Reconstructing the Origins of the Somatostatin and Allatostatin-C Signaling Systems Using the Accelerated Evolution of Biodiverse Cone Snail Toxins

Somatostatin and its related peptides (SSRPs) form an important family of hormones with diverse physiological roles. The ubiquitous presence of SSRPs in vertebrates and several invertebrate deuterostomes suggests an ancient origin of the SSRP signaling system. However, the existence of SSRP genes outside of deuterostomes has not been established, and the evolutionary history of this signaling system remains poorly understood. Our recent discovery of SSRP-like toxins (consomatins) in venomous marine cone snails (Conus) suggested the presence of a related signaling system in mollusks and potentially other protostomes. Here, we identify the molluscan SSRP-like signaling gene that gave rise to the consomatin family. Following recruitment into venom, consomatin genes experienced strong positive selection and repeated gene duplications resulting in the formation of a hyperdiverse family of venom peptides. Intriguingly, the largest number of consomatins was found in worm-hunting species (>400 sequences), indicating a homologous system in annelids, another large protostome phylum. Consistent with this, comprehensive sequence mining enabled the identification of SSRP-like sequences (and their corresponding orphan receptor) in annelids and several other protostome phyla. These results established the existence of SSRP-like peptides in many major branches of bilaterians and challenge the prevailing hypothesis that deuterostome SSRPs and protostome allatostatin-C are orthologous peptide families. Finally, having a large set of predator–prey SSRP sequences available, we show that although the cone snail’s signaling SSRP-like genes are under purifying selection, the venom consomatin genes experience rapid directional selection to target receptors in a changing mix of prey.     

Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars

Background  

The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state-of-the-art algorithms. The pfold model couples a stochastic context-free grammar to phylogenetic analysis for a high accuracy in predictions, but the time complexity of the algorithm and underflow errors have prevented its use for long alignments. Here we present PPfold, a multithreaded version of pfold, which is capable of predicting the structure of large RNA alignments accurately on practical timescales.     

Ornithodoros moubata complement inhibitor is an equally effective C5 inhibitor in pigs and humans

Experimental evidence suggests that C inhibition and more particularly combined inhibition of C and the TLR coreceptor CD14 may be of therapeutic benefit in sepsis and other inflammatory conditions. A barrier to the testing and further development of many inhibitors is that their activity is species specific. Pig is a relevant species for experimental models of human disease, and this study undertakes a comprehensive comparison of the inhibitory efficacy of the C5 inhibitor Ornithodoros moubata C inhibitor (OmCI) in human and porcine whole blood ex vivo models of Escherichia coli-induced sepsis. The effect of OmCI on complement activity in pigs undergoing E. coli sepsis was also examined. Porcine and human serum, and whole blood anticoagulated with lepirudin, was incubated with E. coli and the effect of OmCI investigated. The ex vivo results were virtually identical in pig and human. OmCI completely ablated the activity of all three C pathways at 0.64 μM. E. coli-induced C activation and expression of CD11b (wCD11R3 in the pig), was abolished ex vivo at 0.32 μM OmCI. Combining anti-CD14 and OmCI reduced the formation of IL-8 and TNF-α more potently than the single inhibitors. OmCI also efficiently bound E. coli-induced leukotriene B(4) in pig and human plasma. In support of our ex vivo findings, in vivo the activity of all C pathways was inhibited at 0.6 mg OmCI/kg pig. In conclusion, OmCI efficiently inhibited pig and human C activation, has accompanying anti-inflammatory effects and is a promising candidate inhibitor for further in vivo studies of sepsis.     

Salicylamide and salicylglycine oxidovanadium complexes with insulin-mimetic properties

Reaction of N-(2-hydroxybenzyl)-N-(2-picolyl) glycine (H₂papy) with VOSO₄ in water gives the oxidovanadium(V) oxido-bridged dimer [{(papy)(VO)}₂ μ-O)] (1). Similarly, reaction of N-(2-hydroxybenzyl) glycine (H₂glysal) with VOSO₄ gives [(glysal)VO(H₂O)] (2) and reaction of salicylamide (Hsalam) with VOSO₄ in methanol gives [(salam)₂VO] (3). The crystal structure of the oxido-bridged complex 1 is reported. The insulin-mimetic activity of all three complexes was evaluated with respect to their ability to phosphorylate protein kinase B (PKB). The speciations of complexes 1 and 2 were studied over the pH range 2-10. Complex 1 shows greater stability over the whole pH range but only 2 and 3 exhibit an insulin-mimetic effect.     

Novel multi-target compounds in the quest for new chemotherapies against Alzheimer’s disease: An experimental and theoretical study

The lack of any effective therapy along with the aging world population anticipates a growth of the worldwide incidence of Alzheimer’s disease (AD) to more than 100 million cases by 2050. Accumulation of extracellular amyloid-β (Aβ) plaques, intracellular tangles in the brain, and formation of reactive oxygen species (ROS) are the major hallmarks of the disease. In the amyloidogenic process, a β-secretase, known as BACE 1, plays a fundamental role in the production of Aβ fragments, and therefore, inhibition of such enzymes represents a major strategy for the rational design of anti-AD drugs. In this work, a series of four multi-target compounds (1–4), inspired by previously described ionophoric polyphenols, have been synthesized and studied. These compounds have been designed to target important aspects of AD, including BACE 1 enzymatic activity, Aβ aggregation, toxic concentrations of Cu²⁺ metal ions and/or ROS production. Two other compounds (5 and 6), previously reported by some of us as antimalarial agents, have also been studied because of their potential as multi-target species against AD. Interestingly, compounds 3 and 5 showed moderate to good ability to inhibit BACE 1 enzymatic activity in a FRET assay, with IC₅₀′s in the low micromolar range (4.4?±?0.3 and 1.7?±?0.3?μM, respectively), comparable to other multi-target species, and showing that the observed activity was in part due to a competitive binding of the compounds at the active site of the enzyme. Theoretical docking calculations overall agreed with FRET assay results, displaying the strongest binding affinities for 3 and 5 at the active site of the enzyme. In addition, all compounds selectively interacted with Cu²⁺ metal ions forming 2:1 complexes, inhibited the production of Aβ-Cu²⁺ catalyzed hydroxyl radicals up to a ～100% extent, and scavenged AAPH-induced peroxyl radical species comparably to resveratrol, a compound used as reference in this work. Our results also show good anti-amyloidogenic ability: compounds 1–6 inhibited both the Cu²⁺-induced and self-induced Aβ(1–40) fibril aggregation to an extent that ranged from 31% to 77%, while they disaggregated pre-formed Aβ(1–40) mature fibrils up to a 37% and a 69% extent in absence and presence of Cu²⁺, respectively. Cytotoxicity was additionally studied in Tetrahymena thermophila and HEK293 cells, and compared to that of resveratrol, showing that compounds 1–6 display lower toxicity than that of resveratrol, a well-known non-toxic polyphenol.     

Estimation of density threshold of gregarization of desert locust hoppers from field sampling in Mauritania

For desert locusts, Schistocerca gregaria (Forskål) (Orthoptera: Acrididae), the hopper density threshold of gregarization remains poorly documented. Field sampling was carried out in traditional seasonal breeding areas of Mauritania during two successive years without invasion to approximate the gregarization threshold. Hopper densities were assessed at numerous sampling sites. Vegetation was also sampled to characterize the habitats. Hopper behavior was analyzed in situ with the help of a behavioral circular arena to test our assumptions on empirical locust phases determination based on physical appearance (coloration and behavior) following FAO guidelines. The results provided a critical density value around 2.45 hoppers m^?2, above which gregarious hoppers were expected to be seen more frequently in nature. Hopper density was confirmed as the main factor explaining the presence of gregarious individuals. The level of involvement of vegetation parameters such as plant density, basal area, volume, distance between plants, greenness, or combinations of these indicators was low in explaining the observation of gregarious hoppers compared with hopper density. Vegetation cover and height were the only vegetation characteristics that could enhance the prediction of phase status with hopper density. The hoppers' phase determined from their behavior observed in the arena was similar to that characterized through FAO guidelines phase assessment, making consistent the field sampling method. Additionnally, the use of this arena illustrated that the grouping behavior of hoppers is a gradual response to density. This study can be seen as a step forward in the estimation of hopper density thresholds of gregarization in the field. This should improve the decision making for intervention during preventive control operations.     

Semiautomated improvement of RNA alignments

We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at (http://sarse.ku.dk).     

An expression relating breaking stress and density of trabecular bone

Bone mineral density (BMD) is the principal diagnostic tool used in clinical settings to diagnose and monitor osteoporosis. Experimental studies on ex vivo bone samples from multiple skeletal locations have been used to propose that their breaking stress bears a power-law relationship to volumetric BMD, with a location-dependent index. We argue that a power-law cannot represent effects of trabecular removal, which is one of the leading causes of reduction in bone strength. A new expression, proposed on the basis of theoretical and numerical analysis of a mathematical model, is tested using previously published data on bone samples from iliac crest and vertebral body. It represents the experimental biomechanical data at least as well as the power-law, and provides means for extrapolating results from small biopsy samples to an entire bone. In addition, changes caused by trabecular thinning and anisotropy can be modeled by the expression.