We study the occurrence and dynamics of rogue waves in three-dimensional deep water using phase-resolved numerical simulations based on a high-order spectral (HOS) method. We obtain a large ensemble of nonlinear wave-field simulations (M = 3 in HOS method), initialized by spectral parameters over a broad range, from which nonlinear wave statistics and rogue wave occurrence are investigated. The HOS results are compared to those from the broad-band modified nonlinear Schrödinger (BMNLS) equations. Our results show that for (initially) narrow-band and narrow directional spreading wave fields, modulational instability develops, resulting in non-Gaussian statistics and a probability of rogue wave occurrence that is an order of magnitude higher than linear theory prediction. For longer times, the evolution becomes quasi-stationary with non-Gaussian statistics, a result not predicted by the BMNLS equations (without consideration of dissipation). When waves spread broadly in frequency and direction, the modulational instability effect is reduced, and the statistics and rogue wave probability are qualitatively similar to those from linear theory. To account for the effects of directional spreading on modulational instability, we propose a new modified Benjamin-Feir index for effectively predicting rogue wave occurrence in directional seas. For short-crested seas, the probability of rogue waves based on number frequency is imprecise and problematic. We introduce an area-based probability, which is well defined and convergent for all directional spreading. Based on a large catalogue of simulated rogue wave events, we analyse their geometry using proper orthogonal decomposition (POD). We find that rogue wave profiles containing a single wave can generally be described by a small number of POD modes.

Plant defense responses to pathogen infection involve the production of active oxygen species, including hydrogen peroxide (H2O2). We obtained transgenic potato plants expressing a fungal gene encoding glucose oxidase, which generates H2O2 when glucose is oxidized. H2O2 levels were elevated in both leaf and tuber tissues of these plants. Transgenic potato tubers exhibited strong resistance to a bacterial soft rot disease caused by Erwinia carotovora subsp carotovora, and disease resistance was sustained under both aerobic and anaerobic conditions of bacterial infection. This resistance to soft rot was apparently mediated by elevated levels of H2O2, because the resistance could be counteracted by exogenously added H2O2-degrading catalase. The transgenic plants with increased levels of H2O2 also exhibited enhanced resistance to potato late blight caused by Phytophthora infestans. The development of lesions resulting from infection by P. infestans was significantly delayed in leaves of these plants. Thus, the expression of an active oxygen species-generating enzyme in transgenic plants represents a novel approach for engineering broad-spectrum disease resistance in plants.

Active oxygen species have been postulated to perform multiple functions in plant defense, but their exact role in plant resistance to diseases is not fully understood. We have recently demonstrated H2O2-mediated disease resistance in transgenic potato (Solanum tuberosum) plants expressing a foreign gene encoding glucose oxidase. In this study we provide further evidence that the H2O2-mediated disease resistance in potato is effective against a broad range of plant pathogens. We have investigated mechanisms underlying the H2O2-mediated disease resistance in transgenic potato plants. The constitutively elevated levels of H2O2 induced the accumulation of total salicylic acid severalfold in the leaf tissue of transgenic plants, although no significant change was detected in the level of free salicylic acid. The mRNAs of two defense-related genes encoding the anionic peroxidase and acidic chitinase were also induced. In addition, an increased accumulation of several isoforms of extracellular peroxidase, including a newly induced one, was observed. This was accompanied by a significant increase in the lignin content of stem and root tissues of the transgenic plants. The results suggest that constitutively elevated sublethal levels of H2O2 are sufficient to activate an array of host defense mechanisms, and these defense mechanisms may be a major contributing factor to the H2O2-mediated disease resistance in transgenic plants.

Heterodera glycines, the soybean cyst nematode, is the number one pathogen of soybean (Glycine max). This nematode infects soybean roots and forms an elaborate feeding site in the vascular cylinder. H. glycines produces an arsenal of effector proteins in the secretory esophageal gland cells. More than 60 H. glycines candidate effectors were identified in previous gland-cell-mining projects. However, it is likely that additional candidate effectors remained unidentified. With the goal of identifying remaining H. glycines candidate effectors, we constructed and sequenced a large gland cell cDNA library resulting in 11,814 expressed sequence tags. After bioinformatic filtering for candidate effectors using a number of criteria, in situ hybridizations were performed in H. glycines whole-mount specimens to identify candidate effectors whose mRNA exclusively accumulated in the esophageal gland cells, which is a hallmark of many nematode effectors. This approach resulted in the identification of 18 new H. glycines esophageal gland-cell-specific candidate effectors. Of these candidate effectors, 11 sequences were pioneers without similarities to known proteins while 7 sequences had similarities to functionally annotated proteins in databases. These putative homologies provided the bases for the development of hypotheses about potential functions in the parasitism process.