Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling

We investigate the measurement of DNA supercoiling density ($\sigma$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $\sigma$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.Comment: 5 pages + Supplementary Info (including 3 figures

Simple scoring system to predict in-hospital mortality after surgery for infective endocarditis

BACKGROUND: Aspecific scoring systems are used to predict the risk of death postsurgery in patients with infective endocarditis (IE). The purpose of the present study was both to analyze the risk factors for in-hospital death, which complicates surgery for IE, and to create a mortality risk score based on the results of this analysis. METHODS AND RESULTS: Outcomes of 361 consecutive patients (mean age, 59.1\ub115.4 years) who had undergone surgery for IE in 8 European centers of cardiac surgery were recorded prospectively, and a risk factor analysis (multivariable logistic regression) for in-hospital death was performed. The discriminatory power of a new predictive scoring system was assessed with the receiver operating characteristic curve analysis. Score validation procedures were carried out. Fifty-six (15.5%) patients died postsurgery. BMI >27 kg/m2 (odds ratio [OR], 1.79; P=0.049), estimated glomerular filtration rate 55 mm Hg (OR, 1.78; P=0.032), and critical state (OR, 2.37; P=0.017) were independent predictors of in-hospital death. A scoring system was devised to predict in-hospital death postsurgery for IE (area under the receiver operating characteristic curve, 0.780; 95% CI, 0.734-0.822). The score performed better than 5 of 6 scoring systems for in-hospital death after cardiac surgery that were considered. CONCLUSIONS: A simple scoring system based on risk factors for in-hospital death was specifically created to predict mortality risk postsurgery in patients with IE

Modélisation du chromosome bactérien en vue de la conception de réseaux biologiques de régulation dans l'espace cellulaire

Superhelicity strongly affects the 3D structure of DNA. When supercoiled, circular dna (or linear DNA with topologically constrained ends) folds and forms loops called plectonemes, bringing some distant parts of the chromosome close to one another in space, thus perturbing the transcription regulation network of the cell. Bacterial chromosomes are negatively supercoiled and superhelicity is known to play a important role in the regulation of the transcription.However, due to the global nature of the topological constraint imposed to the DNA, current methods have only been able to simulate small molecules (up to a few kilobasepairs, kb). This thesis presents a novel algorithm used to performed monte-carlo simulations of supercoiled DNA, featuring a local approach to the topological constraint via the computation of the twist of the molecule.Using this efficient algorithm, simulations of long molecules (tens of kb) were performed and shed a new light on debated questions about the structure of supercoiled dna at this scale. This method allows to study the effect of the position of genes along the DNA on their co-localisation and co-regulation, and to envision the possibility of simulating the folding of a whole bacterial chromosome.La structure spatiale de l'adn est fortement affectée par le surenroulement. Lorsqu'il est surenroulé, l'ADN circulaire (ou linéaire et contraint topologiquement aux extrémités) se replie et forme des boucles appelées plectonèmes, rapprochant dans l'espace des régions éloignées du chromosome, perturbant ainsi le réseau de régulation de la transcription de la cellule. Les chromosomes bactériens sont surenroulés négativement et ce surenroulement est connu pour jouer un rôle important dans la régulation de la transcription.Cependant, à cause de la nature globale de la contrainte topologique imposée à l'ADN, les méthodes actuelles ne sont capables de simuler que de petites molécules (jusqu'à quelques milliers de paires de bases, kb). Cette thèse présente un nouvel algorithme utilisé pour réaliser des simulations de Monte-Carlo d'adn surenroulé, basé sur une approche locale de la contrainte topologique, via le calcul du twist de la molécule.Cet algorithme a été utilisé pour réaliser des simulations de longues molécules (plusieurs dizaines de kb) et apporter un nouvel éclairage sur des questions encore débattues à propos de la structure de l'ADN surenroulé à cette échelle. Cette méthode permet d'étudier l'effet de la position des gènes le long de l'ADN sur leur co-localisation et leur co-régulation, et laisse entrevoir la possibilité de simuler le repliement d'un chromosome bactérien entier

Modeling of the bacterial chromosome to design biological regulatory network in the celular space

La structure spatiale de l'ADN est fortement affectée par le surenroulement. Lorsqu'il est surenroulé, l'ADN circulaire (ou linéaire et contraint topologiquement aux extrémités) se replie et forme des boucles appelées plectonèmes, rapprochant dans l'espace des régions éloignées du chromosome, perturbant ainsi de l réseau de régulation de la transcription de la cellule. Les chromosomes bactériens sont surenroulés négativement et ce surenroulement est connu pour jouer un rôle important dans la régulation de la transcription. Cependant, à cause de la nature globale de la contrainte topologique associée à l'ADN, les méthodes actuelles ne sont capables de simuler que de petites molécules (jusqu'à quelques milliers de paires de bases, KB). Cette thèse présente un nouvel algorithme utilisé pour réaliser des simulations de Monte-Carlo d'ADN surenroulé, basé sur une molécule. Cet algorithme a été utilisé pour réaliser des simulations de longues molécules (plusieurs dizaines de KB) et apporter un nouvel éclairage sur des questions encore débattues à propos de la structure de l'ADN surenroulé à cette échelle. Cette méthode permet d'étudier l'effet de la position des gènes le long de l'ADN sur leur co-localisation et leur co-régulation, et laisse entrevoir la possibilité de simuler le repliement d'un chromosome bactérien entier.Superhelicity strongly affects the 3D structure of DNA. When supercoiled, circular DNA (or linear DNA with topolocically constrained ends) folds and forms loops called plectonemes, bringing some distant parts of the chromosme close to one another in space, thus perturbing the transcription regulation network of the cell. Bacterial chromosomes are negatively supercoiled and superhelicity is known to play a important role in the regulation of the transcription. However, due to the global nature of the topological constraint imposed to the DNA, current methods have only been able to simulate small moelcules (up to a few kilobasepairs, KB). This thesis presents a novel algorithm used to performed Monte-Carlo simulations of supercoiled DNA, featuring a local approach to the topological constraint via the computation of the twist of the molecule. Using this efficient algorithm, stimulations of long molecules (tens of KB) were performed and shed a new light on debated questions about the structure of supercoiled DNA at this scale. This method allows to study the effect of the position of genes along the DNA on their co-localisation and co-regulation, and to envision the possibility of simulating the folding of a whole bacterial chromosome

A polymer model of bacterial supercoiled DNA including structural transitions of the double helix

International audienceDNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of braided superstructures (plectonemes), or it may locally destabilize canonical B-DNA to generate denaturation bubbles, left-handed Z-DNA and other functional alternative forms. Prediction of the relative fraction of these structures has been limited because of a lack of predictive polymer models that can capture the multiscale properties of long DNA molecules. In this work, we address this issue by extending the self-avoiding rod-like chain model of DNA so that every site of the chain is allocated with an additional structural degree of freedom reflecting variations of DNA forms. Efficient simulations of the model reveal its relevancy to capture multiscale properties of long chains (here up to 21 kb) as reported in magnetic tweezers experiments. Well-controlled approximations further lead to accurate analytical estimations of thermodynamic properties in the high force regime, providing, in combination with experiments, a simple, yet powerful framework to infer physical parameters describing alternative forms. In this regard, using simulated data, we find that extension curves at forces above 2 pN may lead, alone, to erroneous parameter estimations as a consequence of an underdetermination problem. We thus revisit published data in light of these findings and discuss the relevancy of previously proposed sets of parameters for both denatured and left-handed DNA forms. Altogether, our work paves the way for a scalable quantitative model of bacterial DNA

Production de biocarburants à partir des sous-produits de l'industrie sucrière

Replacement of petroleum by other energy sources is one of the principal challenges of contemporary engineering. One of the most promising substitutes for petroleum is biomass, chemically converted into biofuels. In particular, crops residues, including sugar industry by-products, are the subject of many R&D efforts. As the world's biggest producer of sugarcane, Brazil generates large quantities of agricultural residues from sugarcane cultivation which could be used to produce biofuels for transportation and aviation (i.e. jet fuel) without much difficulty. Furthermore, sugar beet industry (mostly in Western Europe) generates important amount of waste that could be valorized into biofuels. The production of jetfuels via gasification of sugarcane bagasse follow by the Fischer-Tropsch process is pertinent. Indeed, the amount of raw material, the requirements of aviation market and the experience of sugarcane bagasse processing are three key factors. On the contrary, sugar beet pulp does not seem to be an interesting raw material for the production of biofuel. Although the available quantity is high, sugar beet pulp is already used to feed cattle. Moreover, its chemical content is more diversified and therefore more interesting for biotechnology. High value added pathways has to be favoured rather than biofuel production in the case of sugar beet pulp

Single and mixed feedstocks biorefining: comparison of primary metabolites recovery and lignin recombination during an alkaline process

Cannabis sp. and Euphorbia sp. are potential candidates as indoor culture for the extraction of their high value-added metabolites for pharmaceutical applications. Both residual lignocellulosic materials recovered after extraction are studied in the present article as single or mixed feedstocks for a closed-loop bioprocesses cascade. An alkaline process (NaOH 3%, 30min 160◦C) is performed to separate the studied biomasses into their main components: lignin and cellulose. Results highlight the advantages of the multi-feedstocks approach over the single biomass in term of lignin yield and purity. Since the structural characteristics of lignin affect the potential applications, a particular attention is drawn on the comprehension of lignin structure alteration and the possible interaction between them during single or mixed feedstocks treatment. FTIR and 2D-NMR spectra revealed similar profiles in term of chemical functions and structure rather than novel chemical bonds formation inexistent in the original biomasses. In addition, thermal properties and molecular mass distribution are conserved whether hemp or euphorbia are single treated or in combination. A second treatment was applied to investigate the effect of prolonged treatment on extracted lignins and the possible interactions. Aggregation, resulting in higher molecular mass, is observed whatever the feedstocks combination. However,mixing biomass does not affect chemical structures of the end product. Therefore, our paper suggests the possibility of gathering lignocellulosic residues during alkali process for lignin extraction and valorization, allowing to forecast lignin structure and make assumptions regarding potential valorization pathway.Programme VERDIR - Portefeuille Tropical Plant Factory - Projet BioResid

Biomass-to-hydrogen: A review of main routes production, processes evaluation and techno-economical assessment

Hydrogen is viewed as a sustainable strategic alternative to fossil fuels, especially in the field of road and air transport. Currently, hydrogen production is derived from fossil fuels or is manufactured by splitting water. A novel option, H2-generation from lignocellulosic biomass, based on renawble resources is currently in a pilot-scale demonstration or at a commercial stage. The present study reviews the thermochemical, biological, and electrochemical approaches used for biomass-to-hydrogen. The advantages, limitations, and major improvements of each process are presented. A techno-economic assessment is also established based on the production cost, technology readiness level, and industrial scalability. The objective is to allow industrial producers to visualise the degree of technological maturity of each option, clarify the necessary development efforts before reaching the commercial stage, determine the most relevant and competitive routes, and assess the suitability of biomass as a feedstock for renewable hydrogen production. In the reviewed results, the thermochemical process, particularly gasification, partial oxidation, and steam reforming, presented the best yield for H2 production. Steam gasification is the best compromise because it is suitable for wet and dry biomass, and it does not require an oxidising agent. As for biological conversion, dark fermentation is more worthwhile than photo-fermentation due to its lower energy consumption. Additionally, the electrochemical process is feasible for biomass. The findings of this study indicate that biomass-hydrogen-based processes are promising options that contribute to the H2 production capacity but require improvements to produce larger competitive volumes

Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex

International audienceParAB S , the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS , and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS -anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParB S complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS . In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (≥ 30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional “leaky” boundaries