Coupled impedance & field potential data analysis of in vitro cardiomyocyte assays

Présentation PosterInternational audienc

Mixed-effects modeling for concentration effect profiling in cardiomyocyte contractility assays

Présentation PosterInternational audienceBackground. With the advent of new realtime technologies such as impedance assays, extracellular field potential measurement and optical sensing for in vitro cardiac safety screening studies, researchers have now to frequently deal with analyzing voluminous amounts of complex time responses. In this context, main issues are to speed up the data analysis process and to extract accurate information for cardiotoxicity profiling. Objectives. A first objective is the development of an innovative computational method able to globally process a large set of in vitro cardiac signals (provided by 96, 384 and 1536-well microplates) instead of analyzing them once at a time. Such a statistical population approach has the advantage the account for the common characteristics between the individual responses. A second objective is to handle qualitative factors (type of cardiomyocytes, compounds and media, etc.) in the computational process. Methods. The proposed estimation method relies on the combination of a dynamic system identification method and a mixed-effect modeling technique. An output-error polynomial model structure is used for the system identification step and a stochastic approximation expectation maximization is implemented for the estimation of the hyperparameters. Input signals to be analyzed are the contractility amplitudes of cardiomyocytes submitted to compounds to be tested. Impedance signals and contractility amplitude were provided by a CardioExcyte96 system (Nanion Technologies). human iPSC-derived cardiomyocytes were provided by Cellartis Takara with 30,000 cells per well. Results. Our data-driven profiling method extracted four parameters that completely fit the contractility time variations and fully characterize the effect of compound concentration on the contractility amplitude. The proposed method not only estimates the values of the model parameters but also their uncertainty distribution. The latter allows to compute p-values associated with each effect.Conclusion. We show that the population-based estimation method developed in this study is suited to the fully characterize dynamic effects in cardiomyocyte contractility assays. Each parameter becomes a profiling characteristics of the concentration effect. It can be applied to estimate concentration and compounds effects with an optimal accuracy and could be extended directly to multielectrode array and optical sensing responses

Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants

BACKGROUND: Experimental animal data show that protection against severe acute respiratory syndrome coronavirus (SARS-CoV) infection with human monoclonal antibodies (mAbs) is feasible. For an effective immune prophylaxis in humans, broad coverage of different strains of SARS-CoV and control of potential neutralization escape variants will be required. Combinations of virus-neutralizing, noncompeting mAbs may have these properties. METHODS AND FINDINGS: Human mAb CR3014 has been shown to completely prevent lung pathology and abolish pharyngeal shedding of SARS-CoV in infected ferrets. We generated in vitro SARS-CoV variants escaping neutralization by CR3014, which all had a single P462L mutation in the glycoprotein spike (S) of the escape virus. In vitro experiments confirmed that binding of CR3014 to a recombinant S fragment (amino acid residues 318–510) harboring this mutation was abolished. We therefore screened an antibody-phage library derived from blood of a convalescent SARS patient for antibodies complementary to CR3014. A novel mAb, CR3022, was identified that neutralized CR3014 escape viruses, did not compete with CR3014 for binding to recombinant S1 fragments, and bound to S1 fragments derived from the civet cat SARS-CoV-like strain SZ3. No escape variants could be generated with CR3022. The mixture of both mAbs showed neutralization of SARS-CoV in a synergistic fashion by recognizing different epitopes on the receptor-binding domain. Dose reduction indices of 4.5 and 20.5 were observed for CR3014 and CR3022, respectively, at 100% neutralization. Because enhancement of SARS-CoV infection by subneutralizing antibody concentrations is of concern, we show here that anti-SARS-CoV antibodies do not convert the abortive infection of primary human macrophages by SARS-CoV into a productive one. CONCLUSIONS: The combination of two noncompeting human mAbs CR3014 and CR3022 potentially controls immune escape and extends the breadth of protection. At the same time, synergy between CR3014 and CR3022 may allow for a lower total antibody dose to be administered for passive immune prophylaxis of SARS-CoV infection

Micro-combs: a novel generation of optical sources

The quest towards the integration of ultra-fast, high-precision optical clocks is reflected in the large number of high-impact papers on the topic published in the last few years. This interest has been catalysed by the impact that high-precision optical frequency combs (OFCs) have had on metrology and spectroscopy in the last decade [1–5]. OFCs are often referred to as optical rulers: their spectra consist of a precise sequence of discrete and equally-spaced spectral lines that represent precise marks in frequency. Their importance was recognised worldwide with the 2005 Nobel Prize being awarded to T.W. Hänsch and J. Hall for their breakthrough in OFC science [5]. They demonstrated that a coherent OFC source with a large spectrum – covering at least one octave – can be stabilised with a self-referenced approach, where the frequency and the phase do not vary and are completely determined by the source physical parameters. These fully stabilised OFCs solved the challenge of directly measuring optical frequencies and are now exploited as the most accurate time references available, ready to replace the current standard for time. Very recent advancements in the fabrication technology of optical micro-cavities [6] are contributing to the development of OFC sources. These efforts may open up the way to realise ultra-fast and stable optical clocks and pulsed sources with extremely high repetition-rates, in the form of compact and integrated devices. Indeed, the fabrication of high-quality factor (high-Q) micro-resonators, capable of dramatically amplifying the optical field, can be considered a photonics breakthrough that has boosted not only the scientific investigation of OFC sources [7–13] but also of optical sensors and compact light modulators [6,14]

Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction

The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N=293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease. On the electrocardiogram, the PR interval reflects conduction from the atria to ventricles and also serves as risk indicator of cardiovascular morbidity and mortality. Here, the authors perform genome-wide meta-analyses for PR interval in multiple ancestries and identify 141 previously unreported genetic loci.Peer reviewe

A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure

Elevated blood pressure (BP), a leading cause of global morbidity and mortality, is influenced by both genetic and lifestyle factors. Cigarette smoking is one such lifestyle factor. Across five ancestries, we performed a genome-wide gene-smoking interaction study of mean arterial pressure (MAP) and pulse pressure (PP) in 129 913 individuals in stage 1 and follow-up analysis in 480 178 additional individuals in stage 2. We report here 136 loci significantly associated with MAP and/or PP. Of these, 61 were previously published through main-effect analysis of BP traits, 37 were recently reported by us for systolic BP and/or diastolic BP through gene-smoking interaction analysis and 38 were newly identified (P <5 x 10(-8), false discovery rate <0.05). We also identified nine new signals near known loci. Of the 136 loci, 8 showed significant interaction with smoking status. They include CSMD1 previously reported for insulin resistance and BP in the spontaneously hypertensive rats. Many of the 38 new loci show biologic plausibility for a role in BP regulation. SLC26A7 encodes a chloride/bicarbonate exchanger expressed in the renal outer medullary collecting duct. AVPR1A is widely expressed, including in vascular smooth muscle cells, kidney, myocardium and brain. FHAD1 is a long non-coding RNA overexpressed in heart failure. TMEM51 was associated with contractile function in cardiomyocytes. CASP9 plays a central role in cardiomyocyte apoptosis. Identified only in African ancestry were 30 novel loci. Our findings highlight the value of multi-ancestry investigations, particularly in studies of interaction with lifestyle factors, where genomic and lifestyle differences may contribute to novel findings.Peer reviewe

Selection for tolerance to aluminum in corn based on genetic parameters and multivariate analysist

O melhoramento de plantas, nos últimos 40 anos, tem empenhado esforços na busca de genótipos de milho com tolerância ao alumínio. A compreensão da variabilidade existente através da distância genética entre genótipos serve como base para definição de cruzamentos que possibilitem a obtenção de ganho genético. O objetivo deste trabalho foi estudar o caráter tolerância ao alumínio em milho com base em parâmetros genéticos e estatística multivariada em gerações precoces. Para tanto foi realizada a estimativa de parâmetros genéticos e análise multivariada em 74 famílias F3:2 originadas de dois cruzamentos contrastantes para o caráter tolerância ao alumínio. A estimativa dos parâmetros genéticos, com base nos componentes da variância, indicou influência do ambiente para todos os caracteres avaliados e dificuldades de seleção em solo ácido. A análise do dendograma gerado com base nas distâncias genéticas revelou a existência de dois grupos principais. Cruzamentos entre linhagens com desempenho superior e obtidas de famílias de diferentes grupos são potencialmente fonte para geração de populações de milho visando ao incremento da tolerância ao alumínio.The improvement of plants, in the last 40 years, has pledged efforts in the search of maize genotypes with aluminum tolerance. The understanding of the existing variability and the genetic distance between genotypes serves as basis for crossings in breeding programs. The objective of this work was to study aluminum tolerance in maize based on multivariate analysis and genetic parameters in early generations. There were 74 families F3:2 originated from two contrasting crosses for aluminum tolerance. The estimation of genetic parameters based on the components of variance, indicated the influence of the environment for all measured traits, which imposes difficulties for selection in acid soils. The analysis of the dendogram on the basis of the genetic distances disclosed the existence of two main groups. Crossings between inbreds with superior performance and families from different groups are potential source for maize populations to increase aluminum tolerance

Selection for tolerance to aluminum in corn based on genetic parameters and multivariate analysist

O melhoramento de plantas, nos últimos 40 anos, tem empenhado esforços na busca de genótipos de milho com tolerância ao alumínio. A compreensão da variabilidade existente através da distância genética entre genótipos serve como base para definição de cruzamentos que possibilitem a obtenção de ganho genético. O objetivo deste trabalho foi estudar o caráter tolerância ao alumínio em milho com base em parâmetros genéticos e estatística multivariada em gerações precoces. Para tanto foi realizada a estimativa de parâmetros genéticos e análise multivariada em 74 famílias F3:2 originadas de dois cruzamentos contrastantes para o caráter tolerância ao alumínio. A estimativa dos parâmetros genéticos, com base nos componentes da variância, indicou influência do ambiente para todos os caracteres avaliados e dificuldades de seleção em solo ácido. A análise do dendograma gerado com base nas distâncias genéticas revelou a existência de dois grupos principais. Cruzamentos entre linhagens com desempenho superior e obtidas de famílias de diferentes grupos são potencialmente fonte para geração de populações de milho visando ao incremento da tolerância ao alumínio.The improvement of plants, in the last 40 years, has pledged efforts in the search of maize genotypes with aluminum tolerance. The understanding of the existing variability and the genetic distance between genotypes serves as basis for crossings in breeding programs. The objective of this work was to study aluminum tolerance in maize based on multivariate analysis and genetic parameters in early generations. There were 74 families F3:2 originated from two contrasting crosses for aluminum tolerance. The estimation of genetic parameters based on the components of variance, indicated the influence of the environment for all measured traits, which imposes difficulties for selection in acid soils. The analysis of the dendogram on the basis of the genetic distances disclosed the existence of two main groups. Crossings between inbreds with superior performance and families from different groups are potential source for maize populations to increase aluminum tolerance