Agonistic interactions between the invasive green crab, Carcinus maenas (Linnaeus) and juvenile American lobster, Homarus americanus (Milne Edwards)

Invasive organisms have the potential for competition with native organisms. In the Southern Gulf of St. Lawrence, juvenile American lobsters have a potential spatial overlap with adult green crabs. Crustaceans use agonistic behaviour to settle disputes, with the larger organism often winning contests for limited resources such as food and shelter. Two experiments were carried out using adult green crabs (53-76 mm carapace width) and juvenile American lobsters (28-57 mm carapace length). The first experiment used a limited food resource. We found that green crabs were the first to the food in all trials, fed in significantly more trials than lobsters and spent a significantly greater proportion of time with the food. The lobsters were only able to displace the green crabs from the food in 2 of 65 attempts. The second experiment was designed to examine shelter competition; unexpectedly some predation by green crabs on lobsters occurred, which allowed us to test hypotheses about how relative size and shelter use affect predation. Green crabs captured and consumed juvenile lobsters in 6 of 11 trials. The lobsters that survived spent significantly more time in shelter. There was no clear relationship between shelter use and size of lobster. The lobsters that were larger in relation to the green crabs suffered a higher rate of predation, which we believe was due to more conspicuous activity and less use of shelter. It appears that green crabs have the potential to negatively impact native juvenile lobster.     

PIPER: an FFT-based protein docking program with pairwise potentials

The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this restriction is removed, and the approach is efficiently used with pairwise interaction potentials that substantially improve the docking results. The basic idea is approximating the interaction matrix by its eigenvectors corresponding to the few dominant eigenvalues, resulting in an energy expression written as the sum of a few correlation functions, and solving the problem by repeated FFT calculations. In addition to describing how the method is implemented, we present a novel class of structure-based pairwise intermolecular potentials. The DARS (Decoys As the Reference State) potentials are extracted from structures of protein-protein complexes and use large sets of docked conformations as decoys to derive atom pair distributions in the reference state. The current version of the DARS potential works well for enzyme-inhibitor complexes. With the new FFT-based program, DARS provides much better docking results than the earlier approaches, in many cases generating 50% more near-native docked conformations. Although the potential is far from optimal for antibody-antigen pairs, the results are still slightly better than those given by an earlier FFT method. The docking program PIPER is freely available for noncommercial applications.     

Barley Yellow Dwarf Virus Multiplication and Host Plant Tolerance in Durum Wheat

A Canadian PAV-like isolate of barley yellow dwarf virus (BYDV) was used to infect durum wheat (Triticum durum) cultivars previously identified in field trials involving artificial inoculation as highly sensitive (12 IDSN74), slightly tolerant (La Dulce), and relatively tolerant (Boohai and 12 IDSN227) to BYDV. The cultivars were inoculated in the greenhouse as seedlings, and indexed for virus accumulation by enzyme-linked immunosorbent assay (ELISA) at various intervals between 3 and 60 days thereafter. Mean ELISA values were somewhat consistent with tolerance levels for 4 durum wheat cultivars, but the use of ELISA to screen for BYDV resistance in durum wheat is not practical. The magnitude of the difference between sensitive and tolerant cultivars for the mean ELISA value is not high enough, and it may be necessary to average readings between 3 and 60 days after inoculation to obtain somewhat meaningful ELISA data. The effect of vector aphid numbers on virus titre and aerial biomass in the sensitive durum wheat cv. Karim was also evaluated. There was no significant effect on virus content in a preliminary trial, but a second trial revealed that more viruliferous aphids per plant resulted in higher ELISA values. Infestation with 32 or 50 viruliferous Rhopalosiphum padi per plant depressed biomass yield below the level observed with 1–10 aphids per plant.     

Comparison of media for their aptitude in wheat anther culture

Different media were evaluated with anthers of five spring wheat (Triticum aestivum L.) genotypes for their ability to produce embryos and green plants in anther culture. Our first experiment showed that the addition of a combination of 19 amino acids significantly increased the number of embryos and green plants obtained. The mean number of green plants per 100 anthers for the two genotypes in this experiment, HY320 and B723, went from 28.2 without amino acids in the medium, to 46.7 with addition of amino acids. Our second experiment with the genotypes HY320, Wim and Laval-19 showed that liquid medium with Ficoll is more efficient for anther culture (9.9 green plants/100 anthers) than solid (0 green plants), gelationous media (2.5 green plants/100 anthers) or liquid medium with Membrane Rafts (0 green plants; Hoechst Celanese Corp.). Our third experiment revealed that the effect of replacement of sucrose by maltose varied with the genotype of the donor plant. Maltose partially inhibited the androgenesis of three responsive genotypes, HY320, Wim and Reliance (40.3 green plants/100 anthers instead of 43.9 with sucrose), while maltose significantly increased the androgenesis of the recalcitrant genotype Laval-19 (10.8 green plants/100 anthers instead of 5.4 with sucrose). An amino acid x maltose interaction was also observed. Amino acids without maltose increased androgenesis, but the addition of maltose to the amino acid-enriched medium eliminated this positive effect of the amino acids.     

Screening for Barley Yellow Dwarf Luteovirus Resistance in Barley on the Basis of Virus Movement

The movement of barley yellow dwarf luteovirus (BYDV) was evaluated in susceptible and resistant barley and bread wheat genotypes. After leaf inoculation, the virus infected the root system and the growing point of susceptible earlier than resistant, barley genotypes. No difference in virus movement occurred in resistant and susceptible wheat genotypes. It was possible to reliably differentiate susceptible from resistant genotypes when root extracts of 41 barley genotypes were tested by DAS-ELISA 3 or 4 days after inoculation at the oneleaf stage. When barley plants inoculated at the two- or three-leaf stage were assayed by tissue-blot ELISA on nitrocellulose membrane, virus was detected in the phloem vessels of the growing points of the susceptible, but not of the resistant genotype, 4–6 days after inoculation. Our results thus suggest that screening for BYDV resistance in barley could be done quickly and cheaply especially when assays are made by the tissue-blot test.     

Production of extracellular lipases by Penicillium cyclopium purification and characterization of a partial acylglycerol lipase

Penicillium cyclopium, grown in stationary culture, produces a type I lipase specific for triacylglycerols while, in shaken culture, it produces a type II lipase only active on partial acylglycerols. Lipase II has been purified by ammonium sulfate precipitation and chromatographies on Sephadex G-75 and DEAE-Sephadex. The enzyme exists in several glycosylated forms of 40-43 kDa, which can be converted to a single protein of 37 kDa by enzymatic deglycosylation. Activity of lipase II is maximal at pH 7.0 and 40 degrees C. The enzyme is stable from pH 4.5 to 7.0. Activity is rapidly lost at temperatures above 50 degrees C. The enzyme specifically hydrolyzes monoacylglycerols and diacylglycerols, especially of medium chain fatty acids. The sequence of the 20 first amino acid residues is similar to the N-terminal region of P. camembertii lipase and partially similar to lipases from Humicola lanuginosa and Aspergillus oryzae, but is different from Penicillium cyclopium lipase I. However, it can be observed that residues of valine and serine at positions 2 and 5 in Penicillium cyclopium lipase II are conserved in Penicillium expansum lipase, of which 16 out of the 20 first amino acid residues are similar to Penicillium cyclopium lipase I.     

Performance of the first protein docking server ClusPro in CAPRI rounds 3-5

To evaluate the current status of the protein-protein docking field, the CAPRI experiment came to life. Researchers are given the receptor and ligand 3-dimensional (3D) coordinates before the cocrystallized complex is published. Human predictions of the complex structure are supposed to be submitted within 3 weeks, whereas the server ClusPro has only 24 h and does not make use of any biochemical information. From the 10 targets analyzed in the second evaluation meeting of CAPRI, ClusPro was able to predict meaningful models for 5 targets using only empirical free energy estimates. For two of the targets, the server predictions were assessed to be among the best in the field. Namely, for Targets 8 and 12, ClusPro predicted the model with the most accurate binding-site interface and the model with the highest percentage of nativelike contacts, among 180 and 230 submissions, respectively. After CAPRI, the server has been further developed to predict oligomeric assemblies, and new tools now allow the user to restrict the search for the complex to specific regions on the protein surface, significantly enhancing the predictive capabilities of the server. The performance of ClusPro in CAPRI Rounds 3-5 suggests that clustering the low free energy (i.e., desolvation and electrostatic energy) conformations of a homogeneous conformational sampling of the binding interface is a fast and reliable procedure to detect protein-protein interactions and eliminate false positives. Not including targets that had a significant structural rearrangement upon binding, the success rate of ClusPro was found to be around 71%.