Integrative modeling of protein-protein interactions with pyDock for the new docking challenges

The seventh CAPRI edition imposed new challenges to the modeling of protein-protein complexes, such as multimeric oligomerization, protein-peptide, and protein-oligosaccharide interactions. Many of the proposed targets needed the efficient integration of rigid-body docking, template-based modeling, flexible optimization, multiparametric scoring, and experimental restraints. This was especially relevant for the multimolecular assemblies proposed in the CASP12-CAPRI37 and CASP13-CAPRI46 joint rounds, which were described and evaluated elsewhere. Focusing on the purely CAPRI targets of this edition (rounds 38-45), we have participated in all 17 assessed targets (considering heteromeric and homomeric interfaces in T125 as two separate targets) both as predictors and as scorers, by using integrative modeling based on our docking and scoring approaches: pyDock, IRaPPA, and LightDock. In the protein-protein and protein-peptide targets, we have also participated with our webserver (pyDockWeb). On these 17 CAPRI targets, we submitted acceptable models (or better) within our top 10 models for 10 targets as predictors, 13 targets as scorers, and 4 targets as servers. In summary, our participation in this CAPRI edition confirmed the capabilities of pyDock for the scoring of docking models, increasingly used within the context of integrative modeling of protein interactions and multimeric assemblies.     

Contrasting sensitivity of nestling and fledgling Barn Swallow Hirundo rustica body mass to local weather conditions

Local weather can influence the growth and development of young birds either indirectly, by modifying prey availability, or directly, by affecting energetic trade-offs. Such effects can have lasting implications for life history traits, but the nature of these effets may vary with the developmental stage of the birds, and over timescales from days to weeks. We examined the interactive effects of temperature, rainfall and wind speed on the mass of nestling and fledgling Barn Swallows Hirundo rustica both on the day of capture and averaging weather across the time since hatching. At the daily timescale, nestling mass was negatively correlated with temperature, but the strength of this association depended on the level of rainfall and wind speed; nestlings were typically heavier on dry or windy days, and the negative effect of temperature was strongest under calm or wet conditions. At the early lifetime timescale (i.e. from hatching to pre-fledging), nestling mass was negatively correlated with temperature at low wind speed. Fledgling body mass was less sensitive to weather; the only weather effect evident was a negative correlation with temperature at the daily scale under high rainfall that became slightly positive under low rainfall. These changes are consistent with weather effects on the availability and distribution of insects within the landscape (e.g. causing high concentrations of flying insects) and with the effects of weather variation on nest microclimate. These results together demonstrate the impacts of weather on chick growth, over immediate (daily) and longer term (nestling/fledgling lifetime) timescales. This shows that sensitivity to local weather conditions varies across the early lifetime of young birds (nestling–fledgling stages) and illustrates the mechanisms by which larger scale (climate) variations influence the body condition of individuals.     

Neotyphodium endophyte strain and superoxide dismutase activity in perennial ryegrass plants under water deficit

The presence of Neotyphodium endophyte in forage grass tillers has been associated with increased tolerance of abiotic stresses. The effect of four endophyte treatments (plants with three different strains of Neotyphodium lolii compared with plants without endophyte) on superoxide dismutase (SOD) (EC1.15.1.1) activity in Lolium perenne cv ‘Grasslands Samson’ was measured under high and low dehydration regimes in a glasshouse experiment. SOD activity was assayed by a microplate method utilising the inhibition of reduction of a tetrazolium dye by superoxide radicals. A progressive increase in dehydration over 2 weeks reduced shoot fresh weight, dry weight and shoot water content for high, compared with low, moisture-stressed plants. Mean shoot fresh weight was significantly lower for plants with strain AR37 endophyte than for plants with strain AR1 endophyte, wild-type or endophyte-free plants, but there was no interaction between endophyte treatment and dehydration treatment. There were no differences in mean SOD activity between the dehydration treatments, and the four endophyte treatments at any of the harvests. All harvest mean SOD levels for plants in both stress groups, however, were significantly different from the preceding harvest value. Between the first and second week of moisture stress there was a significant endophyte by harvest interaction for mean percentage change in SOD activity when activity in plants with wild-type strain endophyte increased more rapidly than in AR1, AR37 or endophyte-free plants. The results are in agreement with earlier reports suggesting that Neotyphodium endophytes do not have major effects on the water stress physiology of perennial ryegrass, although water deficits applied were not extreme.     

Rapid Sample Processing for Detection of Food-Borne Pathogens via Cross-Flow Microfiltration

This paper reports an approach to enable rapid concentration and recovery of bacterial cells from aqueous chicken homogenates as a preanalytical step of detection. This approach includes biochemical pretreatment and prefiltration of food samples and development of an automated cell concentration instrument based on cross-flow microfiltration. A polysulfone hollow-fiber membrane module having a nominal pore size of 0.2 μm constitutes the core of the cell concentration instrument. The aqueous chicken homogenate samples were circulated within the cross-flow system achieving 500- to 1,000-fold concentration of inoculated Salmonella enterica serovar Enteritidis and naturally occurring microbiota with 70% recovery of viable cells as determined by plate counting and quantitative PCR (qPCR) within 35 to 45 min. These steps enabled 10 CFU/ml microorganisms in chicken homogenates or 10² CFU/g chicken to be quantified. Cleaning and sterilizing the instrument and membrane module by stepwise hydraulic and chemical cleaning (sodium hydroxide and ethanol) enabled reuse of the membrane 15 times before replacement. This approach begins to address the critical need for the food industry for detecting food pathogens within 6 h or less.     

Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle

The replication and life cycle of the influenza virus is governed by an intricate network of intracellular regulatory events during infection, including interactions with an even more complex system of biochemical interactions of the host cell. Computational modeling and systems biology have been successfully employed to further the understanding of various biological systems, however, computational studies of the complexity of intracellular interactions during influenza infection is lacking. In this work, we present the first large-scale dynamical model of the infection and replication cycle of influenza, as well as some of its interactions with the host’s signaling machinery. Specifically, we focus on and visualize the dynamics of the internalization and endocytosis of the virus, replication and translation of its genomic components, as well as the assembly of progeny virions. Simulations and analyses of the models dynamics qualitatively reproduced numerous biological phenomena discovered in the laboratory. Finally, comparisons of the dynamics of existing and proposed drugs, our results suggest that a drug targeting PB1:PA would be more efficient than existing Amantadin/Rimantaine or Zanamivir/Oseltamivir.     

Description of a new species of Neralsia Cameron with a wide distribution in the American continent: N. incompleta n. sp. (Hymenoptera: Figitidae: Figitinae)

In this study a new species of Neralsia is described, N. incompleta n. sp. The radial cell shape allows to distinguish it clearly from the rest of species of the genus. The distribution of Neralsia incompleta n. sp. is probably the entire American continent, having been collected from Canada to Paraguay. In spite of its abundance, the associated biology is unknown, although it should be related with parasitism of Diptera Cyclorrhapha.     

Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716

The RXopJ4 resistance locus from the wild accession Solanum pennellii (Sp) LA716 confers resistance to bacterial spot disease of tomato (S. lycopersicum, Sl) caused by Xanthomonas perforans (Xp). RXopJ4 resistance depends on recognition of the pathogen type III effector protein XopJ4. We used a collection of Sp introgression lines (ILs) to narrow the RXopJ4 locus to a 4.2-Mb segment on the long arm of chromosome 6, encompassed by the ILs 6-2 and 6-2-2. We then adapted or developed a collection of 14 molecular markers to map on a segregating F₂ population from a cross between the susceptible parent Sl FL8000 and the resistant parent RXopJ4 8000 OC₇. In the F₂ population, a 190-kb segment between the markers J350 and J352 cosegregated with resistance. This fine mapping will enable both the identification of candidate genes and the detection of resistant plants using cosegregating markers. The RXopJ4 resistance gene(s), in combination with other recently characterized genes and a quantitative trait locus (QTL) for bacterial spot disease resistance, will likely be an effective tool for the development of durable resistance in cultivated tomato.     

Uncovering the Lactobacillus plantarum WCFS1 Gallate Decarboxylase Involved in Tannin Degradation

Lactobacillus plantarum is a lactic acid bacterium able to degrade tannins by the subsequent action of tannase and gallate decarboxylase enzymes. The gene encoding tannase had previously been identified, whereas the gene encoding gallate decarboxylase is unknown. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of gallic-acid induced L. plantarum extracts showed a 54-kDa protein which was absent in the uninduced cells. This protein was identified as Lp_2945, putatively annotated UbiD. Homology searches identified ubiD-like genes located within three-gene operons which encoded the three subunits of nonoxidative aromatic acid decarboxylases. L. plantarum is the only bacterium in which the lpdC (lp_2945) gene and the lpdB and lpdD (lp_0271 and lp_0272) genes are separated in the chromosome. Combination of extracts from recombinant Escherichia coli cells expressing the lpdB, lpdC, and lpdC genes demonstrated that LpdC is the only protein required to yield gallate decarboxylase activity. However, the disruption of these genes in L. plantarum revealed that the lpdB and lpdC gene products are essential for gallate decarboxylase activity. Similar to L. plantarum tannase, which exhibited activity only in esters derived from gallic and protocatechuic acids, purified His6-LpdC protein from E. coli showed decarboxylase activity against gallic and protocatechuic acids. In contrast to the tannase activity, gallate decarboxylase activity is widely present among lactic acid bacteria. This study constitutes the first genetic characterization of a gallate decarboxylase enzyme and provides new insights into the role of the different subunits of bacterial nonoxidative aromatic acid decarboxylases.     

Occurrence of Poecilochirus austroasiaticus (Acari: Parasitidae) in forensic autopsies and its application on postmortem interval estimation

Despite the fact that mites were used at the dawn of forensic entomology to elucidate the postmortem interval, their use in current cases remains quite low for procedural reasons such as inadequate taxonomic knowledge. A special interest is focused on the phoretic stages of some mite species, because the phoront-host specificity allows us to deduce in many occasions the presence of the carrier (usually Diptera or Coleoptera) although it has not been seen in the sampling performed in situ or in the autopsy room. In this article, we describe two cases where Poecilochirus austroasiaticus Vitzthum (Acari: Parasitidae) was sampled in the autopsy room. In the first case, we could sample the host, Thanatophilus ruficornis (Küster) (Coleoptera: Silphidae), which was still carrying phoretic stages of the mite on the body. That attachment allowed, by observing starvation/feeding periods as a function of the digestive tract filling, the establishment of chronological cycles of phoretic behavior, showing maximum peaks of phoronts during arrival and departure from the corpse and the lowest values in the phase of host feeding. From the sarcosaprophagous fauna, we were able to determine in this case a minimum postmortem interval of 10 days. In the second case, we found no Silphidae at the place where the corpse was found or at the autopsy, but a postmortem interval of 13 days could be established by the high specificity of this interspecific relationship and the departure from the corpse of this family of Coleoptera.