Local Control Model of a Human Ventricular Myocyte: An Exploration of Frequency-Dependent Changes and Calcium Sparks.

Calcium (Ca2+) sparks are the elementary events of excitation-contraction coupling, yet they are not explicitly represented in human ventricular myocyte models. A stochastic ventricular cardiomyocyte human model that adapts to intracellular Ca2+ ([Ca2+]i) dynamics, spark regulation, and frequency-dependent changes in the form of locally controlled Ca2+ release was developed. The 20,000 CRUs in this model are composed of 9 individual LCCs and 49 RyRs that function as couplons. The simulated action potential duration at 1 Hz steady-state pacing is ~0.280 s similar to human ventricular cell recordings. Rate-dependence experiments reveal that APD shortening mechanisms are largely contributed by the L-type calcium channel inactivation, RyR open fraction, and [Ca2+]myo concentrations. The dynamic slow-rapid-slow pacing protocol shows that RyR open probability during high pacing frequency (2.5 Hz) switches to an adapted "nonconducting" form of Ca2+-dependent transition state. The predicted force was also observed to be increased in high pacing, but the SR Ca2+ fractional release was lower due to the smaller difference between diastolic and systolic [Ca2+]SR. Restitution analysis through the S1S2 protocol and increased LCC Ca2+-dependent activation rate show that the duration of LCC opening helps modulate its effects on the APD restitution at different diastolic intervals. Ultimately, a longer duration of calcium sparks was observed in relation to the SR Ca2+ loading at high pacing rates. Overall, this study demonstrates the spontaneous Ca2+ release events and ion channel responses throughout various stimuli.

Structural Analysis of Mitochondria in Cardiomyocytes: Insights into Bioenergetics and Membrane Remodeling.

Mitochondria in mammalian cardiomyocytes display considerable structural heterogeneity, the significance of which is not currently understood. We use electron microscopic tomography to analyze a dataset of 68 mitochondrial subvolumes to look for correlations among mitochondrial size and shape, crista morphology and membrane density, and organelle location within rat cardiac myocytes. A tomographic analysis guided the definition of four classes of crista morphology: lamellar, tubular, mixed and transitional, the last associated with remodeling between lamellar and tubular cristae. Correlations include an apparent bias for mitochondria with lamellar cristae to be located in the regions between myofibrils and a two-fold larger crista membrane density in mitochondria with lamellar cristae relative to mitochondria with tubular cristae. The examination of individual cristae inside mitochondria reveals local variations in crista topology, such as extent of branching, alignment of fenestrations and progressive changes in membrane morphology and packing density. The findings suggest both a rationale for the interfibrillar location of lamellar mitochondria and a pathway for crista remodeling from lamellar to tubular morphology.

Automated measurement for image distortion analysis in 2D panoramic imaging of dental CBCT system: A phantom study.

INTRODUCTION: The daily image quality assessment involves large datasets that consume a lot of time and effort. This study aims to evaluate a proposed automated calculator for image distortion analysis in 2-dimensional (2D) panoramic imaging mode for a dental cone beam computed tomography (CBCT) system in comparison with present manual calculations. METHODS: A ball phantom was scanned using panoramic mode of the Planmeca ProMax 3D Mid CBCT unit (Planmeca, Helsinki, Finland) with standard exposure settings used in clinical practice (60 kV, 2 mA, and maximum FOV). An automated calculator algorithm was developed in MATLAB platform. Two parameters associated with panoramic image distortion such as balls diameter and distance between middle and tenth balls were measured. These automated measurements were compared with manual measurement using the Planmeca Romexis and ImageJ software. RESULTS: The findings showed smaller deviation in distance difference measurements by proposed automated calculator (ranged 3.83 mm) as compared to manual measurements (ranged 5.00 for Romexis and 5.12 mm for ImageJ software). There was a significant difference (p < 0.05) on the mean measured ball diameter between automated and manual measurement. For ball diameter measurement, there is a moderate positive correlation between automated measurement with the manual measurements (r = 0.6024 and r = 0.6358 for Romexis and ImageJ, respectively). However, there is a negative correlation between automated measurement for the distance difference with manual methods (r = -0.3484 and r = -0.3494 for Romexis and ImageJ, respectively). There was a good approximation between automated and ImageJ measurement of ball diameter in comparison to reference value. CONCLUSION: In conclusion, the proposed automated calculator provides faster method with an accurate and acceptable results for daily-basis image quality test in dental panoramic mode of a Dental CBCT imaging system in comparison to current manual method. IMPLICATIONS FOR PRACTICE: An automated calculator is recommended for image distortion analysis on phantom images in routine image quality assessment for dental panoramic mode of Dental CBCT imaging system that may involve analysis of large image datasets. It offers improvement in routine image quality practice in term of time and accuracy.

Subthalamic Nucleus (STN)-Deep Brain Stimulation Reduces the Power of Mu and Beta Rhythms and Enhances Synchrony at the Motor Cortices in Parkinson's Disease: A Report of Two Cases.

The motor circuit in Parkinson's disease (PD) involves the basal ganglia, thalamus, motor cortex, and cerebellum. Hence, subthalamic nucleus (STN) or globus pallidus internus deep brain stimulation is commonly used in treating refractory Parkinson's patients. During the procedure, the local field potential (LPF) is commonly made along the trajectory of the STN. Two cases were assessed, where an electroencephalographic recording at the sensorimotor cortices was also performed with and without stimulation at the optimal STN electrode site. The 'on' stimulation state associated with clinical improvement correlated with a marked reduction in the late theta (7.5 Hz), alpha (10.5 Hz) (Mu wave), and beta (20 Hz) wave power. Besides, more synchronized and coherent brainwaves were noted when the stimulation was 'on'.

Prediction of outcomes in traumatic brain injury: The IMPACT and CRASH prognostic models in a single neurosurgical center, Malaysia.

BACKGROUND: Traumatic brain injury (TBI) has recently become a major concern for public health care and a socioeconomic burden internationally. Prognostic models are mathematical models developed from specific populations which are used to predict the mortality and unfavorable outcomes especially in trauma centers. Hence, we formulate a study to perform an external validation of the IMPACT and CRASH prognostic models; the CRASH model to predict 14-day mortality and 6-month unfavorable outcome and the IMPACT model to estimate 6-month mortality and unfavorable outcome in a single center cohort of TBI patients in Malaysia. METHODS: All patients with traumatic brain injury (mild, moderate, and severe) who were admitted to Queen Elizabeth Hospital from November 1, 2017, to January 31, 2019, were prospectively analyzed through a data collection sheet. The discriminatory power of the models was assessed as area under the receiver operating characteristic curve and calibration was assessed using the Hosmer-Lemeshow (H-L) goodness-of-fit test and Cox calibration regression analysis. RESULTS: We analyzed 281 patients with significant TBI treated in a single neurosurgical center in Malaysia over a 2-year period. The overall observed 14-day mortality was 9.6%, a 6-month unfavorable outcome of 23.5%, and a 6-month mortality of 13.2%. Overall, both the CRASH and IMPACT models showed good discrimination with AUCs ranging from 0.88 to 0.94 and both models calibrating satisfactorily H-L GoF P>0.05 and calibration slopes >1.0 although IMPACT seemed to be slightly more superior compared to the CRASH model. CONCLUSIONS: The CRASH and IMPACT prognostic models displayed satisfactory overall performance in our cohort of TBI patients, but further investigations on factors contributing to TBI outcomes and continuous updating on both models remain crucial.

Reverse Cervical Lordosis Caused by Giant Vertebral Artery Aneurysm in von Recklinghausen Disease.

Neurofibromatosis type 1 (NF1) is a variable penetrance autosomal dominant condition predominantly involving the peripheral nervous system. NF1 exhibits a wide spectrum of clinical patterns involving the skin, eye, brain, spinal cord, and, to a lesser extent, long bones and arteries. Arterial stenosis or aneurysms have been variously studied, but the association with NF1 has not been firmly established. A 31-year-old gentleman with NF1 experienced progressive neck pain over a five-month period, associated with limited range of motion and dysphagia. Magnetic resonance imaging (MRI) of the cervical spine suggests paraspinal plexiform neurofibromas with excessive reverse cervical lordosis. Further workups revealed a large left vertebral artery fusiform aneurysm and a pseudoaneurysm. The patient made a full recovery following endovascular embolization. It is crucial to maintain a high index of suspicion for vascular malformations in patients with NF1. The pathogenesis of vascular manifestations in NF1 and options for therapeutic management were discussed.

Understanding the Dynamics of the Transient and Permanent Opening Events of the Mitochondrial Permeability Transition Pore with a Novel Stochastic Model.

The mitochondrial permeability transition pore (mPTP) is a non-selective pore in the inner mitochondrial membrane (IMM) which causes depolarization when it opens under conditions of oxidative stress and high concentrations of Ca2+. In this study, a stochastic computational model was developed to better understand the dynamics of mPTP opening and closing associated with elevated reactive oxygen species (ROS) in cardiomyocytes. The data modeled are from "photon stress" experiments in which the fluorescent dye TMRM (tetramethylrhodamine methyl ester) is both the source of ROS (induced by laser light) and sensor of the electrical potential difference across the IMM. Monte Carlo methods were applied to describe opening and closing of the pore along with the Hill Equation to account for the effect of ROS levels on the transition probabilities. The amplitude distribution of transient mPTP opening events, the number of transient mPTP opening events per minute in a cell, the time it takes for recovery after transient depolarizations in the mitochondria, and the change in TMRM fluorescence during the transition from transient to permanent mPTP opening events were analyzed. The model suggests that mPTP transient open times have an exponential distribution that are reflected in TMRM fluorescence. A second multiple pore model in which individual channels have no permanent open state suggests that 5-10 mPTP per mitochondria would be needed for sustained mitochondrial depolarization at elevated ROS with at least 1 mPTP in the transient open state.

Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning.

Coronaviruses, including the recent pandemic strain SARS-Cov-2, use a multifunctional 2'-O-methyltransferase (2'-O-MTase) to restrict the host defense mechanism and to methylate RNA. The nonstructural protein 16 2'-O-MTase (nsp16) becomes active when nonstructural protein 10 (nsp10) and nsp16 interact. Novel peptide drugs have shown promise in the treatment of numerous diseases and new research has established that nsp10 derived peptides can disrupt viral methyltransferase activity via interaction of nsp16. This study had the goal of optimizing new analogous nsp10 peptides that have the ability to bind nsp16 with equal to or higher affinity than those naturally occurring. The following research demonstrates that in silico molecular simulations can shed light on peptide structures and predict the potential of new peptides to interrupt methyltransferase activity via the nsp10/nsp16 interface. The simulations suggest that misalignments at residues F68, H80, I81, D94, and Y96 or rotation at H80 abrogate MTase function. We develop a new set of peptides based on conserved regions of the nsp10 protein in the Coronaviridae species and test these to known MTase variant values. This results in the prediction that the H80R variant is a solid new candidate for potential new testing. We envision that this new lead is the beginning of a reputable foundation of a new computational method that combats coronaviruses and that is beneficial for new peptide drug development.

Active site prediction of phosphorylated SARS-CoV-2 N-Protein using molecular simulation.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid protein (N-protein) is responsible for viral replication by assisting in viral RNA synthesis and attaching the viral genome to the replicase-transcriptase complex (RTC). Numerous studies suggested the N-protein as a drug target. However, the specific N-protein active sites for SARS-CoV-2 drug treatments are yet to be discovered. The purpose of this study was to determine active sites of the SARS-CoV-2 N-protein by identifying torsion angle classifiers for N-protein structural changes that correlated with the respective angle differences between the active and inactive N-protein. In the study, classifiers with a minimum accuracy of 80% determined from molecular simulation data were analyzed by Principal Component Analysis and cross-validated by Logistic Regression, Support Vector Machine, and Random Forest Classification. The ability of torsion angles ψ252 and φ375 to differentiate between phosphorylated and unphosphorylated structures suggested that residues 252 and 375 in the RNA binding domain might be important in N-protein activation. Furthermore, the φ and ψ angles of residue S189 correlated to a 90.7% structural determination accuracy. The key residues involved in the structural changes identified here might suggest possible important functional sites on the N-protein that could be the focus of further study to understand their potential as drug targets.

Understanding Calmodulin Variants Affecting Calcium-Dependent Inactivation of L-Type Calcium Channels through Whole-Cell Simulation of the Cardiac Ventricular Myocyte.

Mutations in the calcium-sensing protein calmodulin (CaM) have been linked to two cardiac arrhythmia diseases, Long QT Syndrome 14 (LQT14) and Catecholaminergic Polymorphic Ventricular Tachycardia Type 4 (CPVT4), with varying degrees of severity. Functional characterization of the CaM mutants most strongly associated with LQT14 show a clear disruption of the calcium-dependent inactivation (CDI) of the L-Type calcium channel (LCC). CPVT4 mutants on the other hand are associated with changes in their affinity to the ryanodine receptor. In clinical studies, some variants have been associated with both CPVT4 and LQT15. This study uses simulations in a model for excitation-contraction coupling in the rat ventricular myocytes to understand how LQT14 variant might give the functional phenotype similar to CPVT4. Changing the CaM-dependent transition rate by a factor of 0.75 corresponding to the D96V variant and by a factor of 0.90 corresponding to the F142L or N98S variants, in a physiologically based stochastic model of the LCC prolonger, the action potential duration changed by a small amount in a cardiac myocyte but did not disrupt CICR at 1, 2, and 4 Hz. Under beta-adrenergic simulation abnormal excitation-contraction coupling was observed above 2 Hz pacing for the mutant CaM. The same conditions applied under beta-adrenergic stimulation led to the rapid onset of arrhythmia in the mutant CaM simulations. Simulations with the LQT14 mutations under the conditions of rapid pacing with beta-adrenergic stimulation drives the cardiac myocyte toward an arrhythmic state known as Ca2+ overload. These simulations provide a mechanistic link to a disease state for LQT14-associated mutations in CaM to yield a CPVT4 phenotype. The results show that small changes to the CaM-regulated inactivation of LCC promote arrhythmia and underscore the significance of CDI in proper heart function.

Machine learning-based prediction of drug and ligand binding in BCL-2 variants through molecular dynamics.

Venetoclax is a BH3 (BCL-2 Homology 3) mimetic used to treat leukemia and lymphoma by inhibiting the anti-apoptotic BCL-2 protein thereby promoting apoptosis of cancerous cells. Acquired resistance to Venetoclax via specific variants in BCL-2 is a major problem for the successful treatment of cancer patients. Replica exchange molecular dynamics (REMD) simulations combined with machine learning were used to define the average structure of variants in aqueous solution to predict changes in drug and ligand binding in BCL-2 variants. The variant structures all show shifts in residue positions that occlude the binding groove, and these are the primary contributors to drug resistance. Correspondingly, we established a method that can predict the severity of a variant as measured by the inhibitory constant (Ki) of Venetoclax by measuring the structure deviations to the binding cleft. In addition, we also applied machine learning to the phi and psi angles of the amino acid backbone to the ensemble of conformations that demonstrated a generalizable method for drug resistant predictions of BCL-2 proteins that elucidates changes where detailed understanding of the structure-function relationship is less clear.

Effect of crista morphology on mitochondrial ATP output: A computational study.

Folding of the mitochondrial inner membrane (IM) into cristae greatly increases the ATP-generating surface area, S IM, per unit volume but also creates diffusional bottlenecks that could limit reaction rates inside mitochondria. This study explores possible effects of inner membrane folding on mitochondrial ATP output, using a mathematical model for energy metabolism developed by the Jafri group and two- and three-dimensional spatial models for mitochondria, implemented on the Virtual Cell platform. Simulations demonstrate that cristae are micro-compartments functionally distinct from the cytosol. At physiological steady states, standing gradients of ADP form inside cristae that depend on the size and shape of the compartments, and reduce local flux (rate per unit area) of the adenine nucleotide translocase. This causes matrix ADP levels to drop, which in turn reduces the flux of ATP synthase. The adverse effects of membrane folding on reaction fluxes increase with crista length and are greater for lamellar than tubular crista. However, total ATP output per mitochondrion is the product of flux of ATP synthase and S IM which can be two-fold greater for mitochondria with lamellar than tubular cristae, resulting in greater ATP output for the former. The simulations also demonstrate the crucial role played by intracristal kinases (adenylate kinase, creatine kinase) in maintaining the energy advantage of IM folding.

Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations.

Distinct missense mutations in a specific gene have been associated with different diseases as well as differing severity of a disease. Current computational methods predict the potential pathogenicity of a missense variant but fail to differentiate between separate disease or severity phenotypes. We have developed a method to overcome this limitation by applying machine learning to features extracted from molecular dynamics simulations, creating a way to predict the effect of novel genetic variants in causing a disease, drug resistance, or another specific trait. As an example, we have applied this novel approach to variants in calmodulin associated with two distinct arrhythmias as well as two different neurodegenerative diseases caused by variants in amyloid-ß peptide. The new method successfully predicts the specific disease caused by a gene variant and ranks its severity with more accuracy than existing methods. We call this method molecular dynamics phenotype prediction model.

T lymphocytes from malignant hyperthermia-susceptible mice display aberrations in intracellular calcium signaling and mitochondrial function.

Gain-of-function RyR1-p.R163C mutation in ryanodine receptors type 1 (RyR1) deregulates Ca2+ signaling and mitochondrial function in skeletal muscle and causes malignant hyperthermia in humans and mice under triggering conditions. We investigated whether T lymphocytes from heterozygous RyR1-p.R163C knock-in mutant mice (HET T cells) display measurable aberrations in resting cytosolic Ca2+ concentration ([Ca2+]i), Ca2+ release from the store, store-operated Ca2+ entry (SOCE), and mitochondrial inner membrane potential (ΔΨm) compared with T lymphocytes from wild-type mice (WT T cells). We explored whether these variables can be used to distinguish between T cells with normal and altered RyR1 genotype. HET and WT T cells were isolated from spleen and lymph nodes and activated in vitro using phytohemagglutinin P. [Ca2+]i and ΔΨm dynamics were examined using Fura 2 and tetramethylrhodamine methyl ester fluorescent dyes, respectively. Activated HET T cells displayed elevated resting [Ca2+]i, diminished responses to Ca2+ mobilization with thapsigargin, and decreased rate of [Ca2+]i elevation in response to SOCE compared with WT T cells. Pretreatment of HET T cells with ryanodine or dantrolene sodium reduced disparities in the resting [Ca2+]i and ability of thapsigargin to mobilize Ca2+ between HET and WT T cells. While SOCE elicited dissipation of the ΔΨm in WT T cells, it produced ΔΨm hyperpolarization in HET T cells. When used as the classification variable, the amplitude of thapsigargin-induced Ca2+ transient showed the best promise in predicting the presence of RyR1-p.R163C mutation. Other significant variables identified by machine learning analysis were the ratio of resting cytosolic Ca2+ level to the amplitude of thapsigargin-induced Ca2+ transient and an integral of changes in ΔΨm in response to SOCE. Our study demonstrated that gain-of-function mutation in RyR1 significantly affects Ca2+ signaling and mitochondrial fiction in T lymphocytes, which suggests that this mutation may cause altered immune responses in its carrier. Our data link the RyR1-p.R163C mutation, which causes inherited skeletal muscle diseases, to deregulation of Ca2+ signaling and mitochondrial function in immune T cells and establish proof-of-principle for in vitro T cell-based diagnostic assay for hereditary RyR1 hyperfunction.

Neuropeptide S receptor gene Asn107 polymorphism in obese male individuals in Pakistan.

Neuropeptide S (NPS) is a naturally occurring appetite stimulant, associated with anxiety, stress, and excitement regulation. Neuropeptide S serves as a hypothalamic energy regulator that enhances food intake with a reduced level of satiety. NPS activates fat angiogenesis and the proliferation of new adipocytes in obesity. NPS has an established role in energy regulation by many pre-clinical investigations; however we have limited data available to support this notion in humans. We found significant association of Neuropeptide S receptor (NPSR1) Asn107Ile (rs324981, A>T) polymorphism with obese male participants. The current investigation carried out genotype screening of NPSR1 allele to assess the spectrum of the Asn107Ile polymorphism in obese and healthy Pakistani individuals. We revealed a significant (p = 0.04) difference between AA vs TT + AT genotype distribution of NPSR1 (SNP rs324981,) between obese and healthy individuals (p = 0.04). In this genotype analysis of (SNP rs324981) of the NPSR1 gene, T allele was marked as risk allele with higher frequency in the obese (38%) compared to its frequency in the controls (25%). Single Nucleotide Polymorphism (SNP, rs324981) Asn107Ile of NPSR1gene, that switches an amino acid from Asn to Ile, has been found associated with increased susceptibility to obesity in Pakistani individuals. Furthermore, molecular simulation studies predicted a lower binding affinity of NPSR1 Asn107Ile variant to NPS than the wild-type consistent with the genotype studies. These molecular simulation studies predict a possible molecular mechanism of this interaction by defining the key amino acid residues. However, a significantly (p<0.0001) lower concentration of NPS was recorded independent of genotype frequencies in obese subjects compared to healthy controls. We believe that large scale polymorphism data of population for important gene players including NPSR1 will be more useful to understand obesity and its associated risk factors.

lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA.

Long non-coding RNA Knowledgebase (lncRNAKB) is an integrated resource for exploring lncRNA biology in the context of tissue-specificity and disease association. A systematic integration of annotations from six independent databases resulted in 77,199 human lncRNA (224,286 transcripts). The user-friendly knowledgebase covers a comprehensive breadth and depth of lncRNA annotation. lncRNAKB is a compendium of expression patterns, derived from analysis of RNA-seq data in thousands of samples across 31 solid human normal tissues (GTEx). Thousands of co-expression modules identified via network analysis and pathway enrichment to delineate lncRNA function are also accessible. Millions of expression quantitative trait loci (cis-eQTL) computed using whole genome sequence genotype data (GTEx) can be downloaded at lncRNAKB that also includes tissue-specificity, phylogenetic conservation and coding potential scores. Tissue-specific lncRNA-trait associations encompassing 323 GWAS (UK Biobank) are also provided. LncRNAKB is accessible at http://www.lncrnakb.org/ , and the data are freely available through Open Science Framework ( https://doi.org/10.17605/OSF.IO/RU4D2 ).

Measurement of radiation attenuation parameters of modified defatted soy flour-soy protein isolate-based mangrove wood particleboards to be used for CT phantom production.

For the first time, Rhizophora spp. (Rh. spp.) particleboard phantoms were developed using defatted soy flour (DSF) and soy protein isolate (SPI) modified by sodium hydroxide and itaconic acid polyamidoamine-epichlorohydrin (IA-PAE) adhesive. The microstructural characterization and X-ray diffraction patterns of the material revealed that the modified DSF and SPI adhesives became more compact and homogeneous when NaOH/IA-PAE was added, which prevented damage by moisture. It was confirmed that the composite is crystalline with (101), (002), and (004) orientations. Phantoms made of this material were scanned with X-ray computed tomography (CT) typically used for abdominal examinations with varying energies corresponding to 80, 120, and 135 kVp, to determine CT numbers, electron densities, and density distribution profiles. The radiation attenuation parameters were found to be not significantly different from those of water (XCOM) with p values [Formula: see text] 0.05 for DSF and SPI. The DSF- and SPI-based particleboard phantoms showed CT numbers close to those of water at the three X-ray CT energies. In addition, electron density and density distribution profiles of DSF-SPI-Rh. spp. particleboard phantoms with 15 wt% IA-PAE content were even closer to those of water and other commercial phantom materials at the three X-ray CT energies. It is concluded that DSF-SPI with NaOH/IA-PAE added can be used as a potential adhesive in Rh. spp. particleboard phantoms for radiation dosimetry.

Rare and Unique Case of Midline Anterior Arch of Atlas Non-formation Mimicking Jefferson Type 1 Fracture.

Cervical spine injuries are rare occurrences in children, especially the congenital anomalies of the atlas vertebra. Any injury involving the craniovertebral junction such as Jefferson fracture, is a valid cause for alarm due to the complex nature of the craniovertebral junction and the morbidity associated with it. We report the case of a 10-year-old male, who had failure of fusion of anterior arch of atlas due to the failure of formation of the anterior midline synchondrosis, and this mimicked a Jefferson fracture. If it was not for the peculiar absence of any corresponding evidence to suggest spinal injury, we might have mistaken this extremely rare but benign anomaly for a Jefferson fracture and subjected the patient to needless surgical treatment. Hence, it is concluded that keen clinical acumen and clear understanding of the developmental anatomy of these patients may be necessary to adequately manage them.

Ca2+ signaling in T lymphocytes: the interplay of the endoplasmic reticulum, mitochondria, membrane potential, and CRAC channels on transcription factor activation.

T cell receptor stimulation initiates a cascade of reactions that cause an increase in intracellular calcium (Ca2+) concentration mediated through inositol 1,4,5-trisphosphate (IP3). To understand the basic mechanisms by which the immune response in T cells is activated, it is useful to understand the signaling pathways that contain important targets for drugs in a quantitative fashion. A computational model helps us to understand how the selected elements in the pathways interact with each other, and which component plays the crucial role in systems. We have developed a mathematical model to explore the mechanism for controlling transcription factor activity, which regulates gene expression, by the modulation of calcium signaling triggered during T cell activation. The model simulates the activation and modulation of Ca2+ release-activated Ca2+ (CRAC) channels by mitochondrial dynamics and depletion of endoplasmic reticulum (ER) store, and also includes membrane potential in T-cells. The model simulates the experimental finding that increases in Ca2+ current enhances the activation of transcription factors and the Ca2+ influx through CRAC is also essential for the NFAT and NFκB activation. The model also suggests that plasma membrane Ca2+-ATPase (PMCA) controls a majority of the extrusion of Ca2+ and modulates the activation of CRAC channels. Furthermore, the model simulations explain how the complex interaction of the endoplasmic reticulum, membrane potential, mitochondria, and ion channels such as CRAC channels control T cell activation.