The ppuI-rsaL-ppuR quorum-sensing system regulates cellular motility,pectate lyase activity,and virulence in potato opportunistic pathogen Pseudomonas sp. StFLB209

Pseudomonas sp. StFLB209 was isolated from potato leaf as an N-acylhomoserine lactone (AHL)-producing bacterium and showed a close phylogenetic relationship with P. cichorii, a known plant pathogen. Although there are no reports of potato disease caused by pseudomonads in Japan, StFLB209 was pathogenic to potato leaf. In this study, we reveal the complete genome sequence of StFLB209, and show that the strain possesses a ppuI-rsaL-ppuR quorum-sensing system, the sequence of which shares a high similarity with that of Pseudomonas putida. Disruption of ppuI results in a loss of AHL production as well as remarkable reduction in motility. StFLB209 possesses strong pectate lyase activity and causes maceration on potato tuber and leaf, which was slightly reduced in the ppuI mutant. These results suggest that the quorum-sensing system is well conserved between StFLB209 and P. putida and that the system is essential for motility, full pectate lyase activity, and virulence in StFLB209.     

Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction

Traditional sequence analysis algorithms fail to identify distant homologies when they lie beyond a detection horizon. In this review, we discuss how co-evolution-based contact and distance prediction methods are pushing back this homology detection horizon, thereby yielding new functional insights and experimentally testable hypotheses. Based on correlated substitutions, these methods divine three-dimensional constraints among amino acids in protein sequences that were previously devoid of all annotated domains and repeats. The new algorithms discern hidden structure in an otherwise featureless sequence landscape. Their revelatory impact promises to be as profound as the use, by archaeologists, of ground-penetrating radar to discern long-hidden, subterranean structures. As examples of this, we describe how triplicated structures reflecting longin domains in MON1A-like proteins, or UVR-like repeats in DISC1, emerge from their predicted contact and distance maps. These methods also help to resolve structures that do not conform to a “beads-on-a-string” model of protein domains. In one such example, we describe CFAP298 whose ubiquitin-like domain was previously challenging to perceive owing to a large sequence insertion within it. More generally, the new algorithms permit an easier appreciation of domain families and folds whose evolution involved structural insertion or rearrangement. As we exemplify with α1-antitrypsin, coevolution-based predicted contacts may also yield insights into protein dynamics and conformational change. This new combination of structure prediction (using innovative co-evolution based methods) and homology inference (using more traditional sequence analysis approaches) shows great promise for bringing into view a sea of evolutionary relationships that had hitherto lain far beyond the horizon of homology detection.     

Testing predictions of beetle community patterns derived empirically using remote sensing

Patterns generated from ecological surveys are rarely tested in similar habitats to assess the accuracy of predictions. Testing empirically derived predictions provides a strong tool for establishing the consistency of general patterns in ecology. We test the consistency of beetle community associations with habitat complexity in open canopy forests and make both community and morphospecies-level comparisons with results from a previous study. We use Normalized Difference Vegetation Indices (NDVIs) from remote sensing as a surrogate for habitat complexity. The positive relationships between NDVIs and site-based beetle species richness and abundance were consistent in open canopy forests both south and north of Sydney, Australia. NDVIs were also useful for predicting differences in beetle composition in open canopy forests. Taxon-specific responses to NDVI differences in 'southern forests' were very similar to responses in 'northern forests', most likely reflecting beetle trophic roles. This study shows that NDVIs can be used as rapid biodiversity indicators, when integrated with identified faunal responses to vegetation structure, provided that the lower vegetation strata may be measured by remote sensing.     

Relationship of Aerial Broad Band Reflectance to Meloidogyne incognita Density in Cotton

Aerial images were obtained on 22 July 1999 and 4 August 2000 from five cotton sites infested with Meloidogyne incognita. Images contained three broad bands representing the green (500-600 nm), red (600-700 nm), and near-infrared (700-900 nm) spectrum. Soil samples were collected and assayed for nematodes in the fall at these sites. Sampling locations were identified from images, by locating the coordinates of a wide range of light intensity (measured as a digital number) for each single band, and combinations of bands. There was no single band or band combination in which reflectance consistently predicted M. incognita density. In all 10 site-year combinations, the minimum number of samples necessary to estimate M. incognita density within 25% of the population mean was greater when sampling by reflectance-based classes (3 to 4 per site) than sampling based on the entire site as one unit. Two sites were sampled at multiple times during the growing season. At these sites, there was no single time during the growing season optimal to take images for nematode sampling. Aerial infrared photography conducted during the growing season could not be used to accurately determine fall population densities of M. incognita.     

Zoning eco-environmental vulnerability for environmental management and protection

Eco-environmental vulnerability assessment is crucial for environmental and resource management. However, evaluation of eco-environmental vulnerability over large areas is a difficult and complex process because it is affected by many variables including hydro-meteorology, topography, land resources, and human activities. The Thua Thien – Hue Province and its largest river system, the Perfume River, are vital to the social-economic development of the north central coastal region of Vietnam, but there is no zoning system for environmental protection in this region. An assessment framework is proposed to evaluate the vulnerable eco-environment in association with 16 variables with 6 of them constructed from Landsat 8 satellite image products. The remaining variables were extracted from digital maps. Each variable was evaluated and spatially mapped with the aid of an analytical hierarchy process (AHP) and geographical information system (GIS). An eco-environmental vulnerability map is assorted into six vulnerability levels consisting of potential, slight, light, medium, heavy, and very heavy vulnerabilities, representing 14%, 27%, 17%, 26%, 13%, 3% of the study area, respectively. It is found that heavy and very heavy vulnerable areas appear mainly in the low and medium lands where social-economic activities have been developing rapidly. Tiny percentages of medium and heavy vulnerable levels occur in high land areas probably caused by agricultural practices in highlands, slash and burn cultivation and removal of natural forests with new plantation forests. Based on our results, three ecological zones requiring different development and protection solutions are proposed to restore local eco-environment toward sustainable development. The proposed integrated method of remote sensing (RS), GIS, and AHP to evaluate the eco-environmental vulnerability is useful for environmental protection and proper planning for land use and construction in the future.     

Presence of Quorum-Sensing-Mediated Gene Regulation in Pathogenic Ice-Nucleation-Active (INA) Bacteria

Nine out of a total of 20 pathogenic ice-nucleation-active bacteria, with different levels of inducible INA, were tested and found positive for their ability to synthesize quorum-sensing (QS) signals. The bacteria were isolated from willow plants and belonged to the genera Bacillus, Erwinia, Pseudomonas and Sphingomonas. As reporter bacteria, to detect the homoserine lactone (HSL) autoinducer, Agrobacterium tumefaciens, Chromobacterium violaceum, Pseudomonas aeroginosa, Aeromonas hydrophila and Vibrio fischeri strains were used. We thus provide evidence that pathogenic ice-nucleation bacteria with inducible INA produce QS signals that in other bacteria have been shown to be in the control of genes of importance for pathogenicity.     

Acoustic mapping using a multibeam echosounder reveals cold-water coral reefs and surrounding habitats

Multibeam surveys were carried out in four areas to the west of Scotland where the coral Lophelia pertusa had previously been recorded. Distinctive seabed mounds were found in one area; video images from the mounds showed coral reef formation, and grab samples recovered L. pertusa reef framework and rubble. Skeleton samples were dated to 3,800 years BP. Grab samples contained 123 species of fauna. The reef structures, termed the Mingulay Reef Complex, were identified as topographic mound-like structures from the bathymetric data and were also visible on the backscatter images. The location of the reefs coincides with Atlantic bottom waters, close to a primary productivity centre and mixing zone, in an area where currents are likely to be accelerated by rocky seafloor ridges. This study shows that multibeam echosounders are powerful tools to locate and map deep-water coral reefs irrespective of water depth. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

根瘤菌与群体感应

细菌在高细胞密度下可以产生群体感应信号分子,调控细菌相关基因的表达,这种信号分子被称为自体诱导物。酰基高丝氨酸内酯类化合物(acyl-HSLs)是在根瘤菌中广泛存在的一类自体诱导物,该群体感应系统与根瘤菌和植物的共生作用密切相关。本文概述了AHLs介导的群体感应系统的组成及调控机制和不同根瘤菌中群体感应调节对根瘤菌生理行为及共生固氮的影响。