A test of the metabolic theory of ecology with two longevity data sets reveals no common cause of scaling in biological times

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Multiple pathways from three types of sugar receptor sites to metabotropic transduction pathways of the blowfly: study by the whole cell-clamp experiments

Differences in the allometric scaling between gut capacity (with body mass, BM^1.00) and food intake (with BM^0.75) should theoretically result in a scaling of digesta retention time with BM^0.25 and therefore a higher digestive efficiency in larger herbivores. This concept is an important part of the so-called ‘Jarman–Bell principle’ (JBP) that explains niche differentiation along a body size gradient in terms of digestive physiology. Empirical data in herbivorous mammals, however, do not confirm the scaling of retention time, or of digestive efficiency, with body mass. Here, we test these concepts in herbivorous reptiles, adding data of an experiment that measured food intake, digesta retention, digestibility and gut capacity in 23 tortoises (Testudo graeca, T. hermanni , Geochelone nigra, G. sulcata, Dipsochelys dussumieri) across a large BM range (0.5–180 kg) to a literature data collection. While dry matter gut fill scaled to BM^1.07 and dry matter intake to BM^0.76, digesta mean retention time (MRT) scaled to BM^0.17; the scaling exponent was not significantly different from zero for species > 1 kg. Food intake level was a major determinant of MRT across reptiles and mammals. In contrast to dietary fibre level, BM was not a significant contributor to dry matter digestibility in a General Linear Model. Digestibility coefficients in reptiles depended on diet nutrient composition in a similar way as described in mammals. Although food intake is generally lower and digesta retention longer in reptiles than in mammals, digestive functions scale in a similar way in both clades, indicating universal principles in herbivore digestive physiology. The reasons why the theoretically derived JBP has little empirical support remain to be investigated. Until then, the JBP should not be evoked to explain niche differentiation along a body size axis in terms of digestive physiology.     

Mass,phylogeny, and temperature are sufficient to explain differences in metabolic scaling across mammalian orders?

Whether basal metabolic rate‐body mass scaling relationships have a single exponent is highly discussed, and also the correct statistical model to establish relationships. Here, we aimed (1) to identify statistically best scaling models for 17 mammalian orders, Marsupialia, Eutheria and all mammals, and (2) thereby to prove whether correcting for differences in species’ body temperature and their shared evolutionary history improves models and their biological interpretability. We used the large dataset from Sieg et al. (The American Naturalist 174 , 2009, 720) providing species’ body mass (BM), basal metabolic rate (BMR) and body temperature (T). We applied different statistical approaches to identify the best scaling model for each taxon: ordinary least squares regression analysis (OLS) and phylogenetically informed analysis (PGLS), both without and with controlling for T. Under each approach, we tested linear equations (log‐log‐transformed data) estimating scaling exponents and normalization constants, and such with a variable normalization constant and a fixed exponent of either ? or ¾, and also a curvature. Only under temperature correction, an additional variable coefficient modeled the influence of T on BMR. Except for Pholidata and Carnivora, in all taxa studied linear models were clearly supported over a curvature by AICc. They indicated no single exponent at the level of orders or at higher taxonomic levels. The majority of all best models corrected for phylogeny, whereas only half of them included T. When correcting for T, the mathematically expected correlation between the exponent (b) and the normalization constant (a) in the standard scaling model y = a x ^b was removed, but the normalization constant and temperature coefficient still correlated strongly. In six taxa, T and BM correlated positively or negatively. All this hampers a disentangling of the effect of BM, T and other factors on BMR, and an interpretation of linear BMR‐BM scaling relationships in the mammalian taxa studied.     

Mid-infrared spectroscopy and short wave infrared hyperspectral imaging—A novel approach in the qualitative assessment of Harpagophytum procumbens and H. zeyheri (Devil's Claw)

Harpagophytum procumbens (Burch.) DC. ex Meisn. subsp. procumbens (Pedaliaceae) is an important African medicinal plant growing in the Kalahari region of southern Africa. This species, together with its close taxonomic ally Harpagophytum zeyheri are collectively referred to as Devil's Claw and are used interchangeably for the treatment of inflammation-related disorders. Although the two taxa are botanically and chemically similar, H. zeyheri contains lower levels of harpagoside and these two species have not been proven to exhibit equipotent pharmacological activity. Due to these taxonomic similarities, effective quality control methods are required to distinguish between the two species. Differentiation between the two species was achieved using single point mid-infrared spectroscopy in combination with chemometric data analysis. The orthogonal projections to latent structures discriminant analysis (OPLS-DA) model had good predictive ability, as illustrated by the model statistics: R²X (cum predictive + orthogonal) = 0.86 and Q² (cum) = 0.63. Short wave infrared (SWIR) hyperspectral imaging could distinguish between the two species with acceptable model statistics: R²X and R²Y of 0.99 and 0.78, respectively. This study demonstrated that both MIR single point spectroscopy and SWIR hyperspectral imaging coupled with chemometric modelling are reliable and rapid methods to determine the authenticity of Harpagophytum spp.     

Spatial patterns of species richness in New World coral snakes and the metabolic theory of ecology

The metabolic theory of ecology (MTE) has attracted great interest because it proposes an explanation for species diversity gradients based on temperature-metabolism relationships of organisms. Here we analyse the spatial richness pattern of 73 coral snake species from the New World in the context of MTE. We first analysed the association between ln-transformed richness and environmental variables, including the inverse transformation of annual temperature (1/kT). We used eigenvector-based spatial filtering to remove the residual spatial autocorrelation in the data and geographically weighted regression to account for non-stationarity in data. In a model I regression (OLS), the observed slope between ln-richness and 1/kT was ?0.626 (r² = 0.413), but a model II regression generated a much steeper slope (?0.975). When we added additional environmental correlates and the spatial filters in the OLS model, the R² increased to 0.863 and the partial regression coefficient of 1/kT was ?0.676. The GWR detected highly significant non-stationarity, in data, and the median of local slopes of ln-richness against 1/kT was ?0.38. Our results expose several problems regarding the assumptions needed to test MTE: although the slope of OLS fell within that predicted by the theory and the dataset complied with the assumption of temperature-independence of average body size, the fact that coral snakes consist of a restricted taxonomic group and the non-stationarity of slopes across geographical space makes MTE invalid to explain richness in this case. Also, it is clear that other ecological and historical factors are important drivers of species richness patterns and must be taken into account both in theoretical modeling and data analysis.     

A multiple free-radical scavenging (MULTIS) study on the antioxidant capacity of a neuroprotective drug,edaravone as compared with uric acid,glutathione, and trolox

Edaravone (3-methyl-1-phenyl-2-pyrazoline-5-one) is a neuroprotective drug that has been used for brain ischemia injury treatment. Because its activity is speculated to be due to free radical scavenging activity, we carried out a quantitative determination of edaravone’s free radical scavenging activity against multiple free radical species. Electron spin resonance (ESR) spin trapping-based multiple free-radical scavenging (MULTIS) method was employed, where target free radicals were hydroxyl radical, superoxide anion, alkoxyl radical, alkylperoxyl radical, methyl radical, and singlet oxygen. Edaravone showed relatively high scavenging abilities against hydroxyl radical (scavenging rate constant k = 2.98 × 10¹¹ M⁻¹ s⁻¹), singlet oxygen (k = 2.75 × 10⁷ M⁻¹ s⁻¹), and methyl radical (k = 3.00 × 10⁷ M⁻¹ s⁻¹). Overall, edaravone’s scavenging activity against multiple free radical species is as robust as other known potent antioxidant such as uric acid, glutathione, and trolox. A radar chart illustration of the MULTIS activity relative to uric acid, glutathione, and trolox indicates that edaravone has a high and balanced antioxidant activity with low specificity.     

A probability distribution model of small -scale species richness in plant communities

We devised a probability distribution model that best expressed species richness per quadrat in grassland communities, and clarified the mechanism by which the mean richness per quadrat was always larger than the variance among quadrats. Our model will aid in the understanding of community structures, and allow comparisons among different communities. The model was constructed based on relatively simple theoretical assumptions about the mechanisms in play in target communities. We assumed in the model that the number of species occurring in an actual quadrat, j, is the sum of “the fundamental number of species”, k (constant), and “a fluctuating number of species”, i (a Poisson variate with the mean of μ); that is, j = k + i, where i, j and k are non-negative integers. The probability that j species occur in a quadrat is given by a Poisson-like distribution (extended Poisson), with two parameters k and μ. The mean species richness in the probability distribution is expressed by λ (= k + μ), and the variance is λ − k. The proposed model afforded a good fit for the observed frequency distribution of species richness per quadrat. If even one species is common among many quadrats, the mean number of species per quadrat is greater than the variance. The greater the number of common species among quadrats is, the larger is the value of k, and then the more pronounced is the difference between the mean and the variance (although the variance does not change). We fitted the model to 55 datasets collected by ourselves from grasslands in various locations (Tibet, Inner Mongolia, Slovakia, or Japan), with varying quadrat size (0.25, 0.0625, or 0.01 m²), and under differing management status (various stocking densities).     

Assessing the Jarman–Bell Principle: Scaling of intake,digestibility, retention time and gut fill with body mass in mammalian herbivores

Differences in allometric scaling of physiological characters have the appeal to explain species diversification and niche differentiation along a body mass (BM) gradient — because they lead to different combinations of physiological properties, and thus may facilitate different adaptive strategies. An important argument in physiological ecology is built on the allometries of gut fill (assumed to scale to BM^1.0) and energy requirements/intake (assumed to scale to BM^0.75) in mammalian herbivores. From the difference in exponents, it has been postulated that the mean retention time (MRT) of digesta should scale to BM^1.0–0.75 = BM^0.25. This has been used to argue that larger animals have an advantage in digestive efficiency and hence can tolerate lower-quality diets. However, empirical data does not support the BM^0.25 scaling of MRT, and the deduction of MRT scaling implies, according to physical principles, no scaling of digestibility; basing assumptions on digestive efficiency on the thus-derived MRT scaling amounts to circular reasoning. An alternative explanation considers a higher scaling exponent for food intake than for metabolism, allowing larger animals to eat more of a lower quality food without having to increase digestive efficiency; to date, this concept has only been explored in ruminants. Here, using data for 77 species in which intake, digestibility and MRT were measured (allowing the calculation of the dry matter gut contents (DMC)), we show that the unexpected shallow scaling of MRT is common in herbivores and may result from deviations of other scaling exponents from expectations. Notably, DMC have a lower scaling exponent than 1.0, and the 95% confidence intervals of the scaling exponents for intake and DMC generally overlap. Differences in the scaling of wet gut contents and dry matter gut contents confirm a previous finding that the dry matter concentration of gut contents decreases with body mass, possibly compensating for the less favorable volume–surface ratio in the guts of larger organisms. These findings suggest that traditional explanations for herbivore niche differentiation along a BM gradient should not be based on allometries of digestive physiology. In contrast, they support the recent interpretation that larger species can tolerate lower-quality diets because their intake has a higher allometric scaling than their basal metabolism, allowing them to eat relatively more of a lower quality food without having to increase digestive efficiency.     

Synthesis,X-ray crystal structure,DNA/protein binding and cytotoxicity studies of five α-aminophosphonate N-derivatives

Five new α-aminophosphonates are synthesized and characterized by EA, FT-IR, ¹H NMR, ¹³C NMR, ³¹P NMR, ESI-MS and X-ray crystallography. The X-ray analyses reveal that the crystal structures of 1–5 are monoclinic or triclinic system with the space group P 21/c, P − 1, P − 1, P2(1)/c and P − 1, respectively. All P atoms of 1–5 have tetrahedral geometries involving two O-ethyl groups, one C_α atom, and a double bond O atom. The binding interaction of five new α-aminophosphonate N-derivatives (1–5) with calf thymus(CT)-DNA have been investigated by UV–visible and fluorescence emission spectrometry. The apparent binding constant (Kapp) values follows the order: 1 (3.38 × 10⁵ M⁻¹) > 2 (3.04 × 10⁵ M⁻¹) > 4 (2.52 × 10⁵ M⁻¹) > 5 (2.32 × 10⁵ M⁻¹) > 3 (2.10 × 10⁵ M⁻¹), suggesting moderate intercalative binding mode between the compounds and DNA. In addition, fluorescence spectrometry of bovine serum albumin (BSA) with the compounds 1–5 showed that the quenching mechanism might be a static quenching procedure. For the compounds 1–5, the number of binding sites were about one for BSA and the binding constants follow the order: 1 (2.72 × 10⁴ M⁻¹) > 2 (2.27 × 10⁴ M⁻¹) > 4 (2.08 × 10⁴ M⁻¹) > 5 (1.79 × 10⁴ M⁻¹) > 3 (1.17 × 10⁴ M⁻¹). Moreover, the DNA cleavage abilities of 1 exhibit remarkable changes and the in vitro cytotoxicity of 1 on tumor cells lines (MCF-7, HepG2 and HT29) have been examined by MTT and shown antitumor effect on the tested cells.     

Shrinking factors of hyperbranched polysaccharide from fungus

The branched structure properties of hyperbranched polysaccharides (TM3a and TM3b), extracted from sclerotia of Pleurotus tuber-regium, were studied by using laser light scattering and viscometry. The configurational shrinking factor (g) and viscometric shrinking factor (g′) of TM3a and TM3b were discussed, where curdlan and pullulan were taken as the linear references for derivation of g and g′. The dependences of g factor, g′ factor, and Flory factor (Φ_branched) on weight average molecular weight (M_w) were established to be g = 1.07 × 10²$M_{\text{w}}^{-0.48\pm 0.09}$, g′ = 3.63 × 10¹$M_{\text{w}}^{-0.43\pm 0.01}$, and Φ_branched = 7.08 × 10²⁰$M_{\text{w}}^{0.39\pm 0.1}$ for TM3a in 0.25 M LiCl/DMSO at 25 °C, when curdlan acted as the linear reference. A power law relationship g′ = 2.71 × 10^?1g^?0.61±0.1 for TM3a was found, and the exponent was approximately same to 0.60 established by Kurata et al. for polystyrene star molecules. The dependence of g factor on M_w for TM3b was found to be g = 1.99 × 10²$M_{\text{w}}^{-0.53\pm 0.02}$, when pullulan was used as the linear reference. On the basis of Zimm–Stockmayer equation for tetrafunctional units, molecular weight of branching unit (M₀) deduced from nonlinear curve fitting of g versus M_w was 8739 ± 564 g/mol and 3961 ± 1245 g/mol for TM3a and TM3b, respectively. The effect of different linear reference curves and polydispersity was discussed. This work gave valuable information on branched structure characterization and insights into the biosynthetic pathways of the hyperbranched polysaccharide from fungus.     

Pseudomonas caspiana sp. nov., a citrus pathogen in the Pseudomonas syringae phylogenetic group

In a screening by multilocus sequence analysis of Pseudomonas strains isolated from diverse origins, 4 phylogenetically closely related strains (FBF58, FBF102^T, FBF103, and FBF122) formed a well-defined cluster in the Pseudomonas syringae phylogenetic group. The strains were isolated from citrus orchards in northern Iran with disease symptoms in the leaves and stems and its pathogenicity against citrus plants was demonstrated. The whole genome of the type strain of the proposed new species (FBF102^T = CECT 9164^T = CCUG 69273^T) was sequenced and characterized. Comparative genomics with the 14 known Pseudomonas species type strains of the P. syringae phylogenetic group demonstrated that this strain belonged to a new genomic species, different from the species described thus far. Genome analysis detected genes predicted to be involved in pathogenesis, such as an atypical type 3 secretion system and two type 6 secretion systems, together with effectors and virulence factors. A polyphasic taxonomic characterization demonstrated that the 4 plant pathogenic strains represented a new species, for which the name Pseudomonas caspiana sp. nov. is proposed.     

Flexible chain conformation of (1 → 3)-β-d-glucan from Poria cocos sclerotium in NaOH/urea aqueous solution

A water-insoluble polysaccharide (PCS3-II) extracted from sclerotium of Poria cocos was identified as a linear (1 → 3)-β-d-glucan by ¹³C NMR and gas chromatography. Aqueous 0.5 M NaOH/0.2 M urea was a good solvent for PCS3-II and the dependence of intrinsic viscosity ([η]) on weight-average molecular weight (M_w) was established in the M_w range from 7.68 × 10⁴ to 5.14 × 10⁵ to be [η] = 3.39 × 10^?2 $M_{\text{W}}^{0.62}{\text{cm}}^3{\text{g}}^{-1}$ at 25 °C by using laser light scattering and viscometry. The chain conformation parameters of PCS3-II in the 0.5 M NaOH/0.2 M urea solution was 2.3 (± 0.3) nm for persistence length (q), 580 g mol^?1 nm^?1 for molar mass per unit contour length (M_L), 0.8 (± 0.2) nm for the diameter of the chain (d) and 3.63 for limited characteristic ratio (C_∞). The results revealed, for the first time, that PCS3-II existed as a flexible chain in 0.5 M NaOH/0.2 M urea aqueous solution.     

Agrobacterium rosae sp. nov., isolated from galls on different agricultural crops

The plant tumorigenic strain NCPPB 1650^T isolated from Rosa × hybrida, and four nonpathogenic strains isolated from tumors on grapevine (strain 384), raspberry (strain 839) and blueberry (strains B20.3 and B25.3) were characterized by using polyphasic taxonomic methods. Based on 16S rRNA gene phylogeny, strains were clustered within the genus Agrobacterium. Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of atpD, recA and rpoB housekeeping genes indicated that five strains studied form a novel Agrobacterium species. Their closest relatives were Agrobacterium sp. R89-1, Agrobacterium rubi and Agrobacterium skierniewicense. Authenticity of the novel species was confirmed by average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) comparisons between strains NCPPB 1650^T and B20.3, and their closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. Whole-genome-based phylogeny further supported distinctiveness of the novel species, that forms together with A. rubi, A. skierniewicense and Agrobacterium sp. R89-1 a well-delineated sub-clade of Agrobacterium spp. named “rubi”. As for other species of the genus Agrobacterium, the major fatty acid of the strains studied was 18:1 w7c (73.42–78.12%). The five strains studied were phenotypically distinguishable from other species of the genus Agrobacterium. Overall, polyphasic characterization showed that the five strains studied represent a novel species of the genus Agrobacterium, for which the name Agrobacterium rosae sp. nov. is proposed. The type strain of A. rosae is NCPPB 1650^T (=DSM 30203^T = LMG 230^T = CFBP 4470^T = IAM 13558^T = JCM 20915^T).     

A Kazal-type serine proteinase inhibitor from chicken liver (clTI-1): Purification,primary structure,and inhibitory properties

Low-molecular-mass trypsin inhibitor (clTI-1; chicken liver Trypsin Inhibitor-1) was purified from chicken liver by extraction with perchloric acid, ammonium sulfate precipitation, a combination of ethanol-acetone fractionation followed by gel filtration, ion-exchange chromatography and RP-HPLC on a C18 column. The inhibitor occurs in two isoforms with molecular masses of 5938.56 and 6026.29 Da (determined by MALDI TOFF mass spectrometry). The complete amino acid sequences of both isoforms were determined (UniProtKB/Swiss-Prot P85000; ISK1L_CHICK). The inhibitor shows a high homology to Kazal-type family inhibitors, especially to trypsin/acrosin inhibitors and pancreatic secretory trypsin inhibitors. clTI-1 inhibits both bovine and porcine trypsin (K_a = 1.1 × 10⁹ M^?1 and 2.5 × 10⁹ M^?1, respectively). Significant differences were shown in the inhibition of the anionic and cationic forms of chicken trypsin (K_a = 4.5 × 10⁸ M^?1 and 1.2 × 10¹⁰ M^?1). Weak interaction with human plasmin (K_a = 1.2 × 10⁷ M^?1) was also revealed.     

Magnesium and strontium compositions of recent symbiont-bearing benthic foraminifera

Minor and trace elements in foraminiferal carbonates are potential paleo-proxies of climate, nutrient and seawater composition. There are very few reports of trace element composition of symbiont-bearing, larger foraminifera that are known to be important constituents of shallow-marine, modern and ancient carbonates. In this paper we examine the range of variation in Mg and Sr content of Recent species of these foraminifera from a lagoon of Lakshadweep Atoll (Indian Ocean) and Akajima Islands, Japan. Two hyaline species, Amphistegina lessonii and Neorotalia calcar,and two porcellaneous species, Amphisorus hemprichii and Marginopora vertebralis were collected live from Lakshadweep islands. Mg / Ca in these foraminifera is of an order of magnitude higher than the values reported for planktonic and symbiont-free benthic foraminifera. The Sr / Ca values are, however, comparable with the reported values in other foraminiferal taxa and they are found to vary within a narrow range. Electron-probe micro-analysis of three symbiont-bearing benthic species indicates spatial heterogeneity of high orders in Mg / Ca composition in all the species. The annual variation in temperature and pH of the lagoon water cannot explain the observed amplitude of the compositional variation. The photosynthesis and respiration of the symbionts and host foraminifera are possibly the major cause of compositional heterogeneity in individual tests, as has also been recently postulated for symbiont-bearing planktonic foraminiferal species. It highlights the need to isolate biological factors and necessitates species-specific paleotemperature scale in paleoclimatic analysis. We also analyzed δ¹⁸O, δ¹³C, Ca, Mg and Sr in carefully dissected chambers of a reef-dwelling, porcellaneous benthic foraminifer, Marginopora kudakajimaensis, collected live in four seasons. A moderate positive correlation is observed between Mg / Ca and temperature. However, large inter- and intra-test variation in Mg limits the precision of Mg / Ca as palaeotemperature proxy. The Sr / Ca of the test calcite is unrelated to temperature of the sea water. The δ¹³C of M. kudakajimaensis does not correlate with δ¹⁸O, Mg / Ca or Sr / Ca.     

Growth and loss of distal tissue in blades of Lessonia nigrescens and Lessonia trabeculata (Laminariales)

Meristematic growth and loss of distal tissue from blades of two ecologically important species in the south-east Pacific, Lessonia nigrescens and Lessonia trabeculata, was evaluated during 1 year. Comparative growth was determined by a hole-punch method, loss of distal tissue from the blades was determined by subtracting final blade length (with loss) from expected blade lengths (without loss); growth and tissue loss were transformed to fresh biomass units for calculation of inter-algae differences. The results showed that blade elongation rate increased at the beginning of spring, and declined towards the end of summer, with mean values between 0.40 and 0.08 cm day⁻¹ for L. nigrescens, and 0.65–0.17 cm day⁻¹ for L. trabeculata. Loss of distal tissue varied seasonally when examined as length units for both species; with mean values between 0.24 and 0.10 cm day⁻¹ for L. nigrescens, and 0.51–0.25 cm day⁻¹ for L. trabeculata. Variations in fresh biomass units were only observed in Lessonia trabeculata, increasing in spring, with mean values to 0.13 g (fresh weight) day⁻¹. Annual growth and loss of distal tissue were higher in L. trabeculata (0.41 and 0.39 cm day⁻¹, respectively) than in L nigrescens (0.19 and 0.15 cm day⁻¹). When growth and tissue loss were considered as fresh biomass, monthly gains significantly outweighed loss of distal tissue in both species, but parallel results based on length data followed a different trend. L. trabeculata released about 50% of its growth biomass as particulate organic matter, while the comparative value for L. nigrescens was about 20%.     

Testing the effectiveness of surrogates for assessing biological diversity of arthropods in cereal agricultural landscapes

Agricultural intensification is altering biodiversity patterns worldwide. Rapid and effective methods are needed to monitor these changes in farmland biodiversity, but it becomes both a cost- and time-prohibitive task, particularly for hyper-diverse groups such as arthropods. We evaluated the effectiveness of surrogates in irrigated and rainfed wheat fields in a Mediterranean farmland in NW Spain in order to get a rapid tool to assess arthropod biodiversity. We studied six groups with different ecological needs (i.e. Aphididae, Aphidiinae, Coccinellidae, Formicidae, Heteroptera and Syrphidae) at species level (147 species), genus (105), family (10, only Heteroptera) and order (19) level. Higher taxa, cross-taxa and subset-taxa or total richness approaches were tested as well as the correlation in composition between levels for the selected groups, and the influence of farming regime. Genus richness was a good surrogate of species richness in all six groups studied (R² = 0.38–0.60), like family and order were for Heteroptera (R² = 0.37 and 0.29, respectively). Cross-taxa analyses showed that Aphididae and Aphidiinae genera (R² = 0.19 and 0.30, respectively) and species (R² = 0.20 and 0.28, respectively) were good surrogates for Aphidiinae and Aphididae species respectively. Coccinellidae genera (R² = 0.26) and species (R² = 0.25) were good surrogates for Heteroptera species. Finally, Aphididae and Coccinellidae both at genera (R² = 0.14 and 0.20, respectively) and at species levels (R² = 0.12–0.22, respectively) were good surrogates for total species richness of all groups. Genera composition was the best surrogate for the species composition within each group. Farming regime had no influence on the relationships between surrogates and species patterns in most cases. Our results suggest that genera level is a useful surrogate for all the studied groups and family is appropriate for Heteroptera. Genus level provided a saving of 15% of identification time in Aphididae and 80% for Coccinellidae. This proves its usefulness to asses and monitor biodiversity in wheat croplands and the possibility to reduce costs.     

Structure and seasonal dynamics of the protozoan community (heterotrophic flagellates,ciliates, amoeboid protozoa) in the plankton of a large river (River Danube,Hungary)

Seasonal dynamics of all major protozoan groups were investigated in the plankton of the River Danube, upstream of Budapest (Hungary), by bi-weekly sampling over a 1-year long period. Sixty-one heterotrophic flagellate, 14 naked amoeba, 50 testate amoeba, 4 heliozoan and 83 ciliate morphospecies were identified. The estimated abundance ranges of major groups throughout the year were as follows: heterotrophic flagellates, 0.27–7.8×10⁶ ind. l^?1; naked amoebae, max. 3300 ind. l^?1; testaceans, max. 1600 ind. l^?1; heliozoans, max. 8500 ind. l^?1; ciliates, 132–34,000 ind. l^?1. In terms of biovolume, heterotrophic flagellates dominated throughout the year (max. 0.58 mm³ l^?1), and ciliates only exceeded their biovolume in summer (max. 0.76 mm³ l^?1). Naked amoeba and heliozoan biovolume was about one, and testacean biovolume 1–3, orders of magnitude lower than that of ciliates. In winter, flagellates, mainly chrysomonads, had the highest biomass, whilst ciliates were dominated by peritrichs. In 2005 from April to July a long spring/summer peak occurred for all protozoan groups. Beside chrysomonads typical flagellates were choanoflagellates, bicosoecids and abundant microflagellates (large chrysomonads and Collodictyon). Most abundant ciliates were oligotrichs, while Phascolodon, Urotricha, Vorticella, haptorids, Suctoria, Climacostomum and Stokesia also contributed significantly to biovolume during rapid succession processes. In October and November a second high protozoan peak occurred, with flagellate dominance, and slightly different taxonomic composition.     

Role of amine oxidase expression to maintain putrescine homeostasis in Rhodococcus opacus

While applications of amine oxidases are increasing, few have been characterised and our understanding of their biological role and strategies for bacteria exploitation are limited. By altering the nitrogen source (NH₄Cl, putrescine and cadaverine (diamines) and butylamine (monoamine)) and concentration, we have identified a constitutive flavin dependent oxidase (EC 1.4.3.10) within Rhodococcus opacus. The activity of this oxidase can be increased by over two orders of magnitude in the presence of aliphatic diamines. In addition, the expression of a copper dependent diamine oxidase (EC 1.4.3.22) was observed at diamine concentrations > 1 mM or when cells were grown with butylamine, which acts to inhibit the flavin oxidase. A Michaelis–Menten kinetic treatment of the flavin oxidase delivered a Michaelis constant (K_M) = 190 μM and maximum rate (k_cat) = 21.8 s^?1 for the oxidative deamination of putrescine with a lower K_M (=60 μM) and comparable k_cat (=18.2 s^?1) for the copper oxidase. MALDI–TOF and genomic analyses have indicated a metabolic clustering of functionally related genes. From a consideration of amine oxidase specificity and sequence homology, we propose a putrescine degradation pathway within Rhodococcus that utilises oxidases in tandem with subsequent dehydrogenase and transaminase enzymes. The implications of PUT homeostasis through the action of the two oxidases are discussed with respect to stressors, evolution and application in microbe-assisted phytoremediation or bio-augmentation.