Structural Elucidation of a Nonpeptidic Inhibitor Specific for the Human Immunoproteasome

Selective inhibition of the immunoproteasome is a promising approach towards the development of immunomodulatory drugs. Recently, a class of substituted thiazole compounds that combine a nonpeptidic scaffold with the absence of an electrophile was reported in a patent. Here, we investigated the mode of action of the lead compound by using a sophisticated chimeric yeast model of the human immunoproteasome for structural studies. The inhibitor adopts a unique orientation perpendicular to the β5i substrate‐binding channel. Distinct interactions between the inhibitor and the subpockets of the human immunoproteasome account for its isotype selectivity.     

A new in situ chemical reactor for studying heterogeneous catalysis by NMR: The GRASSHopper

A new device/technique, Gas Reactor And Solid Sample Hopper designated GRASSHopper II, is described as an alternative to magic-angle spinning (MAS) for in situ NMR experiments on reacting heterogeneous systems. It is capable of supporting NMR studies of heterogeneous catalysis in the batch mode, in the flow reactor mode and for measurements of chemical kinetics. This new approach is based on the technique of magic-angle hopping (MAH). Characteristics, advantages, limitations and potential areas of application are described. Preliminary results are shown on the formation, subsequent hydrolysis and then regeneration (via dehydration) of (C₆H₅)₃C⁺ carbocations in zeolite HY cavities, and on the gas–solid polymerization of ethylene on a Cp₂ZrCl₂/MAO/SiO₂ ‘supported' catalyst.     

Five Functional Aspects of the Epidermal Barrier

The epidermis is a living, multilayered barrier with five functional levels, including a physical, a chemical, a microbial, a neuronal, and an immune level. Altogether, this complex organ contributes to protect the host from external aggression and to preserve its integrity. In this review, we focused on the different functional aspects.     

As the number falls,alternatives to the Hagberg–Perten falling number method: A review

This review examines the application, limitations, and potential alternatives to the Hagberg–Perten falling number (FN) method used in the global wheat industry for detecting the risk of poor end-product quality mainly due to starch degradation by the enzyme α-amylase. By viscometry, the FN test indirectly detects the presence of α-amylase, the primary enzyme that digests starch. Elevated α-amylase results in low FN and damages wheat product quality resulting in cakes that fall, and sticky bread and noodles. Low FN can occur from preharvest sprouting (PHS) and late maturity α-amylase (LMA). Moist or rainy conditions before harvest cause PHS on the mother plant. Continuously cool or fluctuating temperatures during the grain filling stage cause LMA. Due to the expression of additional hydrolytic enzymes, PHS has a stronger negative impact than LMA. Wheat grain with low FN/high α-amylase results in serious losses for farmers, traders, millers, and bakers worldwide. Although blending of low FN grain with sound wheat may be used as a means of moving affected grain through the marketplace, care must be taken to avoid grain lots from falling below contract-specified FN. A large amount of sound wheat can be ruined if mixed with a small amount of sprouted wheat. The FN method is widely employed to detect α-amylase after harvest. However, it has several limitations, including sampling variability, high cost, labor intensiveness, the destructive nature of the test, and an inability to differentiate between LMA and PHS. Faster, cheaper, and more accurate alternatives could improve breeding for resistance to PHS and LMA and could preserve the value of wheat grain by avoiding inadvertent mixing of high- and low-FN grain by enabling testing at more stages of the value stream including at harvest, delivery, transport, storage, and milling. Alternatives to the FN method explored here include the Rapid Visco Analyzer, enzyme assays, immunoassays, near-infrared spectroscopy, and hyperspectral imaging.     

Novel TTLL5 Variants Associated with Cone-Rod Dystrophy and Early-Onset Severe Retinal Dystrophy

Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.     

Translesion Synthesis or Repair by Specialized DNA Polymerases Limits Excessive Genomic Instability upon Replication Stress

DNA can experience “replication stress”, an important source of genome instability, induced by various external or endogenous impediments that slow down or stall DNA synthesis. While genome instability is largely documented to favor both tumor formation and heterogeneity, as well as drug resistance, conversely, excessive instability appears to suppress tumorigenesis and is associated with improved prognosis. These findings support the view that karyotypic diversity, necessary to adapt to selective pressures, may be limited in tumors so as to reduce the risk of excessive instability. This review aims to highlight the contribution of specialized DNA polymerases in limiting extreme genetic instability by allowing DNA replication to occur even in the presence of DNA damage, to either avoid broken forks or favor their repair after collapse. These mechanisms and their key regulators Rad18 and Polθ not only offer diversity and evolutionary advantage by increasing mutagenic events, but also provide cancer cells with a way to escape anti-cancer therapies that target replication forks.     

A Practical Method for Animating Anisotropic Elastoplastic Materials

This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly-shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re-use popular isotropic plasticity models like the Drucker-Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate.     

A long-time limit for world subway networks

We study the temporal evolution of the structure of the world''s largest subway networks in an exploratory manner. We show that, remarkably, all these networks converge to a shape that shares similar generic features despite their geographical and economic differences. This limiting shape is made of a core with branches radiating from it. For most of these networks, the average degree of a node (station) within the core has a value of order 2.5 and the proportion of k = 2 nodes in the core is larger than 60 per cent. The number of branches scales roughly as the square root of the number of stations, the current proportion of branches represents about half of the total number of stations, and the average diameter of branches is about twice the average radial extension of the core. Spatial measures such as the number of stations at a given distance to the barycentre display a first regime which grows as r² followed by another regime with different exponents, and eventually saturates. These results—difficult to interpret in the framework of fractal geometry—confirm and yield a natural explanation in the geometric picture of this core and their branches: the first regime corresponds to a uniform core, while the second regime is controlled by the interstation spacing on branches. The apparent convergence towards a unique network shape in the temporal limit suggests the existence of dominant, universal mechanisms governing the evolution of these structures.     

Sensory and physicochemical evolution of tropical cooked peeled shrimp inoculated by Brochothrix thermosphacta and Lactococcus piscium CNCM I-4031 during storage at 8°C

This study investigated the sensory quality and physicochemical evolution (pH, glucose, l-lactic acid, biogenic amine, free amino-acids and volatile compounds) during storage at 8 °C of cooked peeled shrimp inoculated with the specific spoilage bacteria Brochothrix thermosphacta alone or mixed with the protective strain Lactococcus piscium CNCM I-4031. Growth of both bacteria was monitored at regular intervals during storage by microbial counts and the thermal temperature gradient gel electrophoresis (TTGE) technique. Bacterial counts showed that L. piscium and B. thermosphacta inoculated at 7 log CFU/g and 3 log CFU/g were well adapted to shrimp, reaching a maximum level of 9 log CFU/g after 4 days and 10 days respectively. In mixed culture, the growth of B. thermosphacta was reduced by 3.2 ± 0.1 log CFU/g. The TTGE technique allowed monitoring the colonisation of the strains on the shrimp matrix and confirming the dominance of L. piscium in mixed culture throughout the experiment. Sensory analysis confirmed that B. thermosphacta spoiled the product after 11 days, when its cell number attained 8 log CFU/g with the emission of strong butter/caramel off-odours. This sensory profile could be linked to the production of 2,3 butanedione, cyclopentanol, 3-methylbutanol, 3-methylbutanal, 2-methylbutanal, 4-methyl-3-chloro-3-pentanol and ethanol, which were produced in more significant quantities in the B. thermosphacta batch than in the batches in which the protective strain was present. On the contrary, TVBN and TMA were not suitable as quality indicators for B. thermosphacta spoilage activity. In the products where the protective L. piscium strain was present, no adverse effect on sensory quality was noted by the sensory panels. Moreover, biogenic amine assessment did not show any histamine or tyramine production by this strain, underlining its safety profile. Both strains produced lactic acid (1850 mg/kg in L. piscium and B. thermosphacta batch on days 3 and 10 respectively; 3830 mg/kg on day 7 in mixed culture) and the pH decrease from 6.6 ± 0.0 to 5.9 ± 0.1 was similar in all batches. Lactic acid production or competition for free amino-acid was not involved in the inhibition mechanism; however rapid glucose consumption by L. piscium could partially explain the growth limitation of the spoilage micro-organism. This study demonstrated the spoilage characteristic of B. thermosphacta and the usefulness of L. piscium as a bioprotective culture for tropical cooked peeled shrimp without any adverse effect on the sensory quality of the product.     

Evaluation of <Emphasis Type="Italic">Rhizopus oryzae</Emphasis> Lipase for the Determination of Regiodistribution in Triacylglycerols with Medium Chain Fatty Acids

The nutritional profile and rheological behaviors of lipids is both due to fatty acid composition and regiodistribution on external and internal positions of triacylglycerol. Actual methods for regiodistribution analysis having some restrictions, there is still a need for investigating a safe, simple and environmentally friendly method for the sn-2 position analysis that could especially be used for the analysis of fats containing medium and short chain fatty acids. The objective of this study was to evaluate the 1,3-selectivity and typoselectivity of Rhizopus oryzae lipase in the presence of short/medium chain fatty acids in partial hydrolysis conditions used for regiodistribution analysis. Structured triacylglycerols containing eight-carbon-chain length fatty acids in the sn -2 position were chemically synthesized using DCC/DMAP coupling agent and purification steps by flash-chromatography. The final product showed very high purity and was used as the substrate for 1,3-selectivity evaluation. Typoselectivity was assessed by investigating partial hydrolysis of equimolar blends of homogeneous TAG. This study confirmed the 1,3-selectivity of Rhizopus oryzae lipase in the hydrolysis conditions used, and revealed that this lipase was less influenced by fatty acids chain length than pancreatic lipase. Considering this, Rhizopus oryzae lipase appeared to be a good candidate for regiodistribution analysis of fats containing medium and short chain fatty acids.