A study of protein structure changes during hydration by diffuse X-ray scattering: II. Fourier transform analysis of diffuse X-ray scattering data

Radial distribution functions were deduced by Fourier transform analysis of the angular dependences of diffuse X-ray scattering intensities for the following proteins with different hydration degrees: water-soluble α-protein myoglobin, water-soluble (α + β) protein lysozyme, and transmembrane proteins from the photosynthetic reaction centers of purple bacteria Rhodobacter sphaeroides and Blastochlorii (Rhodopseudomonas) viridis. The results of Fourier transform analysis of X-ray scattering intensities give quantitative characteristics of the mechanism underlying the influence of water on the formation of biological macromolecules. On the one hand, water loosens the network of hydrogen bonds, which results in a considerable conformational mobility in the molecules of lysozyme and myoglobin and the reaction centers. On the other hand, water stabilizes and orders the protein globule. A strict correlation was found between the shift of the “first” maximum of the radial distribution function, loosening of the intraglobular hydrogen bonds, increase in the intramolecular mobility, and appearance of pronounced functional activity in macromolecules. The pattern of behavior of the first maximum in the transmembrane proteins of the reaction center was similar to that observed for the water-soluble proteins. However, the first maximum reached the limiting value of 2.9 Å at a considerably lower hydration degree compared with the water-soluble proteins. A quick transition of the protein complex of the reaction center to its native state is due to the fact that the dehydrated conformation of this complex is very close to the native conformation. Comparison of the radial distribution function for water, water-soluble proteins, and transmembrane proteins suggests a quantitative conclusion that water is the least densely packed and ordered system, the water-soluble proteins are more densely packed than water, and the transmembrane proteins are the most densely packed and ordered system.     

Surface Rheology Parameters of Source-Specific Surfactant Films as Indicators of Organic Matter Dynamics

The paper contains the results of natural film experiments carried out on inland and coastal waters in the Dead Vistula catchment area and mouth during 2000–2002, using the integrated Langmuir trough–Wilhelmy plate system. The static film parameters result from the generalized scaling procedures applied to the surface pressure–area isotherms. They appear to reflect in a quantitative and sensitive way the film composition (A_lim, M_w, E_isoth), film solubility and the miscibility of its components (via R, ΔS_c and y factors), and surface concentration (π_eq, Γ_eq). The adsorption kinetics parameters: effective diffusion coefficient D_eff/D and activation energy barrier E_a/RT are derived from dynamic surface pressure. There is a reason to suggest that certain classes of film-forming components or ‘end-members’ may dominate the static and dynamic surface properties. Variation in the surface rheological parameters of source-specific biosurfactants is postulated to reflect organic matter dynamics in natural waters and were measured for the Dead Vistula river, its tributaries and the adjacent coastal area.     

Testing the Sensitivity of Phytoplankton Communities to Changes in Water Temperature and Nutrient Load, in a Temperate Lake

Freshwater lakes are biologically sensitive to changes in the surrounding environment and the impacts that such changes have on their water quality are of considerable ecological, recreational and economic importance. In this study the phytoplankton community model, PROTECH, was used to experiment with the effects of elevated temperatures and increased nutrient load on phytoplankton succession and productivity. The response of a phytoplankton community to combined incremental changes in these drivers was analysed, in order to elucidate the resulting ecological changes. Annual mean phytoplankton biomass increased with increases in temperature and nutrient loading, although the latter had the larger effect. The phenology of the dominant phytoplankton taxa changed with increasing water temperature; the three spring blooming species all peaked earlier in the year. The simulated summer bloom of Anabaena became earlier in the year and the Chlorella bloom later. The increased phytoplankton biomass was largely dominated by the cyanobacterium Anabaena, which was especially prevalent during the summer bloom. This resulted in a progressive loss of phytoplankton biodiversity with increasing water temperature and nutrient supply. Model experimentation showed that whilst both factors greatly affected the community, the changes to nutrient loading generally had the greater effect and that at low nutrient levels the effect of water temperature change was reduced considerably. Finally, the model predicted that cyanobacteria have the potential to dominate the phytoplankton community, with clear consequences for water quality, and that this dominance was at its greatest when high water temperatures were combined with high nutrient loads.     

New material of Pleistocene cats (Carnivora, Felidae) from Southern South America, with comments on biogeography and the fossil record

In this paper the systematic position and age of several Pleistocene cat remains found in southern South American are studied, in an attempt to more fully document the scarce record of the group and clear up their obscure Quaternary history. The fossils are compared with a large sample of recent specimens by means of qualitative and quantitative characters, as well as multivariate methods (discriminant analysis). The age of previous records is restricted using recent chronostratigraphic and biostratigraphic studies. Ly. colocolo is recorded in the late Ensenadan (0.78-0.5 Ma BP) and Bonaerian/Lujanian (0.5 Ma-8.5 Ka BP) ages of the Pampean Region (Argentina) and in the late Pleistocene or Holocene of Tierra del Fuego (Chile). An incomplete hemimandible found in the Bonaerian of the Pampean Region is referred to cf. Herpailurus and could be the earliest record of this lineage. Two other remains could belong to On. geoffroyi, but their incompleteness and some differences prevent their assignation to this recent species. The age of “Felis” vorohuensis is restricted to the late Ensenadan. The fossil record of the Ocelot Lineage is very fragmentary, but it is at least as old as late Ensenadan. Taphonomic biases are responsible for this poor fossil record and this fact could partially explain the hiatus with respect to the timing estimated by molecular divergence. The combination of data suggests that Ly. colocolo, On. guigna, On. geoffroyi and Oreailurus jacobita speciated in South America, supporting previous opinions. If the molecular divergence dates are right the recent diversity of this group could be explained by a minimum of five to six immigrations.     

Using soil profiles of seeds and molecular markers as proxies for sawgrass and wet prairie slough vegetation in Shark Slough, Everglades National Park

We measured the abundance of Cladium jamaicense (Crantz) seeds and three biomarkers in freshwater marsh soils in Shark River Slough (SRS), Everglades National Park (ENP) to determine the degree to which these paleoecological proxies reflect spatial and temporal variation in vegetation. We found that C. jamaicense seeds and the biomarkers Paq, total lignin phenols (TLP) and kaurenes analyzed from surface soils were all significantly correlated with extant aboveground C. jamaicense biomass quantified along a vegetation gradient from a C. jamaicense to a wet prairie/slough (WPS) community. Our results also suggest that these individual proxies may reflect vegetation over different spatial scales: Paq and kaurenes correlated most strongly (R ² = 0.88 and 0.99, respectively) with vegetation within 1 m of a soil sample, while seeds and TLP reflected vegetation 0–20 m upstream of soil samples. These differences in the spatial scale depicted by the different proxies may be complementary in understanding aspects of historic landscape patterning. Soil profiles of short (25 cm) cores showed that downcore variation in C. jamaicense seeds was highly correlated with two of the three biomarkers (Paq, R ² = 0.84, p<0.005; TLP, R ² = 0.97, p<0.0001), and all four of the proxies indicated a recent increase in C. jamaicense biomass at the site. Using a preliminary depth-to-age relationship based on matching charcoal peaks with available ENP fire records (1980-present) specific to our coring site, we found that peak-depths in C. jamaicense seed concentration appeared to correspond to recent minimum water levels (e.g., 1989 and 2001), and low seed abundance corresponded to high water levels (e.g., 1995), consistent with the known autecology of C. jamaicense. In summary, the combination of C. jamaicense seeds and biomarkers may be useful for paleoecological reconstruction of vegetation change and ultimately in guaging the success of ongoing efforts to restore historic hydrologic conditions in the South Florida Everglades.     

A preliminary analysis of the correlation of food-web characteristics with hydrology and nutrient gradients in the southern Everglades

We estimated trophic position and carbon source for three consumers (Florida gar, Lepisosteus platyrhincus; eastern mosquitofish, Gambusia holbrooki; and riverine grass shrimp, Palaemonetes paludosus) from 20 sites representing gradients of productivity and hydrological disturbance in the southern Florida Everglades, U.S.A. We characterized gross primary productivity at each site using light/dark bottle incubation and stem density of emergent vascular plants. We also documented nutrient availability as total phosphorus (TP) in floc and periphyton, and the density of small fishes. Hydrological disturbance was characterized as the time since a site was last dried and the average number of days per year the sites were inundated for the previous 10 years. Food-web attributes were estimated in both the wet and dry seasons by analysis of δ¹⁵N (trophic position) and δ¹³C (food-web carbon source) from 702 samples of aquatic consumers. An index of carbon source was derived from a two-member mixing model with Seminole ramshorn snails (Planorbella duryi) as a basal grazing consumer and scuds (amphipods Hyallela azteca) as a basal detritivore. Snails yielded carbon isotopic values similar to green algae and diatoms, while carbon values of scuds were similar to bulk periphyton and floc; carbon isotopic values of cyanobacteria were enriched in C₁₃ compared to all consumers examined. A carbon source similar to scuds dominated at all but one study site, and though the relative contribution of scud-like and snail-like carbon sources was variable, there was no evidence that these contributions were a function of abiotic factors or season. Gar consistently displayed the highest estimated trophic position of the consumers studied, with mosquitofish feeding at a slightly lower level, and grass shrimp feeding at the lowest level. Trophic position was not correlated with any nutrient or productivity parameter, but did increase for grass shrimp and mosquitofish as the time following droughts increased. Trophic position of Florida gar was positively correlated with emergent plant stem density.     

Identification of QuiP, the Product of Gene PA1032, as the Second Acyl-Homoserine Lactone Acylase of Pseudomonas aeruginosa PAO1

The relevance of the acyl homoserine lactone (acyl-HSL) quorum signals N-3-oxododecanoyl-homoserine lactone (3OC12HSL) and N-butanoyl-homoserine lactone to the biology and virulence of Pseudomonas aeruginosa is well investigated. Previously, P. aeruginosa was shown to degrade long-chain, but not short-chain, acyl-HSLs as sole carbon and energy sources (J. J. Huang, J.-I. Han, L.-H. Zhang, and J. R. Leadbetter, Appl. Environ. Microbiol. 69:5941-5949, 2003). A gene encoding an enzyme with acyl-HSL acylase activity, pvdQ (PA2385), was identified, but it was not required for acyl-HSL utilization. This indicated that P. aeruginosa encodes another acyl-HSL acylase, which we identify here. A comparison of total cell proteins of cultures grown with long-acyl acyl-HSLs versus other substrates implicated the involvement of a homolog of PvdQ, the product of gene PA1032, for which we propose the name QuiP. Transposon mutants of quiP were defective for growth when P. aeruginosa was cultured in medium containing decanoyl-HSL as a sole carbon and energy source. Complementation with a functional copy of quiP rescued this growth defect. When P. aeruginosa was grown in buffered lysogeny broth, constitutive expression of QuiP in P. aeruginosa led to decreased accumulations of the quorum signal 3OC12HSL, relative to the wild type. Heterologous expression of QuiP was sufficient to confer long-chain acyl-HSL acylase activity upon Escherichia coli. Examination of gene expression patterns during acyl-HSL-dependent growth of P. aeruginosa further supported the involvement of quiP in signal decay and revealed other genes also possibly involved. It is not yet known under which “natural” conditions quiP is expressed or how P. aeruginosa balances the expression of its quorum-sensing systems with the expression of its acyl-HSL acylase activities.     

Use of Optical Density Detection Times To Assess the Effect of Acetic Acid on Single-Cell Kinetics

The growth of Listeria innocua at different acetic acid concentrations (0 to 2,000 ppm) was monitored by optical density measurements in a Bioscreen (Labsystems, Vantaa, Finland). The generated populations came from low inocula that were obtained by serial dilution. A new method to estimate both the growth rate and the lag time of single cells from the detection times (time to reach an optical density of 0.11) was developed. It assumes that the single-cell lag times follow a gamma distribution and takes into account the randomness of the inoculation level. (The initial cell number per well was assumed to follow a Poisson distribution.) In this way, relatively small numbers of replicates are sufficient to obtain a robust estimation of the distribution of single-cell lag times. The results were validated with plate count experiments. It was found that logarithms of both the growth rates and of population lag times increased linearly with the acetic acid concentration. The logarithm of the scale parameter of the gamma distribution of the single-cell lag times also increased linearly with the acetic acid concentration irrespective of the phase of the inoculum.