Theoretical Biology and Medical Modelling最新文献

{"title":"The effects of low-impact mutations in digital organisms.","authors":"Chase W Nelson,&nbsp;John C Sanford","doi":"10.1186/1742-4682-8-9","DOIUrl":"https://doi.org/10.1186/1742-4682-8-9","url":null,"abstract":"<p><strong>Background: </strong>Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.</p><p><strong>Results: </strong>When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida's default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.</p><p><strong>Conclusions: </strong>Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2011-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29822343","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}

{"title":"A mathematical model of quorum sensing regulated EPS production in biofilm communities.","authors":"Mallory R Frederick,&nbsp;Christina Kuttler,&nbsp;Burkhard A Hense,&nbsp;Hermann J Eberl","doi":"10.1186/1742-4682-8-8","DOIUrl":"https://doi.org/10.1186/1742-4682-8-8","url":null,"abstract":"<p><strong>Background: </strong>Biofilms are microbial communities encased in a layer of extracellular polymeric substances (EPS). The EPS matrix provides several functional purposes for the biofilm, such as protecting bacteria from environmental stresses, and providing mechanical stability. Quorum sensing is a cell-cell communication mechanism used by several bacterial taxa to coordinate gene expression and behaviour in groups, based on population densities.</p><p><strong>Model: </strong>We mathematically model quorum sensing and EPS production in a growing biofilm under various environmental conditions, to study how a developing biofilm impacts quorum sensing, and conversely, how a biofilm is affected by quorum sensing-regulated EPS production. We investigate circumstances when using quorum-sensing regulated EPS production is a beneficial strategy for biofilm cells.</p><p><strong>Results: </strong>We find that biofilms that use quorum sensing to induce increased EPS production do not obtain the high cell populations of low-EPS producers, but can rapidly increase their volume to parallel high-EPS producers. Quorum sensing-induced EPS production allows a biofilm to switch behaviours, from a colonization mode (with an optimized growth rate), to a protection mode.</p><p><strong>Conclusions: </strong>A biofilm will benefit from using quorum sensing-induced EPS production if bacteria cells have the objective of acquiring a thick, protective layer of EPS, or if they wish to clog their environment with biomass as a means of securing nutrient supply and outcompeting other colonies in the channel, of their own or a different species.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2011-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29803144","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}

{"title":"Proof-of-principle investigation of an algorithmic model of adenosine-mediated angiogenesis.","authors":"Francisco Azuaje,&nbsp;Frédérique Léonard,&nbsp;Magali Rolland-Turner,&nbsp;Yvan Devaux,&nbsp;Daniel R Wagner","doi":"10.1186/1742-4682-8-7","DOIUrl":"https://doi.org/10.1186/1742-4682-8-7","url":null,"abstract":"<p><strong>Background: </strong>We investigated an algorithmic approach to modelling angiogenesis controlled by vascular endothelial growth factor (VEGF), the anti-angiogenic soluble VEGF receptor 1 (sVEGFR-1) and adenosine (Ado). We explored its feasibility to test angiogenesis-relevant hypotheses. We illustrated its potential to investigate the role of Ado as an angiogenesis modulator by enhancing VEGF activity and antagonizing sVEGFR-1.</p><p><strong>Results: </strong>We implemented an algorithmic model of angiogenesis consisting of the dynamic interaction of endothelial cells, VEGF, sVEGFR-1 and Ado entities. The model is based on a logic rule-based methodology in which the local behaviour of the cells and molecules is encoded using if-then rules. The model shows how Ado may enhance angiogenesis through activating and inhibiting effects on VEGF and sVEGFR-1 respectively. Despite the relative simplicity of the model, it recapitulated basic features observed in in vitro models. However, observed disagreements between our models and in vitro data suggest possible knowledge gaps and may guide future experimental directions.</p><p><strong>Conclusions: </strong>The proposed model can support the exploration of hypotheses about the role of different molecular entities and experimental conditions in angiogenesis. Future expansions can also be applied to assist research planning in this and other biomedical domains.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2011-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29801865","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}

{"title":"Module-based multiscale simulation of angiogenesis in skeletal muscle.","authors":"Gang Liu,&nbsp;Amina A Qutub,&nbsp;Prakash Vempati,&nbsp;Feilim Mac Gabhann,&nbsp;Aleksander S Popel","doi":"10.1186/1742-4682-8-6","DOIUrl":"https://doi.org/10.1186/1742-4682-8-6","url":null,"abstract":"<p><strong>Background: </strong>Mathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem.</p><p><strong>Results: </strong>We present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis.</p><p><strong>Conclusions: </strong>This systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2011-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29791743","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}

{"title":"Disruption of cell wall fatty acid biosynthesis in Mycobacterium tuberculosis using a graph theoretic approach.","authors":"Veeky Baths,&nbsp;Utpal Roy,&nbsp;Tarkeshwar Singh","doi":"10.1186/1742-4682-8-5","DOIUrl":"https://doi.org/10.1186/1742-4682-8-5","url":null,"abstract":"<p><p>Fatty acid biosynthesis of Mycobacterium tuberculosis was analyzed using graph theory and influential (impacting) proteins were identified. The graphs (digraphs) representing this biological network provide information concerning the connectivity of each protein or metabolite in a given pathway, providing an insight into the importance of various components in the pathway, and this can be quantitatively analyzed. Using a graph theoretic algorithm, the most influential set of proteins (sets of {1, 2, 3}, etc.), which when eliminated could cause a significant impact on the biosynthetic pathway, were identified. This set of proteins could serve as drug targets. In the present study, the metabolic network of Mycobacterium tuberculosis was constructed and the fatty acid biosynthesis pathway was analyzed for potential drug targeting. The metabolic network was constructed using the KEGG LIGAND database and subjected to graph theoretical analysis. The nearness index of a protein was used to determine the influence of the said protein on other components in the network, allowing the proteins in a pathway to be ordered according to their nearness indices. A method for identifying the most strategic nodes to target for disrupting the metabolic networks is proposed, aiding the development of new drugs to combat this deadly disease.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2011-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29781703","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}

{"title":"Maximum likelihood estimation of reviewers' acumen in central review setting: categorical data.","authors":"Wei Zhao,&nbsp;James M Boyett,&nbsp;Mehmet Kocak,&nbsp;David W Ellison,&nbsp;Yanan Wu","doi":"10.1186/1742-4682-8-3","DOIUrl":"https://doi.org/10.1186/1742-4682-8-3","url":null,"abstract":"<p><p>Successfully evaluating pathologists' acumen could be very useful in improving the concordance of their calls on histopathologic variables. We are proposing a new method to estimate the reviewers' acumen based on their histopathologic calls. The previously proposed method includes redundant parameters that are not identifiable and results are incorrect. The new method is more parsimonious and through extensive simulation studies, we show that the new method relies less on the initial values and converges to the true parameters. The result of the anesthetist data set by the new method is more convincing.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2011-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29770220","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}

{"title":"Theoretical basis to measure the impact of short-lasting control of an infectious disease on the epidemic peak.","authors":"Ryosuke Omori,&nbsp;Hiroshi Nishiura","doi":"10.1186/1742-4682-8-2","DOIUrl":"https://doi.org/10.1186/1742-4682-8-2","url":null,"abstract":"<p><strong>Background: </strong>While many pandemic preparedness plans have promoted disease control effort to lower and delay an epidemic peak, analytical methods for determining the required control effort and making statistical inferences have yet to be sought. As a first step to address this issue, we present a theoretical basis on which to assess the impact of an early intervention on the epidemic peak, employing a simple epidemic model.</p><p><strong>Methods: </strong>We focus on estimating the impact of an early control effort (e.g. unsuccessful containment), assuming that the transmission rate abruptly increases when control is discontinued. We provide analytical expressions for magnitude and time of the epidemic peak, employing approximate logistic and logarithmic-form solutions for the latter. Empirical influenza data (H1N1-2009) in Japan are analyzed to estimate the effect of the summer holiday period in lowering and delaying the peak in 2009.</p><p><strong>Results: </strong>Our model estimates that the epidemic peak of the 2009 pandemic was delayed for 21 days due to summer holiday. Decline in peak appears to be a nonlinear function of control-associated reduction in the reproduction number. Peak delay is shown to critically depend on the fraction of initially immune individuals.</p><p><strong>Conclusions: </strong>The proposed modeling approaches offer methodological avenues to assess empirical data and to objectively estimate required control effort to lower and delay an epidemic peak. Analytical findings support a critical need to conduct population-wide serological survey as a prior requirement for estimating the time of peak.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2011-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29628356","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}

{"title":"Using an agent-based model to analyze the dynamic communication network of the immune response.","authors":"Virginia A Folcik,&nbsp;Gordon Broderick,&nbsp;Shunmugam Mohan,&nbsp;Brian Block,&nbsp;Chirantan Ekbote,&nbsp;John Doolittle,&nbsp;Marc Khoury,&nbsp;Luke Davis,&nbsp;Clay B Marsh","doi":"10.1186/1742-4682-8-1","DOIUrl":"https://doi.org/10.1186/1742-4682-8-1","url":null,"abstract":"<p><strong>Background: </strong>The immune system behaves like a complex, dynamic network with interacting elements including leukocytes, cytokines, and chemokines. While the immune system is broadly distributed, leukocytes must communicate effectively to respond to a pathological challenge. The Basic Immune Simulator 2010 contains agents representing leukocytes and tissue cells, signals representing cytokines, chemokines, and pathogens, and virtual spaces representing organ tissue, lymphoid tissue, and blood. Agents interact dynamically in the compartments in response to infection of the virtual tissue. Agent behavior is imposed by logical rules derived from the scientific literature. The model captured the agent-to-agent contact history, and from this the network topology and the interactions resulting in successful versus failed viral clearance were identified. This model served to integrate existing knowledge and allowed us to examine the immune response from a novel perspective directed at exploiting complex dynamics, ultimately for the design of therapeutic interventions.</p><p><strong>Results: </strong>Analyzing the evolution of agent-agent interactions at incremental time points from identical initial conditions revealed novel features of immune communication associated with successful and failed outcomes. There were fewer contacts between agents for simulations ending in viral elimination (win) versus persistent infection (loss), due to the removal of infected agents. However, early cellular interactions preceded successful clearance of infection. Specifically, more Dendritic Agent interactions with TCell and BCell Agents, and more BCell Agent interactions with TCell Agents early in the simulation were associated with the immune win outcome. The Dendritic Agents greatly influenced the outcome, confirming them as hub agents of the immune network. In addition, unexpectedly high frequencies of Dendritic Agent-self interactions occurred in the lymphoid compartment late in the loss outcomes.</p><p><strong>Conclusions: </strong>An agent-based model capturing several key aspects of complex system dynamics was used to study the emergent properties of the immune response to viral infection. Specific patterns of interactions between leukocyte agents occurring early in the response significantly improved outcome. More interactions at later stages correlated with persistent inflammation and infection. These simulation experiments highlight the importance of commonly overlooked aspects of the immune response and provide insight into these processes at a resolution level exceeding the capabilities of current laboratory technologies.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2011-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29610052","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}

{"title":"Immunologgical self-tolerance in allophenic and embryo-aggregated mice.","authors":"Richmond T Prehn,&nbsp;Liisa M Prehn","doi":"10.1186/1742-4682-7-38","DOIUrl":"https://doi.org/10.1186/1742-4682-7-38","url":null,"abstract":"<p><p>Allophenic mice, supposedly containing almost equal numbers of cells derived from embryos of mouse strains C57Bl and FVB, were shown in a recent paper to grow the B16 melanoma, a long transplanted tumor of C57Bl origin, much better than did mice of either the parental C57Bl strain or the C57Bl x FVB F1 hybrid. Mice containing smaller proportions of C57Bl cells rejected the tumor. A reconsideration of these suprising data, in light of the current literature, suggests that the better growth of the tumor in the 50-50% allophenics than in the C57Bl parental strain was almost certainly caused by the tumor stimulation engendered by a weak anti-C57Bl immune reaction in the overtly healthy allophenic mice.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"38"},"PeriodicalIF":0.0,"publicationDate":"2010-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-7-38","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40080567","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}

{"title":"Pathological axes of wound repair: gastrulation revisited.","authors":"Maria-Angeles Aller,&nbsp;Jose-Ignacio Arias,&nbsp;Jaime Arias","doi":"10.1186/1742-4682-7-37","DOIUrl":"https://doi.org/10.1186/1742-4682-7-37","url":null,"abstract":"<p><p>Post-traumatic inflammation is formed by molecular and cellular complex mechanisms whose final goal seems to be injured tissue regeneration.In the skin -an exterior organ of the body- mechanical or thermal injury induces the expression of different inflammatory phenotypes that resemble similar phenotypes expressed during embryo development. Particularly, molecular and cellular mechanisms involved in gastrulation return. This is a developmental phase that delineates the three embryonic germ layers: ectoderm, endoderm and mesoderm. Consequently, in the post-natal wounded skin, primitive functions related with the embryonic mesoderm, i.e. amniotic and yolk sac-derived, are expressed. Neurogenesis and hematogenesis stand out among the primitive function mechanisms involved.Interestingly, in these phases of the inflammatory response, whose molecular and cellular mechanisms are considered as traces of the early phases of the embryonic development, the mast cell, a cell that is supposedly inflammatory, plays a key role.The correlation that can be established between the embryonic and the inflammatory events suggests that the results obtained from the research regarding both great fields of knowledge must be interchangeable to obtain the maximum advantage.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"37"},"PeriodicalIF":0.0,"publicationDate":"2010-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-7-37","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40067780","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}