scholarly journals FPtool a software tool to obtain in silico genotype-phenotype signatures and fingerprints based on massive model simulations

2018 ◽  
Author(s):  
Guido Santos ◽  
Julio Vera
Keyword(s):  
Mathematical Model ◽  
In Silico ◽  
Software Tool ◽  
Biochemical Network ◽  
Qualitative Behaviour ◽  
Model Simulations

Fptool is an intuitive tool that provides to the user a preliminary fingerprint of the behaviour simulated by a mathematical model of a biochemical network when comparing two biological scenarios defined by the user. Here we present the tool and we applied to an already published mathematical model of lung legionella infection. The fingerprint obtained correlates with the results obtained in the original article. This tool is optimal for the users that would like to obtain a fast and preliminary view of the qualitative behaviour of a mathematical model before deciding for more elaborate analyses.

The ancient Lake Albano tunnel: origins and considerations regarding the hydraulic regulation achieved

2007 ◽  
Vol 7 (1) ◽  
pp. 269-276
Author(s):  
R. Drusiani ◽  
P. Bersani ◽  
P. Penta
Keyword(s):  
Mathematical Model ◽  
Ancient Lake ◽  
Model Simulations ◽  
Volcanic Lakes ◽  
Colli Albani ◽  
Atmospheric Phenomena

A brief description of the geomorphological, historical, and archaeological aspects of the Colli Albani area, where the volcanic lakes of Albano and Nemi are situated, is followed by an examination on the problem of the policies of lake Albano regulation, by means of an ancient tunnel dating at least to the 5th century BC. In particular, it is investigated how, in the presence of even severe atmospheric phenomena, it was possible to control fluctuations in the level of the lake on the banks of which there were large settlements. Mathematical model simulations indicate the effectiveness of the ancient tunnel in achieving these objectives.

Usefulness of collaboration between mathematical models and cell engineering for elucidating complex disease mechanisms and discover effective drugs

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
H Kohjitani ◽  
A Kashiwa ◽  
T Makiyama ◽  
F Toyoda ◽  
Y Yamamoto ◽  
...  
Keyword(s):  
Mathematical Model ◽  
In Silico ◽  
Complex Disease ◽  
Ion Selectivity ◽  
Public Institution ◽  
Cell Engineering ◽  
Funding Source ◽  
Patch Clamp Technique ◽  
In Silico Model

Abstract Background A missense mutation, CACNA1C-E1115K, located in the cardiac L-type calcium channel (LTCC), was recently reported to be associated with diverse arrhythmias. Several studies reported in-vivo and in-vitro modeling of this mutation, but actual mechanism and target drug of this disease has not been clarified due to its complex ion-mechanisms. Objective To reveal the mechanism of this diverse arrhythmogenic phenotype using combination of in-vitro and in-silico model. Methods and results Cell-Engineering Phase: We generated human induced pluripotent stem cell (hiPSC) from a patient carrying heterozygous CACNA1C-E1115K and differentiated into cardiomyocytes. Spontaneous APs were recorded from spontaneously beating single cardiomyocytes by using the perforated patch-clamp technique. Mathematical-Modeling Phase: We newly developed ICaL-mutation mathematical model, fitted into experimental data, including its impaired ion selectivity. Furthermore, we installed this mathematical model into hiPSC-CM simulation model. Collaboration Phase: Mutant in-silico model showed APD prolongation and frequent early afterdepolarization (EAD), which are same as in-vitro model. In-silico model revealed this EAD was mostly related to robust late-mode of sodium current occurred by Na+ overload and suggested that mexiletine is capable of reducing arrhythmia. Afterward, we applicated mexiletine onto hiPSC-CMs mutant model and found mexiletine suppress EADs. Conclusions Precise in-silico disease model can elucidate complicated ion currents and contribute predicting result of drug-testing. Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists

scholarly journals CARTmath—A Mathematical Model of CAR-T Immunotherapy in Preclinical Studies of Hematological Cancers

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2941
Author(s):  
Luciana R. C. Barros ◽  
Emanuelle A. Paixão ◽  
Andrea M. P. Valli ◽  
Gustavo T. Naozuka ◽  
Artur C. Fassoni ◽  
...  
Keyword(s):  
Mathematical Model ◽  
T Cells ◽  
T Cell ◽  
Mouse Models ◽  
In Silico ◽  
Car T Cells ◽  
Car T Cell ◽  
Cell Immunotherapy ◽  
Car T ◽  
T Cell Immunotherapy

Immunotherapy has gained great momentum with chimeric antigen receptor T cell (CAR-T) therapy, in which patient’s T lymphocytes are genetically manipulated to recognize tumor-specific antigens, increasing tumor elimination efficiency. In recent years, CAR-T cell immunotherapy for hematological malignancies achieved a great response rate in patients and is a very promising therapy for several other malignancies. Each new CAR design requires a preclinical proof-of-concept experiment using immunodeficient mouse models. The absence of a functional immune system in these mice makes them simple and suitable for use as mathematical models. In this work, we develop a three-population mathematical model to describe tumor response to CAR-T cell immunotherapy in immunodeficient mouse models, encompassing interactions between a non-solid tumor and CAR-T cells (effector and long-term memory). We account for several phenomena, such as tumor-induced immunosuppression, memory pool formation, and conversion of memory into effector CAR-T cells in the presence of new tumor cells. Individual donor and tumor specificities are considered uncertainties in the model parameters. Our model is able to reproduce several CAR-T cell immunotherapy scenarios, with different CAR receptors and tumor targets reported in the literature. We found that therapy effectiveness mostly depends on specific parameters such as the differentiation of effector to memory CAR-T cells, CAR-T cytotoxic capacity, tumor growth rate, and tumor-induced immunosuppression. In summary, our model can contribute to reducing and optimizing the number of in vivo experiments with in silico tests to select specific scenarios that could be tested in experimental research. Such an in silico laboratory is an easy-to-run open-source simulator, built on a Shiny R-based platform called CARTmath. It contains the results of this manuscript as examples and documentation. The developed model together with the CARTmath platform have potential use in assessing different CAR-T cell immunotherapy protocols and its associated efficacy, becoming an accessory for in silico trials.

scholarly journals Synthesis, in silico studies and antibacterial activity of some novel 2-substituted benzimidazole derivatives

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Ramakrishna Chintakunta ◽  
Geethavani Meka
Keyword(s):  
Antibacterial Activity ◽  
Melting Point ◽  
In Silico ◽  
Software Tool ◽  
Benzimidazole Derivatives ◽  
Recrystallization Process ◽  
Standard Drug ◽  
In Silico Studies ◽  
Drug Synthesis ◽  
Percentage Absorption

Abstract Background The o-phenylenediamine is a versatile starting material for several compounds. Synthesized o-phenylenediamine and amino acids (glycine, alanine, aspartic acid, and l-proline) undergo condensation via Phillips reaction. The synthesized compound showed the promising antibacterial activity of Bacillus subtilis and Pseudomonas aeruginosa at the concentration of 100, 50, 25, 12.5, 6.25, 3.12, 1.6, 0.8, 0.4, and 0.2 μg/ml. Ciprofloxacin was used as standard drug. Synthesis of benzimidazole derivatives was carried out and purified by recrystallization process using ethanol. Substituted derivatives were characterized by melting point, TLC and spectroscopic methods include FT-IR and 1H-NMR. Results In silico studies were adopted for synthetic derivatives by Molinspiration, ChemDraw, and online software tool. Minimum inhibitory concentration (MIC) values of B. subtilis and P. aeruginosa were reported, and benzimidazole ligands and Molinspiration scores were generated and listed. Conclusion The more negative values indicate a higher binding affinity. The generated ligand observations can be visualized. Physical constants of synthesized derivates such as solubility and melting point were determined. Bioactivity scores were noted for different derivatives and predicted percentage absorption in the gut. The antibacterial activity was performed using the MIC method (aerobic).

Ouabain modulation of cellular calcium stores and signaling

2007 ◽  
Vol 293 (5) ◽  
pp. F1518-F1532 ◽  
Author(s):  
Aurélie Edwards ◽  
Thomas L. Pallone
Keyword(s):  
Mathematical Model ◽  
Sarcoplasmic Reticulum ◽  
Active Transport ◽  
Intracellular Localization ◽  
Calcium Stores ◽  
Model Simulations ◽  
Store Depletion ◽  
Intracellular Ca ◽  
Atpase Inhibition ◽  
Predominant Effect

Ouabain-like factors modulate intracellular Ca2+ concentrations and Ca2+ stores. Recently, a role for Na+-K+-ATPase Na+ transport inhibition as a pivotal event in ouabain signaling was questioned (Kaunitz JD. Am J Physiol Renal Physiol 290: F995–F996, 2006). In the present study, we used a mathematical model of Ca2+ trafficking in cytoplasm and subplasmalemmal microdomains to simulate the pathways through which ouabain can affect Ca2+ signaling: inhibition of active transport by Na+-K+-ATPase α1- and α2-isoforms, activation of inositol trisphosphate (IP3) production, and increased IP3 receptor (IP3R) conductance. A fundamental prediction is that Na+-K+-ATPase inhibition favors sarcoplasmic reticulum Ca2+ store loading, whereas Src-mediated increases in IP3 production and IP3R sensitization favor store depletion. The model predicts that α2-isoform inhibition generates a peak-and-plateau pattern of cytosolic Ca2+ concentration ([Ca2+]cyt) elevation, whereas α1-isoform inhibition yields a monophasic rise. The effects of ouabain-mediated increases in IP3 production or IP3R conductance on [Ca2+]cyt depend on their relative distributions between cellular microdomains and the bulk cytoplasm. Simulations suggest that the intracellular localization of IP3 production is a pivotal determinant of the changes in compartmental Ca2+ concentrations that can be induced by ouabain. As a consequence of sequestration of the ouabain-sensitive α2-isoform into microdomains, inhibition of the α2-isoform in rodents is not predicted to significantly affect cytosolic Na+ concentration. Model simulations support the hypothesis that ouabain can enhance agonist-evoked [Ca2+]cyt transients when its predominant effect is to inhibit α2-isoform Na+ transport and, thereby, increase Ca2+ loading into sarcoplasmic reticulum stores.

scholarly journals Quantitative regulation of the dynamic steady state of actin networks

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Angelika Manhart ◽  
Téa Aleksandra Icheva ◽  
Christophe Guerin ◽  
Tobbias Klar ◽  
Rajaa Boujemaa-Paterski ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Steady State ◽  
Heterogeneous Networks ◽  
In Silico ◽  
Actin Network ◽  
Network Nodes ◽  
Actin Networks ◽  
Cell Functions ◽  
Selective Disassembly

Principles of regulation of actin network dimensions are fundamentally important for cell functions, yet remain unclear. Using both in vitro and in silico approaches, we studied the effect of key parameters, such as actin density, ADF/Cofilin concentration and network width on the network length. In the presence of ADF/Cofilin, networks reached equilibrium and became treadmilling. At the trailing edge, the network disintegrated into large fragments. A mathematical model predicts the network length as a function of width, actin and ADF/Cofilin concentrations. Local depletion of ADF/Cofilin by binding to actin is significant, leading to wider networks growing longer. A single rate of breaking network nodes, proportional to ADF/Cofilin density and inversely proportional to the square of the actin density, can account for the disassembly dynamics. Selective disassembly of heterogeneous networks by ADF/Cofilin controls steering during motility. Our results establish general principles on how the dynamic steady state of actin network emerges from biochemical and structural feedbacks.

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