Molecular Evolution of Metazoan Hypoxia-inducing Factors

Most metazoans rely on aerobic energy production, which is dependent on adequate oxygen supply. In the case of reduced oxygen supply (hypoxia), the most profound changes in gene expression are mediated by transcription factors named hypoxia-inducible factors (HIF alpha). These proteins are post-translationally regulated by prolyl-4-hydroxylase (PHD) enzymes that are direct “sensors” of cellular oxygen levels. This thesis examines the molecular evolution of metazoan HIF systems. In early metazoans the HIF system emerged from pre-existing PHD oxygen sensors and early bHLH-PAS transcription factors. In invertebrates our analysis revealed an unexpected diversity of PHD genes and HIF alpha sequence characteristics. An early branching vertebrate, the epaulette shark (Hemiscyllium ocellatum) was chosen for sequencing and hypoxia preconditioning studies of HIF alpha and PHD genes. As no quantitative PCR reference genes were available, this thesis includes the first study of reference genes in cartilaginous fish species. Applying multiple statistical analysis we also discoveredthat commonly used reference gene software may perform poorly with some data sets. Novel reference genes allowed accurate measurements of the mRNAlevels of the studied target genes. Cartilaginous fishes have three genomic duplicates of both HIF alpha and PHD genes like mammals and teleost fishes. Combining functional divergence and selection analyses it was possible to describe how sequence changes in both HIF alpha and PHD duplicates may have contributed to the differential oxygen sensitivityof HIF alphas. Additionally, novel teleost HIF-1 alpha sequences were produced and used to reveal the molecular evolution of HIF-1 alpha in this lineage rich with hypoxia tolerant species.

Monooxygenase Diversity and Oxygen Activation within Polyketide Antibiotic Biosynthesis

Molecular oxygen (O2) is a key component in cellular respiration and aerobic life. Through the redox potential of O2, the amount of free energy available to organisms that utilize it is greatly increased. Yet, due to the nature of the O2 electron configuration, it is non-reactive to most organic molecules in the ground state. For O2 to react with most organic compounds it must be activated. By activating O2, oxygenases can catalyze reactions involving oxygen incorporation into organic compounds. The oxygen activation mechanisms employed by many oxygenases to have been studied, and they often include transition metals and selected organic compounds. Despite the diversity of mechanisms for O2 activation explored in this thesis, all of the monooxygenases studied in the experimental part activate O2 through a transient carbanion intermediate. One of these enzymes is the small cofactorless monooxygenase SnoaB. Cofactorless monooxygenases are unusual oxygenases that require neither transition metals nor cofactors to activate oxygen. Based on our biochemical characterization and the crystal structure of this enzyme, the mechanism most likely employed by SnoaB relies on a carbanion intermediate to activate oxygen, which is consistent with the proposed substrate-assisted mechanism for this family of enzymes. From the studies conducted on the two-component system AlnT and AlnH, both the functions of the NADH-dependent flavin reductase, AlnH, and the reduced flavin dependent monooxygenase, AlnT, were confirmed. The unusual regiochemistry proposed for AlnT was also confirmed on the basis of the structure of a reaction product. The mechanism of AlnT, as with other flavin-dependent monooxygenases, is likely to involve a caged radical pair consisting of a superoxide anion and a neutral flavin radical formed from an initial carbanion intermediate. In the studies concerning the engineering of the S-adenosyl-L-methionine (SAM) dependent 4-O-methylase DnrK and the homologous atypical 10-hydroxylase RdmB, our data suggest that an initial decarboxylation of the substrate is catalyzed by both of these enzymes, which results in the generation of a carbanion intermediate. This intermediate is not essential for the 4-O-methylation reaction, but it is important for the 10-hydroxylation reaction, since it enables substrate-assisted activation of molecular oxygen involving a single electron transfer to O2 from a carbanion intermediate. The only role for SAM in the hydroxylation reaction is likely to be stabilization of the carbanion through the positive charge of the cofactor. Based on the DnrK variant crystal structure and the characterizations of several DnrK variants, the insertion of a single amino acid in DnrK (S297) is sufficient for gaining a hydroxylation function, which is likely caused by carbanion stabilization through active site solvent restriction. Despite large differences in the three-dimensional structures of the oxygenases and the potential for multiple oxygen activation mechanisms, all the enzymes in my studies rely on carbanion intermediates to activate oxygen from either flavins or their substrates. This thesis provides interesting examples of divergent evolution and the prevalence of carbanion intermediates within polyketide biosynthesis. This mechanism appears to be recurrent in aromatic polyketide biosynthesis and may reflect the acidic nature of these compounds, propensity towards hydrogen bonding and their ability to delocalize π-electrons.

The Ferritin-like superfamily: evolution of the biological iron storeman from a rubrerythrin-like ancestor

Background: The Ferritins are part of the extensive ‘Ferritin-like superfamily’ which have diverse functions but are linked by the presence of a common four-helical bundle domain. The role performed by Ferritins as the cellular repository of excess iron is unique. In many ways Ferritins act as tiny organelles in their ability to secrete iron away from the delicate machinery of the cell, and then to release it again in a controlled fashion avoiding toxicity. The Ferritins are ancient proteins, being common in all three domains of life. This ubiquity reflects the key contribution that Ferritins provide in achieving iron homeostasis. Scope of the review: This review compares the features of the different Ferritins and considers how they, and other members of the Ferritin-like superfamily, have evolved. It also considers relevant features of the eleven other known families within the Ferritin-like superfamily, particularly the highly diverse rubrerythrins. Major conclusions: The Ferritins have travelled a considerable evolutionary journey, being derived from far more simplistic rubrerythrin-like molecules which play roles in defence against toxic oxygen species. The forces of evolution have moulded such molecules into three distinct types of iron storing (or detoxifying) protein: the classical and universal 24-meric ferritins; the haem-containing 24-meric bacterioferritins of prokaryotes; and the prokaryotic 12-meric Dps proteins. These three Ferritin types are similar, but also possess unique properties that distinguish them and enable then to achieve their specific physiological purposes. General significance: A wide range of biological functions have evolved from a relatively simple structural unit.

A mechanism for the formation of oxygen and iron bimodal radial distribution in the disc of our Galaxy

Recently, it has been proposed that there are two type Ia supernova progenitors: short-lived and long-lived. On the basis of this idea, we develop a theory of a unified mechanism for the formation of the bimodal radial distribution of iron and oxygen in the Galactic disc. The underlying cause for the formation of the fine structure of the radial abundance pattern is the influence of the spiral arms, specifically the combined effect of the corotation resonance and turbulent diffusion. From our modelling, we conclude that in order to explain the bimodal radial distributions simultaneously for oxygen and iron and to obtain approximately equal total iron output from different types of supernovae, the mean ejected iron mass per supernova event should be the same as quoted in the literature if the maximum mass of stars, which eject heavy elements, is 50 M(circle dot). For the upper mass limit of 70 M(circle dot), the production of iron by a type II supernova explosion should increase by about 1.5 times.

Morphological evolution of tin oxide nanobelts after phase transition

This article reports a study of the thermal stability and morphological changes in tin oxide nanobelts grown in the orthorhombic SnO phase. The nanobelts were heat-treated in a differential scanning calorimetry (DSC) furnace at 800 degrees C for I It in argon, oxygen, or synthetic air atmospheres. The samples were then characterized by DSC, X-ray diffraction (XRD), high resolution transmission electron microscopy (HRTEM), and high resolution field emission scanning electron microscopy (FE-SEM). The results confirmed that the orthorhombic SnO phase is thermodynamically unstable, causing the belts to transform into the SnO2 phase when heat-treated. During the phase transition, if oxygen is available in the furnace atmosphere, nanofibers grow at the edge of nanobelts at about 50 degrees of the belts' growth direction, while particles grow on the belt surface in the absence of oxygen. Although the decomposition process reduces the nanobelt cell volume by 22%, most belts remain monocrystalline after the heat treatment. The results confirm that phase transition is a decomposition process, which explains the morphological changes in the belts based on metallic tin generated in the process.

Evolution of CaCu3Ti4O12 varistor properties during heat treatment in vacuum

Calcium copper titanate (CaCu3Ti4O12) ceramic varistors were prepared by solid-state method. The samples were several times heat treated in vacuum and the evolution of electrical characteristics were monitored by current density versus electric field measurements and impedance spectroscopy. Repeated heat treatments in vacuum (900 degrees C for 1 h, 0.01 Torr) lead to a desorption of oxygen adsorbed at the grain boundaries and consequently to a degradation of the varistor properties. During further successive heat treatments some oxygen from the grain interior moves to the grain boundary thereby partially restoring the varistor properties. (c) 2006 Elsevier Ltd and Techna Group S.r.l. All rights reserved.

CeO2 nanoparticles synthesized by a microwave-assisted hydrothermal method: evolution from nanospheres to nanorods

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pore size evolution during sintering of ceramic oxides

This paper reviews the influence of particle size distribution, agglomerates, rearrangement, sintering atmospheres and impurities on the pore evolution of some commonly studied oxides. These factors largely affect sintering mechanisms due to modifications of diffusion coefficients or evaporation-condensation. Very broad particle size distribution leads to grain growth and agglomerates densify first. Rearrangement of particles due to neck asymmetry mainly in the early stage of sintering is responsible for a high rate of densification in the first minutes of sintering by collapse of large pores. Sintering atmospheres play an important role in both densification and pore evolution. The chemical interaction of water molecules with several oxides like MgO, ZnO and SnO2 largely affects surface diffusion. As a consequence, there is an increase in the rates of pore growth and densification for MgO and ZnO and in the rate of pore growth for SnO2. Carbon dioxide does not affect the rate of sintering of MgO but greatly affects both rates of pore growth and densification of ZnO. Oxygen concentration in the atmosphere can especially affect semiconductor oxides but significantly affects the rate of pore growth of SnO2. Impurities like chlorine ions increase the rate of pore growth in MgO due to evaporation of HCl and Mg(OH)Cl, increasing the rate of densification and particle cuboidization. CuO promotes densification in SnO2, and is more effective in dry air. The rate of densification decrease and pore widening are promoted in argon. An inert atmosphere favors SnO2 evaporation due to reduction of CuO. © 1990.

Effect of lithium doping on the evolution of rheological and structural properties during gelation of siloxane-poly(oxypropylene) nanocomposites

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Formation and evolution of TiO2 nanotubes in alkaline synthesis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Thoughts on the diversity of convergent evolution of bioluminescence on earth

The widespread independent evolution of analogous bioluminescent systems is one of the most impressive and diverse examples of convergent evolution on earth. There are roughly 30 extant bioluminescent systems that have evolved independently on Earth, with each system likely having unique enzymes responsible for catalysing the bioluminescent reaction. Bioluminescence is a chemical reaction involving a luciferin molecule and a luciferase or photoprotein that results in the emission of light. Some independent systems utilize the same luciferin, such as the use of tetrapyrrolic compounds by krill and dinoflagellates, and the wide use of coelenterazine by marine organisms, while the enzymes involved are unique. One common thread among all the different bioluminescent systems is the requirement of molecular oxygen. Bioluminescence is found in most forms of life, especially marine organisms. Bioluminescence in known to benefit the organism by: attraction, repulsion, communication, camouflage, and illumination. The marine ecosystem is significantly affected by bioluminescence, the only light found in the pelagic zone and below is from bioluminescent organisms. Transgenic bioluminescent organisms have revolutionized molecular research, medicine and the biotechnology industry. The use of bioluminescence in studying molecular pathways and disease allows for non-invasive and real-time analysis. Bioluminescence-based assays have been developed for several analytes by coupling luminescence to many enzyme-catalysed reactions. Received 17 February 2012, accepted 27 March 2012, first published online 2 May 2012

OXYGEN ABUNDANCES IN LOW- AND HIGH-alpha FIELD HALO STARS AND THE DISCOVERY OF TWO FIELD STARS BORN IN GLOBULAR CLUSTERS

Oxygen abundances of 67 dwarf stars in the metallicity range -1.6 < [Fe/H] < -0.4 are derived from a non-LTE analysis of the 777 nm O I triplet lines. These stars have precise atmospheric parameters measured by Nissen and Schuster, who find that they separate into three groups based on their kinematics and alpha-element (Mg, Si, Ca, Ti) abundances: thick disk, high-alpha halo, and low-alpha halo. We find the oxygen abundance trends of thick-disk and high-alpha halo stars very similar. The low-alpha stars show a larger star-to-star scatter in [O/Fe] at a given [Fe/H] and have systematically lower oxygen abundances compared to the other two groups. Thus, we find the behavior of oxygen abundances in these groups of stars similar to that of the a elements. We use previously published oxygen abundance data of disk and very metal-poor halo stars to present an overall view (-2.3 < [Fe/H] < +0.3) of oxygen abundance trends of stars in the solar neighborhood. Two field halo dwarf stars stand out in their O and Na abundances. Both G53-41 and G150-40 have very low oxygen and very high sodium abundances, which are key signatures of the abundance anomalies observed in globular cluster (GC) stars. Therefore, they are likely field halo stars born in GCs. If true, we estimate that at least 3% +/- 2% of the local field metal-poor star population was born in GCs.

CeO2 nanoparticles synthesized by a microwave-assisted hydrothermal method: evolution from nanospheres to nanorods

Ceria (CeO2) plays a vital role in emerging technologies for environmental and energy-related applications. The catalytic efficiency of ceria nanoparticles depends on its morphology. In this study, CeO2 nanoparticles were synthesized by a microwave-assisted hydrothermal method under different synthesis temperatures. The samples were characterized by X-ray diffraction, transmission electron microscopy, Raman scattering spectroscopy, electron paramagnetic resonance spectroscopy and by the Brunauer-Emmett-Teller method. The X-ray diffraction and Raman scattering results indicated that all the synthesized samples had a pure cubic CeO2 structure. Rietveld analysis and Raman scattering also revealed the presence of structural defects due to an associated reduction in the valence of the Ce4+ ions to Ce3+ ions caused by an increasing molar fraction of oxygen vacancies. The morphology of the samples was controlled by varying the synthesis temperature. The TEM images show that samples synthesized at 80 degrees C consisted of spherical particles of about 5 nm, while those synthesized at 120 degrees C presented a mix of spherical and rod-like nanoparticles and the sample synthesized at 160 degrees C consisted of nanorods with 10 nm average diameter and 70 nm length. The microwave-assisted method proved to be highly efficient for the synthesis of CeO2 nanoparticles with different morphologies.

The submarine volcano eruption off El Hierro Island: Effects on the scattering migrant biota and the evolution of the pelagic communities

[EN] The submarine volcano eruption off El Hierro Island (Canary Islands) on 10 October 2011 promoted dramatic perturbation of the water column leading to changes in the distribution of pelagic fauna. To study the response of the scattering biota, we combined acoustic data with hydrographic profiles and concurrent sea surface turbidity indexes from satellite imagery. We also monitored changes in the plankton and nekton communities through the eruptive and post-eruptive phases. Decrease of oxygen, acidification, rising temperature and deposition of chemicals in shallow waters resulted in a reduction of epipelagic stocks and a disruption of diel vertical migration (nocturnal ascent) of mesopelagic organisms. Furthermore, decreased light levels at depth caused by extinction in the volcanic plume resulted in a significant shallowing of the deep acoustic scattering layer. Once the eruption ceased, the distribution and abundances of the pelagic biota returned to baseline levels. There was no evidence of a volcano-induced bloom in the plankton community.

Die molekulare Evolution der Hämocyaninsuperfamilie der Arthropoden

In vielen Arthropoden wird Sauerstoff mittels des Kupferproteins Hämocyanin transportiert. In der vorliegenden Arbeit wurde das Hämocyanin einiger Vertreter der Arthropoden molekularbiologisch untersucht. Bei den Crustaceen (Homarus americanus und Palinurus elephas) konnten vier Untereinheiten isoliert werden, bei denen es sich um Hämocyanine des a-Typs handelt. Bei den Myriapoden (Chilopoda, Scutigera coleoptrata und Diplopoda, Spirostreptus spec.) konnten drei unterschiedliche Hämocyaninuntereinheiten gefunden werden. Erst seit einiger Zeit ist das Hämocyanin bei Myriapoden biochemisch charakterisiert und bei diesen Hämocyaninsequenzen handelt es sich um die ersten von Myriapoden. Bei den Onychophoren (Epiperipatus spec.) konnte ebenfalls erstmals ein Hämocyanin isoliert und sequenziert werden. Hierbei handelt es sich um den ersten Hinweis, dass Onychophoren über ein respiratorisches Protein verfügen. In einer phylogenetischen Analyse der Hämocyaninsequenzen konnte ein Stammbaum der Hämocyaninsuperfamilie erstellt werden. Innerhalb der Crustacea ordnen sich die verschiedenen Hämocyaninuntereinheiten in distinkten Ästen an. Die Hämocyanine der Myriapoda sind monophyletisch, wobei die Auftrennung in distinkte Untereinheiten bereits vor der Trennung der Chilopoden und Diplopoden erfolgte; die phylogenetische Stellung der Myriapoda kann anhand der Hämocyaninsequenzen nicht zuverlässig aufgelöst werden. Eine gemeinsame Anordnung mit den Hexapoda ('Tracheata'-Hypothese) kann jedoch mit hoher Sicherheit ausgeschlossen werden. Die Onychophora stehen im Arthropodenstammbaum an basaler Position und können somit als Proarthropoda angesprochen werden. Es konnte gezeigt werden, dass die Hämocyaninevolution der Arthropodenevolution entspricht.