Self-organizing ontology of biochemically relevant small molecules

Background  

The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest.     

Synthesis and Enzymatic Deprotection of Fully Protected 2′‐5′ Oligoadenylates (2‐5A): Towards a Prodrug Strategy for Short 2‐5A

Fully protected pA2′p5′A2′p5′A trimers 1a and 1b have been prepared as prodrug candidates for a short 2′‐5′ oligoadenylate, 2‐5A, and its 3′‐O‐Me analog, respectively. The kinetics of hog liver carboxyesterase (HLE)‐triggered deprotection in HEPES buffer (pH 7.5) at 37° has been studied. The deprotection of 1a turned out to be very slow, and 2‐5A never appeared in a fully deprotected form. By contrast, a considerable proportion of 1b was converted to the desired 2‐5A trimer, although partial removal of the 3′‐O‐[(acetyloxy)methyl] group prior to exposure of the adjacent phosphodiester linkage resulted in 2′,5′→3′,5′ phosphate migration and release of adenosine as side reactions.     

MDA5 participates in the detection of paramyxovirus infection and is essential for the early activation of dendritic cells in response to Sendai Virus defective interfering particles

Defective interfering (DI) particles are byproducts of virus replication that potently enhance dendritic cell (DC) maturation by virus infection. DI particles have been reported for many different viruses and are strong inducers of type I IFNs. The cellular mechanisms involved in the response to DI particles are not known. In this study, we show that 1) DI particles are recognized by more than one viral sensor independently of TLRs and type I IFN signaling; 2) The helicase MDA5 participates in the detection of DI genomes as MDA5-deficient DCs respond inefficiently to Sendai virus stocks containing DI particles; 3) DI particles stimulate the expression of IRF3-responsive genes by a uniquely potent mechanism when compared with other prototypic viral stimulus; and 4) the efficient detection of DI particles overcomes virus immune antagonism. These data highlight the outstanding adjuvant capacity of DI particles in stimulating mouse and human DCs. They also offer biological relevance to the previously reported inhibition of MDA5 by different paramyxovirus V proteins. The unique mechanism by which DI particles trigger the maturation of DCs represents a novel strategy that could be further exploited for the development of potent adjuvant molecules.     

Bill and hyoid apparatus of pigeons (Columbidae) and sandgrouse (Pteroclididae): a common adaptation to vegetarian feeding?

For the present study, 15 species of pigeons representing the 5 sub-families usually recognized, and 3 species of sandgrouse were examined. The skeleton and musculature of the bill and hyoid apparatus are described. Morpho-functional analyses show that from a key adaptation to the removal and deglutition (without processing) of attached plant items, pigeons would have followed two pathways, one based on the joint muscular control of the movement of the jaws (Columbinae, Treroninae, Gourinae), the other on the separate muscular control (Didunculinae, Otidiphabinae). Sandgrouse would have diverged from this latter, developing the ability to very selectively remove attached plant items as well as to peck particularly small seeds on the ground. Unexpected differences appeared between sandgrouse species which raise eco-ethological problems.     

A rapid effect of applied brassinolide on abscisic acid concentrations in <Emphasis Type="Italic">Brassica napus</Emphasis> leaf tissue subjected to short-term heat stress

Three-week old canola (Brassica napus L.) seedlings grown at 20/16°C (day/night) were subjected to short-term (4 and 8 h) heat stress (45°C) or maintained at a normal temperature of 20°C. Half of the plants under each treatment received a 10⁻⁶ M solution of brassinolide (BL) 1 h prior to beginning the temperature treatments. The concentration (ng/g dry weight) of endogenous abscisic acid (ABA) was subsequently determined in young leaves via the stable isotope dilution method. Applied BL had no effect on endogenous ABA for plants maintained at normal temperatures. However, ABA concentration was significantly elevated by heat stress alone and doubled by heat stress + BL. These results suggest that the well-known enhancement of tolerance to high temperature stress that can be obtained by BL or 24-epi-BL applications may be caused by a brassinosteroid-induced elevation in endogenous ABA concentration.