qNABpredict: Quick,accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids

Protein sequence-based predictors of nucleic acid (NA)-binding include methods that predict NA-binding proteins and NA-binding residues. The residue-level tools produce more details but suffer high computational cost since they must predict every amino acid in the input sequence and rely on multiple sequence alignments. We propose an alternative approach that predicts content (fraction) of the NA-binding residues, offering more information than the protein-level prediction and much shorter runtime than the residue-level tools. Our first-of-its-kind content predictor, qNABpredict, relies on a small, rationally designed and fast-to-compute feature set that represents relevant characteristics extracted from the input sequence and a well-parametrized support vector regression model. We provide two versions of qNABpredict, a taxonomy-agnostic model that can be used for proteins of unknown taxonomic origin and more accurate taxonomy-aware models that are tailored to specific taxonomic kingdoms: archaea, bacteria, eukaryota, and viruses. Empirical tests on a low-similarity test dataset show that qNABpredict is 100 times faster and generates statistically more accurate content predictions when compared to the content extracted from results produced by the residue-level predictors. We also show that qNABpredict's content predictions can be used to improve results generated by the residue-level predictors. We release qNABpredict as a convenient webserver and source code at http://biomine.cs.vcu.edu/servers/qNABpredict/ . This new tool should be particularly useful to predict details of protein–NA interactions for large protein families and proteomes.     

Signalling pathways in the pathogenesis of Cryptococcus

Efficient communication with the environment is critical for all living organisms. Fungi utilize complex signalling systems to sense their environments and control proliferation, development and in some cases virulence. Well-studied signalling pathways include the protein kinase A/cyclic AMP (cAMP), protein kinase C (PKC)/mitogen-activated protein kinase (MAPK), lipid signalling cascades, and the calcium–calcineurin signalling pathway. The human pathogenic basidiomycetous fungus Cryptococcus neoformans deploys sensitive signalling systems to survive in the human host, leading to life-threatening meningoencephalitis. Known virulence traits of this fungus, including the antioxidant melanin production, the antiphagocytic polysaccharide capsule and the ability to grow at 37°C, are orchestrated by complex signalling networks, whose understanding is crucial to better treat, diagnose and prevent cryptococcosis.     

Suppression of citrus leafminer, Phyllocnistis citrella, with an attract-and-kill formulation

The citrus leafminer, Phyllocnistis citrella Stainton (Lepidoptera: Gracillariidae), is a worldwide pest of citrus crops and is responsible for proliferation of citrus bacterial canker, Xanthomonas axonopodis (Hasse) pv. citri (Gamma Proteobacteria: Xanthomonadaceae). We developed and evaluated an attracticide formulation, termed MalEx, for control of P. citrella. MalEx is a viscous paste with UV‐protective properties that is dispensed as 50‐μl droplets using custom‐made calibrated pumps. A formulation containing 0.016%P. citrella pheromone [3:1 blend of (Z,Z,E)‐7,11,13‐hexadecatrienal and (Z,Z)‐7,11‐hexadecadienal] and 6% permethrin was found to suppress male response to pheromone in the field better than formulations containing 10× less pheromone. Although formulations without permethrin showed some suppression of male activity because of mating disruption, addition of 6% permethrin to the formulation was required for optimal efficacy. When MalEx, containing 0.016% pheromone and 6% permethrin, was applied at 3 000 point sources ha^?1, the application height did not influence efficacy of male P. citrella suppression within mature 4‐m tall citrus trees. Decreasing the rate of MalEx from 3 000 to 1 500 droplets ha^?1 reduced efficacy as measured by both male P. citrella activity and larval infestation. Although 4 500 droplets ha^?1 did not result in statistically better efficacy than 3 000 droplets ha^?1, there was a noticeable trend for higher efficacy as droplet density increased. Continuous treatment of 0.5‐ha blocks of citrus with MalEx over the course of 112 days reduced larval infestation of new flush, as compared with those in untreated control plots, by 3.6–7.2× depending on droplet application density. In laboratory behavioral bioassays, the attractiveness of MalEx droplets to male P. citrella was drastically reduced after 21 days of field aging. However, our laboratory investigation confirmed that 100% of males contacting MalEx droplets, aged up to 35 days in the field, were killed within 24 h. Direct observation of male P. citrella behavior in the field confirmed that attracted males made contact with droplets. Control of P. citrella with MalEx should reduce the number of required broad spectrum sprays for leafminer management in both field and citrus nursery settings.     

Structural characterization of a dimer of RNA duplexes composed of 8-bromoguanosine modified CGG trinucleotide repeats: a novel architecture of RNA quadruplexes

Fragile X syndrome and fragile X-associated tremor/ataxia syndrome (FXTAS) are neurodegenerative disorders caused by the pathogenic expansion of CGG triplet repeats in the FMR1 gene. FXTAS is likely to be caused by a ‘toxic’ gain-of-function of the FMR1 mRNA. We provide evidence for the existence of a novel quadruplex architecture comprising CGG repeats. The 8-bromoguanosine (^BrG)-modified molecule GC^BrGGCGGC forms a duplex in solution and self-associates via the major groove to form a four-stranded, antiparallel (GC^BrGGCGGC)₄ RNA quadruplex with ^BrG3:G6:^BrG3:G6 tetrads sandwiched between mixed G:C:G:C tetrads. Self-association of Watson–Crick duplexes to form a four-stranded structure has previously been predicted; however, no experimental evidence was provided. This novel four-stranded RNA structure was characterized using a variety of experimental methods, such as native gel electrophoresis, NMR spectroscopy, small-angle X-ray scattering and electrospray ionization mass spectrometry.     

Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2.8 Å resolution

The structure of 2-keto-3-deoxy-6-phosphogluconate aldolase has been extended to 2.8 Å resolution from 3.5 Å resolution by multiple isomorphous replacement methods using three heavy-atom derivatives and anomalous Bijvoet differences to 6 Å resolution (〈m〉 = 0.72). The replacement phases were improved and refined by electron density modification procedures coupled with inverse transform phase angle calculations. A Kendrew model of the molecule was built, which contained all 225 residues of a recently determined amino acid sequence, whereas only 173 were accounted for at 3.5 Å resolution. The missing residues were found to be part of the interior of the molecule and not simply an appendage. The molecule folds to form an eight-strand α/β-barrel structure strikingly similar to triosephosphate isomerase, the A-domain of pyruvate kinase and Taka amylase. With a knowledge of the sequence, the nature of the interfaces of the two kinds of crystallographic trimers have been examined, from which it was concluded that the choice of trimers selected in the 3.5 Å resolution work was probably correct for trimers in solution. The active site region has been established from the position of the Schiff base forming Lys144 but it has not been possible to confirm it conclusively in independent derivative experiments. An apparent anomaly exists in the location of Glu56 (about 25 Å from Lys144). The latter has been reported to assist in catalysis.     

The effect of oral ethanol ingestion on the diurnal neurotensin secretion in man.

Neurotensin is a tridecapeptide, present in the central nervous system and the gastrointestinal tract in man and animals. The affect of orally administered ethanol (1 g/kg body weight) on the neurotensin secretion over 24 hr period was studied in eight young healthy men. No significant circadian rhythm of neurotensin secretion was detected in the eight subjects studied. Ethanol produced a progressive rise in the plasma level of neurotensin reaching a maximum at 12:00 (13.8 +/- 8.6 pmol/l). At 12:00 and 14:00, the neurotensin concentrations were significantly higher than on the placebo day (p < 0.05). The secretion rate of neurotensin was determined approximately using the area under the curve method. Ethanol produced a transient rise in neurotensin secretion over the first 12 hrs period (08:00-20:00 h) after its administration (p < 0.02). The observation that ethanol increases transiently the neurotensin secretion in man supports the hypothesis that neurotensin may be involved in the biological effect of ethanol. The source of its secretion remains to be elucidated.