Aerodynamic optimization of the flat-plate leading edge for experimental studies of laminar and transitional boundary layers

This work is concerned with the design of a leading edge for a flat-plate model used to study laminar and transitional boundary layers. For this study, the flow over the complete boundary-layer model, including leading edge, flat section, and trailing-edge flap, is modeled. The effect of important geometrical features of the leading edge on the resulting pressure distribution, starting from the well-known symmetric modified super ellipse, is investigated. A minimal pressure gradient on the measurement side of the plate is achieved using an asymmetrical configuration of modified super ellipses, with a thickness ratio of 7/24. An aerodynamic shape optimization is performed to obtain a novel leading edge shape that greatly reduces the length of the non-zero pressure gradient region and the adverse pressure gradient region compared to geometries defined by ellipses. Wind tunnel testing is used to validate the numerical solutions.     

Physical complexity of variable length symbolic sequences

A measure called physical complexity is established and calculated for a population of sequences, based on statistical physics, automata theory, and information theory. It is a measure of the quantity of information in an organism’s genome. It is based on Shannon’s entropy, measuring the information in a population evolved in its environment, by using entropy to estimate the randomness in the genome. It is calculated from the difference between the maximal entropy of the population and the actual entropy of the population when in its environment, estimated by counting the number of fixed loci in the sequences of a population. Up until now, physical complexity has only been formulated for populations of sequences with the same length. Here, we investigate an extension to support variable length populations. We then build upon this to construct a measure for the efficiency of information storage, which we later use in understanding clustering within populations. Finally, we investigate our extended physical complexity through simulations, showing it to be consistent with the original.     

Ultrasound promoted synthesis of thioesters from 2-mercaptobenzoxa(thia)zoles

An ultrasound-enhanced method has been developed for the synthesis of a variety of thioesters from benzoyl chlorides and 2-mercaptobenzoxa(thia)zoles. Applying this methodology, 14 compounds were synthesized in excellent yields.     

A Synthetic Substrate of DNA Polymerase Deviating from the Bases,Sugar, and Leaving Group of Canonical Deoxynucleoside Triphosphates

1. Download : Download high-res image (116KB)
2. Download : Download full-size image

Highlights? A highly modified nucleotide as substrate for polymerases ? The reversibility of the polymerase reaction at the template level ? Synthesis of a nucleoside with two anomeric centers     

N-Glycosidase treatment with 18O labeling and de novo sequencing argues for flagellin FliC glycopolymorphism in Pseudomonas aeruginosa

In prokaryote organisms, N-glycosylation of proteins is often correlated to cell–cell recognition and extracellular events. Those glycoproteins are potential targets for infection control. To date, many surface-glycosylated proteins from bacterial pathogens have been described. However, N-linked Pseudomonas surface-associated glycoproteins remain underexplored. We report a combined enrichment and labeling strategy to identify major glycoproteins on the outside of microorganisms. More precisely, bacteria were exposed to a mix of biotinylated lectins able to bind with glycoproteins. The latter were then recovered by avidin beads, digested with trypsin, and submitted to mass spectrometry. The targeted mixture of glycoproteins was additionally deglycosylated in the presence of H₂ ¹⁸O to incorporate ¹⁸O during PNGase F treatment and were also analyzed using mass spectrometry. This approach allowed us to identify a few tens of potential N-glycoproteins, among which flagellin FliC was the most abundant. To detect the possible sites of FliC modifications, a de novo sequencing step was also performed to discriminate between spontaneous deamidation and N-glycan loss. This approach led to the proposal of three potential N-glycosylated sites on the primary sequence of FliC: N26, N69, and N439, with two of these three asparagines belonging to an N-X-(S/T) consensus sequence. These observations suggest that flagellin FliC is a heterogeneous protein mixture containing both O- and N-glycoforms.

PCR-based detection of gene transfer vectors: application to gene doping surveillance

Athletes who illicitly use drugs to enhance their athletic performance are at risk of being banned from sports competitions. Consequently, some athletes may seek new doping methods that they expect to be capable of circumventing detection. With advances in gene transfer vector design and therapeutic gene transfer, and demonstrations of safety and therapeutic benefit in humans, there is an increased probability of the pursuit of gene doping by athletes. In anticipation of the potential for gene doping, assays have been established to directly detect complementary DNA of genes that are top candidates for use in doping, as well as vector control elements. The development of molecular assays that are capable of exposing gene doping in sports can serve as a deterrent and may also identify athletes who have illicitly used gene transfer for performance enhancement. PCR-based methods to detect foreign DNA with high reliability, sensitivity, and specificity include TaqMan real-time PCR, nested PCR, and internal threshold control PCR.     

Hippocampal metabolomics using ultrahigh-resolution mass spectrometry reveals neuroinflammation from Alzheimer’s disease in CRND8 mice

In the wake of genomics, metabolomics characterizes the small molecular metabolites revealing the phenotypes induced by gene mutants. To address the metabolic signatures in the hippocampus of the amyloid-beta (Aβ) peptides produced in transgenic (Tg) CRND8 mice, high-field ion cyclotron resonance–Fourier transform mass spectrometry supported by LC-LTQ-Orbitrap was introduced to profile the extracted metabolites. More than 10,000 ions were detected in the mass profile for each sample. Subsequently, peak alignment and the 80 % rule followed by feature selection based on T score computation were performed. The putative identification was also conducted using the highly accurate masses with isotopic distribution by interfacing the MassTRIX database as well as MS/MS fragmentation generated in the LTQ-Orbitrap after chromatographic separation. Consequently, 58 differentiating masses were tentatively identified while up to 44 differentiating elemental compositions could not be biologically annotated in the databases. Nonetheless, of the putatively annotated masses, eicosanoids in arachidonic acid metabolism, fatty acid beta-oxidation disorders as well as disturbed glucose metabolism were highlighted as metabolic traits of Aβ toxicity in Tg CRND8 mice. Furthermore, a web-based bioinformatic tool was used for simulation of the metabolic pathways. As a result of the obtained metabolic signatures, the arachidonic acid metabolism dominates the metabolic perturbation in hippocampal tissues of Tg CRND8 mice compared to non-Tg littermates, indicating that Aβ toxicity functions neuroinflammation in hippocampal tissue and new theranostic opportunities might be offered by characterization of altered arachidonic acid metabolism for Alzheimer’s disease.