon the effect of activation and repression on mutual information, net synergy, and signal-to-noise ratio. Using the Gaussian framework and linear noise approximation, we derive the analytic expressions for these metrics to establish their underlying relationships in terms of the biochemical parameters. We also verify our approximations through stochastic simulations.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39488165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complexities in viral replication strategies as a potential explanation for prevalence of asymptomatic carriers in Covid-19 infections: analytical observation on SARS-Cov2 genome characteristics.","authors":"Himanshu Priyadarshi, Rekha Das","doi":"10.1007/s12064-021-00349-3","DOIUrl":"10.1007/s12064-021-00349-3","url":null,"abstract":"<p><p>Analytical observations (in silico) indicate molecular features of SARS-Cov2 genome that potentially explains the high prevalence of asymptomatic cases in Covid-19 pandemic. We observed that the virus maintains a low preference for 'GGG' codon for glycine (3%) in its genome. We also observed multiple putative introns of 26-44 nucleotide (nt) length in the genomic region between the coding regions of Nsp10 and RPol in the viral ORF1ab, like several other beta-coronaviruses of similar infectivity levels. It appears that the virus employs a dual strategy to ensure unhindered replication within the host. One of the strategies employ a (- )1 frameshift translation event through programmed ribosomal slippage at the ribosomal slippage site in the ORF1ab. The alternate strategy relies on intron excision to generate a read through frame. The presence of 'GGG' in this conserved ribosomal slippage site ensures adequate tRNA in cytoplasm to match the codon, implying no additional frameshift translation due to ribosomal stalling. With fewer replication events, viral load remains low and resulting in asymptomatic cases. We suggest that this strategy is the primary reason for the prevalence of asymptomatic cases in the disease, enabling the virus to spread rapidly.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8191711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39084239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methodological notes on pandemic virus SARS-CoV-2 research.","authors":"Gianluigi Zangari Del Balzo","doi":"10.1007/s12064-021-00355-5","DOIUrl":"10.1007/s12064-021-00355-5","url":null,"abstract":"<p><p>In the fight against the COVID-19 pandemic, many brilliant results have been achieved, but the thermodynamics of the novel SARS-CoV-2 coronavirus has been completely neglected. This is a serious systematic error, which can compromise the results of the entire pandemic virus SARS-CoV-2 research. In the present work, we therefore study the thermodynamics of SARS-CoV-2 in its environment, from air to endosome and endosome-independent cell entry pathways. In the study of the thermodynamics of the new coronavirus SARS-CoV-2 in air, the presence of pollen, bacteria, other viruses, spores, dust, but more particularly, that of nanoparticles of health interest at the same scale threshold as the spike proteins of the pandemic virus, such as particulate matter, cannot be neglected. This work therefore starts from a comparative study of the air environments in China and Italy, the first countries affected by the infection. Currently, a correlation between the spread of infection and pollution is still very controversial. But our paper is not concerned with this. We propose some methodological notes which lead us to the formulation of a general mathematical apparatus (an energy landscape theory), suitable to explain at the molecular level the energetic configurations of the quasi-species of the pandemic virus SARS-CoV-2 in its environment. We focus on complexes between the viral particle and other objects in its environment at the scale threshold of the spikes of the viral particle. Then, we wondered if such complexes can lead to the generation of more aggressive viral variants and how to predict their populations and energy configurations, in order to plan an adequate prophylaxis.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8423596/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10317628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Geometry and symmetry in biochemical reaction systems.","authors":"Raffaella Mulas, Rubén J Sánchez-García, Ben D MacArthur","doi":"10.1007/s12064-021-00353-7","DOIUrl":"10.1007/s12064-021-00353-7","url":null,"abstract":"<p><p>Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph representations only describe pairwise interactions between molecular species and so are not well suited to modelling complex sets of reactions that may involve numerous reactants and/or products. Here, we make use of a recently developed hypergraph theory of chemical reactions that naturally allows for higher-order interactions to explore the geometry and quantify functional redundancy in biochemical reactions systems. Our results constitute a general theory of automorphisms for oriented hypergraphs and describe the effect of automorphism group structure on hypergraph Laplacian spectra.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8568762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39192088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The biological Maxwell's demons: exploring ideas about the information processing in biological systems.","authors":"Eduardo Mizraji","doi":"10.1007/s12064-021-00354-6","DOIUrl":"10.1007/s12064-021-00354-6","url":null,"abstract":"<p><p>This work is based on ideas supported by some of the biologists who discovered foundational facts of twentieth-century biology and who argued that Maxwell's demons are physically implemented by biological devices. In particular, JBS Haldane first, and later J. Monod, A, Lwoff and F. Jacob argued that enzymes and molecular receptors implemented Maxwell's demons that operate in systems far removed from thermodynamic equilibrium and that were responsible for creating the biological order. Later, these ideas were extended to other biological processes. In this article, we argue that these biological Maxwell's demons (BMD) are systems that have information processing capabilities that allow them to select their inputs and direct their outputs toward targets. In this context, we propose the idea that these BMD are information catalysts in which the processed information has broad thermodynamic consequences.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8568868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39357635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Flow analysis of Carreau fluid model induced by the ciliary cells, smooth muscle cells and pressure gradient at the ampullar region entrance.","authors":"H Ashraf,&nbsp;A M Siddiqui,&nbsp;M A Rana","doi":"10.1007/s12064-021-00352-8","DOIUrl":"https://doi.org/10.1007/s12064-021-00352-8","url":null,"abstract":"<p><p>This theoretical analysis considers a biomechanical model in which the Carreau fluid model characterizes the viscoelastic nature of growing human embryo and secreted fluid. This model incorporates transport mechanisms that involve the swaying motions of ciliary cells, peristaltic contractions of smooth muscle cells and pressure gradient at the ampullar region entrance. Series form solutions of the resulting partial differential equations are obtained using the regular perturbation method. A theoretical estimate of effects of the condition of pressure gradient, geometric parameters and fluid model parameters on the flow variables that have relevance to the problem of growing embryo transport in the human fallopian tube is presented through the discussion of graphs. Furthermore, an analogy between the linearly viscous fluid, and the shear thinning and shear thickening characteristics of the Carreau fluid model is also presented. The pertinence of the obtained results with growing embryo transport in the human fallopian tube revealed that when shear thickening characteristics of the Carreau fluid model are considered then complete mitotic divisions take place properly with an estimated appropriate residue time about 3-4 days. Smaller size trapped boluses of the secreted fluid make the smooth forwarding of the growing embryo in the human fallopian tube when shear thinning characteristics of the Carreau fluid model are taken into account. Key modulators: progesterone ([Formula: see text] and estradiol ([Formula: see text]), prostaglandin [Formula: see text] ([Formula: see text]) and prostaglandin [Formula: see text] ([Formula: see text]) constraint the growing embryo transport.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00352-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39157430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nutrient supply, cell spatial correlation and Gompertzian tumor growth.","authors":"P Castorina,&nbsp;D Carco'","doi":"10.1007/s12064-021-00344-8","DOIUrl":"https://doi.org/10.1007/s12064-021-00344-8","url":null,"abstract":"<p><p>Gompertzian tumor growth can be reproduced by mitosis, related to nutrient supply, with local spatial cell correlations. The global energy constraint alone does not reproduce in vivo data by the observed values of the nutrient expenditure for the cell activities. The depletion of the exponential growth, described by the Gompertz law, is obtained by mean field spatial correlations or by a small word network among cells. The well-known interdependence between the two parameters of the Gompertz growth naturally emerges and depends on the cell volume and on the tumor density.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00344-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38982577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimal allocation in annual plants with density-dependent fitness.","authors":"Sergiy Koshkin,&nbsp;Zachary Zalles,&nbsp;Michael F Tobin,&nbsp;Nicolas Toumbacaris,&nbsp;Cameron Spiess","doi":"10.1007/s12064-021-00343-9","DOIUrl":"https://doi.org/10.1007/s12064-021-00343-9","url":null,"abstract":"<p><p>We study optimal two-sector (vegetative and reproductive) allocation models of annual plants in temporally variable environments that incorporate effects of density-dependent lifetime variability and juvenile mortality in a fitness function whose expected value is maximized. Only special cases of arithmetic and geometric mean maximizers have previously been considered in the literature, and we also allow a wider range of production functions with diminishing returns. The model predicts that the time of maturity is pushed to an earlier date as the correlation between individual lifetimes increases, and while optimal schedules are bang-bang at the extremes, the transition is mediated by schedules where vegetative growth is mixed with reproduction for a wide intermediate range. The mixed growth lasts longer when the production function is less concave allowing for better leveraging of plant size when generating seeds. Analytic estimates are obtained for the power means that interpolate between arithmetic and geometric mean and correspond to partially correlated lifetime distributions.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00343-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25584593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of integrated noise in pathway-specific signal propagation in feed-forward loops.","authors":"Mintu Nandi","doi":"10.1007/s12064-021-00338-6","DOIUrl":"https://doi.org/10.1007/s12064-021-00338-6","url":null,"abstract":"<p><p>Cells impose optimal noise control mechanism in diverse situations to cope with distinct environmental cues. Sometimes, it is desirable for the cell to utilize fluctuations for noise-driven processes. In other cases, noise can be harmful to the cell to show optimal fitness. It is, therefore, important to unravel the noise propagation mechanism inside the cell. Such noise controlling mechanism is accomplished by using gene transcription regulatory networks. One such gene regulatory network is feed-forward loop, having three regulatory nodes S, X and Y. Here, we consider the most abundant type 1 of coherent and incoherent feed-forward loops with both OR and AND logic functions, forming four different architectures. In OR logic function, the functions representing S and X act additively for the regulation of Y, while in AND logic function, the same functions (S and X) act multiplicatively for the regulation of Y. Measurement of susceptibility of the signal at output Y is done using elasticity of each regulation in FFLs. Using susceptibility, we demonstrate the nature of pathway integration by which one-step and two-step pathways get overlapped. The integration type is competitive for motifs having OR gate, while it is noncompetitive for the same with AND gate. The pathway integration property explains the output noise behavior of the motifs properly but cannot infer about the mechanism by which the upstream noise propagates to output. To account this, the total output noise is decomposed, which results in integrated noise as an additional noise source along with pathway-specific noise components. The integrated noise is found to appear as a consequence of integration between the pathways and has different functional characteristics explaining noise amplification and noise attenuation property of coherent and incoherent feed-forward loops, respectively. The noise decomposition also quantifies the contribution of different noise sources toward total noise. Finally, the noise propagation is being tuned as a function of input signal noise and its time scale of fluctuations, which shows considerable intrinsic noise strength and relatively slow relaxation time scale causes a higher degree of noise propagation in FFLs.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":null,"pages":null},"PeriodicalIF":1.1,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s12064-021-00338-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25504545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}