Isolation and characterization of Dehalococcoides sp. strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe

A strictly anaerobic bacterium was isolated from tetrachloroethene (PCE)-to-ethene dechlorinating microcosms established with river sediment without prior exposure to chlorinated solvents. The isolation procedure included the addition of 2-bromoethanesulfonate to select against methanogenic archaea, >50 consecutive 1-2% (v/v) transfers to reduced mineral salts medium amended with trichloroethene (TCE), acetate, and hydrogen, the addition of ampicillin, and the dilution-to-extinction principle. Culture-dependent and 16S rRNA gene-targeted approaches suggested culture purity. Microscopic examination revealed a homogeneous culture of an organism with a distinct, disc-shaped morphology. The isolate shared >99% 16S rRNA gene sequence similarity with members of the Pinellas group of the Dehalococcoides cluster, and was designated Dehalococcoides sp. strain FL2. Strain FL2 could be propagated with TCE, cis-1,2-dichloroethene (cis-DCE), or trans-DCE as the electron acceptors, acetate as the carbon source, and hydrogen as the electron donor in defined, completely synthetic medium. No other growth-supporting redox couples were identified. Trichloroethene, cis-DCE and trans-DCE were dechlorinated at rates of 27.5, 30.4 and 18.8 micromol l-1 day-1 respectively. Quantitative real-time polymerase chain reaction (PCR) with a fluorescently labelled linear hybridization probe confirmed growth with these electron acceptors, and suggested that strain FL2 captures energy from both the TCE-to-cis-DCE and 1,2-DCE-to-VC dechlorination steps. Tetrachloroethene and vinyl chloride (VC) were slowly and cometabolically dechlorinated in the presence of a growth-supporting chloroethene, but ethene formation was incomplete, even after prolonged incubation. At room temperature, strain FL2 grew with a doubling time of 2.4 days, and yielded 166.1+/-10.2 mg of protein per mole of chloride released. In the presence of excess electron acceptor, strain FL2 consumed hydrogen to a concentration of 0.061+/-0.016 nM. Dechlorination ceased following the addition of 0.5 mM sulfite, whereas sulfate (10 mM) and nitrate (5 mM) had no inhibitory effects.     

Landscape effects on large scale abundance patterns of turtle doves Streptopelia turtur in Portugal

The European turtle dove is both a highly valued game species and a species of conservation concern, which is declining due probably to a combination of habitat degradation and unsustainable hunting. Although declines seem to be less severe in the Mediterranean region, it remains uncertain the extent to which ongoing land use changes will negatively affect this species. This study examined this issue, by estimating the effects of landscape composition on the broad scale abundance pattern of breeding turtle doves in continental Portugal. Turtle doves were surveyed in the breeding seasons of 2002 and 2003, from 3160 point counts spaced at about 1-km intervals along 158 transects of about 20 km, evenly covering the country. The frequency of occurrence of turtle doves at each transect was used as a proxy of species abundance, and related using GAM modelling to 21 variables describing land cover and woody linear features (e.g., hedgerows and riparian galleries). Turtle doves were most abundant in north- and central-eastern Portugal, with high abundances also recorded in the regions around Lisbon and along the Guadiana valley. Abundances were positively related to forest cover, particularly by broadleaved forests and by pine stands without woody understory, to cover by permanent crops, and to the density of woody linear habitats. Results suggest that conservation of Mediterranean turtle doves requires policies and management strategies reversing the pervasive trends of forest management neglect and agricultural abandonment, while preserving hedgerows and riparian galleries in more intensive agricultural landscapes.     

Herbivory: effects on plant abundance, distribution and population growth

Plants are attacked by many different consumers. A critical question is how often, and under what conditions, common reductions in growth, fecundity or even survival that occur due to herbivory translate to meaningful impacts on abundance, distribution or dynamics of plant populations. Here, we review population-level studies of the effects of consumers on plant dynamics and evaluate: (i) whether particular consumers have predictably more or less influence on plant abundance, (ii) whether particular plant life-history types are predictably more vulnerable to herbivory at the population level, (iii) whether the strength of plant-consumer interactions shifts predictably across environmental gradients and (iv) the role of consumers in influencing plant distributional limits. Existing studies demonstrate numerous examples of consumers limiting local plant abundance and distribution. We found larger effects of consumers on grassland than woodland forbs, stronger effects of herbivory in areas with high versus low disturbance, but no systematic or unambiguous differences in the impact of consumers based on plant life-history or herbivore feeding mode. However, our ability to evaluate these and other patterns is limited by the small (but growing) number of studies in this area. As an impetus for further study, we review strengths and challenges of population-level studies, such as interpreting net impacts of consumers in the presence of density dependence and seed bank dynamics.     

Productivity and abundance of large sponge populations on Flinders Reef flats,Coral Sea

Large populations of flattened sponges with cyanobacterial symbionts were observed on the shallow reef-flats of the Flinders Reefs, Coral Sea. Estimates of these populations indicated as many as 60 individuals with a total wet biomass of 1.2 kg per m² in some areas. Along a metre wide transect across 1.3 km of reef flat the population was estimated at 530 kg wet weight sponge (mean 411 g m^-2). The four prominent species had instantaneous P/R ratios between 1.3 and 1.8 at optimum light such that photosynthetic productivity was calculated to provide between 61 and 80% of sponge energy requirements in summer and 48 to 64% in winter. While such sponge beds are a prominent feature of these reefs, they appear to contribute less than 10% of gross reef-flat productivity.Contribution no. 352 from the Australian Institute of Marine Science     

Beneficial effects of alternate dietary regimen on liver inflammation, atherosclerosis and renal activation

Background

Alternate day calorie restriction (CR) has been shown to be almost as beneficial as daily CR. The question arises whether this concept is also applicable to alternating dietary composition.

Objective

To seek evidence that alternating high cholesterol (HC) - cholesterol-free (CON) Western diet can effectively diminish hepatic and renal inflammation and cardiovascular risk factors as compared with daily HC-supplemented Western diet.

Design

Four groups of ApoE*3Leiden mice, a humanized model for atherosclerosis, were subjected to different feeding treatments for 16 weeks. Mice were fed CON diet; CON diet with 1% w/w cholesterol (HC); alternate (ALT) diet regimen of CON (4 days) and HC (3 days); or CON diet supplemented with 0.43% (w/w) cholesterol (MC), with overall dietary cholesterol intake equal to ALT. Plasma was analyzed for cardiovascular risk factors, aorta for atherosclerotic lesion formation, and liver and kidney for inflammation.

Results

ALT diet but not MC was almost as effective as daily CON feeding in preventing disease development. Compared to HC, the ALT group showed 62% lower hepatic nuclear factor kappa B (NF-κB) activity (P<0.001), a reduction of the circulating inflammatory markers E-selectin (−20%; P<0.05), vascular cell adhesion molecule 1 (VCAM-1; −15%; P<0.05) and Serum Amyloid A (SAA; −31%; P<0.05), smaller atherosclerotic lesion sizes (−51%; 46497±10791 µm² vs. 94664±16470 µm²; P<0.05) and diminished renal expression of specific inflammation and activation markers (VCAM-1, −27%; P<0.05; monocyte chemotactic protein-1 (MCP-1); −37%; P<0.01).

Conclusion

Alternate HC-CON feeding reproduced most of the beneficial effects of daily cholesterol-free diet, including strongly diminished hepatic, vascular and renal activation and inflammation; also atherosclerosis was reduced by half as compared to HC, albeit still higher compared to the CON group.     

Models for scopolamine,atropine and amphetamine effects on an alternate bar pressing paradigm

A hypothetical neural network is presented to account for errors made by food-deprived albino-rats in a bar-pressing situation (Carlton, 1964). The rats were required to press alternately on two bars in order to activate a device that releases milk to them. When-ever an animal pressed consecutively on the same bar, no milk was released and the animal was scored as having committed an error. In the first part of the paper, a time-independent neural network, part of which is equivalent to the psychophysical discrimination network of H. D. Landahl (1938), is used to interpret the effects on the animals’ performances of the drugs amphetamine, scopolamine and atropine. Suggestions for further experiments are made on the basis of the initial form to the model. In the second part of the paper, certain parameters of the initial form of the model are assumed to be time-dependent and a further generalization occurs through the introduction of the interresponse time distribution. It is shown that, under specified conditions, the second form of the model reduces to the first. The time-dependent form of the model allows certain features to be discussed that could not be discussed in the time-independent form [e.g. P. Dew’s (1961) notion of a possible mode of action for a variety of the behavioral effects of amphetamine]. Furthermore, experiments of an essentially different type from those discussed in the first part can be proposed to aid in the development of a theory for this kind of behavioral situation.     

Relative influence of temperature and electron donor and electron acceptor concentrations on bacterial sulfate reduction in saltmarsh sediment

The relative importance of three environmental variables known to influence the rate of bacterial sulfate reduction was examined using sediment from a saltmarsh pan. The variables investigated were temperature, electron donor concentration, and electron acceptor concentration. Their relative influence on the rate of bacterial sulfate reduction was examined with multiple replicate sediment samples in which the variables were experimentally adjusted. Sulfate reduction rates were measured with³⁵SO₄^2–.The relative importance of each variable to sulfate reduction rate was assessed with multiple regression analysis by calculating the standardized partial regression coefficients, and the results were compared with the ranges of the three variables encountered in the natural sediment. Temperature proved to have the greatest influence, followed by electron donor and electron acceptor concentrations, in that order. The sulfate concentration was shown to have little influence on sulfate reduction rate at seawater concentrations of sulfate, but its effect increased if sulfate concentrations were diminished compared to those of seawater.     

Spatial, bottom-up, and top-down effects on the abundance of a leaf miner

Many plant and animal species have higher densities at the centre of their distribution, with a gradual decline in abundance towards the edge of the range, though reasons for this pattern is not well known. We examined the abundance of the leaf miner Cameraria sp. nova over the range of its host plant Quercus myrtifolia in Florida and addressed how bottom-up and top-down factors varied over its whole distribution. Leaf miner densities, plant quality and natural enemy effects on mine survivorship were evaluated in 40 sites and spatially structured models were used to determine the effects of spatial location on the abundance of Cameraria and effects of both bottom-up (tannin concentration, foliar nitrogen, soil nitrogen, and leaf area) and top-down factors (larval parasitism and predation) on abundance and survivorship. Cameraria mines were, on average, three times more abundant on edge/coastal sites compared to centre/inland sites and did not support the hypothesis of higher abundance on the centre of the distribution. Differences in plant quality, larval parasitism and successful emergence of mines on edge versus central sites might be partially responsible for this finding. A trend surface equation with latitude and longitude combined explained almost 52% of the variation in Cameraria density and a trend surface map also revealed peaks of Cameraria abundance on the edges of the plant distribution. Correlograms also indicated a significant spatial structure of Cameraria as mines were positively spatially autocorrelated at small distances (≈122 km). Partial regression analyses indicated that 69% of the variation in Cameraria abundance was explained by the effects of latitude, longitude, elevation and percentage of foliar nitrogen. Our results indicated that variation in Cameraria abundance was mostly explained by spatial position and significant effects of bottom-up and top-down factors were not detected in our large-scale study.     

Deuteration effects on the in vivo EPR spectrum of the reduced secondary photosystem I electron acceptor A1 in cyanobacteria

The photoreduction of the secondary PSI electron acceptor A1 in vivo has recently been detected via X-band EPR spectroscopy in intact spinach chloroplasts and in marine cyanobacteria Synechococcus PCC 7002 [Klughammer, C., and Pace, R. J. (1997) Biochim. Biophys. Acta 1318, 133-144]. A further study of the A1- EPR spectrum of Synechococcus PCC 7002 at room temperature with higher-field resolution revealed partially resolved hyperfine structure which was dominated by 0.4 mT splittings of three equivalent protons. The hyperfine splitting was not significantly affected by incubation of the cyanobacteria in 2H2O medium for 20 h, but was absent in fully deuterated cyanobacteria that were grown in 2H2O medium. Anisotropic g-factors consistent with a phylloquinone radical were derived by spectra simulation. Biosynthetic protonation of quinones via the CH3 donor L-methionine in deuterated cells maintained hyperfine structure in the A1- spectrum, indicating the incorporation of CH3 groups in 60% of the deuterated, photoactive A1 molecules. Conversely, biosynthetic quinone deuteration via L-[methyl-d3]methionine in protonated cells led to the loss of the 0. 4 mT splittings in 54% of the A1 molecules. These observations confirm the conclusion of Heathcote et al. [(1996) Biochemistry 35, 6644-6650] of the identity of EPR-detected, photoreduced A1- in vivo with a phylloquinone (vitamin K1) radical in PSI. The partially resolved hyperfine structure of the A1- spectrum indicates an altered spin distribution in the bound vitamin K1- radical in vivo compared to that of unbound vitamin K1- in vitro.     

The interaction of methanol dehydrogenase and its electron acceptor, cytochrome cL in methylotrophic bacteria.

The interactions of methanol dehydrogenase (MDH, EC1.1.99.8) with its specific electron acceptor cytochrome cL has been investigated in Methylobacterium extorquens and Methylophilus methylotrophus. The MDHs of these two very different methylotrophs have the same alpha 2 beta 2 structure; the interaction of these MDHs with their specific electron acceptor, cytochrome cL, has been studied using a novel assay system. Electrostatic reactions are involved in 'docking' of the two proteins. EDTA inhibits the reaction by a process involving neither metal chelation nor the 'docking' process. Chemical modification studies showed that the two proteins interact by a 'docking' process involving interactions of lysyl residues on MDH and carboxyl residues on cytochrome cL. When 'zero length', two stage cross-linking was done (with proteins from both bacteria), the alpha-subunits of MDH cross-linked with cytochrome cL by way of lysyl groups on MDH and carboxyl groups on the cytochrome. Tuna mitochondrial cytochrome c provided a model for cytochrome cH which is the electron acceptor for cytochrome cL in the 'methanol oxidase' electron transport chain. Tuna cytochrome c was shown to form crosslinked products with carboxyl-modified cytochrome cL. MDH and tuna cytochrome c competed for the same domain on cytochrome cL. It was concluded that MDH reacts with cytochrome cL by an electrostatic reaction which involves carboxyl groups on cytochrome cL and amino groups on the alpha-subunit of MDH. The same domain on cytochrome cL is involved in subsequent 'docking' with its electron acceptor.     

Management strategy, shade, and landscape composition effects on urban landscape plant quality and arthropod abundance

Intensity and type of management, the cultural variable shade, and the combination of woody and herbaceous annual and perennial plants were evaluated for their effect on key landscape arthropod pests. Azalea lace bugs, Stephanitis pyrioides (Scott), and twolined spittlebugs, Prosapia bicincta (Say), were most effectively suppressed in landscape designed with resistant plant species of woody ornamentals and turf. Landscapes containing susceptible plant counterparts were heavily infested by these two insect species in untreated control plots. A traditional management program of prescribed herbicide, insecticide, and fungicide applications effectively suppressed azalea lace bug and produced a high-quality landscape. Targeted integrated pest management with solely horticultural oils resulted in intermediate levels of azalea lace bug. Neither program completely controlled twolined spittlebug on hollies or turf. Carabidae, Staphylinidae, Formicidae, and Araneae were not reduced by any management strategy. Lace bugs (Stephanitis) were more common in plots with 50% shade than those in full sun. Spittlebugs (Prosapia) were more common in the shade during 1996 and in the sun during 1997. Spiders and ants were more often collected in full sun plots. Carabids, staphylinids, and spiders were more commonly collected from pitfall traps in turf than in wood-chip mulched plant beds, whereas ants were equally common in both locations. The addition of herbaceous plants to the landscape beds had little effect on pest insect abundance.     

Genetic and soil-nutrient effects on the abundance of herbivores on willow

The effects of soil-nutrient environment, plant genotype, and the interaction between the two on the resistance of the willow, Salix sericea, to insect species in a diverse herbivore community was measured. We found that soil-nutrient environment influenced plant growth and the abundance of most herbivores of S. sericea. However, environmental effects on herbivore abundance were often modified by plant genetics; the abundance of four of seven herbivores exhibited significant genotypeby-environment interaction effects. Pure genotype effects were mostly small and non-significant. The effects of fertilization differed among herbivores. Several herbivores were more abundant on fertilized plants, one was less abundant, and the abundance of others did not change. We found that feeding guild was a poor predictor of herbivore response. Finally we found significant phenotypic and genetic correlations among growth rate, internode length, and the abundances of several herbivores.     

Temporal variation in site fidelity: scale-dependent effects of forage abundance and predation risk in a non-migratory large herbivore

Large herbivores are typically confronted by considerable spatial and temporal variation in forage abundance and predation risk. Although animals can employ a range of behaviours to balance these limiting factors, scale-dependent movement patterns are expected to be an effective strategy to reduce predation risk and optimise foraging opportunities. We tested this prediction by quantifying site fidelity of global positioning system-collared, non-migratory female elk (Cervus canadensis manitobensis) across multiple nested temporal scales using a long-established elk–wolf (Canis lupus) system in Manitoba, Canada. Using a hierarchical analytical approach, we determined the combined effect of forage abundance and predation risk on variation in site fidelity within four seasons across four nested temporal scales: monthly, biweekly, weekly, daily. Site fidelity of female elk was positively related to forage-rich habitat across all seasons and most temporal scales. At the biweekly, weekly and daily scales, elk became increasingly attached to low forage habitat when risk was high (e.g. when wolves were close or pack sizes were large), which supports the notion that predator-avoidance movements lead to a trade-off between energetic requirements and safety. Unexpectedly, predation risk at the monthly scale increased fidelity, which may indicate that elk use multiple behavioural responses (e.g. movement, vigilance, and aggregation) simultaneously to dilute predation risk, especially at longer temporal scales. Our study clearly shows that forage abundance and predation risk are important scale-dependent determinants of variation in site fidelity of non-migratory female elk and that their combined effect is most apparent at short temporal scales. Insight into the scale-dependent behavioural responses of ungulate populations to limiting factors such as predation risk and forage variability is essential to infer the fitness costs incurred.     

Plant neighbours mediate bird predation effects on arthropod abundance and herbivory

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Catalytic mechanism of scytalone dehydratase: site-directed mutagenisis, kinetic isotope effects, and alternate substrates.

On the basis of the X-ray crystal structure of scytalone dehydratase complexed with an active center inhibitor [Lundqvist, T., Rice, J., Hodge, C. N., Basarab, G. S., Pierce, J. and Lindqvist, Y. (1994) Structure (London) 2, 937-944], eight active-site residues were mutated to examine their roles in the catalytic mechanism. All but one residue (Lys73, a potential base in an anti elimination mechanism) were found to be important to catalysis or substrate binding. Steady-state kinetic parameters for the mutants support the native roles for the residues (Asn131, Asp31, His85, His110, Ser129, Tyr30, and Tyr50) within a syn elimination mechanism. Relative substrate specificities for the two physiological substrates, scytalone and veremelone, versus a Ser129 mutant help assign the orientation of the substrates within the active site. His85Asn was the most damaging mutation to catalysis consistent with its native roles as a general base and a general acid in a syn elimination. The additive effect of Tyr30Phe and Tyr50Phe mutations in the double mutant is consistent with their roles in protonating the substrate's carbonyl through a water molecule. Studies on a synthetic substrate, which has an anomeric carbon atom which can better stabilize a carbocation than the physiological substrate (vermelone), suggest that His110Asn prefers this substrate over vermelone in order to balance the mutation-imposed weakness in promoting the elimination of hydroxide from substrates. All mutant enzymes bound a potent active-site inhibitor in near 1:1 stoichiometry, thereby supporting their active-site integrity. An X-ray crystal structure of the Tyr50Phe mutant indicated that both active-site waters were retained, likely accounting for its residual catalytic activity. Steady-state kinetic parameters with deuterated scytalone gave kinetic isotope effects of 2.7 on kcat and 4.2 on kcat/Km, suggesting that steps after dehydration partially limit kcat. Pre-steady-state measurements of a single-enzyme turnover with scytalone gave a rate that was 6-fold larger than kcat. kcat/Km with scytalone has a pKa of 7.9 similar to the pKa value for the ionization of the substrate's C6 phenolic hydroxyl, whereas kcat was unaffected by pH, indicating that the anionic form of scytalone does not bind well to enzyme. With an alternate substrate having a pKa above 11, kcat/Km had a pKa of 9.3 likely due to the ionization of Tyr50. The non-enzyme-catalyzed rate of dehydration of scytalone was nearly a billion-fold slower than the enzyme-catalyzed rate at pH 7.0 and 25 degrees C. The non-enzyme-catalyzed rate of dehydration of scytalone had a deuterium kinetic isotope effect of 1.2 at pH 7.0 and 25 degrees C, and scytalone incorporated deuterium from D2O in the C2 position about 70-fold more rapidly than the dehydration rate. Thus, scytalone dehydrates through an E1cb mechanism off the enzyme.