Modeling SILAC Data to Assess Protein Turnover in a Cellular Model of Diabetic Nephropathy.

Protein turnover rate is finely regulated through intracellular mechanisms and signals that are still incompletely understood but that are essential for the correct function of cellular processes. Indeed, a dysfunctional proteostasis often impacts the cell's ability to remove unfolded, misfolded, degraded, non-functional, or damaged proteins. Thus, altered cellular mechanisms controlling protein turnover impinge on the pathophysiology of many diseases, making the study of protein synthesis and degradation rates an important step for a more comprehensive understanding of these pathologies. In this manuscript, we describe the application of a dynamic-SILAC approach to study the turnover rate and the abundance of proteins in a cellular model of diabetic nephropathy. We estimated protein half-lives and relative abundance for thousands of proteins, several of which are characterized by either an altered turnover rate or altered abundance between diabetic nephropathic subjects and diabetic controls. Many of these proteins were previously shown to be related to diabetic complications and represent therefore, possible biomarkers or therapeutic targets. Beside the aspects strictly related to the pathological condition, our data also represent a consistent compendium of protein half-lives in human fibroblasts and a rich source of important information related to basic cell biology.

Physiologically based modelling of the antiplatelet effect of aspirin: A tool to characterize drug responsiveness and inform precision dosing.

A computational approach involving mathematical modeling and in silico experiments was used to characterize the determinants of extent and duration of platelet cyclooxygenase (COX)-1 inhibition by aspirin and design precision dosing in patients with accelerated platelet turnover or reduced drug bioavailability. To this purpose, a recently developed physiologically-based pharmacokinetics (PK) and pharmacodynamics (PD) model of low-dose aspirin in regenerating platelets and megakaryocytes, was used to predict the main features and determinants of platelet COX-1 inhibition. The response to different aspirin regimens in healthy subjects and in pathological conditions associated with alterations in aspirin PK (i.e., severely obese subjects) or PD (i.e., essential thrombocytemya patients), were simulated. A model sensitivity analysis was performed to identify the main processes influencing COX-1 dynamics. In silico experiments and sensitivity analyses indicated a major role for megakaryocytes and platelet turnover in determining the extent and duration of COX-1 inhibition by once-daily, low-dose aspirin. They also showed the superiority of reducing the dosing interval vs increasing the once-daily dose in conditions of increased platelet turnover, while suggested specific dose adjustments in conditions of possible reduction in drug bioavailability. In conclusion, the consistency of our model-based findings with experimental data from studies in healthy subjects and patients with essential thrombocythemia supports the potential of our approach for describing the determinants of platelet inhibition by aspirin and informing precision dosing which may guide personalized antithrombotic therapy in different patient populations, especially in those under-represented in clinical trials or in those associated with poor feasibility.

Reduced Effective Connectivity in the Motor Cortex in Parkinson's Disease.

Fast rhythms excess is a hallmark of Parkinson's Disease (PD). To implement innovative, non-pharmacological, neurostimulation interventions to restore cortical-cortical interactions, we need to understand the neurophysiological mechanisms underlying these phenomena. Here, we investigated effective connectivity on source-level resting-state electroencephalography (EEG) signals in 15 PD participants and 10 healthy controls. First, we fitted multivariate auto-regressive models to the EEG source waveforms. Second, we estimated causal connections using Granger Causality, which provide information on connections' strength and directionality. Lastly, we sought significant differences connectivity patterns between the two populations characterizing the network graph features-i.e., global efficiency and node strength. Causal brain networks in PD show overall poorer and weaker connections compared to controls quantified as a reduction of global efficiency. Motor areas appear almost isolated, with a strongly impoverished information flow particularly from parietal and occipital cortices. This striking isolation of motor areas may reflect an impaired sensory-motor integration in PD. The identification of defective nodes/edges in PD network may be a biomarker of disease and a potential target for future interventional trials.

Corrigendum to "Genetic perturbation of IFN-α transcriptional modulators in human endothelial cells uncovers pivotal regulators of angiogenesis" [Comput Struct Biotechnol J. 2020 Dec 2;18:3977-3986. doi: https://doi.org//10.1016/j.csbj.2020.11.048. eCollection 2020].

[This corrects the article DOI: 10.1016/j.csbj.2020.11.048.].

Genetic perturbation of IFN-α transcriptional modulators in human endothelial cells uncovers pivotal regulators of angiogenesis.

Interferon-α (IFN-α) comprises a family of 13 cytokines involved in the modulation of antiviral, immune, and anticancer responses by orchestrating a complex transcriptional network. The activation of IFN-α signaling pathway in endothelial cells results in decreased proliferation and migration, ultimately leading to suppression of angiogenesis. In this study, we knocked-down the expression of seven established or candidate modulators of IFN-α response in endothelial cells to reconstruct a gene regulatory network and to investigate the antiangiogenic activity of IFN-α. This genetic perturbation approach, along with the analysis of interferon-induced gene expression dynamics, highlighted a complex and highly interconnected network, in which the angiostatic chemokine C-X-C Motif Chemokine Ligand 10 (CXCL10) was a central node targeted by multiple modulators. IFN-α-induced secretion of CXCL10 protein by endothelial cells was blunted by the silencing of Signal Transducer and Activator of Transcription 1 (STAT1) and of Interferon Regulatory Factor 1 (IRF1) and it was exacerbated by the silencing of Ubiquitin Specific Peptidase 18 (USP18). In vitro sprouting assay, which mimics in vivo angiogenesis, confirmed STAT1 as a positive modulator and USP18 as a negative modulator of IFN-α-mediated sprouting suppression. Our data reveal an unprecedented physiological regulation of angiogenesis in endothelial cells through a tonic IFN-α signaling, whose enhancement could represent a viable strategy to suppress tumor neoangiogenesis.

Stochastic modeling of human papillomavirusearly promoter gene regulation.

High risk forms of human papillomaviruses (HPVs) promote cancerous lesions and are implicated in almost all cervical cancer. Of particular relevance to cancer progression is regulation of the early promoter that controls gene expression in the initial phases of infection and can eventually lead to pre-cancer progression. Our goal was to develop a stochastic model to investigate the control mechanisms that regulate gene expression from the HPV early promoter. Our model integrates modules that account for transcriptional, post-transcriptional, translational and post-translational regulation of E1 and E2 early genes to form a functioning gene regulatory network. Each module consists of a set of biochemical steps whose stochastic evolution is governed by a chemical Master Equation and can be simulated using the Gillespie algorithm. To investigate the role of noise in gene expression, we compared our stochastic simulations with solutions to ordinary differential equations for the mean behavior of the system that are valid under the conditions of large molecular abundances and quasi-equilibrium for fast reactions. The model produced results consistent with known HPV biology. Our simulation results suggest that stochasticity plays a pivotal role in determining the dynamics of HPV gene expression. In particular, the combination of positive and negative feedback regulation generates stochastic bursts of gene expression. Analysis of the model reveals that regulation at the promoter affects burst amplitude and frequency, whereas splicing is more specialized to regulate burst frequency. Our results also suggest that splicing enhancers are a significant source of stochasticity in pre-mRNA abundance and that the number of viruses infecting the host cell represents a third important source of stochasticity in gene expression.

A rule-based model of insulin signalling pathway.

BACKGROUND: The insulin signalling pathway (ISP) is an important biochemical pathway, which regulates some fundamental biological functions such as glucose and lipid metabolism, protein synthesis, cell proliferation, cell differentiation and apoptosis. In the last years, different mathematical models based on ordinary differential equations have been proposed in the literature to describe specific features of the ISP, thus providing a description of the behaviour of the system and its emerging properties. However, protein-protein interactions potentially generate a multiplicity of distinct chemical species, an issue referred to as "combinatorial complexity", which results in defining a high number of state variables equal to the number of possible protein modifications. This often leads to complex, error prone and difficult to handle model definitions. RESULTS: In this work, we present a comprehensive model of the ISP, which integrates three models previously available in the literature by using the rule-based modelling (RBM) approach. RBM allows for a simple description of a number of signalling pathway characteristics, such as the phosphorylation of signalling proteins at multiple sites with different effects, the simultaneous interaction of many molecules of the signalling pathways with several binding partners, and the information about subcellular localization where reactions take place. Thanks to its modularity, it also allows an easy integration of different pathways. After RBM specification, we simulated the dynamic behaviour of the ISP model and validated it using experimental data. We the examined the predicted profiles of all the active species and clustered them in four clusters according to their dynamic behaviour. Finally, we used parametric sensitivity analysis to show the role of negative feedback loops in controlling the robustness of the system. CONCLUSIONS: The presented ISP model is a powerful tool for data simulation and can be used in combination with experimental approaches to guide the experimental design. The model is available at http://sysbiobig.dei.unipd.it/ was submitted to Biomodels Database ( https://www.ebi.ac.uk/biomodels-main/ # MODEL 1604100005).

Reconstruction of gene regulatory modules from RNA silencing of IFN-α modulators: experimental set-up and inference method.

BACKGROUND: Inference of gene regulation from expression data may help to unravel regulatory mechanisms involved in complex diseases or in the action of specific drugs. A challenging task for many researchers working in the field of systems biology is to build up an experiment with a limited budget and produce a dataset suitable to reconstruct putative regulatory modules worth of biological validation. RESULTS: Here, we focus on small-scale gene expression screens and we introduce a novel experimental set-up and a customized method of analysis to make inference on regulatory modules starting from genetic perturbation data, e.g. knockdown and overexpression data. To illustrate the utility of our strategy, it was applied to produce and analyze a dataset of quantitative real-time RT-PCR data, in which interferon-α (IFN-α) transcriptional response in endothelial cells is investigated by RNA silencing of two candidate IFN-α modulators, STAT1 and IFIH1. A putative regulatory module was reconstructed by our method, revealing an intriguing feed-forward loop, in which STAT1 regulates IFIH1 and they both negatively regulate IFNAR1. STAT1 regulation on IFNAR1 was object of experimental validation at the protein level. CONCLUSIONS: Detailed description of the experimental set-up and of the analysis procedure is reported, with the intent to be of inspiration for other scientists who want to realize similar experiments to reconstruct gene regulatory modules starting from perturbations of possible regulators. Application of our approach to the study of IFN-α transcriptional response modulators in endothelial cells has led to many interesting novel findings and new biological hypotheses worth of validation.

Low-frequency rTMS inhibitory effects in the primary motor cortex: Insights from TMS-evoked potentials.

The neuromodulatory effects of repetitive transcranial magnetic stimulation (rTMS) have been mostly investigated by peripheral motor-evoked potentials (MEPs). New TMS-compatible EEG systems allow a direct investigation of the stimulation effects through the analysis of TMS-evoked potentials (TEPs). We investigated the effects of 1-Hz rTMS over the primary motor cortex (M1) of 15 healthy volunteers on TEP evoked by single pulse TMS over the same area. A second experiment in which rTMS was delivered over the primary visual cortex (V1) of 15 healthy volunteers was conducted to examine the spatial specificity of the effects. Single-pulse TMS evoked four main components: P30, N45, P60 and N100. M1-rTMS resulted in a significant decrease of MEP amplitude and in a significant increase of P60 and N100 amplitude. There was no effect after V1-rTMS. 1-Hz rTMS appears to increase the amount of inhibition following a TMS pulse, as demonstrated by the higher N100 and P60, which are thought to originate from GABAb-mediated inhibitory post-synaptic potentials. Our results confirm the reliability of the TMS-evoked N100 as a marker of cortical inhibition and provide insight into the neuromodulatory effects of 1-Hz rTMS. The present finding could be of relevance for therapeutic and diagnostic purposes.

Minimal modeling of insulin secretion in the perfused rat pancreas: a drug effect case study.

The experimental protocol of the perfused rat pancreas is commonly used to evaluate ß-cell function. In this context, mathematical models become useful tools through the determination of indexes that allow the assessment of ß-cell function in different experimental groups and the quantification of the effects of antidiabetic drugs, secretagogues, or treatments. However, a minimal model applicable to the isolated perfused rat pancreas has so far been unavailable. In this work, we adapt the C-peptide minimal model applied previously to the intravenous glucose tolerance test to obtain a specific model for the experimental settings of the perfused pancreas. Using the model, it is possible to estimate indexes describing ß-cell responsivity for first (ΦD) and second phase (ΦS, T) of insulin secretion. The model was initially applied to untreated pancreata and afterward used for the assessment of pharmacologically relevant agents (the gut hormone GLP-1, the potent GLP-1 receptor agonist lixisenatide, and a GPR40/FFAR1 agonist, SAR1) to quantify and differentiate their effect on insulin secretion. Model fit was satisfactory, and parameters were estimated with good precision for both untreated and treated pancreata. Model application showed that lixisenatide reaches improvement of ß-cell function similarly to GLP-1 (11.7- vs. 13.1-fold increase in ΦD and 2.3- vs. 2.8-fold increase in ΦS) and demonstrated that SAR1 leads to an additional improvement of ß-cell function in the presence of postprandial GLP-1 levels.

Effect of voluntary repetitive long-lasting muscle contraction activity on the BOLD signal as assessed by optimal hemodynamic response function.

OBJECTIVE: Among other neuroimaging techniques, functional magnetic resonance imaging (fMRI) can be useful for studying the development of motor fatigue. The aim of this study was to identify differences in cortical neuronal activation in nine subjects on three motor tasks: right-hand movement with minimum, maximum, and post-fatigue maximum finger flexion. MATERIALS AND METHODS: fMRI activation maps for each subject and during each condition were obtained by estimating the optimal model of the hemodynamic response function (HRF) out of four standard HRF models and an individual-based HRF model (ibHRF). RESULTS: ibHRF was selected as the optimal model in six out of nine subjects for minimum movement, in five out of nine for maximum movement, and in eight out of nine for post-fatigue maximum movement. As compared to maximum movement, a large reduction in the total number of active voxels (primary sensorimotor area, supplementary motor area and cerebellum) was observed in post-fatigue maximum movement. CONCLUSION: This is the first approach to the evaluation of long-lasting contraction effort in healthy subjects by means of the fMRI paradigm with the use of an individual-based hemodynamic response. The results may be relevant for defining a baseline in future studies on central fatigue in patients with neuropathological disorders.

Automatic selection of resting-state networks with functional magnetic resonance imaging.

Functional magnetic resonance imaging (fMRI) during a resting-state condition can reveal the co-activation of specific brain regions in distributed networks, called resting-state networks, which are selected by independent component analysis (ICA) of the fMRI data. One of the major difficulties with component analysis is the automatic selection of the ICA features related to brain activity. In this study we describe a method designed to automatically select networks of potential functional relevance, specifically, those regions known to be involved in motor function, visual processing, executive functioning, auditory processing, memory, and the default-mode network. To do this, image analysis was based on probabilistic ICA as implemented in FSL software. After decomposition, the optimal number of components was selected by applying a novel algorithm which takes into account, for each component, Pearson's median coefficient of skewness of the spatial maps generated by FSL, followed by clustering, segmentation, and spectral analysis. To evaluate the performance of the approach, we investigated the resting-state networks in 25 subjects. For each subject, three resting-state scans were obtained with a Siemens Allegra 3 T scanner (NYU data set). Comparison of the visually and the automatically identified neuronal networks showed that the algorithm had high accuracy (first scan: 95%, second scan: 95%, third scan: 93%) and precision (90%, 90%, 84%). The reproducibility of the networks for visual and automatic selection was very close: it was highly consistent in each subject for the default-mode network (≥92%) and the occipital network, which includes the medial visual cortical areas (≥94%), and consistent for the attention network (≥80%), the right and/or left lateralized frontoparietal attention networks, and the temporal-motor network (≥80%). The automatic selection method may be used to detect neural networks and reduce subjectivity in ICA component assessment.

The human brain pacemaker: Synchronized infra-slow neurovascular coupling in patients undergoing non-pulsatile cardiopulmonary bypass.

In non-pulsatile cardiopulmonary bypass surgery, middle cerebral artery blood flow velocity (BFV) is characterized by infra-slow oscillations of approximately 0.06Hz, which are paralleled by changes in total EEG power variability (EEG-PV), measured in 2s intervals. Since the origin of these BFV oscillations is not known, we explored their possible causative relationships with oscillations in EEG-PV at around 0.06Hz. We monitored 28 patients undergoing non-pulsatile cardiopulmonary bypass using transcranial Doppler sonography and scalp electroencephalography at two levels of anesthesia, deep (prevalence of burst suppression rhythm) and moderate (prevalence of theta rhythm). Under deep anesthesia, the EEG bursts suppression pattern was highly correlative with BFV oscillations. Hence, a detailed quantitative picture of the coupling between electrical brain activity and BFV was derived, both in deep and moderate anesthesia, via linear and non linear processing of EEG-PV and BFV signals, resorting to widely used measures of signal coupling such as frequency of oscillations, coherence, Granger causality and cross-approximate entropy. Results strongly suggest the existence of coupling between EEG-PV and BFV. In moderate anesthesia EEG-PV mean dominant frequency is similar to frequency of BFV oscillations (0.065±0.010Hz vs 0.045±0.019Hz); coherence between the two signals was significant in about 55% of subjects, and the Granger causality suggested an EEG-PV→BFV causal effect direction. The strength of the coupling increased with deepening anesthesia, as EEG-PV oscillations mean dominant frequency virtually coincided with the BFV peak frequency (0.062±0.017Hz vs 0.060±0.024Hz), and coherence became significant in a larger number (65%) of subjects. Cross-approximate entropy decreased significantly from moderate to deep anesthesia, indicating a higher level of synchrony between the two signals. Presence of a subcortical brain pacemaker that drives vascular infra-slow oscillations in the brain is proposed. These findings allow to suggest an original hypothesis explaining the mechanism underlying infra-slow neurovascular coupling.

The disposition index: from individual to population approach.

To correctly evaluate the glucose control system, it is crucial to account for both insulin sensitivity and secretion. The disposition index (DI) is the most widely accepted method to do so. The original paradigm (hyperbolic law) consists of the multiplicative product of indices related to insulin sensitivity and secretion, but more recently, an alternative formula has been proposed with the exponent α (power function law). Traditionally, curve-fitting approaches have been used to evaluate the DI in a population: the algorithmic implementations often introduce some critical issues, such as the assumption that one of the two indices is error free or the effects of the log transformation on the measurement errors. In this work, we review the commonly used approaches and show that they provide biased estimates. Then we propose a novel nonlinear total least square (NLTLS) approach, which does not need to use the approximations built in the previously proposed alternatives, and show its superiority. All of the traditional fit procedures, including NLTLS, account only for uncertainty affecting insulin sensitivity and secretion indices when they are estimated from noisy data. Thus, they fail when part of the observed variability is due to inherent differences in DI values between individuals. To handle this inevitable source of variability, we propose a nonlinear mixed-effects approach that describes the DI using population hyperparameters such as the population typical values and covariance matrix. On simulated data, this novel technique is much more reliable than the curve-fitting approaches, and it proves robust even when no or small population variability is present in the DI values. Applying this new approach to the analysis of real IVGTT data suggests a value of α significantly smaller than 1, supporting the importance of testing the power function law as an alternative to the simpler hyperbolic law.

Time-frequency analysis of short-lasting modulation of EEG induced by intracortical and transcallosal paired TMS over motor areas.

Dynamic changes in spontaneous electroencephalogram (EEG) rhythms can be seen to occur with a high rate of variability. An innovative method to study brain function is by triggering oscillatory brain activity with transcranial magnetic stimulation (TMS). EEG-TMS coregistration was performed on five healthy subjects during a 1-day experimental session that involved four steps: baseline acquisition, unconditioned single-pulse TMS, intracortical inhibition (ICI, 3 ms) paired-pulse TMS, and transcallosal stimulation over left and right primary motor cortex (M1). A time-frequency analysis based on the wavelet method was used to characterize rapid modifications of oscillatory EEG rhythms induced by TMS. Single, paired, and transcallosal TMS applied on the sensorimotor areas induced rapid desynchronization over the frontal and central-parietal electrodes mainly in the alpha and beta bands, followed by a rebound of synchronization, and rapid synchronization of delta and theta activity. Wavelet analysis after a perturbation approach is a novel way to investigate modulation of oscillatory brain activity. The main findings are consistent with the concept that the human motor system may be based on networklike oscillatory cortical activity and might be modulated by single, paired, and transcallosal magnetic pulses applied to M1, suggesting a phenomenon of fast brain activity resetting and triggering of slow activity.

Electroencephalography in patients with cirrhosis.

BACKGROUND & AIMS: Electroencephalography has not been completely quantified in patients with cirrhosis. We investigated the electroencephalogram (EEG) dynamics in patients with cirrhosis. METHODS: We performed closed-eye EEGs on 175 patients with cirrhosis (age, 55 ± 11 years; 24% Child-Pugh class A, 48% class B, and 285 class C), conducted clinical and psychometric assessments for hepatic encephalopathy (HE), and followed the patients for 1 year. EEG characteristics were assessed in the frequency domain, in the frontal (F3-F4) and parietal (P3-P4) derivations. Intrahemispheric (frontoparietal, right, and left) and interhemispheric (F3-F4 and P3-P4) coherence were computed. The EEGs of 50 healthy volunteers (age, 56 ± 17 years) served as controls. RESULTS: Compared with controls, the EEGs of patients with cirrhosis had a reduced frequency in the posterior derivations (P3/P4 mean dominant frequency, 9.1 ± 1.8 and 8.9 ± 1.7 Hz vs 10.4 ± 1.3 and 10.2 ± 1.3 Hz, respectively; P < .01) and an increase in interhemispheric parietal relative coherence within the theta band (22.3% ± 5.5% vs 18.9% ± 3.5%; P < .01). These features were more prominent in patients with Child class C and in patients with a history of overt HE; they correlated with hyperammonemia and hyponatremia. The decrease in EEG frequency, along with the increase in interhemispheric theta coherence in the posterior derivations, was inversely associated with survival and the occurrence of overt HE during the follow-up period. CONCLUSIONS: In patients with cirrhosis, alterations in the EEG were significantly associated with the severity of liver disease and HE; the EEG might be used in determining prognosis.

Integrating EEG and fMRI in epilepsy.

Integrating electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) studies enables to non-invasively investigate human brain function and to find the direct correlation of these two important measures of brain activity. Presurgical evaluation of patients with epilepsy is one of the areas where EEG and fMRI integration has considerable clinical relevance for localizing the brain regions generating interictal epileptiform activity. The conventional analysis of EEG-fMRI data is based on the visual identification of the interictal epileptiform discharges (IEDs) on scalp EEG. The convolution of these EEG events, represented as stick functions, with a model of the fMRI response, i.e. the hemodynamic response function, provides the regressor for general linear model (GLM) analysis of fMRI data. However, the conventional analysis is not automatic and suffers of some subjectivity in IEDs classification. Here, we present an easy-to-use and automatic approach for combined EEG-fMRI analysis able to improve IEDs identification based on Independent Component Analysis and wavelet analysis. EEG signal due to IED is reconstructed and its wavelet power is used as a regressor in GLM. The method was validated on simulated data and then applied on real data set consisting of 2 normal subjects and 5 patients with partial epilepsy. In all continuous EEG-fMRI recording sessions a good quality EEG was obtained allowing the detection of spontaneous IEDs and the analysis of the related BOLD activation. The main clinical finding in EEG-fMRI studies of patients with partial epilepsy is that focal interictal slow-wave activity was invariably associated with increased focal BOLD responses in a spatially related brain area. Our study extends current knowledge on epileptic foci localization and confirms previous reports suggesting that BOLD activation associated with slow activity might have a role in localizing the epileptogenic region even in the absence of clear interictal spikes.

Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates.

Neisseria meningitidis is a human-specific pathogen known for its capability to cause sepsis and meningitis. Here we report the availability of 2 draft genome sequences obtained from patients infected during the same epidemic outbreak. Both bacterial isolates belong to serogroup C, but their genome sequences show local and remarkable differences compared with each other or with the reference genome of strain FAM18.

An optimized data structure for high-throughput 3D proteomics data: mzRTree.

As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard XML-based portable formats. The structures that are currently employed to manage these data can be highly inefficient, especially when dealing with high-throughput profile data. LC-MS datasets are usually accessed through 2D range queries. Optimizing this type of operation could dramatically reduce the complexity of data analysis. We propose a novel data structure for LC-MS datasets, called mzRTree, which embodies a scalable index based on the R-tree data structure. mzRTree can be efficiently created from the XML-based data formats and it is suitable for handling very large datasets. We experimentally show that, on all range queries, mzRTree outperforms other known structures used for LC-MS data, even on those queries these structures are optimized for. Besides, mzRTree is also more space efficient. As a result, mzRTree reduces data analysis computational costs for very large profile datasets.

Retrovirus HTLV-1 gene circuit: a potential oscillator for eukaryotes.

Retrovirus HTLV-1 gene circuit is characterized by positive and negative feedback phenomena, thus candidating it as a potential relaxation oscillator deliverable into eukaryotes. Here we describe a model of HTLV-1 which, by providing predictions of genes and proteins kinetics, can be helpful for designing gene circuits for eukaryotes, or for optimizing gene therapy approaches which are currently carried out by means of lentiviral vectors or re-engineered adenoviruses. Oscillatory patterns of HTLV-1 gene circuit are predicted when positive feedback is faster than negative feedback. Techniques to mutate the retroviral genome in order to implement practically the above conditions are discussed. Finally, the effect of stochasticity on the system behavior is tested by means of Gillespie algorithm. Simulations show the difficulties to preserve synchronization in viral expression for a multiplicity of cells, while the long tail of the density probability function of the master regulator gene tax/rex, due to its steady state fluctuations, suggests an activation mechanism of HTLV-1 similar to that recently proposed for HIV(1): the virus tends to latency but under certain circumstances, the master regulator gene reaches high values of expression, whose persistence induces the viral replication.