Université PSL

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Metabolic changes in Medaka fish induced by cyanobacterial exposures in mesocosms: an integrative approach combining proteomic and metabolomic analyses OPEN
Laboratoire Spectrométrie de masse biologique et protéomique - Benoît Sotton, Alain Paris, Séverine Le Manach, Alain Blond, Gérard Lacroix, Alexis Millot, Charlotte Duval, Hélène Huet, Qin Qiao, Sophie Labrut, Giovanni Chiappetta, Joelle Vinh, Arnaud Catherine & Benjamin Marie
Scientific Reports - 7 4051 - DOI: 10.1038/s41598-017-04423-z - 2018
Cyanobacterial blooms pose serious threats to aquatic organisms and strongly impact the functioning of aquatic ecosystems. Due to their ability to produce a wide range of potentially bioactive secondary metabolites, so called cyanotoxins, cyanobacteria have been extensively studied in the past decades. Proteomic and metabolomic analyses provide a unique opportunity to evaluate the global response of hundreds of proteins and metabolites at a glance. In this study, we provide the first combined utilization of these methods targeted to identify the response of fish to bloom-forming cyanobacteria. Medaka fish (Oryzias latipes) were exposed for 96 hours either to a MC-producing or to a non-MC-producing strain of Microcystis aeruginosa and cellular, proteome and metabolome changes following exposure to cyanobacteria were characterized in the fish livers. The results suggest that a short-term exposure to cyanobacteria, producing or not MCs, induces sex-dependent molecular changes in medaka fish, without causing any cellular alterations. Globally, molecular entities involved in stress response, lipid metabolism and developmental processes exhibit the most contrasted changes following a cyanobacterial exposure. Moreover, it appears that proteomic and metabolomic analyses are useful tools to verify previous information and to additionally bring new horizons concerning molecular effects of cyanobacteria on fish.
Advances on non-invasive physically triggered nucleic acid delivery from nanocarriers
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Hai Doan Do, Brice Martin Couillaud, Bich-Thuy Doan, Yohann Corvis, Nathalie Mignet
Review - 138 3-17 - DOI: 10.1016/j.addr.2018.10.006 - 2018
Nucleic acids (NAs) have been considered as promising therapeutic agents for various types of diseases. However, their clinical applications still face many limitations due to their charge, high molecular weight, instability in biological environment and low levels of transfection. To overcome these drawbacks, therapeutic NAs should be carried in a stable nanocarrier, which can be viral or non-viral vectors, and released at specific target site. Various controllable gene release strategies are currently being evaluated with interesting results. Endogenous stimuli-responsive systems, for example pH-, redox reaction-, enzymatic-triggered approaches have been widely studied based on the physiological differences between pathological and normal tissues. Meanwhile, exogenous triggered release strategies require the use of externally non-invasive physical triggering signals such as light, heat, magnetic field and ultrasound. Compared to internal triggered strategies, external triggered gene release is time and site specifically controllable through active management of outside stimuli. The signal induces changes in the stability of the delivery system or some specific reactions which lead to endosomal escape and/or gene release. In the present review, the mechanisms and examples of exogenous triggered gene release approaches are detailed. Challenges and perspectives of such gene delivery systems are also discussed.
Clickable-Zwitterionic Copolymer Capped-Quantum Dots for in Vivo Fluorescence Tumor Imaging
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Laura Trapiella-Alfonso, Thomas Pons , Nicolas Lequeux , Ludovic Leleu, Juliette Grimaldi, Mariana Tasso, Edward Oujagir, Johanne Seguin, Fanny d'Orlyé, Christian Girard, Bich-Thuy Doan,
ACS Appl. Mater. Interfaces - 10-20 17107–17116 - doi.org/10.1021/acsami.8b04708 - 2018
In the last decades, fluorescent quantum dots (QDs) have appeared as high-performance biological fluorescent nanoprobes and have been explored for a variety of biomedical optical imaging applications. However, many central challenges still exist concerning the control of the surface chemistry to ensure high biocompatibility, low toxicity, antifouling, and specific active targeting properties. Regarding in vivo applications, circulation time and clearance of the nanoprobe are also key parameters to control the design and characterization of new optical imaging agents. Herein, the complete design and characterization of a peptide-near-infrared-QD-based nanoprobe for biomedical optical imaging is presented from the synthesis of the QDs and the zwitterionic-azide copolymer ligand, enabling a bio-orthogonal coupling, till the final in vivo test through all the characterization steps. The developed nanoprobes show high fluorescence emission, controlled grafting rate, low toxicity, in vitro active specific targeting, and in vivo long circulating blood time. This is, to our knowledge, the first report characterizing the in vivo circulation kinetics and tumor accumulation of targeted zwitterionic QDs.
The enzyme-like catalytic activity of cerium oxide nanoparticles and its dependency on Ce3+ surface area concentration
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - V. Baldim, F. Bedioui, N. Mignet, I. Margaillc and J.-F. Berret
ACS Appl. Mater. Interfaces - 10 6971-6980 - doi.org/10.1039/C8NR00325D - 2018
Cerium oxide nanoparticles are known to catalyze the decomposition of reactive oxygen species such as the superoxide radical and hydrogen peroxide. Herein, we examine the superoxide dismutase (SOD) and catalase (CAT) mimetic catalytic activities of nanoceria and demonstrate the existence of generic behaviors. For particles of sizes 4.5, 7.8, 23 and 28 nm, the SOD and CAT catalytic activities exhibit the characteristic shape of a Langmuir isotherm as a function of cerium concentration. The results show that the catalytic effects are enhanced for smaller particles and for the particles with the largest Ce3+ fraction. The SOD-like activity obtained from the different samples is found to superimpose on a single master curve using the Ce3+ surface area concentration as a new variable, indicating the existence of particle independent redox mechanisms. For the CAT assays, the adsorption of H2O2 molecules at the particle surface modulates the efficacy of the decomposition process and must be taken into account. We design an amperometry-based experiment to evaluate the H2O2 adsorption at nanoceria surfaces, leading to the renormalization of the particle specific area. Depending on the particle type the amount of adsorbed H2O2 molecules varies from 2 to 20 nm−2. The proposed scalings are predictive and allow the determination of the SOD and CAT catalytic properties of cerium oxide solely from physicochemical features.
The enzyme-like catalytic activity of cerium oxide nanoparticles and its dependency on Ce3+ surface area concentration
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Oliveira R, Sella C, Souprayen C, Ait-Yahiatene E, Slim C, Griveau S, Thouin L, Bedioui F
Electrochimica Acta - 286 365-373 - DOI10.1016/j.electacta.2018.07.158 - 2018
The detection of reactive oxygen and nitrogen species is of utmost importance in several pathological situations. Indeed, these reactive species are biomarkers of oxidative stress and their real-time monitoring is crucial to adapt medical treatments. We report here on the electrochemical detection of nitric oxide (NO center dot) in the presence of hydrogen peroxide (H2O2). The detection was performed by using different sensing microdevices involving either static solutions in wells or flowing solutions in microfluidic channels. Furthermore, an original strategy was proposed to further enhance the selectivity of NO center dot detection at Pt/poly(eugenol) modified platinum electrodes by designing a dual-electrode microfluidic device based on a pre-electrolysis of interfering species including H2O2 at an upstream electrode prior to NO center dot detection. (C) 2018 Elsevier Ltd. All rights reserved.
Electrochemical Behavior of Stainless Steels for Sudomotor Dysfunction Applications
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Fethi Bedioui Abdulghani Ismail Sophie Griveau
ELSEVIER - 12 42-50 - DOI : 10.1016/j.coelec.2018.04.014 - 2018
Electrochemical detection of nitric oxide using different electrode materials and strategies exploded after the discovery of nitric oxide as important biological messenger. S-nitrosothiols (RSNOs), which result from interaction of NO with peptides and proteins, were shown to be important pools of NO that interfere in different physiological and pathological conditions. This lead to development of several decomposition methods to detect RSNOs electrochemically. This mini-review summarizes the beginning and the current investigations in electrochemical methods to detect NO and RSNOs. Indeed, it describes the latest trends to detect NO and RSNO using microfluidic technologies coupled to electrochemistry and discuss the future of NO and RSNOs detection.
Integrated microfluidic device for the separation, decomposition and detection of low molecular weight S-nitrosothiols
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Gerson F Duarte-Junior, Abdulghani Ismail, Sophie Griveau, Fanny d'Orlyé , José Alberto Fracassi da Silva, Wendell K T Coltro, Fethi Bedioui , Anne Varenne
Analyst - 144(1) 180-185 - doi: 10.1039/c8an00757h - 2018
S-nitrosothiols (RSNOs) are very important biomolecules that play crucial roles in many physiological and physiopathological processes. They act as NO-donors and are candidates for future medicines. Their identification and quantitation are therefore important for biomedical applications. One, two or more RSNOs can then be combined to design a drug and therefore, the quantification of each is important to establish an acceptable quality control process. Till date, miniaturized devices have been used to detect RSNOs based on their total quantitation without a preceding separation step. This study reports on an original and integrated microdevice allowing for the successive electrokinetic separation of low molecular weight RSNOs, their decomposition under metal catalysis, and their quantitation by amperometric detection of the produced nitrite in the end-channel arrangement, leading to their quantitation in a single run. For this purpose, a commercial SU-8/Pyrex microfluidic system was coupled to a portable and wireless potentiostat. Different operating and running parameters were optimized to achieve the best analytical data, allowing for an LOD equal to 20 μM. The simultaneous separation of S-nitrosoglutathione and S-nitrosocysteine was successfully obtained within 75 s. The proposed methodology using SU-8/Pyrex microfluidic devices opens new possibilities to investigate future drug candidates for NO-donors.
In vitro distinction between proinflammatory and antiinflammatory macrophages with gadolinium-liposomes and ultrasmall superparamagnetic iron oxide particles at 3.0T
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Wassef Khaled, Joao Piraquive , Benjamin Leporq , Jing Hong Wan , Simon A Lambert 1, Nathalie Mignet , Bich-Thuy Doan , Sophie Lotersztajn , Philippe Garteiser , Bernard E Van Beers
J Magn Reson Imaging - 49(4) 1166-1173 - doi: 10.1002/jmri.26331 - 2018
Background: Inflammation involves a heterogeneous macrophage population, for which there is no readily available MR assessment method.

Purpose: To assess the feasibility of distinguishing proinflammatory M1 and antiinflammatory M2 macrophages at MRI enhanced with gadolinium liposomes or ultrasmall superparamagnetic iron oxide particles.

Study type: In vitro.

Specimen: We employed cultured RAW macrophages. M0 macrophages were polarized with lipopolysaccharide (LPS) or interleukin-4 (IL-4), resulting in M1 or M2 macrophages. The macrophages were incubated with gadolinium (±rhodamine) liposomes or iron oxide particles and cell pellets were prepared for MRI.

Field strength/sequence: Transverse relaxation rates and quantitative susceptibility were obtained at 3.0T with multiecho turbo spin echo and spoiled gradient echo sequences.

Assessment: MRI results were compared with confocal microscopy, flow cytometry, and expression of endocytosis, M1 and M2 genes.

Statistical tests: Mann-Whitney and Kruskal-Wallis tests were performed.

Results: Higher transverse relaxation rates and susceptibility were observed in M1 than in M2 and M0 macrophages (P < 0.01 both with liposomes and USPIO) and significantly different susceptibility in M2 and M0 macrophages (P < 0.01 both with liposomes and USPIO). These MRI results were confirmed at confocal microscopy and flow cytometry. LPS macrophages displayed M1 gene expression, whereas IL-4 macrophages showed M2 polarization and lower endocytosis gene expression rates.

Data conclusion: These in vitro results show that it is feasible to distinguish between proinflammatory M1 and antiinflammatory M2 macrophages according to their level of contrast agent uptake at MRI.

Level of evidence: 1 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;49:1166-1173.

Keywords: gadolinium liposomes; macrophage imaging; macrophage phagocytosis; magnetic resonance imaging of inflammation; quantitative susceptibility mapping; ultrasmall iron oxide particles.
In Vivo Evaluation of Magnetic Targeting in Mice Colon Tumors with Ultra-Magnetic Liposomes Monitored by MRI
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Thébault C, Ramniceanu G, Michel A, Beauvineau C, Girard C, Seguin J, Mignet N, Ménager C, Doan BT
Molecular Imaging and Biology - 21(2) 269-278 - DOI: 10.1007/s11307-018-1238-3 - 2018
PURPOSE:The development of theranostic nanocarriers as an innovative therapy against cancer has been improved by targeting properties in order to optimize the drug delivery to safely achieve its desired therapeutic effect. The aim of this paper is to evaluate the magnetic targeting (MT) efficiency of ultra-magnetic liposomes (UML) into CT26 murine colon tumor by magnetic resonance imaging (MRI). PROCEDURES:Dynamic susceptibility contrast MRI was applied to assess the bloodstream circulation time. A novel semi-quantitative method called %I0.25, based on the intensity distribution in T2*-weighted MRI images was developed to compare the accumulation of T2 contrast agent in tumors with or without MT. To evaluate the efficiency of magnetic targeting, the percentage of pixels under the intensity value I0.25 (I0.25 = 0.25(Imax - Imin)) was calculated on the intensity distribution histogram. RESULTS:This innovative method of processing MRI images showed the MT efficiency by a %I0.25 that was significantly higher in tumors using MT compared to passive accumulation, from 15.3 to 28.6 %. This methodology was validated by ex vivo methods with an iron concentration that is 3-fold higher in tumors using MT. CONCLUSIONS:We have developed a method that allows a semi-quantitative evaluation of targeting efficiency in tumors, which could be applied to different T2 contrast agents.
Electrochemical behavior of electrode materials (nickel and stainless steels) for sudomotor dysfunction applications : a review
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Fethi Bedioui Virginie Lair Sophie Griveau Armelle Ringuedé José Zagal Michel Cassir
Chimie analytique - - DOI : 10.1002/elan.201800439 - 2018
This is an overview of the electrochemical characterization of nickel and stainless steel as electrodes in medical devices for the early diagnosis of small fiber neuropathy that originates from type-2 diabetes or cystic fibrosis. The electrical current responses obtained during the clinical tests are related to the amount of chloride present on the sweat. Stainless steel electrodes are now used to replace nickel because this later not only presents problems with chloride sensitivity but its contact with skin can cause possible allergic reactions for some patients. For the above reasons, several types of stainless steels were studied. It was shown that some of them perform well and have lower costs than Ni electrodes. We discuss the state of the art of the electrochemical studies conducted with nickel and steels under physiological or biomimetic conditions and discuss the advantages of a particular steel over the others depending on the conditions, especially chloride concentration.
AGuIX ® from bench to bedside-Transfer of an ultrasmall theranostic gadolinium-based nanoparticle to clinical medicine
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - François Lux, Vu Long Tran, Eloïse Thomas, Sandrine Dufort , Fabien Rossetti , Matteo Martini, Charles Truillet, Tristan Doussineau, Guillaume Bort, Franck Denat, Frédéric Boschetti, Goran Angelovski, Alexandre Detappe, Yannic
Br J Radiol - 92(1093) 20180365 - doi: 10.1259/bjr.20180365 - 2018
AGuIX® are sub-5 nm nanoparticles made of a polysiloxane matrix and gadolinium chelates. This nanoparticle has been recently accepted in clinical trials in association with radiotherapy. This review will summarize the principal preclinical results that have led to first in man administration. No evidence of toxicity has been observed during regulatory toxicity tests on two animal species (rodents and monkeys). Biodistributions on different animal models have shown passive uptake in tumours due to enhanced permeability and retention effect combined with renal elimination of the nanoparticles after intravenous administration. High radiosensitizing effect has been observed with different types of irradiations in vitro and in vivo on a large number of cancer types (brain, lung, melanoma, head and neck…). The review concludes with the second generation of AGuIX nanoparticles and the first preliminary results on human.
Information-theoretic analysis of the directional influence between cellular processes
Laboratoire Biochimie - Sourabh Lahiri, Philippe Nghe, Sander J. Tans, Martin Luc Rosinberg, David Lacoste
- 12(11) - https://doi.org/10.1371/journal.pone.0187431 - 2017
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback. We re-analyze the experimental data from Kiviet et al. (2014) where fluctuations in gene expression of metabolic enzymes and growth rate have been measured in single cells of E. coli. We confirm the formerly detected modes between growth and gene expression, while prescribing more stringent conditions on the structure of noise sources. We furthermore point out practical requirements in terms of length of time series and sampling time which must be satisfied in order to infer optimally transfer entropy from times series of fluctuations.
Single-cell deep phenotyping of IgG-secreting cells for high-resolution immune monitoring
Laboratoire Biochimie - Eyer K, Doineau RCL, Castrillon CE, Briseño-Roa L, Menrath V, Mottet G, England P, Godina A, Brient-Litzler E, Nizak C, Jensen A, Griffiths AD, Bibette J, Bruhns P4, Baudry J.
Nat Biotechnol. - 35(10) 977-982 - doi: 10.1038/nbt.3964 - 2017
Studies of the dynamics of the antibody-mediated immune response have been hampered by the absence of quantitative, high-throughput systems to analyze individual antibody-secreting cells. Here we describe a simple microfluidic system, DropMap, in which single cells are compartmentalized in tens of thousands of 40-pL droplets and analyzed in two-dimensional droplet arrays using a fluorescence relocation-based immunoassay. Using DropMap, we characterized antibody-secreting cells in mice immunized with tetanus toxoid (TT) over a 7-week protocol, simultaneously analyzing the secretion rate and affinity of IgG from over 0.5 million individual cells enriched from spleen and bone marrow. Immunization resulted in dramatic increases in the range of both single-cell secretion rates and affinities, which spanned at maximum 3 and 4 logs, respectively. We observed differences over time in dynamics of secretion rate and affinity within and between anatomical compartments. This system will not only enable immune monitoring and optimization of immunization and vaccination protocols but also potentiate antibody screening.
Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase.
Laboratoire Biochimie - Obexer R, Godina A, Garrabou X, Mittl PR, Baker D, Griffiths AD, Hilvert D.
Nat Chem. - 9(1) 50-56 - doi: 10.1038/nchem.2596 - 2017
Designing catalysts that achieve the rates and selectivities of natural enzymes is a long-standing goal in protein chemistry. Here, we show that an ultrahigh-throughput droplet-based microfluidic screening platform can be used to improve a previously optimized artificial aldolase by an additional factor of 30 to give a >109 rate enhancement that rivals the efficiency of class I aldolases. The resulting enzyme catalyses a reversible aldol reaction with high stereoselectivity and tolerates a broad range of substrates. Biochemical and structural studies show that catalysis depends on a Lys-Tyr-Asn-Tyr tetrad that emerged adjacent to a computationally designed hydrophobic pocket during directed evolution. This constellation of residues is poised to activate the substrate by Schiff base formation, promote mechanistically important proton transfers and stabilize multiple transition states along a complex reaction coordinate. The emergence of such a sophisticated catalytic centre shows that there is nothing magical about the catalytic activities or mechanisms of naturally occurring enzymes, or the evolutionary process that gave rise to them.
Topological and thermodynamic factors that influence the evolution of small networks of catalytic RNA species.
Laboratoire Biochimie - Yeates JAM, Nghe P, Lehman N.
RNA. - 23(7) 1088-1096 - doi: 10.1261/rna.061093.117 - 2017
An RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks could have been an important feature of the RNA world during the nascent evolution of life on the Earth. However, the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self-assemble via genotype-selfish and genotype-cooperative interactions into full-length ribozymes to investigate the dynamics of small (three- and four-membered) networks. We focused on the influence of a three-membered core network on the incorporation of additional nodes, and on the degree and direction of connectivity as single new nodes are added to this core. We confirmed experimentally the predictions that additional links to a core should enhance overall network growth rates, but that the directionality of the link (a "giver" or a "receiver") impacts the growth of the core itself. Additionally, we used a simple mathematical model based on the first-order effects of lower-level interactions to predict the growth of more complex networks, and find that such a model can, to a first approximation, predict the ordinal rankings of nodes once a steady-state distribution has been reached.
Synthesis of new hydrophilic rhodamine based enzymatic substrates compatible with droplet-based microfluidic assays
Laboratoire Biochimie - Johan Fenneteau, Dany Chauvin,b Andrew D. Griffiths,b Clément Nizak,b and Janine Cossy
Chem. Comm. - 53 5437-5440 - DOI: 10.1039/C7CC01506B - 2017
Here we report the conception, synthesis and evaluation of new hydrophilic rhodamine-based enzymatic substrates for detection of peptidase activity compatible with high-throughput screening using droplet-based microfluidics.
Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica
Laboratoire Biochimie - Beneyton T, Thomas S, Griffiths AD, Nicaud JM, Drevelle A, Rossignol T.
Microb Cell Fact. - 16(1) 18 - doi: 10.1186/s12934-017-0629-5. - 2017
BACKGROUND:
Droplet-based microfluidics is becoming an increasingly attractive alternative to microtiter plate techniques for enzymatic high-throughput screening (HTS), especially for exploring large diversities with lower time and cost footprint. In this case, the assayed enzyme has to be accessible to the substrate within the water-in-oil droplet by being ideally extracellular or displayed at the cell surface. However, most of the enzymes screened to date are expressed within the cytoplasm of Escherichia coli cells, which means that a lysis step must take place inside the droplets for enzyme activity to be assayed. Here, we take advantage of the excellent secretion abilities of the yeast Yarrowia lipolytica to describe a highly efficient expression system particularly suitable for the droplet-based microfluidic HTS.
RESULTS:
Five hydrolytic genes from Aspergillus niger genome were chosen and the corresponding five Yarrowia lipolytica producing strains were constructed. Each enzyme (endo-β-1,4-xylanase B and C; 1,4-β-cellobiohydrolase A; endoglucanase A; aspartic protease) was successfully overexpressed and secreted in an active form in the crude supernatant. A droplet-based microfluidic HTS system was developed to (a) encapsulate single yeast cells; (b) grow yeast in droplets; (c) inject the relevant enzymatic substrate; (d) incubate droplets on chip; (e) detect enzymatic activity; and (f) sort droplets based on enzymatic activity. Combining this integrated microfluidic platform with gene expression in Y. lipolytica results in remarkably low variability in the enzymatic activity at the single cell level within a given monoclonal population (<5%). Xylanase, cellobiohydrolase and protease activities were successfully assayed using this system. We then used the system to screen for thermostable variants of endo-β-1,4-xylanase C in error-prone PCR libraries. Variants displaying higher thermostable xylanase activities compared to the wild-type were isolated (up to 4.7-fold improvement).
CONCLUSIONS:
Yarrowia lipolytica was used to express fungal genes encoding hydrolytic enzymes of interest. We developed a successful droplet-based microfluidic platform for the high-throughput screening (105 strains/h) of Y. lipolytica based on enzyme secretion and activity. This approach provides highly efficient tools for the HTS of recombinant enzymatic activities. This should be extremely useful for discovering new biocatalysts via directed evolution or protein engineering approaches and should lead to major advances in microbial cell factory development.
Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments.
Laboratoire Biochimie - Huguet JM1,2, Ribezzi-Crivellari M3, Bizarro CV4, Ritort F1,5.
Nucleic Acids Res. - 120 158101 - doi: 10.1093/nar/gkx1161. - 2017
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.
Information-theoretic analysis of the directional influence between cellular processes
Laboratoire Biochimie - Sourabh Lahiri, Philippe Nghe, Sander J. Tans, Martin Luc Rosinberg, David Lacoste
Nucleic Acids Res. - - doi.org/10.1371/journal.pone.0187431 - 2017
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback. We re-analyze the experimental data from Kiviet et al. (2014) where fluctuations in gene expression of metabolic enzymes and growth rate have been measured in single cells of E. coli. We confirm the formerly detected modes between growth and gene expression, while prescribing more stringent conditions on the structure of noise sources. We furthermore point out practical requirements in terms of length of time series and sampling time which must be satisfied in order to infer optimally transfer entropy from times series of fluctuations
Evolutionary Applications
Laboratoire Biochimie - Calcagno, V., Mitoyen, C., Audiot, P., Ponsard, S., Gao, G.-Z., Lu, Z.-Z., Wang, Z.-Y., He, K.-L., and Bourguet, D. Parallel
Semin Cell Dev Biol. - 10 9 - DOI: 10.1111/eva.12481 - 2017
Maize was introduced into opposite sides of Eurasia 500 years ago, in Western Europe and in Asia. This caused two host-shifts in the phytophagous genus Ostrinia; O. nubilalis (the European corn borer; ECB) and O. furnacalis (the Asian corn borer; ACB) are now major pests of maize worldwide. They originated independently from Dicot-feeding ancestors, similar to O. scapulalis(the Adzuki bean borer; ABB). Unlike other host-plants, maize is yearly harvested, and harvesting practices impose severe mortality on larvae found above the cut-off line. Positive geotaxis in the ECB has been proposed as a behavioural adaptation to harvesting practices, allowing larvae to move below the cut-off line and thus escape harvest mortality. Here, we test whether the same behavioural adaptation evolved independently in Europe and in Asia. We sampled eight genetically differentiated ECB, ACB and ABB populations in France and China and monitored geotaxis through the entire larval development in artificial stacks mimicking maize stems. We find that all ECB and ACB populations show a similar tendency to move down during the latest larval stages, a behaviour not observed in any European or Asian ABB population. The behaviour is robustly expressed regardless of larval density, development mode or environmental conditions. Our results indicate that maize introduction triggered parallel behavioural adaptations in Europe and Asia, harvest selection presumably being the main driver.

515 publications.