Common Chemical Inductors of Replication Stress: Focus on Cell-Based Studies.

DNA replication is a highly demanding process regarding the energy and material supply and must be precisely regulated, involving multiple cellular feedbacks. The slowing down or stalling of DNA synthesis and/or replication forks is referred to as replication stress (RS). Owing to the complexity and requirements of replication, a plethora of factors may interfere and challenge the genome stability, cell survival or affect the whole organism. This review outlines chemical compounds that are known inducers of RS and commonly used in laboratory research. These compounds act on replication by direct interaction with DNA causing DNA crosslinks and bulky lesions (cisplatin), chemical interference with the metabolism of deoxyribonucleotide triphosphates (hydroxyurea), direct inhibition of the activity of replicative DNA polymerases (aphidicolin) and interference with enzymes dealing with topological DNA stress (camptothecin, etoposide). As a variety of mechanisms can induce RS, the responses of mammalian cells also vary. Here, we review the activity and mechanism of action of these compounds based on recent knowledge, accompanied by examples of induced phenotypes, cellular readouts and commonly used doses

Patient-Specific Virtual Insertion of Electrode Array for Electrical Simulations of Cochlear Implants

International audienceSensorineural hearing loss is becoming one the most common reasons of disability. Worldwide 278 million people (around 25% of people above 45 years) suffer from moderate to several hearing disorders. Cochlear implantation (CI) enables to convert sound to an electrical signal that directly stimulates the auditory nerves via the electrode array surgically placed. However, this technique is intrinsically patient-dependent and its range of outcomes is very broad. A major source of outcome variability resides in the electrode array insertion. It has been reported to be one of the most important steps in cochlear implant surgery. In this context, we propose a method for patient-specific virtual electrode insertion further used into a finite element electrical simulation, and consequently improving the planning of the surgical implantation. The anatomical parameters involved in the electrode insertion such as the curvature and the number of turns of the cochlea, make virtual insertion highly challenging. Moreover, the influence of the insertion parameters and the use of different manufactured electrode arrays increase the range of scenarios to be considered for the implantation of a given patient. To this end, the method we propose is fast, easily parameterizable and applicable to a wide range of anatomies and insertion configurations. Our method is novel for targeting automatic virtual electrode insertion. Also, it combines high-resolution imaging techniques and clinical data to be further used into a finite element study and predict implantation outcomes in humans

Automatic Generation of a Computational Model for Monopolar Stimulation of Cochlear Implants

International audienceCochlear implants have the potential to significantly improve severe sensorineural hearing loss. However, the outcome of this technique is highly variable and depends on patient-specific factors. We previously proposed a method for patient-specific electrical simulation after CI, which can assist in surgical planning of the CI and determination of the electrical stimulation pattern. However, the virtual implant placement and mesh generation were carried out manually and the process was not easily applied automatically for further cochlear anatomies. Moreover, in order to optimize the implant designs, it is important to develop a way to stimulate the results of the implantation in a population of virtual patients. In this work we propose an automatic framework for patient-specific electrical simulation in CI surgery. To the best of our knowledge, this is the first method proposed for patient-specific generation of hearing models which combines high-resolution imaging techniques, clinical CT data and virtual electrode insertion. Furthermore, we show that it is possible to use the computational models of virtual patients to simulate the results of the electrical activation of the implant in the cochlea and surrounding bone. This is an important step because it allows us to advance towards a complete surgical planning and implant optimization procedure

Molecular Studies on the Interaction of Leptin With Its Receptor

Leptin is a hormonal protein involved in energy homeostasis, acting to inhibit food intake, stimulate energy expenditure and influence insulin secretion, lipo-lysis and sugar transport. Its action is mediated by a specific receptor whose activation is highly controversial. As a member of the cytokine receptor super-family, it has been predicted to be activated by ligand-induced dimerization. However, recent evidence has suggested that this receptor exists as a dimer in both ligand-free and ligand-bound states. The aim of this project was to determine the kinetics and stoichiometry of leptin receptor interaction with its ligand, using a variety of biophysical techniques, namely BiaCore and microcalorimetry. To achieve this, it was necessary to express the leptin receptor. Because the receptor cDNA was not available at the start of this project, the initial goal was to obtain the cDNA encoding the extracellular domain of the receptor by RT-PCR. The open reading frame consisting of 839 a.a. encoded by 2517 nucleotides was generated by several molecular approaches, as the mRNA is a rare species. To generate large amounts of the receptor required for microcalorimetry, Baculovirus expression system for the leptin receptor production was devel-oped. At the same time BiaCore analysis of the interaction was performed since it requires small amounts of protein, and commercially available protein could be used. BiaCore was used to measure the thermodynamics of the interaction. Hu-man or mouse receptor chimeras comprising two receptor extracellular domains fused to the Fc region of IgGI were captured on to the sensor via Protein G. The kinetics and stoichiometry of interactions with human, mouse or rat lep-tin were measured. This data demonstrated a high affinity interaction. The KD was 0.2 +/- 0.1 nM, with ka = (1.9 +/- 0.4) x10e6 M-1s-1 and kd = (4.6 +/- 0.9) x10e-4 s-1 for human leptin with its cognate receptor. The observed stoichiometry was 1:1. Little difference was observed for different species of leptin. Thus, leptin forms a very stable 1:1 complex with its receptor. This observation indicates that the leptin receptor oligomerization state is not altered during its interaction with a ligand. This contradicts the common paradigm of cytokine receptor activation. A truncated version of the leptin molecule with deleted glutamine at position 28 was also expressed in E. coli. Its affinity for human and mouse leptin receptor chimeras was analysed by BiaCore, which revealed a 10-fold decrease in affinity, indicating a possible involvement of Q28 in binding

Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

This review explores the latest developments in Fourier transform mass spectrometry and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing high resolution mass spectrometry data

Serial measurements of cardiac biomarkers in patients after allogeneic hematopoietic stem cell transplantation

<p>Abstract</p> <p>Background</p> <p>Previous therapy with anthracyclines (ANT) and conditioning regimen followed by hematopoietic stem cell transplantation (HSCT) represents a high risk for development of cardiotoxicity. The aim of this study was to assess subclinical myocardial damage after HSCT using echocardiography and cardiac biomarkers - high sensitive cardiac troponin T (hs-cTnT) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) and to identify patients at risk of developing clinical cardiotoxicity.</p> <p>Patients and methods</p> <p>Thirty-seven patients who were treated with allogeneic HSCT for hematologic diseases at median age of 28 years at time of HSCT were studied. Conditioning regimen included either chemotherapy without total body irradiation (TBI) or combination of chemotherapy with TBI. Twenty-nine (78,3%) patients were pretreated with ANT therapy. Cardiac biomarkers were serially measured before conditioning regimen and at days 1, 14 and 30 after HSCT. Cardiac systolic and diastolic functions were assessed before conditioning regimen and 1 month after HSCT by echocardiography.</p> <p>Results</p> <p>The changes in plasma NT-proBNP and hs-cTnT levels during the 30 days following the HSCT were statistically significant (<it>P </it>< 0,01 v.s. <it>P </it>< 0,01). Persistent elevations of NT-proBNP and hs-cTnT simultaneously for a period exceeding 14 days after HSCT were found in 29,7% patients. Serum concentrations of cardiomarkers were significantly elevated in ANT group compared to non-ANT group. These observations were underscored by the echocardiographic studies which did reveal significant changes in systolic and diastolic parameters. Five of 37 (13,5%) patients developed clinical manifestation of cardiotoxicity.</p> <p>Conclusions</p> <p>Elevations in both cardiac biomarkers were found before clinical signs of cardiotoxicity developed. Persistent elevations in NT-pro-BNP and hs-cTnT concentrations simultaneously for a period exceeding 14 days might be used for identification of patients at risk of developing cardiotoxicity and requiring further cardiological follow up.</p

Computational evaluation of cochlear implant surgery outcomes accounting for uncertainty and parameter variability

Cochlear implantation (CI) is a complex surgical procedure that restores hearing in patients with severe deafness. The successful outcome of the implanted device relies on a group of factors, some of them unpredictable or difficult to control. Uncertainties on the electrode array position and the electrical properties of the bone make it difficult to accurately compute the current propagation delivered by the implant and the resulting neural activation. In this context, we use uncertainty quantification methods to explore how these uncertainties propagate through all the stages of CI computational simulations. To this end, we employ an automatic framework, encompassing from the finite element generation of CI models to the assessment of the neural response induced by the implant stimulation. To estimate the confidence intervals of the simulated neural response, we propose two approaches. First, we encode the variability of the cochlear morphology among the population through a statistical shape model. This allows us to generate a population of virtual patients using Monte Carlo sampling and to assign to each of them a set of parameter values according to a statistical distribution. The framework is implemented and parallelized in a High Throughput Computing environment that enables to maximize the available computing resources. Secondly, we perform a patient-specific study to evaluate the computed neural response to seek the optimal post-implantation stimulus levels. Considering a single cochlear morphology, the uncertainty in tissue electrical resistivity and surgical insertion parameters is propagated using the Probabilistic Collocation method, which reduces the number of samples to evaluate. Results show that bone resistivity has the highest influence on CI outcomes. In conjunction with the variability of the cochlear length, worst outcomes are obtained for small cochleae with high resistivity values. However, the effect of the surgical insertion length on the CI outcomes could not be clearly observed, since its impact may be concealed by the other considered parameters. Whereas the Monte Carlo approach implies a high computational cost, Probabilistic Collocation presents a suitable trade-off between precision and computational time. Results suggest that the proposed framework has a great potential to help in both surgical planning decisions and in the audiological setting process