Dipole source localization by the mottled sculpin II. The role of lateral line excitation patterns

Extracellular, single unit recording techniques were used to measure the responses of posterior lateral line nerve fibers to a 50-Hz dipole source that slowly changed its location along the length of the fish. The flow-field equations for a dipole source were used to model the pressure gradient pattern and thus, the expected excitation pattern along a linear array of lateral line receptor organs for different source locations. Finally, excitation patterns were similarly modeled along the left and right side of the fish's head for actual steps taken by sculpin in approach pathways to the 50-Hz dipole source. Spatial histograms of posterior lateral line nerve fiber responses to different locations of the dipole source could be predicted from pressure gradient patterns modeled from the flow-field equations, confirming that the modeling approach applied to behavioral results was a good predictor of excitation patterns likely to be encoded by the lateral line periphery. An examination of how modeled excitation patterns changed from one position to the next in typical approach pathways and how patterns differed between positions from which successful and unsuccessful strikes were launched suggests that approach and strike strategies can indeed be explained by the information available in excitation patterns. In particular, changes in the spatial distribution of pressure gradient directions (polarities), available only when the source is lateral (as opposed to directly in front of the fish), appear to enhance the ability of sculpin to determine source distance. Without such information, misses are more likely to occur and successful strikes are more likely to be launched from short distances only. Accepted: 23 October 1996     

Structural basis for the allosteric regulation and substrate recognition of human cytosolic 5'-nucleotidase II

Cytosolic 5′-nucleotidase II (cN-II) catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5′-monophosphates and participates in the regulation of purine nucleotide pools within the cell. It interferes with the phosphorylation-dependent activation of nucleoside analogues used in the treatment of cancer and viral diseases. It is allosterically activated by a number of phosphate-containing cellular metabolites such as ATP, diadenosine polyphosphates, and 2,3-bisphosphoglycerate, which couple its activity with the metabolic state of the cell. We present seven high-resolution structures of human cN-II, including a ligand-free form and complexes with various substrates and effectors. These structures reveal the structural basis for the allosteric activation of cN-II, uncovering a mechanism where an effector-induced disorder-to-order transition generates rearrangements within the catalytic site and the subsequent coordination of the catalytically essential magnesium. Central to the activation is the large transition of the catalytically essential Asp356. This study also provides the structural basis for the substrate specificity of cN-II, where Arg202, Asp206, and Phe157 seem to be important residues for purine/pyrimidine selectivity. These structures provide a comprehensive structural basis for the design of cN-II inhibitors. They also contribute to the understanding of how the nucleotide salvage pathway is regulated at a molecular level.     

Crystal structure of the passenger domain of the Escherichia coli autotransporter EspP

Autotransporters represent a large superfamily of known and putative virulence factors produced by Gram-negative bacteria. They consist of an N-terminal “passenger domain” responsible for the specific effector functions of the molecule and a C-terminal “β-domain” responsible for translocation of the passenger across the bacterial outer membrane. Here, we present the 2.5-Å crystal structure of the passenger domain of the extracellular serine protease EspP, produced by the pathogen Escherichia coli O157:H7 and a member of the serine protease autotransporters of Enterobacteriaceae (SPATEs). Like the previously structurally characterized SPATE passenger domains, the EspP passenger domain contains an extended right-handed parallel β-helix preceded by an N-terminal globular domain housing the catalytic function of the protease. Of note, however, is the absence of a second globular domain protruding from this β-helix. We describe the structure of the EspP passenger domain in the context of previous results and provide an alternative hypothesis for the function of the β-helix within SPATEs.     

Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding

Human salivary α-amylase (HSAmy) has three distinct functions relevant to oral health: (1) hydrolysis of starch, (2) binding to hydroxyapatite (HA), and (3) binding to bacteria (e.g., viridans streptococci). Although the active site of HSAmy for starch hydrolysis is well-characterized, the regions responsible for bacterial binding are yet to be defined. Since HSAmy possesses several secondary saccharide-binding sites in which aromatic residues are prominently located, we hypothesized that one or more of the secondary saccharide-binding sites harboring the aromatic residues may play an important role in bacterial binding. To test this hypothesis, the aromatic residues at five secondary binding sites were mutated to alanine to generate six mutants representing either single (W203A, Y276A, and W284A), double (Y276A/W284A and W316A/W388A), or multiple [W134A/W203A/Y276A/W284A/W316A/W388A; human salivary α-amylase aromatic residue multiple mutant (HSAmy-ar)] mutations. The crystal structure of HSAmy-ar as an acarbose complex was determined at a resolution of 1.5 Å and compared with the existing wild-type acarbose complex. The wild-type and the mutant enzymes were characterized for their abilities to exhibit enzyme activity, starch-binding activity, HA-binding activity, and bacterial binding activity. Our results clearly showed that (1) mutation of aromatic residues does not alter the overall conformation of the molecule; (2) single or double mutants showed either moderate or minimal changes in both starch-binding activity and bacterial binding activity, whereas HSAmy-ar showed significant reduction in these activities; (3) starch-hydrolytic activity was reduced by 10-fold in HSAmy-ar; (4) oligosaccharide-hydrolytic activity was reduced in all mutants, but the action pattern was similar to that of the wild-type enzyme; and (5) HA binding was unaffected in HSAmy-ar. These results clearly show that the aromatic residues at the secondary saccharide-binding sites in HSAmy play a critical role in bacterial binding and in starch-hydrolytic functions of HSAmy.     

Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool

GeoCAT is an open source, browser based tool that performs rapid geospatial analysis to ease the process of Red Listing taxa. Developed to utilise spatially referenced primary occurrence data, the analysis focuses on two aspects of the geographic range of a taxon: the extent of occurrence (EOO) and the area of occupancy (AOO). These metrics form part of the IUCN Red List categories and criteria and have often proved challenging to obtain in an accurate, consistent and repeatable way. Within a familiar Google Maps environment, GeoCAT users can quickly and easily combine data from multiple sources such as GBIF, Flickr and Scratchpads as well as user generated occurrence data. Analysis is done with the click of a button and is visualised instantly, providing an indication of the Red List threat rating, subject to meeting the full requirements of the criteria. Outputs including the results, data and parameters used for analysis are stored in a GeoCAT file that can be easily reloaded or shared with collaborators. GeoCAT is a first step toward automating the data handling process of Red List assessing and provides a valuable hub from which further developments and enhancements can be spawned.     

Pollution risk assessment based on source apportionment in a groundwater resource area,NE China

Pollution risk assessment of a groundwater resource area is instrumental in contributing to groundwater protection. This study considered the evaluation results of source apportionment by combining a principal component analysis (PCA) with a factor analysis (FA) to identify potential risk sources. The vulnerability was evaluated using a DRASTIC model as the main pollution pathway, and groundwater quality as a pollution receptor, in order to validate the risk of pollution in a typical groundwater resource area of northeastern China. Results showed that four principal potential pollution sources were point source pollution such as water-rock interaction, dissolution of iron and manganese bearing minerals due to geological processes, non-point source pollution of nitrogen such as agriculture fertilizers, and organic pollution resulting from domestic and industrial wastewater. A “high” and “relatively high” pollution risk occurred mainly at the northwestern and southeastern edges of the region, respectively, with a widely distributed “moderate” pollution risk over the majority of the study area, and a “relatively low” and “low” pollution risk located mainly in the central of the Limin Groundwater Resources area, which showed that the potential pollution sources, especially due to human activity, have significantly changed the distribution of pollution risk in groundwater resource areas.     

Modeling and measuring lateral line excitation patterns to changing dipole source locations

In order to determine excitation patterns to the lateral line system from a nearby 50 Hz oscillating sphere, dipole flow field equations were used to model the spatial distribution of pressures along a linear array of lateral line canal pores. Modeled predictions were then compared to pressure distributions measured for the same dipole source with a miniature hydrophone placed in a small test tank used for neurophysiological experiments. Finally, neural responses from posterior lateral line nerve fibers in the goldfish were measured in the test tank to demonstrate that modeled and measured pressure gradient patterns were encoded by the lateral line periphery. Response patterns to a 50 Hz dipole source that slowly changed location along the length of the fish included (1) peaks and valleys in spike-rate responses corresponding to changes in pressure gradient amplitudes, (2) 180° phase-shifts corresponding to reversals in the direction of the pressure gradient and (3) distance-dependent changes in the locations of peaks, valleys and 180° phase-shifts. Modeled pressure gradient patterns also predict that the number of neural amplitude peaks and phase transitions will vary as a function of neuromast orientation and axis of source oscillation. The faithful way in which the lateral line periphery encodes pressure gradient patterns has implications for how source location and distance might be encoded by excitation patterns in the CNS. Phase-shift information may be important for (1) inhibitory/excitatory sculpting of receptive fields and (2) unambiguously encoding source distance so that increases in source distance are not confused with decreases in source amplitude.     

Temperature-dependent feedback inhibition of photosynthesis in peanut

Arachis hypogaea L. is a tropical crop that is slow-growing at temperatures below 25°C. Unadapted CO₂-assimilation rate (A) showed insufficient variation between 15 and 30°C in the short term (hours) to explain this marked reduction in growth. However, at longer periods (12 d), A was depressed as were growth rate and leafproduction rate. To examine the possible relationship between growth, A and sink demand plants were transferred from 30°C, which is near the optimum for growth, to a suboptimal temperature (19°C). In the first 2 d of cooling, A decreased by 50–70%, the stomata stayed open, and the intercellular CO₂ concentration (c_i) rose, i.e. the decrease in A of the cooled plants was the result of non-stomatal factors. Changes in dark respiration did not account for the decline in A.Clear evidence was obtained of sink control of A by independently manipulating the temperature of different leaves on the plant. Cooling (to 19°C) most of the plant (the sink) led to a 70% decline in A of the remaining leaves at 30°C after 3 d, whereas the converse treatments (30°C sink, 19°C source) resulted in small changes (17%). In plants at 19°C which were exposed to low CO₂ concentration to prevent photosynthesis, A was not reduced when measured at normal CO₂ concentrations, indicating that carbohydrate accumulation was responsible for the decline in A. Dry-matter build-up at suboptimal temperature was also consistent with end-product inhibition of photosynthesis.Abbreviations and symbols A (mol·m^-2·s^-1) rate of net CO₂ assimilation - C_i (l·l^-1) substomatal CO₂ concentration - DW (g) dry weight - g (mol·m^-2·s^-1) stomatal conductance to diffusion of water vapour - PFD (mol·m^-2·s^-1) photon flux density