BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data

Activation of CD4⁺ T cells requires the recognition of peptides that are presented by HLA class II molecules and can be assessed experimentally using the ELISpot assay. However, even given an individual’s HLA class II genotype, identifying which class II molecule is responsible for a positive ELISpot response to a given peptide is not trivial. The two main difficulties are the number of HLA class II molecules that can potentially be formed in a single individual (3–14) and the lack of clear peptide binding motifs for class II molecules. Here, we present a Bayesian framework to interpret ELISpot data (BIITE: Bayesian Immunogenicity Inference Tool for ELISpot); specifically BIITE identifies which HLA-II:peptide combination(s) are immunogenic based on cohort ELISpot data. We apply BIITE to two ELISpot datasets and explore the expected performance using simulations. We show this method can reach high accuracies, depending on the cohort size and the success rate of the ELISpot assay within the cohort.     

The contribution of olfactory receptor neurons to the perception of pheromone component ratios in male redbanded leafroller moths

Summary (Z)-11-tetradecenyl acetate (Z-11, 14:AC) must be in a 1009 ratio with (E)-11-tetradecenyl acetate (E-11,14:AC) to produce maximal wing fanning and attraction in male redbanded leafrollers. Earlier electrophysiological studies had indicated that mixtures of these pheromone components elicited responses from olfactory receptor neurons that appeared to differ from those expected on the basis of the responses to the individual components. Here we evaluate whether the behavioral sensitivity to particular ratios of Z- and E-11,14:AC has a correlate in the response properties of olfactory receptor neurons.The stimuli included the ratios of Z- and E-11, 14:AC used in earlier behavioral work plus several different mixtures of the seven components found in the pheromone blend, and equivalent amounts of the individual components. These stimuli were presented over a range of intensities to individual trichoid sensilla on the male antenna. In common with earlier results, the receptor neuron with the larger amplitude action potential responded most strongly to Z-11,14:AC, whereas the companion receptor neuron in the sensillum responded most strongly to E-11,14:AC. In contrast with earlier results, each receptor neuron responded exclusively to its own most effective stimulus, without regard to the presence of any other compound. They failed to respond uniquely to any of the other five compounds in the female pheromone blend, or to any of the tested combinations of these compounds. These minor components also failed to modulate the responses elicited in receptor neurons by appropriate ratios of Z- and E-11,14:AC. Thus, the responses of the two types of olfactory receptor neurons found in trichoid sensilla failed to show an optimum at the pheromone ratio known to elicit peak behavioral activity.Abbreviation RBLR redbanded leafroller moth     

Na movements and their oscillations during fertilization and the cell cycle in sea urchin eggs

We have analysed in detail the Na⁺ content and Na⁺ influx during fertilization and first divisions of the sea urchin egg (Paracentrotus lividus) using a filtration technique devised to eliminate rapidly contamination by the Na⁺ of external sea water. In the first 5 min following fertilization the egg fills up with Na⁺ (+ 30%). Thereafter Na⁺ is extruded and the Na⁺ content stabilizes at about 60% of the unfertilized egg level by the second cleavage (2 h). The initial increase in Na⁺ content is due to a large increase in Na⁺ influx already detected at 20 sec. The Na⁺ influx reaches its maximum at 1 min and its minimum at 5 min. H⁺ excretion follows the same kinetics. A second increase in Na⁺ influx is noted 5–10 min after fertilization; it reaches its maximum at prophase metaphase (30 min) and its minimum during cleavage (60 min). These oscillations in Na⁺ influx were observed for the first three divisions. Fertilization also immediately stimulates the Na⁺ efflux which remains elevated throughout the cell cycle and is responsible for the depletion of the Na⁺ content of the embryos. Activation of the eggs by weak amine bases (5 mM NH₄Cl) which bypasses the early cortical reaction produces only a depletion in the Na⁺ content of the egg similar to that produced by fertilization. NH₄Cl also increases the Na⁺ influx soon after fertilization, although no transient variations are noted.     

Assessment of Wall Elasticity Variations on Intraluminal Haemodynamics in Descending Aortic Dissections Using a Lumped-Parameter Model

Descending aortic dissection (DAD) is associated with high morbidity and mortality rates. Aortic wall stiffness is a variable often altered in DAD patients and potentially involved in long-term outcome. However, its relevance is still mostly unknown. To gain more detailed knowledge of how wall elasticity (compliance) might influence intraluminal haemodynamics in DAD, a lumped-parameter model was developed based on experimental data from a pulsatile hydraulic circuit and validated for 8 clinical scenarios. Next, the variations of intraluminal pressures and flows were assessed as a function of wall elasticity. In comparison with the most rigid-wall case, an increase in elasticity to physiological values was associated with a decrease in systolic and increase in diastolic pressures of up to 33% and 63% respectively, with a subsequent decrease in the pressure wave amplitude of up to 86%. Moreover, it was related to an increase in multidirectional intraluminal flows and transition of behaviour as 2 parallel vessels towards a vessel with a side-chamber. The model supports the extremely important role of wall elasticity as determinant of intraluminal pressures and flow patterns for DAD, and thus, the relevance of considering it during clinical assessment and computational modelling of the disease.     

Bone Cell-autonomous Contribution of Type 2 Cannabinoid Receptor to Breast Cancer-induced Osteolysis

The cannabinoid type 2 receptor (CB2) has previously been implicated as a regulator of tumor growth, bone remodeling, and bone pain. However, very little is known about the role of the skeletal CB2 receptor in the regulation of osteoblasts and osteoclasts changes associated with breast cancer. Here we found that the CB2-selective agonists HU308 and JWH133 reduced the viability of a variety of parental and bone-tropic human and mouse breast cancer cells at high micromolar concentrations. Under conditions in which these ligands are used at the nanomolar range, HU308 and JWH133 enhanced human and mouse breast cancer cell-induced osteoclastogenesis and exacerbated osteolysis, and these effects were attenuated in cultures obtained from CB2-deficient mice or in the presence of a CB2 receptor blocker. HU308 and JWH133 had no effects on osteoblast growth or differentiation in the presence of conditioned medium from breast cancer cells, but under these circumstances both agents enhanced parathyroid hormone-induced osteoblast differentiation and the ability to support osteoclast formation. Mechanistic studies in osteoclast precursors and osteoblasts showed that JWH133 and HU308 induced PI3K/AKT activity in a CB2-dependent manner, and these effects were enhanced in the presence of osteolytic and osteoblastic factors such as RANKL (receptor activator of NFκB ligand) and parathyroid hormone. When combined with published work, these findings suggest that breast cancer and bone cells exhibit differential responses to treatment with CB2 ligands depending upon cell type and concentration used. We, therefore, conclude that both CB2-selective activation and antagonism have potential efficacy in cancer-associated bone disease, but further studies are warranted and ongoing.     

La séquence de Moulin Quignon est-elle une séquence archéologique ?

The sequence of the Moulin Quignon quarry yielded archaeological findings (faunal remains, artefacts) and some of them are well located in the stratigraphy thanks to Jacques Boucher de Perthes and colleagues. These remains are often used to attest the early age of the site and the human remains. Some bifaces have been found in close relationship to the human remains and, in particular, the mandible found in 1863. Thanks to the handwritten label put on the pieces and their deposit at the National Museum of Natural History (Paris), it is possible to study them again in relation with the sequence. The study concerns the rare faunal remains and the bifaces given, among others, by Boucher de Perthes to the Museum. The paleontological and technological analyses allow us replacing the lithic material among the north-western European data. The material is presented according to the historical context of his discovery.     

On the evolution of structure in aminoacyl-tRNA synthetases.

The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. The evolution of the tRNA synthetases is of fundamental importance with respect to the nature of the biological cell and the transition from an RNA world to the modern world dominated by protein-enzymes. We present a structure-based phylogeny of the aminoacyl-tRNA synthetases. By using structural alignments of all of the aminoacyl-tRNA synthetases of known structure in combination with a new measure of structural homology, we have reconstructed the evolutionary history of these proteins. In order to derive unbiased statistics from the structural alignments, we introduce a multidimensional QR factorization which produces a nonredundant set of structures. Since protein structure is more highly conserved than protein sequence, this study has allowed us to glimpse the evolution of protein structure that predates the root of the universal phylogenetic tree. The extensive sequence-based phylogenetic analysis of the tRNA synthetases (Woese et al., Microbiol. Mol. Biol. Rev. 64:202-236, 2000) has further enabled us to reconstruct the complete evolutionary profile of these proteins and to make connections between major evolutionary events and the resulting changes in protein shape. We also discuss the effect of functional specificity on protein shape over the complex evolutionary course of the tRNA synthetases.     

Assessment of lake sturgeon (Acipenser fulvescens) recruitment in a regulated spawning tributary of Rainy Lake,Ontario

Continued study of the relationship between lake sturgeon (Acipenser fulvescens) recruitment and hydroelectric dams and operations, in a variety of river systems and habitat types is needed to improve the ability to predict and monitor impacts of the hydroelectric industry on this species. Herein, we present results of a juvenile lake sturgeon study aimed at addressing concerns over an inferred lack of recruitment resulting from spawning downstream of a hydroelectric generating station (HGS). Two years of sampling (2015 and 2016) were conducted in five sections of a 41 km long reach of the Seine River, Ontario, a lake sturgeon spawning tributary of Rainy Lake. Using an established gillnetting method, deepwater habitat was targeted to capture juvenile lake sturgeon to assess relative abundance, recruitment (cohort strength), and growth. Deepwater habitat, defined as water depths >6 m in this system, comprised only 2.1% of the wetted area in this study area. Within these habitats, a total of 331 lake sturgeon capture events were observed over the 2-years study period. The majority of the lake sturgeon catch (85%) was comprised of age-0 to age-5 individuals (both sampling years combined). Although inter-annual variation in cohort strength was apparent, each cohort between 2006 and 2016 was represented. The spatial distribution of cohorts varied among river reaches with younger individuals (age-0 and age-1) occupying reaches proximal to the Sturgeon Falls HGS, and larger, older individuals (age-2 to age-5) occupying reaches further downstream. The rarity of age-6+ individuals can likely be explained by ongoing downstream redistribution of juveniles over time, out of the Seine River and into Rainy Lake. Growth of juvenile lake sturgeon captured in the Seine River was above average relative to conspecifics from other rivers in the Hudson Bay drainage. Unfortunately, baseline data sets required to facilitate comparisons of contemporary (post-construction Sturgeon Falls HGS) versus historical (i.e. pre- Sturgeon Falls HGS) lake sturgeon recruitment, or to evaluate the influence of the Seine River Water Management Plan (2004) on lake sturgeon recruitment, are lacking. However, juvenile Lake Sturgeon are more abundant in this system than what had been surmised based on recent studies which implemented random sampling. Results indicate that juvenile lake sturgeon may reside in spawning tributaries for several years (age-0 to age-5) prior to seeking alternate habitats and highlights the value of targeted sampling (i.e. by depth) along the flow axis of rivers downstream of spawning areas when assessing lake sturgeon recruitment patterns.