Olivier Bernard

High-throughput sequence analysis of the tyrosine kinome in acute myeloid leukemia

To determine whether aberrantly activated tyrosine kinases other than FLT3 and c-KIT contribute to acute myeloid leukemia (AML) pathogenesis, we used high-throughput (HT) DNA sequence ana-lysis to screen exons encoding the activation loop and juxtamembrane domains of 85 tyrosine kinase genes in 188 AML patients without FLT3 or c-KIT mutations. The screen identified 30 nonsynonymous sequence variations in 22 different kinases not previously reported in single-nucleotide polymorphism (SNP) databases. These included a novel FLT3 activating allele and a previously described activating mutation in MET (METT1010I). The majority of novel sequence variants were stably expressed in factor-dependent Ba/F3 cells. Apart from one FLT3 allele, none of the novel variants showed constitutive phosphorylation by immunoblot analysis and none transformed Ba/F3 cells to factor-independent growth. These findings indicate the majority of these alleles are not potent tyrosine kinase activators in this cellular context and that a significant proportion of nonsynonymous sequence variants identified in HT DNA sequencing screens may not have functional significance. Although some sequence variants may represent SNPs, these data are consistent with recent reports that a significant fraction of such sequence variants are passenger rather than driver alleles and underscore the importance of functional assessment of candidate disease alleles.

The effects of a controlled fluctuating nutrient environment on continuous cultures of phytoplankton monitored by computers

Abstract A completely automatic continuous phytoplankton culturing device is described. This computer-controlled system monitors simultaneously and automatically the basic culture parameters of several chemostats, i.e., limiting nutrient concentrations, cell size spectra, cell densities and temperatures. Culture pH can also be regulated. The dilution rate and the limiting nutrient concentration in the enrichment medium may be programmed to follow different dynamic patterns with time. An example is given with a sinusoidal variation of the dilution rate. Applications are discussed, which concern the advantages to modelling gained by acquiring information from continuously fluctuating systems rather than from nutrient-pulsed systems.

Models for electrokinetic phenomena in montmorillonite

Abstract Clays present remarkable electrokinetic features since they exist from very dilute colloidal state to nanoporous materials, depending on the water/clay ratio. The case of low volume fraction Vwater/Vtot which corresponds to compact systems is examined. The ionic distributions have been evaluated by Poisson–Boltzmann like models and compared to discrete solvent simulations. Several electrokinetic properties (electroosmosis and conductance) have been calculated, in the framework of the mean spherical approximation introduced in the Fuoss–Onsager transport theory. It is found that Onsagers limiting laws in terms of external concentration are not valid on the grounds of the Donnan effect.

Modelling of Microalgae Culture Systems with Applications to Control and Optimization

Mathematical modeling is becoming ever more important to assess the potential, guide the design, and enable the efficient operation and control of industrial-scale microalgae culture systems (MCS). The development of overall, inherently multiphysics, models involves coupling separate submodels of (i) the intrinsic biological properties, including growth, decay, and biosynthesis as well as the effect of light and temperature on these processes, and (ii) the physical properties, such as the hydrodynamics, light attenuation, and temperature in the culture medium. When considering high-density microalgae culture, in particular, the coupling between biology and physics becomes critical. This chapter reviews existing models, with a particular focus on the Droop model, which is a precursor model, and it highlights the structure common to many microalgae growth models. It summarizes the main developments and difficulties towards multiphysics models of MCS as well as applications of these models for monitoring, control, and optimization purposes.

Liver nodules after portal systemic shunt surgery for extrahepatic portal vein obstruction in children

BACKGROUNDnLiver nodules have been reported after portal systemic shunt surgery (PSSS) in animal experiments or in humans with liver cirrhosis. The aim of our study was to assess the incidence of liver nodules after surgery for extrahepatic portal vein obstruction (EHPVO) in children without associated liver disease.nnnMETHODSnWe retrospectively reviewed the charts of 45 children who had surgery from 1979 to 2005 for EHPVO in our institution, consisting of 38 PSSS and 7 portal reperfusion procedures (PRPs). We assessed the presence of liver nodules on ultrasonography.nnnRESULTSnOf 45 patients, 7 (15%) had liver nodules during a median of 80 months of follow-up. All the nodules occurred after PSSS. Five nodules were subjected to biopsy; we found 2 liver cell adenomas and 3 focal nodular hyperplasias.nnnCONCLUSIONSnIn this study, liver nodules occurred in 18% of cases after PSSS for EHPVO in children and not after PRP. As many children have undergone PSSS throughout the world, the presence of liver nodules should be considered during the follow-up of those patients.

Hereditary fructose intolerance: Frequency and spectrum mutations of the aldolase B gene in a large patients cohort from France—Identification of eight new mutations

We investigated the molecular basis of hereditary fructose intolerance (HFI) in 160 patients from 92 families by means of a PCR-based mutation screening strategy, consisting of restriction enzyme digestion and direct sequencing. Sixteen different mutations of the aldolase B (ALDOB) gene were identified in HFI patients. As in previous studies, p.A150P (64%), p.A175D (16%) and p.N335K (5%) were the most common mutated alleles, followed by p.R60X, p.A338V, c.360_363delCAAA (p.N120KfsX30), c.324G>A (p.K108K) and c.625-1G>A. Eight novel mutations were also identified in 10 families with HFI: a one-base deletion (c.146delT (p.V49GfsX27)), a small deletion (c.953del42bp), a small insertion (c.689ins TGCTAA (p.K230MfsX136)), one splice site mutation (c.112+1G>A), one nonsense mutation (c.444G>A (p.W148X)), and three missense mutations (c.170G>C (p.R57P), c.839C>A (p.A280P) and c.932T>C (p.L311P)). Our strategy allows to diagnose 75% of HFI patients using restriction enzymatic analysis and to enlarge the diagnosis to 97% of HFI patients when associated with direct sequencing.

Long‐term adaptive response to high‐frequency light signals in the unicellular photosynthetic eukaryote Dunaliella salina

Productivity of microalgal cultivation processes is tightly related to photosynthetic efficiency, and therefore to light availability at the cell scale. In an agitated, highly turbid suspension,the light signal received by a single phytoplankton cell moving in a dense culture is a succession of flashes. The growth characteristics of microalgae under such dynamic light conditions are thus fundamental information to understand nonlinear properties of the photosynthetic process and to improve cultivation process design and operation. Studies of the long term consequences of dynamic illumination regime on photosynthesis require a very specific experimental set‐up where fast varying signals are applied on the long term. In order to investigate the growth response of the unicellular photosynthetic eukaryote Dunaliella salina (Chlorophyceae) to intermittent light exposure, different light regimes using LEDs with the same average total light dose were applied in continuous cultures. Flashing light with different durations of light flashes (△t of 30u2009s, 15u2009s, 2u2009s and 0.1u2009s) followed by dark periods of variable length (0.67u2009≤u2009L:Du2009≤u20092) yielding flash frequencies in the range 0.017–5u2009Hz, were compared to continuous illumination. Specific growth rate, photosynthetic pigments, lipid productivity and elemental composition were measured on two duplicates for each irradiance condition. The different treatments of intermittent light led to specific growth rates ranging from 0.25 to 0.93 day−1. While photosynthetic efficiency was enhanced with increased flash frequency, no significant differences were observed in the particular carbon and chlorophyll content. Pigment analysis showed that within this range of flash frequency, cells progressively photoacclimated to the average light intensity. Biotechnol. Bioeng. 2015;112: 1111–1121.

Phytoplankton plasticity drives large variability in carbon fixation efficiency

Phytoplankton C:N stoichiometry is highly flexible due to physiological plasticity, which could lead to high variations in carbon fixation efficiency (carbon consumption relatively to nitrogen). However, the magnitude, as well as the spatial and temporal scales of variability, remain poorly constrained. We used a high resolution biogeochemical model resolving various scales from small to high, spatially and temporally, in order to quantify and better understand this variability. We find that phytoplankton C:N ratio is highly variable at all spatial and temporal scales (5-12 molC/molN), from meso- to regional scale, and is mainly driven by nitrogen supply. Carbon fixation efficiency varies accordingly at all scales (± 30%), with higher values under oligotrophic conditions and lower values under eutrophic conditions. Hence phytoplankton plasticity may act as a buffer by attenuating carbon sequestration variability. Our results have implications for in situ estimations of C:N ratios and for future predictions under high CO 2 world.

Dynamic coupling of photoacclimation and photoinhibition in a model of microalgae growth.

The development of mathematical models that can predict photosynthetic productivity of microalgae under transient conditions is crucial for enhancing large-scale industrial culturing systems. Particularly important in outdoor culture systems, where the light irradiance varies greatly, are the processes of photoinhibition and photoacclimation, which can affect photoproduction significantly. The former is caused by an excess of light and occurs on a fast time scale of minutes, whereas the latter results from the adjustment of the light harvesting capacity to the incoming irradiance and takes place on a slow time scale of days. In this paper, we develop a dynamic model of microalgae growth that simultaneously accounts for the processes of photoinhibition and photoacclimation, thereby spanning multiple time scales. The properties of the model are analyzed in connection to PI-response curves, under a quasi steady-state assumption for the slow processes and by neglecting the fast dynamics. For validation purposes, the model is calibrated and compared against multiple experimental data sets from the literature for several species. The results show that the model can describe the difference in photosynthetic unit acclimation strategies between Dunaliella tertiolecta (n-strategy) and Skeletonema costatum (s-strategy).

Mesenchymal stem cells protect from hypoxia-induced alveolar epithelial-mesenchymal transition.

Administration of bone marrow-derived human mesenchymal stem cells (hMSC) reduces lung inflammation, fibrosis, and mortality in animal models of lung injury, by a mechanism not completely understood. We investigated whether hMSC would prevent epithelial-mesenchymal transition (EMT) induced by hypoxia in primary rat alveolar epithelial cell (AEC). In AEC cultured on semipermeable filters, prolonged hypoxic exposure (1.5% O2 for up to 12 days) induced phenotypic changes consistent with EMT, i.e., a change in cell morphology, a decrease in transepithelial resistance (Rte) and in the expression of epithelial markers [zonula occludens-1 (ZO-1), E-cadherin, AQP-5, TTF-1], together with an increase in mesenchymal markers [vimentin, α-smooth muscle actin (α-SMA)]. Expression of transcription factors driving EMT such as SNAIL1, ZEB1, and TWIST1 increased after 2, 24, and 48 h of hypoxia, respectively. Hypoxia also induced TGF-β1 mRNA expression and the secretion of active TGF-β1 in apical medium, and the expression of connective tissue growth factor (CTGF), two inducers of EMT. Coculture of AEC with hMSC partially prevented the decrease in Rte and in ZO-1, E-cadherin, and TTF-1 expression, and the increase in vimentin expression induced by hypoxia. It also abolished the increase in TGF-β1 expression and in TGF-β1-induced genes ZEB1, TWIST1, and CTGF. Finally, incubation with human recombinant KGF at a concentration similar to what was measured in hMSC-conditioned media restored the expression of TTF-1 and prevented the increase in TWIST1, TGF-β1, and CTGF in hypoxic AEC. Our results indicate that hMSC prevent hypoxia-induced alveolar EMT through the paracrine modulation of EMT signaling pathways and suggest that this effect is partly mediated by KGF.