Use of Restored Small Wetlands by Breeding Waterfowl in Prince Edward Island, Canada

Abstract Since 1990 under the Eastern Habitat Joint Venture over 100 small wetlands have been restored in Prince Edward Island, Canada. Wetlands were restored by means of dredging accumulated sediment from erosion to emulate pre‐disturbance conditions (i.e., open water and extended hydroperiod). In 1998 and 1999 we compared waterfowl pair and brood use on 22 restored and 24 reference wetlands. More pairs and broods of Ring‐necked Ducks, Gadwall, Green‐winged Teal, and American Black Ducks used restored versus reference wetlands. In restored wetlands waterfowl pair density and species richness were positively correlated with wetland/cattail area, percent cattail cover, and close proximity to freshwater rivers. In addition, a waterfowl reproductive index was positively correlated with percent cattail cover. Green‐winged Teal pair occurrence in restored wetlands was positively correlated with greater amounts of open water and water depths. American Black Duck pairs occurred on most (86%) restored wetlands. Restored small wetlands likely served as stopover points for American Black Duck broods during overland or stream movements, whereas they likely served as a final brood‐rearing destination for Green‐winged Teal broods. We suggest that wetland restoration is a good management tool for increasing populations of Green‐winged Teal and American Black Ducks in Prince Edward Island.     

The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences.

In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with the observed ones to appraise the behaviour of a known x-ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time-consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined. A simulation of hydrophobic effects in an aqueous environment is also proposed which seems to provide a better approximation of the observed solution structure of the protein.     

Possible role of a short extra loop of the long-chain flavodoxin from Azotobacter chroococcum in electron transfer to nitrogenase: Complete 1H, 15N and 13C backbone assignments and secondary solution structure of the flavodoxin

Summary The ¹H, ¹⁵N and ¹³C backbone and ¹H and ¹³C beta resonance assignments of the long-chain flavodoxin from Azotobacter chroococcum (the 20-kDa nifF product, flavodoxin-2) in its oxidized form were made at pH 6.5 and 30°C using heteronuclear multidimensional NMR spectroscopy. Analysis of the NOE connectivities, together with amide exchange rates, ³J_Hn_H coupling constants and secondary chemical shifts, provided extensive solution secondary structure information. The secondary structure consists of a five-stranded parallel -sheet and five -helices. One of the outer regions of the -sheet shows no regular extended conformation, whereas the outer strand 4/6 is interrupted by a loop, which is typically observed in long-chain flavodoxins. Two of the five -helices are nonregular at the N-terminus of the helix. Loop regions close to the FMN are identified. Negatively charged amino acid residues are found to be mainly clustered around the FMN, whereas a cluster of positively charged residues is located in one of the -helices. Titration of the flavodoxin with the Fe protein of the A. chroococcum nitrogenase enzyme complex revealed that residues Asn¹¹, Ser⁶⁸ and Asn⁷² are involved in complex formation between the flavodoxin and Fe protein. The interaction between the flavodoxin and the Fe protein is influenced by MgADP and is of electrostatic nature.Abbreviations SQ semiquinone - FMN riboflavin 5-monophosphate; nif, nitrogen fixation - TSP 3-(trimethylsilyl)propionate sodium salt - DSS 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt Supplementary Material is available on request, comprising a Materials and Methods section for the expression and purification of the A. chroococcum flavodoxin, a Table S1 containing the parameters of the titration of A. chroococcum flavodoxin with the Fe protein, and a Table S2 containing the ¹⁵N, H^N, ¹³C, ¹H, ¹³C, ¹H and ¹³CO chemical shifts.To whom correspondence should be addressed.     

Ecological compensation of the impacts of a road. Preliminary method for the A50 road link (Eindhoven-Oss, The Netherlands)

After years of efforts to avoid or reduce the impact of infrastructure projects on nature, the principle of ecological compensation has been incorporated in Dutch governmental policy. Ecological compensation aims to recover those ecological functions and natural values that still remain affected after maximum effort has been made to reduce the impact of the intervention (mitigation). The accepted aim of current policy is thus no-net-loss of area and quality by means of mitigative and compensatory measures. As part of the planning process for construction of a stretch of road in The Netherlands, viz., the A50 road link in the province of North Brabant, a Nature Compensation Plan (NCP) was required to be drawn up. This work has recently been completed by the Regional Directorate of Public Works and Water Management, the initiator of the intervention. The NCP, initially presented as a Draft Plan, was drawn up by the Regional Directorate using a preliminary method designed by the Centre of Environmental Science of Leiden University for deriving compensatory measures. After an opportunity for public comment, the Draft Plan was revised to form a Final NCP. This article describes, firstly, the preliminary method for deriving ecological compensatory measures. The method starts by quantifying the effects of habitat loss, habitat disturbance (by changes in noise emissions, in the water table and in outdoor recreational patterns), barrier action and fauna casualties. Following mitigation of impacts on nature, compensation for non-mitigable effects focuses successively on area size, derived from the impacts on breeding birds, and on area quality, derived from the habitat requirements of the vegetation and fauna groups affected by the road. Guidelines for identifying appropriate locations for compensation are also formulated. Secondly, the compensation method is applied to calculate the mitigative and compensatory measures for the A50 trajectory between Eindhoven and Oss. Thirdly, two comparisons are made: the Draft NCP is compared with the results of the preliminary method, and the Draft and the Final NCP are compared with one another in order to identify the role of the interest groups that played a major role in commenting on the Draft Plan. Finally, realization of the compensatory measures and development of the preliminary method itself are discussed. On the basis of the experience with the A50 case study, a more robust compensation method for road projects is to be developed.     

Effects of pond size and consequent predator density on two species of tadpoles

Experimental ponds were used as a model system of habitat patches to study the effect of habitat size on the relative growth performance of tadpoles of Bufo americanus and Pseudacris triseriata, and on colonization by predatory insects. Three pond depths and surface areas were habitat size treatments in a replicated, factorial experiment. Tadpoles of both species were astablished together at a single density and ponds were left open to natural colonization by aquatic insects. Pond area had a significant effect on the multivariate response of P. triseriata larval period, survival, and metamorphic mass. P. triseriata survived better relative to B. americanus in larger ponds. However, increasing pond area led to greater incidence of predacious beetle larvae (Dytiscus, Coleoptera: Dytiscidae). Dytiscus larvae had a significant negative effect on the survival of P. triseriata and led to reduced P. triseriata survival relative to B. americanus in colonized ponds. The results suggest that habitat size can influence community structure by altering the distribution of predation among habitat patches.     

Temperature coefficients of peptides dissolved in hexafluoroisopropanol monitor distortions of helices

Temperature coefficients are widely used as an indication of solvent accessibility to amide protons. Low temperature coefficients are related to low accessibility and are often interpreted as evidence for intramolecular hydrogen bonding. Conformational shifts, i.e. the difference between chemical shifts of a particular residue in a structured and in a random-coil conformation, provide information on secondary structure. In particular, negative CH conformational shifts are often used to delineate the extent of helical stretches. NH conformational shifts show large oscillations within a helix that have been interpreted as the result of helix distortions affecting hydrogen bond lengths. In the course of the study of different peptides that adopt a helical structure in the presence of the structure-inducing solvent hexafluoroisopropanol (HFIP), we have found a strong correlation between temperature coefficients and amide conformational shifts. However, contrary to the initial expectations, lower temperature coefficients were associated to amide protons involved in longer, and presumably weaker, hydrogen bonds. The correlation can be explained, however, assuming that, in helical peptides dissolved in HFIP, temperature affects the chemical shift of amide protons mainly by changing the average length of intramolecular hydrogen bonds and changes in solvent accessibility play only a secondary role under these experimental conditions. The pattern of temperature coefficients in helical peptides can therefore be used to identify short or long hydrogen bonds causing bending of the helix axis.     

Spectral regions in which aquatic insects see reflected polarized light

For diverse water insects (species of Hydrophilidae, Hadraenidae, Dytiscidae, Haliplidae and aquatic Heteroptera), the attractiveness of an artificial water surface was found to vary when the polarization of the reflected light, the property by which these insects identify water, was abolished in different regions of the spectrum. The sensitivity maxima of their reflection-polarization visual systems (max(POL)) thus determined were in various spectral regions, between < 360 nm (UV) and ca. 550 nm (yellow-green). Species with max(POL) at the short-wavelength end of the spectrum would be able to identify bodies of water by polarization regardless of whether the subsurface reflection was bright or dark; nevertheless, this group includes forms that avoid water with a bright subsurface because of the intensity of the reflected light. Species with max(POL) in the long-wavelength region fail to use certain bodies of water with a bright subsurface as habitats because the light they reflect at the longer wavelengths is insufficiently polarized. That the POL system of a species has a large max could affect habitat choice; on the other hand, it could also be that systems operating in the long-wavelength region were produced in the course of adaptation to the light conditions in or above the habitat.Abbreviations max(POL) spectral sensitivity maximum for polarization vision     

The ecology of ruffe,Gymnocephalus cernuus (Pisces: Percidae) introduced to Mildevatn,western Norway

Synopsis Diet, habitat use, diel and seasonal activity and a number of population parameters were studied on ruffe,Gymnocephalus cernuus, introduced to Mildevatn, western Norway. This lake is sited outside the natural range of the ruffe and has a lower fish diversity and a different fish species composition than within its native range. From June through September the ruffe was planktivorous and mainly caught at 4 to 6 m depth in the benthic zone. At other times of year ruffe was feeding on zoobenthos and caught deeper in the benthic zone. Ruffe was mainly day active. Zooplankton feeding during summer is the clearest difference compared to ruffe populations living within its natural range. Presence of large zooplankton organisms available for ruffe is suggested as the main reason for the difference found in food choice. The availability of large zooplankton is probably due to community structure caused by a predator and lack of interspecific competition for zooplankton in the deeper parts of the lake. Piscivorous brown trout.Salmo trutta, restrict the habitat of threespined stickleback,Gasterosteus aculeatus, to the zone of littoral vegetation, allowing high densities of larger zooplankton species likeBythotrephes longimanus to be present in the lake. Brown trout is present only in the upper light and well oxygenated parts of the lake, leaving a refuge for the ruffe, where they can feed on the rich zooplankton community.     

‘Random coil’ 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG

Summary Proton chemical shifts of a series of disordered linear peptides (H-Gly-Gly-X-Gly-Gly-OH, with X being one of the 20 naturally occurring amino acids) have been obtained using 1D and 2D ¹H NMR at pH 5.0 as a function of temperature and solvent composition. The use of 2D methods has allowed some ambiguities in side-chain assignments in previous studies to be resolved. An additional benefit of the temperature data is that they can be used to obtain ‘random coil’ amide proton chemical shifts at any temperature between 278 and 318 K by interpolation. Changes of chemical shift as a function of trifluoroethanol concentration have also been determined at a variety of temperatures for a subset of peptides. Significant changes are found in backbone and side-chain amide proton chemical shifts in these ‘random coil’ peptides with increasing amounts of trifluoroethanol, suggesting that caution is required when interpreting chemical shift changes as a measure of helix formation in peptides in the presence of this solvent. Comparison of the proton chemical shifts obtained here for H-Gly-Gly-X-Gly-Gly-OH with those for H-Gly-Gly-X-Ala-OH [Bundi, A. and Wüthrich, K. (1979) Biopolymers, 18, 285–297] and for Ac-Gly-Gly-X-Ala-Gly-Gly-NH₂ [Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67–81] generally shows good agreement for CH protons, but reveals significant variability for NH protons. Amide proton chemical shifts appear to be highly sensitive to local sequence variations and probably also to solution conditions. Caution must therefore be exercised in any structural interpretation based on amide proton chemical shifts.     

Chemical shifts and three-dimensional protein structures

Summary During the past three years it has become possible to compute ab initio the ¹³C, ¹⁵N and ¹⁹F NMR chemical shifts of many sites in native proteins. Chemical shifts are beginning to become a useful supplement to more established methods of solution structure determination, and may find utility in solid-state analysis as well. From ¹³C NMR, information on , and torsions can be obtained, permitting both assignment verification, and structure refinement and prediction. For ¹⁵N, both torsional and hydrogen-bonding effects are important, while for ¹⁹F, chemical shifts are primarily indicators of the local charge field. Chemical shift calculations are still slow, but shielding hypersurfaces — the shift as a function of the dihedral angles that define the molecular conformation — are becoming accessible. Over the next few years, theoretical and computer hardware improvements will enable more routine use of chemical shifts in structural studies, including the study of metal-ligand interactions, the analysis of drug and substrate binding and catalysis, the study of folding/unfolding pathways, as well as the characterization of conformational substates. Rather than simply being a necessary prerequisite for multidimensional NMR, chemical shifts and chemical shift non-equivalence due to folding are now beginning to be useful for structural characterization.