Characterization of the peridinin–chlorophyll a-protein complex in the dinoflagellate Symbiodinium

The water-soluble peridinin–chlorophyll a-proteins (PCPs) are one of the major light harvesting complexes in photosynthetic dinoflagellates. PCP contains the carotenoid peridinin as its primary pigment. In this study, we identified and characterized the PCP protein and the PCP gene organization in Symbiodinium sp. CS-156. The protein molecular mass is 32.7 kDa, revealing that the PCP is of the monomeric form. The intronless PCP genes are organized in tandem arrays. The PCP gene cassette is composed of 1095-bp coding regions and spacers in between. Despite the heterogeneity of PCP gene tandem repeats, we identified a single form of PCP, the sequence of which exactly matches the deduced sequence of PCP gene clone 7 (JQ395030) by LC–MS/MS analysis of tryptic digested PCP, revealing the mature PCP apoprotein is 312 amino acids in length. Pigment analysis showed a peridinin-to-Chl a ratio of 4. The peridinin-to-Chl a Q_y energy transfer efficiency is 95% in this complex.     

Which Environmental Factors Predict Seasonal Variation in the Coral Health of Acropora digitifera and Acropora spicifera at Ningaloo Reef?

The impact of physico-chemical factors on percent coral cover and coral health was examined on a spatial basis for two dominant Acropora species, A. digitifera and A. spicifera, at Ningaloo Reef (north-western Australia) in the southeast Indian Ocean. Coral health was investigated by measuring metabolic indices (RNA/DNA ratio and protein concentration), energy levels (lipid ratio) and autotrophic indices (chlorophyll a (chl a) and zooxanthellae density) at six stations during typical seasons (austral autumn 2010 (March and April), austral winter 2010 (August)) and during an extreme La Niña event in summer 2011 (February). These indices were correlated with 15 physico-chemical factors (measured immediately following coral sampling) to identify predictors for health indices. Variations in metabolic indices (protein concentration and RNA/DNA ratio) for A. spicifera were mainly explained by nitrogen, temperature and zooplankton concentrations under typical conditions, while for A. digitifera, light as well as phytoplankton, in particular picoeukaryotes, were important, possibly due to higher energy requirement for lipid synthesis and storage in A. digitifera. Optimum metabolic values occurred for both Acropora species at 26–28°C when autotrophic indices (chl a and zooxanthellae density) were lowest. The extreme temperature during the La Niña event resulted in a shift of feeding modes, with an increased importance of water column plankton concentrations for metabolic rates of A. digitifera and light and plankton for A. spicifera. Our results suggest that impacts of high sea surface temperatures during extreme events such as La Niña may be mitigated via reduction on metabolic rates in coral host. The high water column plankton concentrations and associated low light levels resulted in a shift towards high symbiont densities, with lower metabolic rates and energy levels than the seasonal norm for the coral host.     

Postnatal transformations of alveolar surfactant in the rabbit: changes in pool size,pool morphology and isoforms of the 32–38 kDa apolipoprotein

To clarify perinatal transformations of surfactant we performed lung lavage in term fetuses and in 0–24-h-old newborn rabbits. Lavage fluid was separated into three pools, namely lavage pellet, lavage supernatant and cells. We found that at birth the pellet contains 94.1 ± 1.4% (S.E.) saturated phosphatidylcholine, while the supernatant and cells contain traces of it. At birth the pellet contains secreted lamellar bodies while the supernatant lacks any recognizable structure. After birth, the alveolar saturated phosphatidylcholine level increases 5.1-times in 24 h, the proportions between pools reaching adult values in 90 min (pellet = 75.9 + 4.8%, supernatant = 22.7 ± 4.9%), and small vesicles appear in the supernatant, probably originating from the turnover of alveolar surfactant during breathing. The saturated phosphatidylcholine associated with cells remains unchanged. At birth, the 32–38 kDa surfactant apolipoprotein appears to be less extensively sialylated than in adult life.     

Structure and floristic composition of the Heard Island “pool complex” community

Summary The stratigraphy, hydrology and vegetation of the Heard Island (sub-Antarctic; 53°05S, 73°30E) pool complex bogs are described. Spatial variation in processes that might have contributed to their formation are discussed. This community occurs where drainage is impeded. with Callitriche antarctica being the indicator species. Particular attention is paid to the interaction of the vegetation, pools and animals. Surface stratigraphy, peat depth, water depth and vegetation composition were measured along transect lines. Species cover abundance data of 300 quadrats were classified using a two-way indicator species analysis program and ordinated using detrended correspondence analysis. The major factors determining vegetation composition were found to be peat depth, surface topography, and the degree and type of animal disturbance. Similarities between the pool complexes on Heard Island and corresponding bogs in Tasmania, and the northern hemisphere temperate and boreal zones appear to diminish as the density of the animals occupying this habitat increases.     

Severe inbreeding depression is predicted by the “rare allele load” in Mimulus guttatus*

Most flowering plants are hermaphroditic and experience strong pressures to evolve self-pollination (automatic selection and reproductive assurance). Inbreeding depression (ID) can oppose selection for selfing, but it remains unclear if ID is typically strong enough to maintain outcrossing. To measure the full cost of sustained inbreeding on fitness, and its genomic basis, we planted highly homozygous, fully genome-sequenced inbred lines of yellow monkeyflower (Mimulus guttatus) in the field next to outbred plants from crosses between the same lines. The cost of full homozygosity is severe: 65% for survival and 86% for lifetime seed production. Accounting for the unmeasured effect of lethal and sterile mutations, we estimate that the average fitness of fully inbred genotypes is only 3–4% that of outbred competitors. The genome sequence data provide no indication of simple overdominance, but the number of rare alleles carried by a line, especially within rare allele clusters nonrandomly distributed across the genome, is a significant negative predictor of fitness measurements. These findings are consistent with a deleterious allele model for ID. High variance in rare allele load among lines and the genomic distribution of rare alleles both suggest that migration might be an important source of deleterious alleles to local populations.     

Is the ubiquinone pool in the respiratory chain of the bacterium Paracoccus denitrificans really unhomogeneous?

We have established the participation of a mobile redox pool in the respiratory chain of anaerobically grown bacterium Paracoccus denitrificans. In testing the kinetical homogeneity of the pool it was found that the ratio of fluxes of electron transport toward the terminal acceptors oxygen and nitrate was coincident for the respiratory substrates NADH and succinate; this provides evidence against the preferential link of one dehydrogenase with a distinct terminal enzyme through the separate pool of ubiquinone. The deviation from the expected behavior observed in comparing the titration of NADH oxidase and succinate oxidase with respiratory inhibitors such as mucidin (inhibitor in the bc₁ region) or cyanide can be accounted for by the activation of succinate dehydrogenase upon the increase in the reduced state of respiratory components during the titration.     

Aggregate index of social–environmental sustainability to evaluate the social–environmental quality in a watershed in the Southern Amazon

The purpose of this study was to build an aggregate index of social–environmental sustainability derived from incorporation of indicators of the quality of soil, water, and vegetation, and social organization and socioeconomic variables, in order to assess the overall social–environmental quality in a micro watershed in the Southern Amazon. From a population of 105 family production units 56 were randomly selected for evaluation of indicators of the quality of soil and water as well as for conducting interviews to evaluate the farmers’ perception of soil, water, and vegetation quality and also of socioeconomic aspects of agroecosystems. The aggregate index built from social–environmental sustainability indicators shows that the selected indicators were adequate for describing social–environmental quality and confirms the hypothesis that the studied micro-watershed in the southern edge of the Amazon is in a state of collapse, and is socially and environmentally degraded.     

Shifting white pox aetiologies affecting Acropora palmata in the Florida Keys, 1994–2014

We propose ‘the moving target hypothesis’ to describe the aetiology of a contemporary coral disease that differs from that of its historical disease state. Hitting the target with coral disease aetiology is a complex pursuit that requires understanding of host and environment, and may lack a single pathogen solution. White pox disease (WPX) affects the Caribbean coral Acropora palmata. Acroporid serratiosis is a form of WPX for which the bacterial pathogen (Serratia marcescens) has been established. We used long-term (1994–2014) photographic monitoring to evaluate historical and contemporary epizootiology and aetiology of WPX affecting A. palmata at eight reefs in the Florida Keys. Ranges of WPX prevalence over time (0–71.4%) were comparable for the duration of the 20-year study. Whole colony mortality and disease severity were high in historical (1994–2004), and low in contemporary (2008–2014), outbreaks of WPX. Acroporid serratiosis was diagnosed for some historical (1999, 2003) and contemporary (2012, 2013) outbreaks, but this form of WPX was not confirmed for all WPX cases. Our results serve as a context for considering aetiology as a moving target for WPX and other coral diseases for which pathogens are established and/or candidate pathogens are identified. Coral aetiology investigations completed to date suggest that changes in pathogen, host and/or environment alter the disease state and complicate diagnosis.     

Modelling the effect of environmental factors on the “trade-off” between growth and defensive compounds in young apple trees

The allocation of plant internal resources to growth processes (primary metabolism) and to defensive compounds (secondary metabolism) is determined by plant internal competition for common substrates and energy. In order to contribute to the discussion about environmental impacts on this trade-off between demands for growth and defence, we extended a complex plant growth model to simulate the formation of defensive compounds on the whole plant level, depending on the dynamics of the environmental conditions light, nutrients and water. In this paper, we present and apply the model to simulate the effects of different N fertilizer applications on growth and resistance of young apple trees (cv Golden Delicious). The results show that model predictions are able to describe the observed relation between growth rate and phenylpropanoid concentrations in young leaves of apple trees, and can assist in the interpretation of experimental findings. Finally, we estimate costs and benefits of investment into defence in a scenario, in which an attack by the leaf pathogen Venturia inaequalis is simulated.     

NAD kinase regulates the size of the NADPH pool and insulin secretion in pancreatic β-cells

NADPH is an important component of the antioxidant defense system and a proposed mediator in glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells. An increase in the NADPH/NADP(+) ratio has been reported to occur within minutes following the rise in glucose concentration in β-cells. However, 30 min following the increase in glucose, the total NADPH pool also increases through a mechanism not yet characterized. NAD kinase (NADK) catalyzes the de novo formation of NADP(+) by phosphorylation of NAD(+). NAD kinases have been shown to be essential for redox regulation, oxidative stress defense, and survival in bacteria and yeast. However, studies on NADK in eukaryotic cells are scarce, and the function of this enzyme has not been described in β-cells. We employed INS-1 832/13 cells, an insulin-secreting rat β-cell line, and isolated rodent islets to investigate the role of NADK in β-cell metabolic pathways. Adenoviral-mediated overexpression of NADK resulted in a two- to threefold increase in the total NADPH pool and NADPH/NADP(+) ratio, suggesting that NADP(+) formed by the NADK-catalyzed reaction is rapidly reduced to NADPH via cytosolic reductases. This increase in the NADPH pool was accompanied by an increase in GSIS in NADK-overexpressing cells. Furthermore, NADK overexpression protected β-cells against oxidative damage by the redox cycling agent menadione and reversed menadione-mediated inhibition of GSIS. Knockdown of NADK via shRNA exerted the opposite effect on all these parameters. These data suggest that NADK kinase regulates intracellular redox and affects insulin secretion and oxidative defense in the β-cell.     

Evolution of “determinants” in sex-determination: A novel hypothesis for the origin of environmental contingencies in avian sex-bias

Sex-determination is commonly categorized as either “genetic” or “environmental”—a classification that obscures the origin of this dichotomy and the evolution of sex-determining factors. The current focus on static outcomes of sex-determination provides little insight into the dynamic developmental processes by which some mechanisms acquire the role of sex determinants. Systems that combine “genetic” pathways of sex-determination (i.e., sex chromosomes) with “environmental” pathways (e.g., epigenetically induced segregation distortion) provide an opportunity to examine the evolutionary relationships between the two classes of processes and, ultimately, illuminate the evolution of sex-determining systems. Taxa with sex chromosomes typically undergo an evolutionary reduction in size of one of the sex chromosomes due to suppressed recombination, resulting in pronounced dimorphism of the sex chromosomes, and setting the stage for emergence of epigenetic compensatory mechanisms regulating meiotic segregation of heteromorphic sex chromosomes. Here we propose that these dispersed and redundant regulatory mechanisms enable environmental contingency in genetic sex-determination in birds and account for frequently documented context-dependence in avian sex-determination. We examine the evolution of directionality in such sex-determination as a result of exposure of epigenetic regulators of meiosis to natural selection and identify a central role of hormones in integrating female reproductive homeostasis, resource allocation to oocytes, and offspring sex. This approach clarifies the evolutionary relationship between sex-specific molecular genetic mechanisms of sex-determination and non-sex-specific epigenetic regulators of meiosis and demonstrates that both can determine sex. Our perspective shows how non-sex-specific mechanisms can acquire sex-determining function and, by establishing the explicit link between physiological integration of oogenesis and sex-determination, opens new avenues to the studies of adaptive sex-bias and sex-specific resource allocation in species with genetic sex-determination.     

Why are pitfall traps so rare in the natural world?

Prey capture by trapping is uncommon taxonomically, and generally requires highly evolved cognitive powers (humans) or specialist self-secreted materials (for example, spiders and caddisfly larvae). The most notable exception to this is the conical traps dug by antlion larvae. The relative uncommonness (taxonomically and ecologically) of such pitfall traps has been described as an unexplained mystery in recent publications. Here we suggest some potential routes that might lead to resolution to this mystery. We argue that although such pitfall traps have numerous benefits and are relatively cheap and easy to construct, they may suffer two significant disadvantages relative to, for example, spiders’ webs. First, pitfall traps may require a quite specialist microhabitat. Second, antlion pitfall traps may only work to retain all but the smallest prey if the antlion is present at the bottom of the pit. Thus, antlion may be more functionally tied to their trap than spiders and (since traps are much more visually conspicuous than their owners) this may make them vulnerable to predators and parasitoids that cue on the traps. Both these hypothesised drawbacks are speculative in the absence of a strong body of data and so we discuss how both potential costs could be explored empirically.     

Does a relationship exist between the urate pool in the body and lipid peroxidation during exercise?

In this study, we investigated whether a relationship exists between the levels of urate in vivo and lipid peroxidation during exercise. Seven healthy male subjects performed exhaustive cycling exercise under the following three conditions. The levels of urate, thiobarbituric acid reactive substances (TBARS) and allantoin in plasma and urine were examined before exercise and during a 3h recovery period. (1) Benzbromarone administration experiment: benzbromarone (an uricosuric agent) was administered orally the day before exercise. (2) IMP administration experiment: inosine 5'-monophosphate disodium salt (a precursor of urate) was administered orally the day before exercise. (3) Control experiment: no test substance was administered. The main results obtained were as follows. Plasma urate levels and total peroxyl radical-trapping antioxidant parameter (TRAP) for deproteinized plasma in the resting period significantly decreased depending on the treatment, in the order of IMP> control > benzbromarone. A significant positive correlation was evident between plasma urate levels and TRAP values for deproteinized plasma. The increase in plasma levels of allantoin was observed only in the case of IMP treatment. A significant negative correlation between plasma levels of urate in the resting period and the amounts of urinary TBARS excreted during the recovery period was recognized. These results suggest that the urate level in vivo before exercise is a factor influencing lipid peroxidation during exhaustive exercise. Furthermore, these findings support the view that urate may serve as an important freeradical scavenger in vivo.     

Does the cellular labile iron pool participate in the oxidation of 2',7'-dichlorodihydrofluorescein?

The fluorogenic probe 2',7'-dichlorodihydrofluorescein diacetate (H₂DCF-DA) is widely used for the estimation of oxidative stress in cells. It is known that 2',7'-dichlorodihydrofluorescein (H₂DCF), product of intracellular hydrolysis of H₂DCF-DA, is oxidized to the fluorescent compound, DCF, mainly by hydrogen peroxide (H₂O₂) in the presence of catalysts. The present study was aimed at answering the question whether the labile iron pool (LIP) may contribute to the oxidation of H₂DCF in cellular systems. The membrane-permeable lipophilic iron chelator salicylaldehyde isonicotinoyl hydrazone (SIH) was found to inhibit oxidation of the probe by H₂O₂ dependent on ferrous ions but not by peroxidase or superoxide dismutase in defined in vitro systems. When applied to cells, the probe inhibited considerably oxidation of H₂DCF in V79 Chinese hamster fibroblasts and two murine lymphoma L5178Y(LY) sublines (LY-R, LY-S) differing in LIP level, the extent of inhibition being greater in the LY-R line of higher LIP level. These results demonstrate that LIP is a significant factor determining the rate of intracellular H₂DCF oxidation.     

Is the impact of environmental noise visible in the dynamics of age-structured populations?

Climate change has ignited lively research into its impact on various population-level processes. The research agenda in ecology says that some of the fluctuations in population size are accountable for by the external noise (e.g. weather) modulating the dynamics of populations. We obeyed the agenda by assuming population growth after a resource-limited Leslie matrix model in an age-structured population. The renewal process was disturbed by superimposing noise on the development of numbers in one or several age groups. We constructed models for iteroparous and semelparous breeders so that, for both categories, the population growth rate was matching. We analysed how the modulated population dynamics correlates with the noise signal with different time-lags. No significant correlations were observed for semelparous breeders, whereas for iteroparous breeders high correlations were frequently observed with time-lags of 71 year or longer. However, the latter occurs under red-coloured noise and for low growth rates when the disturbance is on the youngest age group only. It is laborious to find any clear signs of the (red) noise- and age group-specific fluctuations if the disturbance influences older age groups only. These results cast doubts on the possibility of detecting the signature of external disturbance after it has modulated temporal fluctuations in age-structured populations.     

The molecular mechanism underlying the “rare allele phenomenon” in a subspecific hybrid zone of the California field mouse,Peromyscus californicus

Natural hybrid zones are known to have unusually high levels of novel or otherwise rare electrophoretic variants (the rare allele phenomenon). These variant alleles are most likely the result either of high levels of unique mutations in hybrids or of intragenic recombination between divergent alleles from the parental populations. This study uses DNA sequence comparisons to determine which process has produced a rare allele of the 6-phosphogluconate dehydrogenase (6PGD) gene in a subspecific hybrid zone of the California field mouse (Peromyscus californicus).About 70% of the coding sequence of 6-PGD was cloned and sequenced from three alleles, including two widespread alleles and one rare allele unique to hybrid populations. Sequence comparisons among the three alleles reveal no patterns that would indicate that the variant was formed by intragenic recombination. Instead, the unique allele of 6-PGD studied seems to have developed by the accumulation of base substitutions, which supports the hypothesis of increased mutation rates in hybrids.     

The gene pool of the Belgorod oblast population: Description of the “genetic landscape” of 22 district populations

Data on the frequencies of all (50412) surnames in a total population of 849399 people have been treated by various methods of multivariate statistics (cluster analysis, multidimensional scaling, and factor analysis) to show that 22 district populations of the Central Chernozem region of Russia form a definite, ordered system of population groups. All raions (administrative districts) of Belgorod oblast (administrative region) have been grouped into four clusters corresponding to the actual geographic locations of the populations. Districts of the eastern cluster are characterized by very specific spectrum and frequencies of surnames; districts of the western cluster differ in a high proportion of Ukrainian surnames