Proton-Detected Solid-State NMR of the Cell-Free Synthesized α-Helical Transmembrane Protein NS4B from Hepatitis C Virus

Proton-detected 100 kHz magic-angle-spinning (MAS) solid-state NMR is an emerging analysis method for proteins with only hundreds of microgram quantities, and thus allows structural investigation of eukaryotic membrane proteins. This is the case for the cell-free synthesized hepatitis C virus (HCV) nonstructural membrane protein 4B (NS4B). We demonstrate NS4B sample optimization using fast reconstitution schemes that enable lipid-environment screening directly by NMR. 2D spectra and relaxation properties guide the choice of the best sample preparation to record 2D ¹H-detected ¹H,¹⁵N and 3D ¹H,¹³C,¹⁵N correlation experiments with linewidths and sensitivity suitable to initiate sequential assignments. Amino-acid-selectively labeled NS4B can be readily obtained using cell-free synthesis, opening the door to combinatorial labeling approaches which should enable structural studies.     

Polarization control in a vertical cavity surface emitting laser submitted to optical feedback

We study experimentally and theoretically two polarization effects in a vertical cavity surface emitting laser submitted to optical feedback. In a first experiment, we obtain flips between two linearly polarized laser modes up to a frequency of 50 MHz using an external cavity with a polarizer. In a second experiment, polarization self modulation is demonstrated up to a frequency of 2.6 GHz, using a quarter wave plate instead. Numerical calculations, based on a four levels model for the active medium, show a good agreement with the experiments.     

The cholesterol-lowering effect of guar gum is not the result of a simple diversion of bile acids toward fecal excretion

The effects of partially hydrolyzed, nonviscous, guar gum (PHGG) on cholesterol metabolism and digestive balance have been compared with those of native guar gum (GUAR) in rats adapted to 0.4% cholesterol diets. Both types of guar gum elicited acidic fermentations in the large intestine, but only GUAR effectively lowered plasma cholesterol (P<0.001), chiefly in the triglyceride-rich lipoprotein fraction. The biliary bile acid excretion was significantly enhanced in rats fed GUAR (P<0.05), as well as the intestinal and cecal bile acid pool (P<0.001). In rats fed GUAR and to a lesser extent in those fed PHGG, the fecal excretion of bile acids and neutral sterol was higher than in controls (P<0.01). The digestive balance (cholesterol intake-steroid excretion) was positive in control rats (+47 μmol/d), whereas it was negative in rats fed GUAR (−20 μmol/d), which could involve a higher rate of endogenous cholesterol synthesis. In rats fed PHGG, the steroid balance remained slightly positive. Liver 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase activity was very low (22 pmol/min/mg protein), owing to cholesterol supplementation, in control rats or in rats fed PHGG, whereas it was markedly higher (+463%) in rats fed GUAR. In conclusion, even if PHGG does alter some parameters of the enterohepatic cycle of cholesterol and bile acids, its effects are not sufficient to elicit a significant cholesterol-lowering effect. The intestinal (ileal or cecal) reabsorption of bile acids was not reduced, but rather increased, by GUAR; nevertheless the intestinal capacities of reabsorption were overwhelmed by the enlargement of the digestive pool of bile acids. In the present model, induction of HMG-CoA reductase probably takes place in the presence of elevated portal bile acid concentrations.     

The minimum information about failures for solving non-local tasks in message-passing systems

We first define the basic notions of local and non-local tasks for distributed systems. Intuitively, a task is local if, in a system with no failures, each process can compute its output value locally by applying some local function on its own input value (so the output value of each process depends only on the process’ own input value, not on the input values of the other processes); a task is nonlocal otherwise. All the interesting distributed tasks, including all those that have been investigated in the literature (e.g., consensus, set agreement, renaming, atomic commit, etc.) are non-local. In this paper we consider non-local tasks and determine the minimum information about failures that is necessary to solve such tasks in message-passing distributed systems. As part of this work, we also introduces weak set agreement—a natural weakening of set agreement—and show that, in some precise sense, it is the weakest nonlocal task in message-passing systems.     

Dialogue in context, towards a referential approach in collective learning

In this article, we present research in the making of a collective work environment within the framework of a distance education course. We base our theoretical and methodological standpoints on examples of dialogical discourses recorded within the framework of this CSCL system called Symba. In fact, the results of previous research lead us to rethink our vision of the study of collaborative moments between participants in a computer-supported human learning environment that proposes several communication tools. Redefining the methodological process aiming at finding and understanding these rich learning moments is also necessary. We intend to describe “socio-technical” instances during which these collaboration phases appear. More generally speaking, our aim is to draw up both new theoretical and methodological perspectives that would be reusable in CSCL environments; in view of the nature of these two perspectives, and the diversity of the domain knowledge (sociology, cognitivism, linguistics, philosophy, statistics, etc.) brought to bear in the study of the environment in question, our approach constitutes a trans-disciplinary reassessment of the uses of the communication tools—and the study thereof—proposed.

Fusarium graminearum Infection Strategy in Wheat Involves a Highly Conserved Genetic Program That Controls the Expression of a Core Effectome

Fusarium graminearum, the main causal agent of Fusarium Head Blight (FHB), is one of the most damaging pathogens in wheat. Because of the complex organization of wheat resistance to FHB, this pathosystem represents a relevant model to elucidate the molecular mechanisms underlying plant susceptibility and to identify their main drivers, the pathogen’s effectors. Although the F. graminearum catalog of effectors has been well characterized at the genome scale, in planta studies are needed to confirm their effective accumulation in host tissues and to identify their role during the infection process. Taking advantage of the genetic variability from both species, a RNAseq-based profiling of gene expression was performed during an infection time course using an aggressive F. graminearum strain facing five wheat cultivars of contrasting susceptibility as well as using three strains of contrasting aggressiveness infecting a single susceptible host. Genes coding for secreted proteins and exhibiting significant expression changes along infection progress were selected to identify the effector gene candidates. During its interaction with the five wheat cultivars, 476 effector genes were expressed by the aggressive strain, among which 91% were found in all the infected hosts. Considering three different strains infecting a single susceptible host, 761 effector genes were identified, among which 90% were systematically expressed in the three strains. We revealed a robust F. graminearum core effectome of 357 genes expressed in all the hosts and by all the strains that exhibited conserved expression patterns over time. Several wheat compartments were predicted to be targeted by these putative effectors including apoplast, nucleus, chloroplast and mitochondria. Taken together, our results shed light on a highly conserved parasite strategy. They led to the identification of reliable key fungal genes putatively involved in wheat susceptibility to F. graminearum, and provided valuable information about their putative targets.     

Thermal conductivity imaging at micrometre-scale resolution for combinatorial studies of materials

Combinatorial methods offer an efficient approach for the development of new materials. Methods for generating combinatorial samples of materials, and methods for characterizing local composition and structure by electron microprobe analysis and electron-backscatter diffraction are relatively well developed. But a key component for combinatorial studies of materials is high-spatial-resolution measurements of the property of interest, for example, the magnetic, optical, electrical, mechanical or thermal properties of each phase, composition or processing condition. Advances in the experimental methods used for mapping these properties will have a significant impact on materials science and engineering. Here we show how time-domain thermoreflectance can be used to image the thermal conductivity of the cross-section of a Nb-Ti-Cr-Si diffusion multiple, and thereby demonstrate rapid and quantitative measurements of thermal transport properties for combinatorial studies of materials. The lateral spatial resolution of the technique is 3.4 microm, and the time required to measure a 100 x 100 pixel image is approximately 1 h. The thermal conductivity of TiCr(2) decreases by a factor of two in crossing from the near-stoichiometric side of the phase to the Ti-rich side; and the conductivity of (Ti,Nb)(3)Si shows a strong dependence on crystalline orientation.     

On querying simple conceptual graphs with negation

We consider basic conceptual graphs, namely simple conceptual graphs (SGs), which are equivalent to the existential conjunctive positive fragment of first-order logic. The fundamental problem, deduction, is performed by a graph homomorphism called projection. The existence of a projection from a SG Q to a SG G means that the knowledge represented by Q is deducible from the knowledge represented by G. In this framework, a knowledge base is composed of SGs representing facts and a query is itself a SG. We focus on the issue of querying SGs, which highlights another fundamental problem, namely query answering. Each projection from a query to a fact defines an answer to the query, with an answer being itself a SG. The query answering problem asks for all answers to a query.

This paper introduces atomic negation into this framework. Several understandings of negation are explored, which are all of interest in real world applications. In particular, we focus on situations where, in the context of incomplete knowledge, classical negation is not satisfactory because deduction can be proven but there is no answer to the query. We show that intuitionistic deduction captures the notion of an answer and can be solved by projection checking. Algorithms are provided for all studied problems. They are all based on projection. They can thus be combined to deal with several kinds of negation simultaneously. Relationships with problems on conjunctive queries in databases are recalled and extended. Finally, we point out that this discussion can be put in the context of semantic web databases.     

An artificial intelligence-based approach to deal with argumentation applied to food quality in a public health policy

Argumentation is a relatively new research area in Artificial Intelligence. Since the early 1980s, its use has been investigated in various frameworks. We propose a general model for recommendation-based argumentation by extending Dung’s seminal argumentation system. This approach is applied to analyse argumentation on food quality in a public health policy. Cereal products, and more specifically bread, are used by decision makers as a healthy lever to fight against diseases such as obesity or diabetes. Our model outputs new recommendations based on stakeholder’s argumentation by targeting some specific audiences.     

Axial impeller selection for anchorage dependent animal cell culture in stirred bioreactors: Methodology based on the impeller comparison at just-suspended speed of rotation

Animal cells, which are nowadays essential for the industrial production of proteinic compounds, are commonly cultivated inside stirred tank bioreactors. In case of anchorage dependent cells, they are usually fixed on microcarriers. The choice of agitation conditions (impeller type, rotational speed…) in this type of process is not an easy task as it has to fulfil three potentially conflicting goals: (1) maintaining microcarriers in complete suspension, (2) homogenizing the culture medium, and (3) limiting mechanical constraints generated by the hydrodynamics on the cells. The aim of this study is to present an original methodology to select the most appropriate axial impeller for this specific application. Seven propellers are preselected on basis of their characteristics available in the literature. Instead of comparing impellers at a given rotational speed or a given power input, they are compared at their respective minimum impeller rotational speed that leads to a complete microcarrier suspension, i.e. at their respective just-suspended speed N_js. They are then compared at higher rotational speeds N, expressed as multiples of N_js. The impeller classification is based on the intensity of mechanical constraints they produced, evaluated from: (1) the macro-shear rate quantified by the spatial derivative of time average velocity fields measured by P.I.V., (2) the micro-shear rate characterized by the ratio between the microcarrier diameter to the average Kolmogorov scale computed from power input measurements, and (3) the impact of microcarrier collisions on cells described via the turbulent collision severity index also computed from power input measurements. Results show that the 125 mm diameter TTP impeller (Mixel) and the 150 mm diameter Elephant Ear impeller (Applikon) produce the smallest mechanical constraints at their just-suspended speed (50 and 20 rpm, respectively). Moreover, the mechanical constraints they produce increase more slowly with the N/N_js ratio than the mechanical constraints produced by other impellers. These propellers are thus even more advantageous if rotational speeds higher than the just-suspended speed have to be used.