PHYCOBILIPROTEIN COMPONENTS AND CHARACTERISTICS OF THE PHYCOBILISOME FROM A THERMOPHILIC CYANOBACTERIUM MYXOSARCINA CONCINNA1

A phycocyanin (PC) and three allophycocyanin (AP) components (designated PC, AP1, AP2, and AP3) were prepared from Myxosarcina concinna Printz phycobilisomes by the native gradient PAGE performed in a neutral buffer system combined with the ion exchange column chromatography on DEAE‐DE52 cellulose. PC contained one β subunit () and two α ones ( and ), and it carried two rod linkers ( and ) and one rod‐core linker (). AP1 and AP3 were characterized as peripheral core APs, whereas AP2 was an inner‐core one. AP2 and AP3 were demonstrated to function as the terminal emitters. Each of the three APs contained two β subunits ( and ), two α subunits ( and ) and an inner‐core linker (). AP2 and AP3 had another subunit of the allophycocyanin B (AP‐B) type () belonging to the β subunit group, and AP1 and AP3 carried their individual specific core linkers ( and ), respectively. No AP component was shown to associate with the core‐membrane linker L_CM. The functions of the linker polypeptides in the phycobilisome (PBS) construction are discussed.     

Relative contribution of AtHAK5 and AtAKT1 to K+ uptake in the high‐affinity range of concentrations

The relative contribution of the high‐affinity K⁺ transporter AtHAK5 and the inward rectifier K⁺ channel AtAKT1 to K⁺ uptake in the high‐affinity range of concentrations was studied in Arabidopsis thaliana ecotype Columbia (Col‐0). The results obtained with wild‐type lines, with T‐DNA insertion in both genes and specific uptake inhibitors, show that AtHAK5 and AtAKT1 mediate the ‐sensitive and the Ba²⁺‐sensitive components of uptake, respectively, and that they are the two major contributors to uptake in the high‐affinity range of Rb⁺ concentrations. Using Rb⁺ as a K⁺ analogue, it was shown that AtHAK5 mediates absorption at lower Rb⁺ concentrations than AtAKT1 and depletes external Rb⁺ to values around 1 μM. Factors such as the presence of K⁺ or during plant growth determine the relative contribution of each system. The presence of in the growth solution inhibits the induction of AtHAK5 by K⁺ starvation. In K⁺‐starved plants grown without , both systems are operative, but when is present in the growth solution, AtAKT1 is probably the only system mediating Rb⁺ absorption, and the capacity of the roots to deplete Rb⁺ is reduced.     

Effects of different Nitrogen forms and osmotic stress on water use efficiency of rice (Oryza sativa)

A hydroponic experiment with simulated water stress induced by polyethylene glycol (PEG) was conducted in greenhouse to study the effects of different nitrogen (N) forms (; and the mixture of and ) on water stress tolerance and water use efficiency (WUE and WUE_T) of different rice cultivars. Two rice cultivars (cv. ‘Shanyou 63’ hybrid indica and ‘Yangdao 6’ indica, China) were grown under non‐water‐ or water‐stressed condition [10% (w/v) PEG, molecular weight 6000] with different N forms for 3 weeks. Under non‐water stress, the biomass of Shanyou 63 was 50.0% and 64.3% and of Yangdao 6 was 6.9% and 87.8% higher under the supply of mixture of and than either under the sole supply of or , respectively; under water stress, the biomass of both rice cultivars decreased in all three nitrogen forms compared with non‐water stress; however, the inhibitory effect of water stress on biomass varied between and nutrition; the reduction of dry matter was significantly higher in than in nutrition. Compared with non‐water stress, under water stressed condition, WUE of both two rice cultivars significantly decreased in supply; WUE did not vary in and the mixture supply. It is concluded that (a) the resistance of water stress of rice seedlings is related to nitrogen form; (b) under water stress, could maintain a higher WUE compared with ; (c) hybrid indica rice seedlings have a higher water stress tolerance than indica rice seedlings.     

INTERACTIONS BETWEEN NITRATE UPTAKE AND NITROGEN FIXATION IN CONTINUOUS CULTURES OF THE MARINE DIAZOTROPH TRICHODESMIUM (CYANOBACTERIA)1

Diazotrophic cyanobacteria can take up combined nitrogen (nitrate, ammonium, amino acids, dissolved organic nitrogen) from solution, but the interaction between N₂ fixation and uptake of combined nitrogen is not well understood. We studied the effects of combined nitrogen ) additions on N₂ fixation rates in the cyanobacterium Trichodesmium erythraeum (IMS‐101) maintained in continuous culture in an N‐free medium (YBCII) and a 12:12‐h light:dark cycle. We measured acetylene reduction rates, nutrient concentrations, and biomass throughout the 12 h of illumination after the addition of nitrate (0.5–20 μM) at the start of the light period. Compared with unamended controls, Trichodesmium showed strong inhibition of acetylene reduction (up to 70%) in the presence of , with apparent saturation of the inhibition effect at an initial concentration of approximately 10 μM. The inhibition of acetylene reduction persisted through much of the light period as concentration in the culture vessel decreased. Recovery of N₂ fixation was observed late in the light period in cultures amended with low concentrations of (<5 μM) when ambient concentrations had decreased to 0.3–0.4 μM in the culture vessel. Nitrate uptake accounted for as much as 86% of total N uptake and, at the higher treatment concentrations, more than made up for the observed decrease in N₂ fixation rates. We conclude that Trichodesmium can obtain significant quantities of N through uptake of nitrate and does so in preference to N₂ fixation when sufficient is available.     

Organic and inorganic nutrient effects on growth rate–irradiance relationships in the Texas brown‐tide alga Aureoumbra lagunensis (Pelagophyceae)1

Pelagophyte species in the genera Aureococcus and Auroumbra form brown tides in coastal bays that cause food‐web disruption and extensive shading of benthic primary producers. Organic nutrients have been suggested as key factors in the origination and persistence of the East Coast (USA) brown‐tide alga Aureococcus anophagefferens Hargraves et Sieburth. To evaluate this finding for the Texas brown‐tide alga Aureoumbra lagunensis D. A. Stockw., DeYoe, Hargraves et P. W. Johnson, we grew strain TBA‐2 with dissolved inorganic nitrogen (DIN; or ) or dissolved organic nitrogen (DON; urea or glutamate) as the nitrogen (N) source under eight light intensities. Maximum growth rates decreased with N source from (1.0 div · d^?1) to (0.48 div · d^?1). Neither growth rate efficiency (α) nor I_k varied significantly between N treatments. Both inorganic phosphorus (P) and β‐glycerophosphate supported growth. Aureoumbra lagunensis can utilize at least some forms of organic N and P and can use them to persist or grow when inorganic forms become limiting. We found no evidence to support the hypothesis that organic utilization enhances or supplements growth at low light levels.     

Are geothermal streams important sites of nutrient uptake in an agricultural and urbanising landscape (Rotorua,New Zealand)?

1. Lakes in the Rotorua region of New Zealand are affected by eutrophication from urbanisation and agricultural land use. Some lake tributaries contain geothermally influenced waters, and it is currently unknown whether geothermal tributaries are active sites of nutrient cycling or represent point sources of nutrients to the lakes. 2. Using government data sets, we characterised the physicochemical conditions of geothermal and non‐geothermal streams. We then measured ecosystem metabolism and reach‐scale uptake of nitrate (), ammonium () and phosphate () in summer 2010 (n = 8 streams). Finally, we used government data to compare annual nutrient flux from geothermal and non‐geothermal surface water inputs to Lake Rotoiti. 3. As expected, geothermal streams had higher temperature, conductivity and nutrient concentrations and lower pH. However, primary production, community respiration and uptake rates in geothermal streams were not different from those in their non‐geothermal counterparts. Uptake rates of were higher in geothermal streams, and uptake was below detection in geothermal streams, probably due to the saturation by naturally high concentrations. 4. A comparison of Lake Rotoiti inputs suggested that geothermal streams are not significant sources of and , while geothermal inputs of represent an average of 46% of total flux from Lake Rotoiti tributaries. 5. Despite their high temperature and low pH, geothermal streams are active sites of photosynthesis, respiration and and cycling, indicating dynamic biofilm communities. 6. Management options for geothermal streams, if any, should focus on retention (e.g. uptake or coupled nitrification and denitrification) but could prove challenging given the persistent, naturally occurring high flux.     

Isolation by distance in a continuous population under stochastic demographic fluctuations

The local density of individuals is seldom uniform in space and time within natural populations. Yet, formal approaches to the process of isolation by distance in continuous populations have encountered analytical difficulties in describing genetic structuring with demographic heterogeneities, usually disregarding local correlations in the movement and reproduction of genes. We formulate exact recursions for probabilities of identity in continuous populations, from which we deduce definitions of effective dispersal () and effective density (D_e) that generalize results relating spatial genetic structure, dispersal and density in lattice models. The latter claim is checked in simulations where estimates of effective parameters obtained from demographic information are compared with estimates derived from spatial genetic patterns in a plant population evolving in a heterogeneous and dynamic habitat. The simulations further suggest that increasing spatio‐temporal correlations in local density reduce and generally decrease the product , with dispersal kurtosis influencing their sensitivity to density fluctuations. As in the lattice model, the expected relationship between the product and the genetic structure statistic a_r holds under fluctuating density, irrespective of dispersal kurtosis. The product D σ² between observed census density and the observed dispersal rate over one generation will generally be an upwardly biased (up to 400% in simulations) estimator of in populations distributed in spatially aggregated habitats.     

Cover Caption: Plant Vascular System

This issue focuses on the plant vascular system, with a comprehensive review article written by Lucas et al. (pp. 294–388). The cover drawing illustrates the phosphate‐stress signaling and response network (pp. 347–351). A Pi deficiency signal is generated in roots and transported to shoots via the xylem (blue lines). This signal is recognized by source leaves to activate the Pi stress response pathway and then to load the subsequent signals into the phloem (red lines). Phloemmobile RNAs move to roots to increase Pi uptake and alter root architecture . Different phloem‐mobile RNAs are also delivered from source leaves to developing leaves and the shoot apex where they regulate development under Pi‐stress conditions.     

PHOTOPHYSIOLOGICAL RESPONSES OF FRAGILARIOPSIS CYLINDRUS (BACILLARIOPHYCEAE) TO NITROGEN DEPLETION AT TWO TEMPERATURES1

The photosynthetic efficiency and photoprotective capacity of the sea‐ice diatom, Fragilariopsis cylindrus (Grunow) W. Krieg., grown in a matrix of nitrogen repletion and depletion at two different temperatures (?1°C and +6°C) was investigated. Temperature showed no significant effect on photosynthetic efficiency or photoprotection in F. cylindrus. Cultures under nitrogen depletion showed enhanced photoprotective capacity with an increase in nonphotochemical quenching (NPQ) when compared with nitrogen‐replete cultures. This phenomenon was achieved at no apparent cost to the photosynthetic efficiency of PSII (F_V/F_M). Nitrogen depletion yielded a partially reduced electron transport chain in which maximum fluorescence (F_M) could only be obtained by adding 3‐(3,4‐dichlorophenyl)‐1,1‐dimethylurea (DCMU). reoxidation curves showed the presence of Q_B nonreducing PSII centers under nitrogen depletion. Fast induction curves (FICs) and electron transport rates (ETRs) revealed slowing of the electrons transferred from the primary (Q_A) to the secondary (Q_B) quinone electron acceptors of PSII. The data presented show that nitrogen depletion in F. cylindrus leads to the formation of Q_B nonreducing PSII centers within the photosystem. On a physiological level, the formation of Q_B nonreducing PSII centers in F. cylindrus provides the cell with protection against photoinhibition by facilitating the rapid induction of NPQ. This strategy provides an important ecological advantage, especially during the Antarctic spring, maintaining photosynthetic efficiency under high light and nutrient‐limiting conditions.     

STRATEGIES AND RATES OF PHOTOACCLIMATION IN TWO MAJOR SOUTHERN OCEAN PHYTOPLANKTON TAXA: PHAEOCYSTIS ANTARCTICA (HAPTOPHYTA) AND FRAGILARIOPSIS CYLINDRUS (BACILLARIOPHYCEAE)1

We investigated rates and mechanisms of photoacclimation in cultures of Phaeocystis antarctica G. Karst. and Fragilariopsis cylindrus (Grunow) Willi Krieg, phytoplankton taxa that each dominate distinct areas of the Ross Sea, Antarctica. Both P. antarctica and F. cylindrus acclimated to increases in irradiance by reducing the effective size of the pigment antenna (σPSII) via xanthophyll‐cycle activity and reductions in chl. While enhanced photoprotection facilitated increases in specific growth rate and eventually led to higher light‐saturated photosynthetic rates (P^cell_m) in P. antarctica, increases in those variables were much smaller in F. cylindrus. In response to a lower irradiance, relaxation of xanthophyll‐cycle activity led to an increase in σPSII in both taxa, which occurred much more slowly in F. cylindrus. A surprising increase in specific growth rate over the first 36 h of acclimation in P. antarctica may have facilitated the significant reductions in P^cell_m observed in that taxon. In general, P. antarctica acclimated more quickly to changes in irradiance than F. cylindrus, exhibited a wider range in photosynthetic rates, but was more susceptible to photoinhibition. This acclimation strategy is consistent with growth in deeply mixed water columns with variations in irradiance that allow time for repair. In contrast, the slower acclimation rates, extensive photoprotection, and low photoinhibition exhibited by F. cylindrus suggest that it does not require the same period for repair as P. antarctica and is best suited for growth in habitats with relatively uniform irradiance, such as shallow mixed layers or sea ice.     

BEFORE OCEAN ACIDIFICATION: CALCIFIER CHEMISTRY LESSONS1

Ocean Acidification (OA) has been an important research topic for a decade. Scientists have focused on how the predicted 56% decline in the seawater carbonate ion () concentration will dramatically impair the ability of calcifiers, ranging from coccolithophores to shellfish, to form calcium carbonate (CaCO₃) structures, and the implications of the reduced carbonate saturation state (Ω) for increased dissolution of such structures. However, many published OA studies have overlooked a fundamental issue: most calcifying organisms do not rely on carbonate from seawater to calcify; they use either bicarbonate () or metabolically‐produced CO₂. The ability of important primary (corals, coralline seaweeds, and coccolithophores) and secondary (mollusks) producers to modify their local carbonate chemistry suggests that the primary threat to them from OA is by dissolution rather than impaired calcification. Here, we draw on calcification research from an era before OA and combine it with recent studies that question the source of the carbonate ion, to provide new insights into how OA might affect calcifying organisms. Organismal modification of local carbonate chemistry may enable some calcifiers to successfully form calcareous structures despite OA.     

NITROGEN UPTAKE AND ASSIMILATION KINETICS IN ALEXANDRIUM MINUTUM (DYNOPHYCEAE): EFFECT OF N‐LIMITED GROWTH RATE ON NITRATE AND AMMONIUM INTERACTIONS1

Uptake and assimilation kinetics of nitrate and ammonium were investigated along with inhibition of nitrate uptake by ammonium in the harmful dinoflagellate Alexandrium minutum Halim at different nitrogen (N)–limited growth rates. Alexandrium minutum had a strong affinity for nitrate and ammonium (K_s=0.26±0.03 and 0.31±0.04 μmol·L^?1, respectively) whatever the degree of N deficiency of the cells. Ammonium was always the preferred form of nitrogen taken up (=0.42–0.50). In the presence of both forms, nitrate uptake was inhibited by ammonium, and inhibition was particularly marked in N‐sufficient cells (I_max～0.9 and K_i=0.31–0.56 μmol·L^?1). In the case of N assimilation, ammonium was also the preferred form in N‐deficient cells (=0.54–0.72), whereas in N‐sufficient cells, both N sources were equally preferred (=0.90–1.00). The comparison of uptake and assimilation rates highlighted the ability of A. minutum to significantly store in 1 h nitrate and ammonium in amounts sufficient to supply twice the daily N requirements of the slowest‐growing N‐deficient cells. Nitrogen uptake kinetic parameters of A. minutum and their ecological implications are discussed.     

The fate of assimilated nitrogen in streams: an in situ benthic chamber study

1. Nitrogen (N) processing in streams has been investigated using whole‐stream ¹⁵N addition experiments that, in general, have found that a large proportion of added nitrate removed from the water column appears to be assimilated by the stream benthos. The long‐term fate of this retained N is unknown, and of particular interest is the possibility that it becomes denitrified through coupled mineralisation–nitrification–denitrification processes (indirect denitrification). 2. We used in situ chambers to produce highly ¹⁵N‐enriched benthic biofilms and removed the chambers to allow biofilms to interact with ambient stream conditions. Nitrogen assimilation and direct denitrification were estimated from the first chamber deployment. Chambers were periodically reinstalled over 4 weeks to measure tracer ¹⁵N in ammonium (), nitrate () and dinitrogen (N₂), from which we estimated subsequent rates of biotic N transformations, including N mineralisation (ammonification), nitrification and indirect denitrification. We also estimated rates of depuration of ¹⁵N tracer from benthic biomass compartments. 3. Nitrate uptake was roughly equivalent in the sand and cobble habitats that dominated the stream. Direct denitrification (denitrification of from the water column) was an order of magnitude higher in cobble habitats than in sand habitats, accounting for c. 26 and 2% of total nitrate uptake in cobble and sand, respectively. 4. Mean residence times of actively cycling organic N in stream benthos (algae and microbes) were 16 days in cobble habitats and 9 days in sand habitats. The difference between habitat types was driven by the influence of N residence time in epilithic biofilms (18 days) on cobbles. 5. Release of enriched ¹⁵ was the primary flux of remineralised N, while release of enriched ¹⁵ was an order of magnitude less. We detected slight ¹⁵N enrichment in dissolved nitrogen gas (N₂) in post‐enrichment sampling, indicating that indirect denitrification was taking place. However, indirect denitrification accounted for <0.1% of the assimilated N. 6. These experiments agree with results of whole‐stream ¹⁵N additions, in that most added N was assimilated rather than directly denitrified. Assimilation was primarily a short‐term N retention mechanism in this stream, and indirect denitrification of assimilated N accounted for only a minor proportion of the observed ¹⁵N loss over time. 7. Remaining possible fates include export of N as particulate organic matter, which may lead to additional storage of assimilated N in downstream habitats, and consumption by grazers.     

Plant–microbial competition for nitrogen uncoupled from soil C:N ratios

A green house experiment was designed to test the idea that competition for inorganic nitrogen (N) between plants and heterotrophic microorganisms occurs in soils with high C:N ratios, qualifying for N limited microbial activity, but not at low C:N ratios. The short‐term (24 h) ¹⁵N uptake by the grass Festuca gigantea and microorganisms in planted and unplanted soils was determined, and the bacterial activity was measured by the ³H‐thymidine incorporation technique. Two deciduous forest soils, with C:N‐ratios of 20 and 31, and the 20 soil amended with litter to a C:N ratio of 34, were used. A novel and important part of the experimental design was the preparation of the unplanted reference soil with plants present until the competition assay started by the addition of ¹⁵N labelled ammonium ( ) or nitrate ). The results suggested that plants and soil microorganisms competed for mineral N but under influence of other factors than the soil C:N ratio. The plants reduced the microbial uptake of and in the soil with low C:N ratio, which also had the lowest bacterial activity. The plants had a larger N uptake than microorganisms in the two natural soils but smaller in the litter‐amended, and their presence enhanced the bacterial activity, especially in the latter soil. The litter‐amended soil with its high C:N ratio and easily decomposable C was the soil that best fulfilled the criteria for competition, including a net consumption of mineral N during the assay, the lowest plant uptake of mineral N due to the high N immobilization by microorganisms, and a reduced microbial ¹⁵N uptake‐to‐bacterial activity in the presence of plants. Thus, other factors, such as the decomposability of the soil C and the bacterial activity, were more important than the soil C:N ratio to the outcome of plant–microbial competition for N.     

Water chemistry in the microenvironment of rainbow trout Oncorhynchus mykiss embryos is affected by development,the egg capsule and crowding

The hypothesis tested was that embryonic metabolism affects the water chemistry in the boundary layer. In addition, embryo crowding would further compound the metabolic effect on the water chemistry in the boundary layer. As development progressed, the magnitude of the boundary layer gradients for O₂ and pH, but not for NH, increased. The presence of the egg capsule hindered the diffusion of O₂ into and H⁺ and NH out of the embryo. The magnitude of the O₂, pH and NH boundary layer gradient was significantly increased when embryos were surrounded by either sham embryos or live embryos. The majority of this crowding effect on embryo boundary layers was due to changes in water flow rather than due to metabolism directly. These results clearly show that the microenvironment adjacent to the developing rainbow trout Oncorhynchus mykiss embryo becomes more stagnant as development progresses in the presence of the egg capsule and is further intensified with embryo crowding.     

LINKING TIME‐DEPENDENT CARBON‐FIXATION EFFICIENCIES IN DUNALIELLA TERTIOLECTA (CHLOROPHYCEAE) TO UNDERLYING METABOLIC PATHWAYS1

The chl‐specific short‐term ¹⁴C‐based production (P^b) measurement is a widely used tool to understand phytoplankton responses to environmental stresses. However, among the metabolic consequences of these stresses is variability in lifetimes of newly fixed carbon that cause P^b to range between chl‐specific net primary production (NPP*) and chl‐specific gross photosynthetic electron flow that is available for carbon reduction () depending on growth rate. To investigate the basis for this discrepancy, photosynthate utilization was characterized in Dunaliella tertiolecta Butcher grown at three different growth rates in N‐limited chemostats. P^b was measured throughout a 2 min to 24 h time course and showed clear growth‐rate‐dependent differences in lifetimes of newly fixed carbon. ¹⁴C pulse‐chase experiments revealed differences in patterns of carbon utilization between growth rates. At high growth rate, the majority of ¹⁴C was initially fixed into polysaccharide and lipid, but the relative contribution of each labeled biochemical pool to the total label changed over 24 h. In fast‐growing cells, labeled polysaccharides decreased 50%, while labeled lipids increased over the first 4 h. At low growth rate, ¹⁴C was initially incorporated primarily into protein, but the contribution of labeled protein to the total label increased over the next 24 h. Together, time‐resolved measurements of P^b and cellular NAD and NADP content suggest an enhanced role for alternative dissipation pathways at very low growth rate. Findings of this study contribute to an integrated understanding of growth‐rate‐dependent shifts in metabolic processes from photosynthesis to net growth.     

Microbial thiosulphate reaction arrays: the interactive roles of Fe(III), O2 and microbial strain on disproportionation and oxidation pathways

In this work, we experimentally evaluate pH and  dynamics associated with abiotic and microbial  oxidation under varying [O₂], [Fe(III)] and microbial strain/consortia (two pure strains, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, their consortia, and two enrichments from an acidic environmental system, Moose Lake 2002 and Moose Lake 2003). Results of the batch experiments demonstrate highly active microbial processing of  while abiotic controls under identical experimental conditions remain static with no pH decrease. When abiotic controls were manually titrated with acid to achieve similar pH decreases to those occurring in the microbial treatments, different S pathways were involved. In particular, disproportionation is a substantial component of initial microbial  processing, and is accelerated by the presence of Fe(III), indicating that recycling of S through intermediate oxidation states is likely to be widespread in acidic mine environments where high [Fe(III)] is common. Furthermore, the microbially mediated S reaction pathways were dependent on both environmental conditions and microbial strain/consortia, indicating that microbial community structure also plays a key role. Collectively, these results highlight the importance of microbial activity, their poor representation by abiotic S models, the likelihood that Fe(III), rather than O₂, is a key control on microbial S processing in acid environments and the need to identify the microbial community/strain involved.     

Functional linkage between N acquisition strategies and aeration capacities of hydrophytes for efficient oxygen consumption in roots

We evaluated the specific strategies of hydrophytes for root O₂ consumption in relation to N acquisition and investigated whether the strategies varied depending on the aeration capacity. Aeration capacity of roots is an important factor for determining hypoxia tolerance in plants. However, some hydrophytes possessing quite different aeration capacities often co‐occur in wetlands, suggesting that root O₂ consumption also strongly affects hypoxia tolerance. We cultivated Phragmites australis with high aeration capacity and Zizania latifolia with low aeration capacity in hypoxic conditions with NH or NO treatment and compared the growth, N uptake, N assimilation and root respiration between the two species. In Z. latifolia grown with NH treatment, high N uptake activity and restrained root growth led to sufficient N acquisition and decrease in whole‐root respiration rate. These characteristics consequently compensated for the low aeration capacity. In contrast, in P. australis, low N uptake activity was compensated by active root growth, but the whole‐root respiration rate was high. This high root respiration rate was allowed by the high aeration capacity. The O₂ consumption‐related traits of hydrophyte roots were closely correlated with N acquisition strategies, which consequently led to a compensational relationship with the root aeration capacity. It is likely that this functional linkage plays an important role as a core mechanism in the adaptation of plants to hypoxic soils.     

Locomotor activity of mice divergently selected for basal metabolic rate: a test of hypotheses on the evolution of endothermy

The aerobic capacity model postulates that high basal metabolic rates (BMR) underlying endothermy evolved as a correlated response to the selection on maximal levels of oxygen consumption () associated with locomotor activity. The recent assimilation capacity model specifically assumes that high BMR evolved as a by‐product of the selection for effective parental care, which required long‐term locomotor activity fuelled by energy assimilated from food. To test both models, we compared metabolic and behavioural correlates in males of laboratory mice divergently selected on body mass‐corrected BMR. elicited by running on the treadmill did not differ between selection lines, which points to the lack of genetic correlation between BMR and . In contrast, there was a positive, genetic correlation between spontaneous long‐term locomotor activity, food intake and BMR. Our results therefore corroborate predictions of the assimilation capacity model of endothermy evolution.     

Bayesian effect estimation accounting for adjustment uncertainty

Summary Model‐based estimation of the effect of an exposure on an outcome is generally sensitive to the choice of which confounding factors are included in the model. We propose a new approach, which we call Bayesian adjustment for confounding (BAC), to estimate the effect of an exposure of interest on the outcome, while accounting for the uncertainty in the choice of confounders. Our approach is based on specifying two models: (1) the outcome as a function of the exposure and the potential confounders (the outcome model); and (2) the exposure as a function of the potential confounders (the exposure model). We consider Bayesian variable selection on both models and link the two by introducing a dependence parameter, , denoting the prior odds of including a predictor in the outcome model, given that the same predictor is in the exposure model. In the absence of dependence (), BAC reduces to traditional Bayesian model averaging (BMA). In simulation studies, we show that BAC, with estimates the exposure effect with smaller bias than traditional BMA, and improved coverage. We, then, compare BAC, a recent approach of Crainiceanu, Dominici, and Parmigiani (2008 , Biometrika 95, 635–651), and traditional BMA in a time series data set of hospital admissions, air pollution levels, and weather variables in Nassau, NY for the period 1999–2005. Using each approach, we estimate the short‐term effects of on emergency admissions for cardiovascular diseases, accounting for confounding. This application illustrates the potentially significant pitfalls of misusing variable selection methods in the context of adjustment uncertainty.