<Emphasis Type="Italic">WUS</Emphasis> and <Emphasis Type="Italic">STM</Emphasis>-based reporter genes for studying meristem development in poplar

We describe the development of a reporter system for monitoring meristem initiation in poplar using promoters of poplar homologs to the meristem-active regulatory genes WUSCHEL (WUS) and SHOOTMERISTEMLESS (STM). When ~3 kb of the 5′ flanking regions of close homologs were used to drive expression of the GUSPlus gene, 50–60% of the transgenic events showed expression in apical and axillary meristems. However, expression was also common in other organs, including in leaf veins (40 and 46% of WUS and STM transgenic events, respectively) and hydathodes (56% of WUS transgenic events). Histochemical GUS staining of explants during callogenesis and shoot regeneration using in vitro stems as explants showed that expression was detectable prior to visible shoot development, starting 3–15 days after explants were placed onto callus inducing medium. A minority of WUS and STM events also showed expression in the cambium, phloem, or xylem of regenerated, greenhouse grown plants undergoing secondary growth. Based on microarray gene expression data, a paralog of poplar WUS was detectably up-regulated during shoot initiation, but the other paralog was not. Both paralogs of poplar STM were down-regulated threefold to sixfold during early callus initiation. We identified 15–35 copies of cytokinin response regulator binding motifs (ARR1AT) and one copy of the auxin response element (AuxRE) in both promoters. Several of the events recovered may be useful for studying the process of primary and secondary meristem development, including treatments intended to stimulate meristem development to promote clonal propagation and genetic transformation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Handling does not affect reproductive signals of male threespine stickleback

We examined the affect of handling on reproductive signal expression in male threespine stickleback, Gasterosteus aculeatus. Spectrophotometric techniques have become popular methods for measuring fish color, but the measurements require handling of the subjects in order to make measurements. Fish can undergo rapid physiological color change in response to stress. As such, handling fish may induce color changes and measured colour may not be representative of signal appearance under non-stressful conditions. We measured the reflectance characteristics of the opercular, ventro-lateral and dorso-lateral areas of 41 reproductive males from Hotel Lake, BC, Canada using spectroradiometry immediately upon capture and again at 2, 3, 4, 5, 10, 15, and 20 min post-capture. Repeated measures ANOVA revealed that post-capture handling did not affect opercular or ventro-lateral reflectance characteristics over the 20 min period. However, we did observe a change in dorso-lateral reflectance characteristics of parental males over the experiment. The results of our study show that handling does not influence reflective properties of two key components of stickleback reproductive signals during a time frame that is reasonable for taking field measurements of signal color.     

Larval aquatic and terrestrial mites infesting a temperate assemblage of mosquitoes

We collected 22,769 adult female mosquitoes, representing 27 species, from light traps in Norfolk, Virginia (2006–2007) and examined them to assess infestation by larval mites. Mosquitoes were parasitized by two species of aquatic (Acari: Arrenuridae: Arrenurus) and three species of terrestrial mites (Acari: Erythraeidae). The prevalence of infestation varied from 0.55% (2006) to 0.17% (2007). The mean intensity of parasitism ranged from 3.6 mites per host (2006) to 1.8 mites per host (2007). The most common host species for aquatic mites was Culex erraticus, while the most common host for terrestrial mites was Anopheles quadrimaculatus. Relationships between biotic and abiotic factors were investigated in an attempt to provide insight into temporal, spatial, and interspecific variation in mite–mosquito interactions. Scanning electron microscopy was used to examine the mode of attachment for larval mites. While the prevalence of aquatic mite parasitism was correlated for Culex erraticus, the invasive mosquito, Aedes albopictus, was never parasitized through the duration of the study. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation

The responses and adaptation mechanisms of the industrial Saccharomyces cerevisiae to vacuum fermentation were explored using proteomic approach. After qualitative and quantitative analyses, a total of 106 spots corresponding to 68 different proteins were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The differentially expressed proteins were involved in amino acid and carbohydrate metabolisms, various signal pathways (Ras/MAPK, Ras–cyclic adenosine monophosphate, and HOG pathway), and heat shock and oxidative responses. Among them, alternations in levels of 17 proteins associated with carbohydrate metabolisms, in particular, the upregulations of proteins involved in glycolysis, trehalose biosynthesis, and the pentose phosphate pathway, suggested vacuum-induced redistribution of the metabolic fluxes. The upregulation of 17 heat stress and oxidative response proteins indicated that multifactors contributed to oxidative stresses by affecting cell redox homeostasis. Taken together with upregulation in 14-3-3 proteins levels, 22 proteins were detected in multispots, respectively, indicating that vacuum might have promoted posttranslational modifications of some proteins in S. cerevisiae. Further investigation revealed that the elevations of the differentially expressed proteins were mainly derived from vacuum stress rather than the absence of oxygen. These findings provide new molecular mechanisms for understanding of adaptation and tolerance of yeast to vacuum fermentation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effect of ultrafine-grained titanium surfaces on adhesion of bacteria

The influence of the ultrafine crystallinity of commercial purity grade 2 (as-received) titanium and titanium modified by equal channel angular pressing (modified titanium) on bacterial attachment was studied. A topographic profile analysis of the surface of the modified titanium revealed a complex morphology of the surface. Its prominent micro- and nano-scale features were 100–200-nm-scale undulations with 10–15 μm spacing. The undulating surfaces were nano-smooth, with height variations not exceeding 5–10 nm. These surface topography characteristics were distinctly different from those of the as-received samples, where broad valleys (up to 40–60 μm) were detected, whose inner surfaces exhibited asperities approximately 100 nm in height spaced at 1–2 μm. It was found that each of the three bacteria strains used in this study as adsorbates, viz. Staphylococcus aureus CIP 68.5, Pseudomonas aeruginosa ATCC 9025 and Escherichia coli K12, responded differently to the two types of titanium surfaces. Extreme grain refinement by ECAP resulted in substantially increased numbers of cells attached to the surface compared to as-received titanium. This enhanced degree of attachment was accompanied with an increased level of extracellular polymeric substances (EPS) production by the bacteria. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phylogenetic position of the monotypic Des Murs’ Wiretail ( Sylviorthorhynchus desmursii , Aves: Furnariidae) based on mitochondrial and nuclear DNA

Parallelisms and paraphyletic assemblages are common among ovenbirds. Molecular markers are therefore the best approach when studying the evolutionary relationships among the members of this unparalleled diversified family. We obtained nucleotide sequence data from mitochondrial (cytochrome b) and nuclear genes (myoglobin and glyceraldehyde-3-phosphodehydrogenase) and used these to deduce the phylogenetic position of a monotypic genus endemic to the austral temperate rainforests of southern South America, the Des Murs’ Wiretail (Sylviorthorhynchus desmursii Des Murs, 1847, Aves: Furnariidae). Phylogenetic analyses based on maximum parsimony, maximum likelihood and Bayesian inference all converged into a congruent topology, with a basal position of Des Murs’ Wiretail within Synallaxinae together with Tit–Spinetails (Leptasthenura). Our data reject the hypothesis of a phylogenetic relationship between Des Murs’ Wiretail and thistletails (Schizoeaca) which exhibit parallelisms in morphology, tail structure and nest architecture. Using a molecular clock based on the myoglobin intron 2 gene, we estimated a divergence time of Des Murs’ Wiretail from Tit-Spinetails of 14–15 Myr, which is associated with the appearance of sclerophyllous forest elements in Chile at the Middle–Upper Miocene. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genome-scale reconstruction and <Emphasis Type="Italic">in silico</Emphasis> analysis of the <Emphasis Type="Italic">Clostridium acetobutylicum</Emphasis> ATCC 824 metabolic network

To understand the metabolic characteristics of Clostridium acetobutylicum and to examine the potential for enhanced butanol production, we reconstructed the genome-scale metabolic network from its annotated genomic sequence and analyzed strategies to improve its butanol production. The generated reconstructed network consists of 502 reactions and 479 metabolites and was used as the basis for an in silico model that could compute metabolic and growth performance for comparison with fermentation data. The in silico model successfully predicted metabolic fluxes during the acidogenic phase using classical flux balance analysis. Nonlinear programming was used to predict metabolic fluxes during the solventogenic phase. In addition, essential genes were predicted via single gene deletion studies. This genome-scale in silico metabolic model of C. acetobutylicum should be useful for genome-wide metabolic analysis as well as strain development for improving production of biochemicals, including butanol. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. J. L. and H. Y. equally contributed to this work.     

Group formation and anemone use in captively reared anemonefish (<Emphasis Type="Italic">Amphiprion frenatus</Emphasis>)

We studied group formation and anemone use in captively reared anemonefish Amphiprion frenatus. Four small fish (23–32 mm total length) were simultaneously released into a central area of the aquaria (ca. 160 l) that was divided in half with an anemone placed on each half, with the opportunity to settle on either side. Four-day trials were conducted for analyzing settlement patterns. Because of the monogamous mating system, we predicted that small fish should settle in pairs. However, all four small fish settled on the same side in 7 of 14 replicates, which was a higher than expected value under random settlement.     

Pacific salmon effects on stream ecosystems: a quantitative synthesis

Pacific salmon (Oncorhynchus spp.) disturb sediments and fertilize streams with marine-derived nutrients during their annual spawning runs, leading researchers to classify these fish as ecosystem engineers and providers of resource subsidies. While these processes strongly influence the structure and function of salmon streams, the magnitude of salmon influence varies widely across studies. Here, we use meta-analysis to evaluate potential sources of variability among studies in stream ecosystem responses to salmon. Results obtained from 37 publications that collectively included 79 streams revealed positive, but highly inconsistent, overall effects of salmon on dissolved nutrients, sediment biofilm, macroinvertebrates, resident fish, and isotopic enrichment. Variation in these response variables was commonly influenced by salmon biomass, stream discharge, sediment size, and whether studies used artificial carcass treatments or observed a natural spawning run. Dissolved nutrients were positively related to salmon biomass per unit discharge, and the slope of the relationship for natural runs was five to ten times higher than for carcass additions. Mean effects on ammonium and phosphorus were also greater for natural runs than carcass additions, an effect attributable to excretion by live salmon. In contrast, we observed larger positive effects on benthic macroinvertebrates for carcass additions than for natural runs, likely because disturbance by live salmon was absent. Furthermore, benthic macroinvertebrates and biofilm associated with small sediments (<32 mm) displayed a negative response to salmon while those associated with large sediments (>32 mm) showed a positive response. This comprehensive analysis is the first to quantitatively identify environmental and methodological variables that influence the observed effects of salmon. Identifying sources of variation in salmon–stream interactions is a critical step toward understanding why engineering and subsidy effects vary so dramatically over space and time, and toward developing management strategies that will preserve the ecological integrity of salmon streams. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of spironolactone and RU486 on gene expression and cell proliferation after freshwater transfer in the euryhaline killifish

We have explored the possible mechanisms by which mineralocorticoid (MR) and glucocorticoid (GR) receptors regulate the response to freshwater transfer in the gills of the euryhaline killifish Fundulus heteroclitus. Killifish were implanted with RU486 (GR antagonist) or spironolactone (MR antagonist) at doses of 0.1–1.0 mg g⁻¹, and subsequently transferred from 10‰ brackish water to freshwater. Compared to brackish water sham fish, mRNA expression of CFTR and NKCC1 decreased in the gills of sham fish transferred to freshwater, whereas Na⁺,K⁺–ATPase α_1a mRNA expression and α protein abundance, as well as cell proliferation (detected using BrdU) increased. Spironolactone inhibited the normal increase in cell proliferation and Na⁺,K⁺-ATPase expression after freshwater transfer. RU486 increased plasma cortisol levels and may have slightly inhibited Na⁺,K⁺–ATPase activity, but did not change α _1a expression. RU486 had no effect on cell proliferation in the non-lamellar region of the gills, but increased proliferation in the lamellar region. Neither antagonist inhibited the suppression of CFTR or NKCC1 expression after freshwater transfer. Glucocorticoid receptor expression was reduced in all sham and antagonist treatments compared to untreated controls, but no other consistent differences were observed. The effects of spironolactone suggest that MR is important for regulating ion transport in killifish gills after freshwater transfer.     

Effect of body mass and water temperature on the standard metabolic rate of juvenile yellow perch, Perca flavescens (Mitchill)

Fish respiration rates that are presumed to represent standard metabolic rates (SMR) may sometimes include an unspecified energy expenditure associated with activity and digestion. This situation may introduce a bias in bioenergetics models because standard metabolism, digestion, and activity may not be affected by the same environmental conditions. The aim of this study was to (1) develop a SMR model for juvenile yellow perch, Perca flavescens (Mitchill), that represent the minimum energy expenditure required to maintain life and (2) compare the results of this study with published perch metabolic rates and bioenergetics models. SMR was estimated for yellow perch over a range of body␣mass (4.4–24.7 g) and water temperature (12–20°C). The intercept of the relationship between fish respiration and swimming velocity obtained during forced swimming experiments was used to determine SMR. SMR estimated by the present study were comparable to values presented by two published studies on Eurasian perch, Perca fluviatilis L. However, estimated SMR were 4.1–20.9 times lower than values of a third respirometry study and predictions of bioenergetics models for perch. The present study suggests that published SMR models may sometimes include a significant fraction of energy expenditures (39.2–75.9%) associated with digestion and activity. This may complicate the implementation and the interpretation of fish bioenergetics models. The present study indicates that the intercept of respiration-velocity relationships and long-term respiration rates during starvation experiments may provide similar and reliable SMR values.     

Salinity tolerance in diapausing embryos of the annual killifish <Emphasis Type="Italic">Austrofundulus limnaeus</Emphasis> is supported by exceptionally low water and ion permeability

The annual killifish Austrofundulus limnaeus inhabits rainwater pools in the Maracaibo basin of Venezuela. This species persists in ephemeral habitats by producing diapausing embryos that are resistant to the stresses imposed by the drying of their aquatic habitat. Embryos of A. limnaeus are likely exposed to a highly variable osmotic environment during development, but their tolerance of osmotic stress has not been characterized. We investigated the capacity of these embryos to survive in hypersaline environments and evaluated the possible mechanisms used to support osmoregulation. Diapausing embryos of A. limnaeus defend their internal osmolality of around 290 mOsmol kg⁻¹ H₂O⁻¹ against salt stress as high as 50 ppt salinity. We find that diapausing embryos of A. limnaeus have a permeability to water that is orders of magnitude lower than other teleost fish embryos. The activity of ion motive ATPases that may be important in the extrusion of ions via mitochondrial rich cells do not appear to be playing a large role in osmoregulation of A. limnaeus embryos. We conclude that for the duration of embryonic development the unique properties of the enveloping cell layer of A. limnaeus embryos acts as a permeability barrier to water and ions and supports osmoregulation in this species in response to a broad range of osmotic environments. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Effects of body lipid content on the resting metabolic rate and postprandial metabolic response in the southern catfish Silurus meridionalis

We assessed the effects of body lipid content on the resting metabolic rate and specific dynamic action (SDA) of the southern catfish Silurus meridionalis. Obese and lean fish were obtained by feeding the fish with two different feeds at 27.5 °C for 4 weeks prior to the experiment. The fish were fed with experimental diets with a meal size of 4% by body mass. A continuous-flow respirometer was used to determine the oxygen consumption rate at 2-h intervals until the postprandial oxygen consumption rate had returned to the preprandial level. The body lipid content of the obese fish was significantly greater than that of the lean fish. The metabolic parameters evaluated (resting metabolic rate, peak metabolic rate (R_peak), factorial ratio, time to peak, duration, energy expended on SDA (SDA_E), or SDA coefficient) were not significantly affected by body fat content in terms of the whole-body or mass-specific values. Increased body fat content did not decrease the resting metabolic rate in the southern catfish, which might be due to the higher levels of highly unsaturated fatty acids in these fish. The results also suggest that the body composition does not appear to affect the SDA response.     

Formation and identification of trimethylimidazole during tetramethylpyrazine production from glucose by <Emphasis Type="Italic">Bacillus</Emphasis> strains

During 2,3,5,6-tetramethylpyrazine production from glucose by Bacillus strains, a novel product was detected and identified as 2,4,5-trimethylimidazole (TMI) by GC/MS. TMI appeared in the culture medium only after glucose had been depleted and then increased to 0.25–0.31 g l⁻¹ in 90–120 h. When the ammonium source was changed from (NH₄)₂SO₄ to (NH₄)₂HPO₄, only about one tenth of TMI was detected. Although the mechanistic events largely remain unclear, both microbial strains tested demonstrated similar dynamic processes of TMI production, suggesting that TMI formation is a genuine feature of Bacillus species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Does habitat structure matter? Spatially explicit population modelling of an Iberian gypsum endemic

Habitat heterogeneity may influence plant demography because conditions for survival, growth, and reproduction vary within a species’ range. We assessed the role of microhabitat spatial structure on the demography of Helianthemum squamatum, a shrubby gypsum specialist endemic to the Iberian Peninsula. We evaluated the demographic effect of microhabitat spatial variation using an approach that combined cellular automata with matrix population models, and included environmental and demographic stochasticty. We collected data on seed bank (2003–2005), seedling emergence (2003–2006), and adult survivorship (2004–2007) for H. squamatum in two independent blocks with different grazing intensity in Belinchón (Cuenca, Spain). We built spatial scenarios for each block based on field data of cover and spatial pattern of four microhabitats: lichenic crust, litter, H. squamatum, and shrub. Seedling survivorship was affected by year, block, and microhabitat, with individuals emerging under conspecifics having the highest survival rate and on litter the lowest in both blocks, whereas the effect of crust and other shrubs differed across blocks. Our models indicated population increase in the block with low grazing, but population decline in the block with intense grazing. We hypothesize that higher pressure of livestock grazing and trampling leads to a shift in relative microhabitat suitability for crust and shrub. This potential effect of grazing on spatial demographic variation opens interesting questions for future research. We emphasize the importance of considering microhabitat spatial structure when evaluating management and conservation strategies. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.