Chromatographic separation of extruded iron-sulfur cores from the apoproteins of Clostridium pasteurianum and spinach ferredoxins in aqueous Triton X-100/urea

Iron-sulfur core extrusions from spinach [( 2Fe-2S]) and Clostridium pasteurianum (2[4Fe-4S]) ferredoxins in aqueous Triton X-100/urea containing excess benzenethiol yield quantitatively [FenSn(SPh)4]2- with n = 2 and n = 4, respectively. The iron-sulfur cluster can be separated from the corresponding apoprotein by rapid passage of the extrusion mixture over a small anaerobic column of Whatman DE-52 anion-exchange cellulose. Essentially quantitative recovery of [FenSn (SPh)4]2- is achieved in the eluate. The apoprotein remaining on the column can be eluted with 0.5 M NaCl. Most of the residual Triton X-100 and benzenethiol can be removed by passage of the apoprotein eluate over a small column of Bio-Beads SM-2, a hydrophobic polystyrene adsorbent. Apoprotein recovery is comparable to that obtained by other chromatographic methods. At least with spinach ferredoxin, the apoprotein prepared in this fashion can be reconstituted. The procedures developed in this work are potentially most applicable to selective removal of [2Fe-2S] and [4Fe-4S] centers from a multicenter enzyme without irreversible denaturation.     

Microhabitat nest‐site selection by ducks in the boreal forest

The boreal forest is one of the North America’s most important breeding areas for ducks, but information about the nesting ecology of ducks in the region is limited. We collected microhabitat data related to vegetation structure and composition at 157 duck nests and paired random locations in Alberta’s boreal forest region from 2016 to 2018. We identified fine‐scale vegetation features selected by ducks for all nests, between nesting guilds, and among five species using conditional logistic regression. Ducks in the boreal forest selected nest sites with greater overhead and graminoid cover, but less forb cover than random sites. Characteristics of the nest sites of upland‐ and overwater‐nesting guilds differed, with species nesting in upland habitat selecting nests that provided greater shrub cover and less lateral concealment and species nesting over water selecting nests with less shrub cover. We examined the characteristics of nest sites of American Wigeon (Mareca americana), Blue‐winged Teal (Spatula discors), Green‐winged Teal (Anas crecca), Mallards (Anas platyrhynchos), and Ring‐necked Ducks (Aythya collaris), and found differences among species that may facilitate species coexistence at a regional scale. Our results suggest that females of species nesting in upland habitat selected nest sites that optimized concealment from aerial predators while also allowing detection of and escape from terrestrial predators. Consequently, alteration in the composition and heterogeneity of vegetation and predator communities caused by climate change and industrial development in the boreal forest of Canada may affect the nest‐site selection strategies of boreal ducks.     

Ordination and classification of operational geographic units in Southwest Sweden

The vascular plant distributions of Dalsland and northern Bohuslän (Southwest Sweden) were subjected to multivariate analyses in order to delimit geographically coherent floristic zones. 271 squares of 5×5 km were the Operational Geographic Units; the data matrix comprises presence/absence species records for each OGU. Different ordination and classification methods were tested and detailed results are presented for detrended correspondence analysis (DCA), UPGMA and ordination space partitioning (OSP). A weighting procedure, neighbour-weighting, which gives pseudo-frequency scores along the nominal scale 0–9 depending on the species' distribution patterns, is introduced. The superior method for delimiting geographically coherent floristic zones was judged to be ordination space partitioning, using DCA and neighbour-weighted species scores.Abbreviations DCA Detrended Correspondence Analysis - OGU Operational Geographical Unit - OSP Ordination Space Partitioning - UPGMA Unweighted Pair-Group Method using Arithmetic Averages     

A unique,thermostable dimer linkage structure of RD114 retroviral RNA

Retroviruses package their genome as RNA dimers linked together primarily by base-pairing between palindromic stem–loop (psl) sequences at the 5′ end of genomic RNA. Retroviral RNA dimers usually melt in the range of 55°C–70°C. However, RNA dimers from virions of the feline endogenous gammaretrovirus RD114 were reported to melt only at 87°C. We here report that the high thermal stability of RD114 RNA dimers generated from in vitro synthesized RNA is an effect of multiple dimerization sites located in the 5′ region from the R region to sequences downstream from the splice donor (SD) site. By antisense oligonucleotide probing we were able to map at least five dimerization sites. Computational prediction revealed a possibility to form stems with autocomplementary loops for all of the mapped dimerization sites. Three of them were located upstream of the SD site. Mutant analysis supported a role of all five loop sequences in the formation and thermal stability of RNA dimers. Four of the five psls were also predicted in the RNA of two baboon endogenous retroviruses proposed to be ancestors of RD114. RNA fragments of the 5′ R region or prolonged further downstream could be efficiently dimerized in vitro. However, this was not the case for the 3′ R region linked to upstream U3 sequences, suggesting a specific mechanism of negative regulation of dimerization at the 3′ end of the genome, possibly explained by a long double-stranded RNA region at the U3-R border. Altogether, these data point to determinants of the high thermostability of the dimer linkage structure of the RD114 genome and reveal differences from other retroviruses.     

Measuring dominance and diversity in ecological communities: choosing the right variables

Abstract. Although there are many studies in searching for the most useful community diversity index, the importance of choosing an appropriate parameter has been neglected. Here, we examined dominance and diversity in early post-fire chaparral communities using different variables, i.e. plant density, cover and biomass. Significant different results were produced by applying different parameters and the difference may be caused by the inconsistency in density, cover, and biomass allocated in each life form. Among the three parameters, biomass was most successful in detecting differences among communities because the apportionment of biomass among species was more variable than that of density. Although the three species variables represent different aspects of community properties and their relative performance may vary among communities, we recommend the use of biomass or productivity data as the most appropriate variable because it can best represent per capita resource use and resource partitioning among organisms in competitive situations.     

Diet partitioning in sympatric Atlantic salmon and brown trout in streams with contrasting riparian vegetation

Prey intake by Atlantic salmon Salmo salar and brown trout Salmo trutta was measured across different riparian vegetation types: grassland, open canopy deciduous and closed canopy deciduous, in upland streams in County Mayo, Western Ireland. Fishes were collected by electrofishing while invertebrates were sampled from the benthos using a Surber sampler and drifting invertebrates collected in drift traps. Aquatic invertebrates dominated prey numbers in the diets of 0+ year Atlantic salmon and brown trout and 1+ year Atlantic salmon, whereas terrestrial invertebrates were of greater importance for diets of 1+ and 2+ year brown trout. Terrestrial prey biomass was generally greater than aquatic prey for 1+ and 2+ year brown trout across seasons and riparian types. Prey intake was greatest in spring and summer and least in autumn apart from 2+ year brown trout that sustained feeding into autumn. Total prey numbers captured tended to be greater for all age classes in streams with deciduous riparian canopy. Atlantic salmon consumed more aquatic prey and brown trout more terrestrial prey with an ontogenetic increase in prey species richness and diversity. Atlantic salmon and brown trout diets were most similar in summer. Terrestrial invertebrates provided an important energy subsidy particularly for brown trout. In grassland streams, each fish age class was strongly associated with aquatic, mainly benthic invertebrates. In streams with deciduous riparian canopy cover, diet composition partitioned between conspecifics with older brown trout associated with surface drifting terrestrial invertebrates and older Atlantic salmon associated with aquatic invertebrates with a high drift propensity in the water column and 0+ year fish feeding on benthic aquatic invertebrates. Deciduous riparian canopy cover may therefore facilitate vertical partitioning of feeding position within the water column between sympatric Atlantic salmon and brown trout. Implications for riparian management are discussed.     

Mg2+-ATPase activity in wheat root plasma membrane vesicles: Time-dependence and effect of sucrose and detergents

Purified plasma membrane vesicles were isolated in the presence of 250 mM sucrose from 7-day-old roots of Triticum aestivum L. cv. Drabant by aqueous polymer two-phase partitioning. When added to a low-salt medium containing 9-aminoacridine (9-AA), the vesicles caused a much larger total decrease in 9-AA fluorescence when sucrose was absent than when sucrose was present. A slow component of the decrease was also larger in the absence of sucrose. Triton X-100 reduced the decrease in 9-AA fluorescence upon vesicle addition and abolished completely the slow component of the decrease. There was no correlation between the time-dependence of 9-AA fluorescence and that of the Mg²⁺-ATPase described below. The time course of Mg²⁺-ATPase activity was followed by sampling at short intervals (down to 10 s) and analyzing for P, released. In the absence of detergent, the rates of P, release were linear from zero minutes, whether 250 mM sucrose was present or not, but the rate was 10^?50% higher in the absence of sucrose than in its presence. Sucrose (250 mM) added during a minus-sucrose assay lowered Mg²⁺-ATPase activity within 2 min to the level observed with 250 mM sucrose present from the start. The effect of 25-1 100 mM sucrose was tested and there was little or no effect below KM) mM. Above 100 mM sucrose the rate of P, release decreased drastically; at 1 100 mM sucrose the rate was ca 20% the rate at 25 mM sucrose. The inhibitory effect of sucrose was not alleviated by increased concentrations of Mg²⁺ and/or ATP. nor was it affected by the presence or absence of Triton X-100. We conclude that sucrose somehow inhibits the Mg²⁺-ATPase directly or affects the conformation of the plasma membrane in such a way as to inhibit the enzyme. The presence of detergents increased Mg²⁺-ATPase activity in the order Triton X-100 (4–5-fold) > Zwittergent 3–14 = Na-cholate = octylglucoside > digitonin (2-fold). In all cases optimal activity was observed at detergent concentrations at or below the critical micellar concentration. The detergent concentration curves could be simulated by the sum of a stimulatory and an inhibitory reaction. At the optimal concentration, digitonin gave a linear time-course of P, release, whereas all the other detergents showed a distinct lag of 1–3 min before maximal rates were attained. The problems of using detergents in polarity assays are discussed.