In Silico Biology最新文献

Modelling speciation: Problems and implications. 建模物种形成:问题和影响。

In Silico Biology Pub Date : 2023-01-01 DOI: 10.3233/ISB-220253

Jonathan B L Bard

{"title":"Modelling speciation: Problems and implications.","authors":"Jonathan B L Bard","doi":"10.3233/ISB-220253","DOIUrl":"10.3233/ISB-220253","url":null,"abstract":"Darwin's and Wallace's 1859 explanation that novel speciation resulted from natural variants that had been subjected to selection was refined over the next 150 years as genetic inheritance and the importance of mutation-induced change were discovered, the quantitative theory of evolutionary population genetics was produced, the speed of genetic change in small populations became apparent and the ramifications of the DNA revolution became clear. This paper first discusses the modern view of speciation in its historical context. It then uses systems-biology approaches to consider the many complex processes that underpin the production of a new species; these extend in scale from genes to populations with the processes of variation, selection and speciation being affected by factors that range from mutation to climate change. Here, events at a particular scale level (e.g. protein network activity) are activated by the output of the level immediately below (i.e. gene expression) and generate a new output that activates the layer above (e.g. embryological development), with this change often being modulated by feedback from higher and lower levels. The analysis shows that activity at each level in the evolution of a new species is marked by stochastic activity, with mutation of course being the key step for variation. The paper examines events at each of these scale levels and particularly considers how the pathway by which mutation leads to phenotypic variants and the wide range of factors that drive selection can be investigated computationally. It concludes that, such is the complexity of speciation, most steps in the process are currently difficult to model and that predictions about future speciation will, apart from a few special cases, be hard to make. The corollary is that opportunities for novel variants to form are maximised.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10741375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10724747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data. scAN1.0：用于处理10X单细胞RNAseq数据的可复制和标准化管道。

In Silico Biology Pub Date : 2023-01-01 DOI: 10.3233/ISB-220252

Maxime Lepetit, Mirela Diana Ilie, Marie Chanal, Gerald Raverot, Philippe Bertolino, Christophe Arpin, Franck Picard, Olivier Gandrillon

引用次数: 0

Where Do CABs Exist? Verification of a specific region containing concave Actin Bundles (CABs) in a 3-Dimensional confocal image. 出租车在哪里?在三维共聚焦图像中包含凹肌动蛋白束(cab)的特定区域的验证。

In Silico Biology Pub Date : 2023-01-01 DOI: 10.3233/ISB-210240

Doyoung Park

{"title":"Where Do CABs Exist? Verification of a specific region containing concave Actin Bundles (CABs) in a 3-Dimensional confocal image.","authors":"Doyoung Park","doi":"10.3233/ISB-210240","DOIUrl":"10.3233/ISB-210240","url":null,"abstract":"CABs (Concave Actin Bundles) are oriented against the scaffold transversally in a manner different from traditional longitudinal F-actin bundles. CABs are present in a specific area, and do not exist in random areas. Biologically, CABs are developed to attach cells to fibers firmly so that CABs are found near cells. Based on this knowledge, we closely examined 3D confocal microcopy images containing fiber scaffolds, actin, and cells. Then, we assumed that the areas containing high values of compactness of fiber, compactness of actin, and density of cells would have many numbers of CABs.In this research, we wanted to prove this assumption. We first incorporated a two-point correlation function to define a measure of compactness. Then, we used the Bayes' theorem to prove the above assumption. As the assumption, our results verified that CABs exist in an area of high compactness of a fiber network, high compactness of actin distribution, and high density of cells. Thus, we concluded that CABs are developed to attach cells to a fibrillar scaffold firmly. This finding may be further verified mathematically in future studies.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10741311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40677600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multiscale modeling of tumor response to vascular endothelial growth factor (VEGF) inhibitor. 肿瘤对血管内皮生长因子(VEGF)抑制剂反应的多尺度模型。

In Silico Biology Pub Date : 2021-01-01 DOI: 10.3233/ISB-210235

Melisa Hendrata, Janti Sudiono

{"title":"Multiscale modeling of tumor response to vascular endothelial growth factor (VEGF) inhibitor.","authors":"Melisa Hendrata, Janti Sudiono","doi":"10.3233/ISB-210235","DOIUrl":"https://doi.org/10.3233/ISB-210235","url":null,"abstract":"Vascular endothelial growth factor (VEGF) has been known as a key mediator of angiogenesis in cancer. Bevacizumab is anti-VEGF monoclonal antibody that has been approved by the FDA as a first-line treatment in many types of cancer. In this paper, we extend a previously validated multiscale tumor model to comprehensively include the multiple roles of VEGF during the course of angiogenesis and its binding mechanism with bevacizumab. We use the model to simulate tumor system response under various bevacizumab concentrations, both in stand-alone treatment and in combination with chemotherapy. Our simulation indicates that periodic administration of bevacizumab with lower concentration can achieve greater efficacy than a single treatment with higher concentration. The simulation of the combined therapy also shows that the continuous administration of bevacizumab during the maintenance phase can lead to antitumor activity which further suppresses its growth. Agreement with experimental results indicates the potential of the model in predicting the efficacy of anti-VEGF therapies and could therefore contribute to developing prospective clinical trials.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/fe/bb/isb-14-isb210235.PMC8842763.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39799967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Modeling and characterization of inter-individual variability in CD8 T cell responses in mice. 小鼠CD8 T细胞反应的个体间变异的建模和表征。

In Silico Biology Pub Date : 2021-01-01 DOI: 10.3233/ISB-200205

Chloe Audebert, Daphné Laubreton, Christophe Arpin, Olivier Gandrillon, Jacqueline Marvel, Fabien Crauste

{"title":"Modeling and characterization of inter-individual variability in CD8 T cell responses in mice.","authors":"Chloe Audebert, Daphné Laubreton, Christophe Arpin, Olivier Gandrillon, Jacqueline Marvel, Fabien Crauste","doi":"10.3233/ISB-200205","DOIUrl":"https://doi.org/10.3233/ISB-200205","url":null,"abstract":"To develop vaccines it is mandatory yet challenging to account for inter-individual variability during immune responses. Even in laboratory mice, T cell responses of single individuals exhibit a high heterogeneity that may come from genetic backgrounds, intra-specific processes (e.g. antigen-processing and presentation) and immunization protocols.To account for inter-individual variability in CD8 T cell responses in mice, we propose a dynamical model coupled to a statistical, nonlinear mixed effects model. Average and individual dynamics during a CD8 T cell response are characterized in different immunization contexts (vaccinia virus and tumor). On one hand, we identify biological processes that generate inter-individual variability (activation rate of naive cells, the mortality rate of effector cells, and dynamics of the immunogen). On the other hand, introducing categorical covariates to analyze two different immunization regimens, we highlight the steps of the response impacted by immunogens (priming, differentiation of naive cells, expansion of effector cells and generation of memory cells). The robustness of the model is assessed by confrontation to new experimental data.Our approach allows to investigate immune responses in various immunization contexts, when measurements are scarce or missing, and contributes to a better understanding of inter-individual variability in CD8 T cell immune responses.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/ISB-200205","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25346132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology. 基于栅格的蒙特卡罗模拟营养浓度和磁场暴露对酵母菌落生长和形态的影响。

In Silico Biology Pub Date : 2021-01-01 DOI: 10.3233/ISB-210233

Rebekah Hall, Daniel A Charlebois

引用次数: 1

Cancer immunoediting: A game theoretical approach. 癌症免疫编辑:一种博弈论方法。

In Silico Biology Pub Date : 2021-01-01 DOI: 10.3233/ISB-200475

Fatemeh Tavakoli, Javad Salimi Sartakhti, Mohammad Hossein Manshaei, David Basanta

{"title":"Cancer immunoediting: A game theoretical approach.","authors":"Fatemeh Tavakoli, Javad Salimi Sartakhti, Mohammad Hossein Manshaei, David Basanta","doi":"10.3233/ISB-200475","DOIUrl":"https://doi.org/10.3233/ISB-200475","url":null,"abstract":"The role of the immune system in tumor development increasingly includes the idea of cancer immunoediting. It comprises three phases: elimination, equilibrium, and escape. In the first phase, elimination, transformed cells are recognized and destroyed by immune system. The rare tumor cells that are not destroyed in this phase may then enter the equilibrium phase, where their growth is prevented by immunity mechanisms. The escape phase represents the final phase of this process, where cancer cells begin to grow unconstrained by the immune system. In this study, we describe and analyze an evolutionary game theoretical model of proliferating, quiescent, and immune cells interactions for the first time. The proposed model is evaluated with constant and dynamic approaches. Population dynamics and interactions between the immune system and cancer cells are investigated. Stability of equilibria or critical points are analyzed by applying algebraic analysis. This model allows us to understand the process of cancer development and might help us design better treatment strategies to account for immunoediting.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/ISB-200475","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38623231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Reverse engineering of a mechanistic model of gene expression using metastability and temporal dynamics. 利用亚稳态和时间动力学的基因表达机制模型的逆向工程。

In Silico Biology Pub Date : 2021-01-01 DOI: 10.3233/ISB-210226

Elias Ventre

{"title":"Reverse engineering of a mechanistic model of gene expression using metastability and temporal dynamics.","authors":"Elias Ventre","doi":"10.3233/ISB-210226","DOIUrl":"https://doi.org/10.3233/ISB-210226","url":null,"abstract":"Differentiation can be modeled at the single cell level as a stochastic process resulting from the dynamical functioning of an underlying Gene Regulatory Network (GRN), driving stem or progenitor cells to one or many differentiated cell types. Metastability seems inherent to differentiation process as a consequence of the limited number of cell types. Moreover, mRNA is known to be generally produced by bursts, which can give rise to highly variable non-Gaussian behavior, making the estimation of a GRN from transcriptional profiles challenging. In this article, we present CARDAMOM (Cell type Analysis from scRna-seq Data achieved from a Mixture MOdel), a new algorithm for inferring a GRN from timestamped scRNA-seq data, which crucially exploits these notions of metastability and transcriptional bursting. We show that such inference can be seen as the successive resolution of as many regression problem as timepoints, after a preliminary clustering of the whole set of cells with regards to their associated bursts frequency. We demonstrate the ability of CARDAMOM to infer a reliable GRN from in silico expression datasets, with good computational speed. To the best of our knowledge, this is the first description of a method which uses the concept of metastability for performing GRN inference.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/00/e7/isb-14-isb210226.PMC8842760.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39718518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. 微生物诱发心血管疾病宿主-病原体蛋白相互作用的网络分析。

In Silico Biology Pub Date : 2021-01-01 DOI: 10.3233/ISB-210238

Nirupma Singh, Sneha Rai, Rakesh Bhatnagar, Sonika Bhatnagar

{"title":"Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases.","authors":"Nirupma Singh, Sneha Rai, Rakesh Bhatnagar, Sonika Bhatnagar","doi":"10.3233/ISB-210238","DOIUrl":"https://doi.org/10.3233/ISB-210238","url":null,"abstract":"Large-scale visualization and analysis of HPIs involved in microbial CVDs can provide crucial insights into the mechanisms of pathogenicity. The comparison of CVD associated HPIs with the entire set of HPIs can identify the pathways specific to CVDs. Therefore, topological properties of HPI networks in CVDs and all pathogens was studied using Cytoscape3.5.1. Ontology and pathway analysis were done using KOBAS 3.0. HPIs of Papilloma, Herpes, Influenza A virus as well as Yersinia pestis and Bacillus anthracis among bacteria were predominant in the whole (wHPI) and the CVD specific (cHPI) network. The central viral and secretory bacterial proteins were predicted virulent. The central viral proteins had higher number of interactions with host proteins in comparison with bacteria. Major fraction of central and essential host proteins interacts with central viral proteins. Alpha-synuclein, Ubiquitin ribosomal proteins, TATA-box-binding protein, and Polyubiquitin-C &B proteins were the top interacting proteins specific to CVDs. Signaling by NGF, Fc epsilon receptor, EGFR and ubiquitin mediated proteolysis were among the top enriched CVD specific pathways. DEXDc and HELICc were enriched host mimicry domains that may help in hijacking of cellular machinery by pathogens. This study provides a system level understanding of cardiac damage in microbe induced CVDs.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a2/91/isb-14-isb210238.PMC8842779.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39801374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

A computational framework for finding parameter sets associated with chaotic dynamics. 寻找混沌动力学相关参数集的计算框架。

In Silico Biology Pub Date : 2021-01-01 DOI: 10.3233/ISB-200476

S Koshy-Chenthittayil, E Dimitrova, E W Jenkins, B C Dean

引用次数: 0