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In order to elucidate factors that determine substrate specificity and activity of mammalian molybdo-flavoproteins we performed site directed mutagenesis of mouse aldehyde oxidase 3 (mAOX3). The sequence alignment of different aldehyde oxidase (AOX) isoforms identified variations in the active site of mAOX3 in comparison to other AOX proteins and xanthine oxidoreductases (XOR). Based on the structural alignment of mAOX3 and bovine XOR, differences in amino acid residues involved in substrate binding in XORs in comparison to AOXs were identified. We exchanged several residues in the active site to the ones found in other AOX homologues in mouse or to residues present in bovine XOR in order to examine their influence on substrate selectivity and catalytic activity. Additionally we analyzed the influence of the [2Fe-2S] domains of mAOX3 on its kinetic properties and cofactor saturation. We applied UV-VIS and EPR monitored redox-titrations to determine the redox potentials of wild type mAOX3 and mAOX3 variants containing the iron-sulfur centers of mAOX1. In addition, a combination of molecular docking and molecular dynamic simulations (MD) was used to investigate factors that modulate the substrate specificity and activity of wild type and AOX variants. The successful conversion of an AOX enzyme to an XOR enzyme was achieved exchanging eight residues in the active site of mAOX3. It was observed that the absence of the K889H exchange substantially decreased the activity of the enzyme towards all substrates analyzed, revealing that this residue has an important role in catalysis.
Recent efforts have applied quantum tomography techniques to the calibration and characterization of complex quantum detectors using minimal assumptions. In this work, we provide detail and insight concerning the formalism, the experimental and theoretical challenges and the scope of these tomographical tools. Our focus is on the detection of photons with avalanche photodiodes and photon-number resolving detectors and our approach is to fully characterize the quantum operators describing these detectors with a minimal set of well-specified assumptions. The formalism is completely general and can be applied to a wide range of detectors.
Owen et al. [Owen. R.B.. Potts, R., Behrensmeyer, A.K., Ditchfield, P. 2008. Diatomaceous sediments and environmental change in the Pleistocene Olorgesailie Formation, southern Kenya Rift Valley. Palaeogeography, Palaeochmatology, Palaeoccology, 269. 17-37], Diatomaceous sediments and environmental change in the Pleistocene Olorgesailie Formation. southern Kenya Rift. Palaeogeography Palaeoclimatology Palaeciecology, 269, 17-37) argued that diatom assemblage variations in the Olorgesailie Formation indicate considerable environmental instability with both wetter and drier periods, contradicting the proposed period of lake stability and wet climatic conditions between ca 11 and 0.9 million years ago as proposed by Trauth et al [Trauth, M.H. Maslin, MA.. Demo. A.. Strecker, M R.. 2005. Late Cenozoic moisture history of East Africa. Science 309. 2051-2053., Trauth, M H. Mashn. M.A., Deino, A., Bergner. A G.N.. Diihnforth, M. Strecker. M.R, 2007 High- and low-latitude forcing of Plio-Pleistocene East African climate and hL.man evolution. journal of Human Evolution 53, 475-486] Contrary to the interpretation of our work by O Nen et al. [Owen. R.B, Potts, R. Behrensmeyer, A.K. Ditchfield. P. 2008], we never said that the proposed periods of large lakes were characterized by stable conditions.
We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RIs) was negatively correlated with the strength of natural selection (RIm), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage.
Organic management is one of the most popular strategies to reduce negative environmental impacts of intensive agriculture. However, little is known about benefits for biodiversity and potential worsening of yield under organic grasslands management across different grassland types, i.e. meadow, pasture and mown pasture. Therefore, we studied the diversity of vascular plants and foliage-living arthropods (Coleoptera, Araneae, Heteroptera, Auchenorrhyncha), yield, fodder quality, soil phosphorus concentrations and land-use intensity of organic and conventional grasslands across three study regions in Germany. Furthermore, all variables were related to the time since conversion to organic management in order to assess temporal developments reaching up to 18 years. Arthropod diversity was significantly higher under organic than conventional management, although this was not the case for Araneae, Heteroptera and Auchenorrhyncha when analyzed separately. On the contrary, arthropod abundance, vascular plant diversity and also yield and fodder quality did not considerably differ between organic and conventional grasslands. Analyses did not reveal differences in the effect of organic management among grassland types. None of the recorded abiotic and biotic parameters showed a significant trend with time since transition to organic management, except soil organic phosphorus concentrations which decreased with time. This implies that permanent grasslands respond slower and probably weaker to organic management than crop fields do. However, as land-use intensity and inorganic soil phosphorus concentrations were significantly lower in organic grasslands, overcoming seed and dispersal limitation by re-introducing plant species might be needed to exploit the full ecological potential of organic grassland management. We conclude that although organic management did not automatically increase the diversity of all studied taxa, it is a reasonable and useful way to support agro-biodiversity.
Two sesquiterpenes, corymbolone and mustakone, isolated from the chloroform extract of the rhizomes of Cyperus articulatus, exhibited significant anti-plasmodial properties. Mustakone was approximately ten times more active than corymbolone against the sensitive strains of the Plasmodium falciparum.
Recent efforts have applied quantum tomography techniques to the calibration and characterization of complex quantum detectors using minimal assumptions. In this work, we provide detail and insight concerning the formalism, the experimental and theoretical challenges and the scope of these tomographical tools. Our focus is on the detection of photons with avalanche photodiodes and photon-number resolving detectors and our approach is to fully characterize the quantum operators describing these detectors with a minimal set of well-specified assumptions. The formalism is completely general and can be applied to a wide range of detectors.
Ironsulfur clusters (ISCs) are important prosthetic groups that define the functions of many proteins. Proteins with ISCs (called ironsulfur or FeS proteins) are present in mitochondria, the cytosol, the endoplasmic reticulum and the nucleus. They participate in various biological pathways including oxidative phosphorylation (OXPHOS), the citric acid cycle, iron homeostasis, heme biosynthesis and DNA repair. Here, we report a homozygous mutation in LYRM4 in two patients with combined OXPHOS deficiency. LYRM4 encodes the ISD11 protein, which forms a complex with, and stabilizes, the sulfur donor NFS1. The homozygous mutation (c.203GT, p.R68L) was identified via massively parallel sequencing of 1000 mitochondrial genes (MitoExome sequencing) in a patient with deficiency of complexes I, II and III in muscle and liver. These three complexes contain ISCs. Sanger sequencing identified the same mutation in his similarly affected cousin, who had a more severe phenotype and died while a neonate. Complex IV was also deficient in her skeletal muscle. Several other FeS proteins were also affected in both patients, including the aconitases and ferrochelatase. Mutant ISD11 only partially complemented for an ISD11 deletion in yeast. Our in vitro studies showed that the l-cysteine desulfurase activity of NFS1 was barely present when co-expressed with mutant ISD11. Our findings are consistent with a defect in the early step of ISC assembly affecting a broad variety of FeS proteins. The differences in biochemical and clinical features between the two patients may relate to limited availability of cysteine in the newborn period and suggest a potential approach to therapy.
Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., "thermophilization" of communities). Lack of community responses to increased temperature, however, has also been reported for several taxa and regions, suggesting that "climatic lags" may be frequent. Here we show that microclimatic effects brought about by forest canopy closure can buffer biotic responses to macroclimate warming, thus explaining an apparent climatic lag. Using data from 1,409 vegetation plots in European and North American temperate forests, each surveyed at least twice over an interval of 12-67 y, we document significant thermophilization of ground-layer plant communities. These changes reflect concurrent declines in species adapted to cooler conditions and increases in species adapted to warmer conditions. However, thermophilization, particularly the increase of warm-adapted species, is attenuated in forests whose canopies have become denser, probably reflecting cooler growing-season ground temperatures via increased shading. As standing stocks of trees have increased in many temperate forests in recent decades, local microclimatic effects may commonly be moderating the impacts of macroclimate warming on forest understories. Conversely, increases in harvesting woody biomass-e.g., for bioenergy-may open forest canopies and accelerate thermophilization of temperate forest biodiversity.
Structural and physicochem. characteristics of mesquite gum (from Prosopis velutina) were investigated using FT- IR spectroscopic, mass spectrometric and chromatog. methods. Four fractions (F-I, F-IIa, F-IIb and F-III) were isolated by hydrophobic interaction chromatog. The samples were characterized and analyzed for their monosaccharide and oligomers compn. by high performance anion-exchange chromatog. with pulsed amperometric detection (HPAEC-PAD). L-Arabinose (L-Ara) and D-galactose (D-Gal) were found as the main carbohydrate constituent residues in the polysaccharides from mesquite gum and their ratio (L-Ara/D-Gal) varied within the range 2.54 to 3.06 among the various fractions. Small amts. of D- glucose (D-Glc), D-mannose (D-Man) and D-xylose (D-Xyl) were also detected, particularly in Fractions IIa, IIb and III. IR spectroscopy identified polysaccharides and protein in all the samples. Data from mass spectrometry (MALDI-TOF MS) was consistent with the idea that the structure corresponding to the periphereal chains of Fraction I is predominantly a chain of pentoses attached to uronic acid. [on SciFinder (R)].
Numerical simulation of the Antartic ice sheet and its dynamic response to external pertubations
(2012)
Shear folding, which is also referred to as slip folding, involves shear along planes that are oriented approximately parallel to the axial plane of the fold structure. These planes, which are typically axial-planar cleavage planes, facilitate high-angle reverse slip leading to fold limb rotation and amplification. This study builds on recent advances in our understanding of the role of weak fault zones in facilitating slip on misoriented faults; i.e., faults at a high angle to the maximum principal tectonic stress (sigma(1)). Analysis of folded marine sedimentary rocks from the Variscan of southern Ireland provides unambiguous microstructural evidence for reverse shear on chemically weakened cleavage domains. Significant silica loss in these cleavage domains, and as a consequence marked mechanical weakening, is seen as the primary cause for the reverse slip associated with the shear folding of these sedimentary rocks.
Plio-pleistocene East African pulsed climate variability and its influence on early human evolution
(2009)
Forest management is known to influence species diversity of various taxa but inconsistent or even contrasting effects are reported for arthropods. Regional differences in management as well as differences in regional species pools might be responsible for these inconsistencies, but, inter-regional replicated studies that account for regional variability are rare. We investigated the effect of forest type on the abundance, diversity, community structure and composition of two important ground-dwelling beetle families, Carabidae and Staphylinidae, in 149 forest stands distributed over three regions in Germany. In particular we focused on recent forestry history, stand age and dominant tree species, in addition to a number of environmental descriptors. Overall management effects on beetle communities were small and mainly mediated by structural habitat parameters such as the cover of forest canopy or the plant diversity on forest stands. The general response of both beetle taxa to forest management was similar in all regions: abundance and species richness of beetles was higher in older than in younger stands and species richness was lower in unmanaged than in managed stands. The abundance ratio of forest species-to-open habitat species differed between regions, but generally increased from young to old stands, from coniferous to deciduous stands and from managed to unmanaged stands. The response of both beetle families to dominant tree species was variable among regions and staphylinid richness varied in the response to recent forestry history. Our results suggest that current forest management practices change the composition of ground-dwelling beetle communities mainly by favoring generalists and open habitat species. To protect important forest beetle communities and thus the ecosystem functions and services provided by them, we suggest to shelter remaining ancient forests and to develop near-to-nature management strategies by prolonging rotation periods and increasing structural diversity of managed forests. Possible geographic variations in the response of beetle communities need to be considered in conservation-orientated forest management strategies. (C) 2014 Elsevier B.V. All rights reserved.
Current evidence suggests that all of the major events in hominin evolution have occurred in East Africa. Over the last two decades, there has been intensive work undertaken to understand African palaeoclimate and tectonics in order to put together a coherent picture of how the environment of East Africa has varied in the past. The landscape of East Africa has altered dramatically over the last 10 million years. It has changed from a relatively flat, homogenous region covered with mixed tropical forest, to a varied and heterogeneous environment, with mountains over 4 km high and vegetation ranging from desert to cloud forest. The progressive rifting of East Africa has also generated numerous lake basins, which are highly sensitive to changes in the local precipitation-evaporation regime. There is now evidence that the presence of precession-driven, ephemeral deep-water lakes in East Africa were concurrent with major events in hominin evolution. It seems the unusual geology and climate of East Africa created periods of highly variable local climate, which, it has been suggested could have driven hominin speciation, encephalisation and dispersal out of Africa. One example is the significant hominin speciation and brain expansion event at -1.8 Ma that seems to have been coeval with the occurrence of highly variable, extensive, deep-water lakes. This complex, climatically very variable setting inspired first the variability selection hypothesis, which was then the basis for the pulsed climate variability hypothesis. The newer of the two suggests that the long-term drying trend in East Africa was punctuated by episodes of short, alternating periods of extreme humidity and aridity. Both hypotheses, together with other key theories of climate-evolution linkages, are discussed in this paper. Though useful the actual evolution mechanisms, which led to early hominins are still unclear and continue to be debated. However, it is clear that an understanding of East African lakes and their palaeoclimate history is required to understand the context within which humans evolved and eventually left East Africa. (C) 2014 The Authors. Published by Elsevier Ltd.
Intensive land use is a driving force for biodiversity decline in many ecosystems. In semi-natural grasslands, land-use activities such as mowing, grazing and fertilization affect the diversity of plants and arthropods, but the combined effects of different drivers and the chain of effects are largely unknown. In this study we used structural equation modelling to analyse how the arthropod communities in managed grasslands respond to land use and whether these responses are mediated through changes in resource diversity or resource quantity (biomass). Plants were considered resources for herbivores which themselves were considered resources for predators. Plant and arthropod (herbivores and predators) communities were sampled on 141 meadows, pastures and mown pastures within three regions in Germany in 2008 and 2009. Increasing land-use intensity generally increased plant biomass and decreased plant diversity, mainly through increasing fertilization. Herbivore diversity decreased together with plant diversity but showed no response to changes in plant biomass. Hence, land-use effects on herbivore diversity were mediated through resource diversity rather than quantity. Land-use effects on predator diversity were mediated by both herbivore diversity (resource diversity) and herbivore quantity (herbivore biomass), but indirect effects through resource quantity were stronger. Our findings highlight the importance of assessing both direct and indirect effects of land-use intensity and mode on different trophic levels. In addition to the overall effects, there were subtle differences between the different regions, pointing to the importance of regional land-use specificities. Our study underlines the commonly observed strong effect of grassland land use on biodiversity. It also highlights that mechanistic approaches help us to understand how different land-use modes affect biodiversity.