Secondary structure prediction: combination of three different methods

A combination of three complementary secondary structure predictionmethods is presented. The methods used are the GOR III method,the Homologue method and a new method, the bit pattern method,which is based on hydrophilic/hydrophobic residue patterns.For this purpose a hydropathy scale was developed and is presentedhere. The combination algorithm (Combine method) was designedto take the best results of each method and use their differencesin order to improve the prediction. The combination yields 65.5%correctly predicted residues in three states: -helix (H), ß-strand(E) and aperiodic structure (C) which is an improvement rangingfrom 2.5 to 6.5% compared with the individual methods when testedwith a 67-polypeptide chain database. Seventy-five per centof the regular secondary structure (H and E) runs are correctlylocated and ß-sheet runs are much better located bythe Combine method in comparison to the other methods.     

Comparative genomics uncovers large tandem chromosomal duplications in Mycobacterium bovis BCG Pasteur

On direct comparison of minimal sets of ordered clones from bacterial artificial chromosome (BAC) libraries representing the complete genomes of Mycobacterium tuberculosis H37Rv and the vaccine strain, Mycobacterium bovis BCG Pasteur, two major rearrangements were identified in the genome of M. bovis BCG Pasteur. These were shown to correspond to two tandem duplications, DU1 and DU2, of 29 668 bp and 36 161 bp, respectively. While DU1 resulted from a single duplication event, DU2 apparently arose from duplication of a 100 kb genomic segment that subsequently incurred an internal deletion of 64 kb. Several lines of evidence suggest that DU2 may continue to expand, since two copies were detected in a subpopulation of BCG Pasteur cells. BCG strains harbouring DU1 and DU2 are diploid for at least 58 genes and contain two copies of oriC, the chromosomal origin of replication. These findings indicate that these genomic regions of the BCG genome are still dynamic. Although the role of DU1 and DU2 in the attenuation and/or altered immunogenicity of BCG is yet unknown, knowledge of their existence will facilitate quality control of BCG vaccine lots and may help in monitoring the efficacy of the world's most widely used vaccine.     

Rayleigh-Mie Doppler wind lidar for atmospheric measurements. II. Mie scattering effect, theory, and calibration

A theoretical and experimental study is conducted for the direct-detection Doppler Lidar developed by the Service d'Aéronomie du Centre National de la Recherche Scientifique. Thanks to a specific design, the double-edge technique that applies primarily to Rayleigh scattering can also be employed in presence of aerosols backscatter. We focus on a careful estimate of the particle-induced error on the wind measurements. With a theoretical model for the Fabry-Perot interferometer and two sets of calibration measurements, the true spectral properties of the interferometer and the calibration curves are recovered. Furthermore, the particle-induced error is estimated for varying values of the scattering ratio at 532 nm. When applied to real atmospheric signals, this error is shown to be negligible. A comparison between ancillary data and the wind and backscatter ratio as retrieved from the Doppler lidar signals confirms our estimate.     

Synthetic peptides for chymosin and pepsin assays: pH effect and pepsin independent-determination in mixtures.

Peptide I [H-Phe-Gly-His-Phe(NO2)-Phe-Ala-Phe-OMe] hydrolyzed by chymosin with kcat=.3+/-.3 s-1 and KM=7+/-3 mM (pH 4.7) inhibited competitively peptide II [H-Leu-Ser-Phe(NO2)-Nle-Ala-Leu-OMe] hydrolysis by chymosin with KI=.23 +/- .12 mM at pH 4.7. In reference conditions (.4 mM peptide, .01 M acetate buffer pH 4.7), the specific activities of porcine pepsin and chymosin on peptide I were 470 +/- 70 nM S-1 and .8 nM S-1 per mg of enzyme. This difference in specific activity for peptide I allowed development of a chymosin-independent pepsin assay for mixtures of these enzymes. In addition, peptide II with a specific activity of 2400 +/- 300 nM S-1 and 154 +/- 20 nM S-1 per mg of porcine pepsin and chymosin provides an alternative to measurement of milk clotting for measurement of chymosin- and pepsin-like activities in commercial rennets. Hydrolysis products of peptide II by chymosin exhibited one ionized group of apparent pK of 3.5 +/- .2 and a molar absorption coefficient change of 1000 +/- 100 at pH 4.7 and at 310 nm. From measurements of the kinetic constants, kcat and KM, from pH 2.5 to 7 with peptide II, chymosin activity depends on the protonation of one group of apparent pK 5.3 +/- .2 in the free enzyme. Rennet powder proved to be fairly stable after a 17-month storage at 4 C. Within the same period, a crystalline chymosin solution kept at --18 C lost 30 to 50% of its activity.     

Technical note: High-throughput method for antifungal activity screening in a cheese-mimicking model

In this study, we developed a high-throughput antifungal activity screening method using a cheese-mimicking matrix distributed in 24-well plates. This method allowed rapid screening of a large variety of antifungal agent candidates: bacterial fermented ingredients, bacterial isolates, and preservatives. Using the proposed method, we characterized the antifungal activity of 44 lactic acid bacteria (LAB) fermented milk-based ingredients and 23 LAB isolates used as protective cultures against 4 fungal targets (Mucor racemosus, Penicillium commune, Galactomyces geotrichum, and Yarrowia lipolytica). We also used this method to determine the minimum inhibitory concentration of a preservative, natamycin, against 9 fungal targets. The results underlined the strain-dependency of LAB antifungal activity, the strong effect of fermentation substrate on this activity, and the effect of the screening medium on natamycin minimum inhibitory concentration. Our method could achieved a screening rate of 1,600 assays per week and can be implemented to evaluate antifungal activity of microorganisms, fermentation products, or purified compounds compatible with dairy technology.     

CAST3M/ARCTURUS: A coupled heat transfer CFD code for thermal–hydraulic analyzes of gas cooled reactors

The safety of gas cooled reactors (High Temperature Reactors (HTR), Very High Temperature Reactors (VHTR) or Gas Cooled Fast Reactors (GFR)) must be ensured by systems (active or passive) which maintain loads on component (fuel) and structures (vessel, containment) within acceptable limits under accidental conditions. To achieve this objective, thermal–hydraulics computer codes are necessary tools to design, enhance the performance and ensure a high safety level of the different reactors. Some key safety questions are related to the evaluation of decay heat removal and containment pressure and thermal loads. This requires accurate simulations of conduction, convection, thermal radiation transfers and energy storage. Coupling with neutronics is also an important modeling aspect for the determination of representative parameters such as neutronics coefficient (Doppler coefficient, Moderator coeffcient, …), critical position of control rods, reactivity insertion aspects, …. For GFR, the high power density of the core and its necessary reduced dimension cannot rely only on passive systems for decay heat removal. Therefore, forced convection using active safety systems (gas blowers, heat exchangers, …) are highly recommended. Nevertheless, in case of station black-out, the safety demonstration of the concept should be guaranteed by natural circulation heat removal. This could be performed by keeping a relatively high back-up pressure for pure helium convection and also by heavy gas injection. So, it is also necessary to model mixing of different gases, the on-set of natural convection and the pressure and thermal loads onto the proximate or guard containment. In this paper, we report on the developments of the CAST3M/ARCTURUS thermal–hydraulics (Lumped Parameter and CFD) code developed at CEA, including its coupling to the neutronics code CRONOS2 and the system code CATHARE. Elementary validation cases are detailed, as well as application of the code to benchmark problems such as the HTR-10 thermal–hydraulic exercise. Examples of containment thermal–hydraulics calculations for fast reactor design (GFR) are also detailed.