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Sample records for biochemical evolution iii

  1. Ordering events of biochemical evolution.

    PubMed

    Cunchillos, C; Lecointre, G

    2007-05-01

    Metabolic pathways exhibit structures resulting from an evolutionary process. Pathways have been inherited through time with modification, from the earliest periods of life. It is possible to compare the structure of pathways as done in comparative anatomy, i.e. for inferring ancestral pathways or parts of it (ancestral enzymatic functions), using standard phylogenetic reconstruction. Thus a phylogenetic tree of pathways provides a relative ordering of the rise of enzymatic functions. It even becomes possible to order the birth of each complete pathway in time. This particular "DNA-free" conceptual approach to evolutionary biochemistry is reviewed, gathering all the justifications given for it. Then, the method of assigning a given pathway to a time span of biochemical development is revisited. The previous method used an implicit "clock" of metabolic development that is difficult to justify. We develop a new clock-free approach, using functional biochemical arguments. Results of the two methods are not significantly different; our method is just more precise. This suggests that the clock assumed in the first method does not provoke any important artefact in describing the development of biochemical evolution. It is just unnecessary to postulate it. As a result, most of the amino acid metabolic pathways develop forwards, confirming former models of amino acid catabolism evolution, but not those for amino acid anabolism. The order of appearance of sectors of universal cellular metabolism is: (1) amino acid catabolism, (2) amino acid anabolism and closure of the urea cycle, (3) glycolysis and glycogenesis, (4) closure of the pentose-phosphate cycle, (5) closure of the Krebs cycle and fatty acids metabolism, (6) closure of the Calvin cycle.

  2. Biochemical and Structural Properties of Mouse Kynurenine Aminotransferase III

    SciTech Connect

    Han, Q.; Robinson, H; Cai, T; Tagle, D; Li, J

    2009-01-01

    Kynurenine aminotransferase III (KAT III) has been considered to be involved in the production of mammalian brain kynurenic acid (KYNA), which plays an important role in protecting neurons from overstimulation by excitatory neurotransmitters. The enzyme was identified based on its high sequence identity with mammalian KAT I, but its activity toward kynurenine and its structural characteristics have not been established. In this study, the biochemical and structural properties of mouse KAT III (mKAT III) were determined. Specifically, mKAT III cDNA was amplified from a mouse brain cDNA library, and its recombinant protein was expressed in an insect cell protein expression system. We established that mKAT III is able to efficiently catalyze the transamination of kynurenine to KYNA and has optimum activity at relatively basic conditions of around pH 9.0 and at relatively high temperatures of 50 to 60C. In addition, mKAT III is active toward a number of other amino acids. Its activity toward kynurenine is significantly decreased in the presence of methionine, histidine, glutamine, leucine, cysteine, and 3-hydroxykynurenine. Through macromolecular crystallography, we determined the mKAT III crystal structure and its structures in complex with kynurenine and glutamine. Structural analysis revealed the overall architecture of mKAT III and its cofactor binding site and active center residues. This is the first report concerning the biochemical characteristics and crystal structures of KAT III enzymes and provides a basis toward understanding the overall physiological role of mammalian KAT III in vivo and insight into regulating the levels of endogenous KYNA through modulation of the enzyme in the mouse brain.

  3. Biochemical Lab Activity Supports Evolution Theory

    ERIC Educational Resources Information Center

    Dyman, Daniel J.

    1974-01-01

    Described is thin-layer chromatography (TLC), a technique that can be conveniently used in the laboratory to generate evidence supporting the principle that degrees of biochemical similarity reflect degrees of evolutionary relatedness among organisms. (Author/PEB)

  4. Characterization of the biochemical properties of Campylobacter jejuni RNase III

    PubMed Central

    Haddad, Nabila; Saramago, Margarida; Matos, Rute G.; Prévost, Hervé; Arraiano, Cecília M.

    2013-01-01

    Campylobacter jejuni is a foodborne bacterial pathogen, which is now considered as a leading cause of human bacterial gastroenteritis. The information regarding ribonucleases in C. jejuni is very scarce but there are hints that they can be instrumental in virulence mechanisms. Namely, PNPase (polynucleotide phosphorylase) was shown to allow survival of C. jejuni in refrigerated conditions, to facilitate bacterial swimming, cell adhesion, colonization and invasion. In several microorganisms PNPase synthesis is auto-controlled in an RNase III (ribonuclease III)-dependent mechanism. Thereby, we have cloned, overexpressed, purified and characterized Cj-RNase III (C. jejuni RNase III). We have demonstrated that Cj-RNase III is able to complement an Escherichia coli rnc-deficient strain in 30S rRNA processing and PNPase regulation. Cj-RNase III was shown to be active in an unexpectedly large range of conditions, and Mn2+ seems to be its preferred co-factor, contrarily to what was described for other RNase III orthologues. The results lead us to speculate that Cj-RNase III may have an important role under a Mn2+-rich environment. Mutational analysis strengthened the function of some residues in the catalytic mechanism of action of RNase III, which was shown to be conserved. PMID:24073828

  5. Galapagos III World Evolution Summit: why evolution matters

    PubMed Central

    Paz-y-Miño-C, Guillermo; Espinosa, Avelina

    2016-01-01

    There is no place on Earth like the Galapagos Islands and no better destination to discuss the reality of evolution. Under the theme ‘Why Does Evolution Matter’, the University San Francisco of Quito (USFQ), Ecuador, and its Galapagos Institute for the Arts and Sciences (GAIAS), organized the III World Evolution Summit in San Cristóbal Island. The 200-attendee meeting took place on 1 to 5 June 2013; it included 12 keynote speakers, 20 oral presentations by international scholars, and 31 posters by faculty, postdocs, and graduate and undergraduate students. The Summit encompassed five sessions: evolution and society, pre-cellular evolution and the RNA world, behavior and environment, genome, and microbes and diseases. USFQ and GAIAS launched officially the Lynn Margulis Center for Evolutionary Biology and showcased the Galapagos Science Center, in San Cristóbal, an impressive research facility conceptualized in partnership with the University of North Carolina at Chapel Hill, USA. USFQ and GAIAS excelled at managing the conference with exceptional vision and at highlighting the relevance of Galapagos in the history of modern evolutionary thinking; Charles Darwin’s visit to this volcanic archipelago in 1835 unfolded unprecedented scientific interest in what today is a matchless World Heritage. PMID:26925190

  6. In silico evolution of oscillatory dynamics in biochemical networks

    NASA Astrophysics Data System (ADS)

    Ali, Md Zulfikar; Wingreen, Ned S.; Mukhopadhyay, Ranjan

    2015-03-01

    We are studying in silico evolution of complex, oscillatory network dynamics within the framework of a minimal mutational model of protein-protein interactions. In our model we consider two different types of proteins, kinase (activator) and phosphatase(inhibitor). In our model. each protein can either be phosphorylated(active) or unphospphorylated (inactive), represented by binary strings. Active proteins can modify their target based on the Michaelis-Menten kinetics of chemical equation. Reaction rate constants are directly related to sequence dependent protein-protein interaction energies. This model can be stuided for non-trivial behavior e.g. oscillations, chaos, multiple stable states. We focus here on biochemical oscillators; some questions we will address within our framework include how the oscillatory dynamics depends on number of protein species, connectivity of the network, whether evolution can readily converge on a stable oscillator if we start with random intitial parameters, neutral evolution with additional protein components and general questions of robustness and evolavability.

  7. Evolution of Class III treatment in orthodontics.

    PubMed

    Ngan, Peter; Moon, Won

    2015-07-01

    Angle, Tweed, and Moyers classified Class III malocclusions into 3 types: pseudo, dentoalveolar, and skeletal. Clinicians have been trying to identify the best timing to intercept a Class III malocclusion that develops as early as the deciduous dentition. With microimplants as skeletal anchorage, orthopedic growth modification became more effective, and it also increased the scope of camouflage orthodontic treatment for patients who were not eligible for orthognathic surgery. However, orthodontic treatment combined with orthognathic surgery remains the only option for patients with a severe skeletal Class III malocclusion or a craniofacial anomaly. Distraction osteogenesis can now be performed intraorally at an earlier age. The surgery-first approach can minimize the length of time that the malocclusion needs to worsen before orthognathic surgery. Finally, the use of computed tomography scans for 3-dimensional diagnosis and treatment planning together with advances in imaging technology can improve the accuracy of surgical movements and the esthetic outcomes for these patients.

  8. The Evolution of Population III Objects

    NASA Astrophysics Data System (ADS)

    de Araujo, J. C. N.; Opher, R.

    1990-11-01

    RESUMEN. Estudiamos el enfriamiento y colapso de las perturbaciones iso- termicas de masa M % Mj (masa de Jeans en la era de recombinaci6n) y M « Mj tomando en consideraci5n la expansi6n del Universo, presi6n, arrastre de fotones, enfriamiento de fotones (calentamiento), fotoioni- zaci6n, ionizaci5n por colisiones y la formaci6n y enfriamiento de mo- leculas de hidr6geno. Tambien estudiamos el efecto de no-esfericidad, rotaci6n y campos magneticos en el colapso de M % Mj debido a perturbaciones residuales que sobreviven para N « Mj. ABSTRACT. We study the cooling and collapse of isothermal perturbations of mass N % Nj (Jeans mass at recombination era) and N « NJ taking into account the expansion of the Universe, pressure, photon-drag, photon -cooling (heating), photoionization, collisional ionization and the formation and cooling of hydrogen molecules. We also study the effect of the nonsphericity, rotation and magnetic fields in the collapse of N % NJ. The formation of protostars from the fragmentation of clouds of mass M % MJ due to the residual perturbations that survive for N « NJ is also investigated. K ok : HYDRODYNANICS - STARS-POPULATION III

  9. Planetary change and biochemical adaptation: molecular evolution of corrinoid and heme biosyntheses.

    PubMed

    Lazcano, Antonio

    2012-04-01

    This review examines the evidence suggesting that the anaerobic biosynthesis of cobalamin (vitamin B12) evolved during early stages of cell evolution and was quickly recruited in the pathway leading to deoxyribonucleotides, the building blocks of DNA genomes. Biochemical evolution preceding the synthesis of the heme group and related molecules is discussed within the framework of geological evolution in which the appearance and accumulation of an oxygen-rich atmosphere stands as one of the major events in the evolution of the planet and the biosphere.

  10. Biochemical Evolution of Iron and Copper Proteins, Substances Vital to Life

    ERIC Educational Resources Information Center

    Frieden, Earl

    1974-01-01

    Summarizes studies in the area of biochemical evolution of iron, copper, and heme proteins to provide an historical outline. Included are lists of major kinds of proteins and enzymes and charts illustrating electron flow in a cytochrome electron transport system and interconversion of jerrous to ferric ion in iron metabolism. (CC)

  11. The role of log-normal dynamics in the evolution of biochemical pathways.

    PubMed

    Nacher, J C; Ochiai, T; Yamada, T; Kanehisa, M; Akutsu, T

    2006-01-01

    The study of the scale-free topology in non-biological and biological networks and the dynamics that can explain this fascinating property of complex systems have captured the attention of the scientific community in the last years. Here, we analyze the biochemical pathways of three organisms (Methanococcus jannaschii, Escherichia coli, Saccharomyces cerevisiae) which are representatives of the main kingdoms Archaea, Bacteria and Eukaryotes during the course of the biological evolution. We can consider two complementary representations of the biochemical pathways: the enzymes network and the chemical compounds network. In this article, we propose a stochastic model that explains that the scale-free topology with exponent in the vicinity of gamma approximately 3/2 found across these three organisms is governed by the log-normal dynamics in the evolution of the enzymes network. Precisely, the fluctuations of the connectivity degree of enzymes in the biochemical pathways between evolutionary distant organisms follow the same conserved dynamical principle, which in the end is the origin of the stationary scale-free distribution observed among species, from Archaea to Eukaryotes. In particular, the log-normal dynamics guarantees the conservation of the scale-free distribution in evolving networks. Furthermore, the log-normal dynamics also gives a possible explanation for the restricted range of observed exponents gamma in the scale-free networks (i.e., gamma > or = 3/2). Finally, our model is also applied to the chemical compounds network of biochemical pathways and the Internet network.

  12. Hydrogen Evolution from Water Coupled with the Oxidation of As(III) in a Photocatalytic System.

    PubMed

    Zou, Jian-Ping; Wu, Dan-Dan; Bao, Shao-Kui; Luo, Jinming; Luo, Xu-Biao; Lei, Si-Liang; Liu, Hui-Long; Du, Hong-Mei; Luo, Sheng-Lian; Au, Chak-Tong; Suib, Steven L

    2015-12-30

    A series of heterostructured CdS/Sr2(Nb17/18Zn1/18)2O7-δ composites with excellent photocatalytic ability for simultaneous hydrogen evolution and As(III) oxidation under simulated sunlight were synthesized and characterized. Among them, 30% CdS/Sr2(Nb17/18Zn1/18)2O7-δ (30CSNZO) has the highest in activity, exhibiting a H2 production rate of 1669.1 μmol·h(-1)·g(-1) that is higher than that of many photocatalysts recently reported in the literature. At pH 9, As(III) is completely oxidized to As(V) over 30CSNZO in 30 min of irradiation of simulated sunlight. In the photocatalytic system, H2 production rate decreases with the increase of As(III) concentration, and the recycle experiments show that 30CSNZO exhibits excellent stability, durability, and recyclability for photocatalytic hydrogen evolution and As(III) oxidation. We propose a mechanism in which superoxide radical (·O2(-)) is the active species for As(III) oxidation and the oxidation of As(III) has an effect on hydrogen evolution. For the first time, it is demonstrated that simultaneous hydrogen evolution and arsenite oxidation is possible in a photocatalytic system. PMID:26650610

  13. Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective.

    PubMed

    Pallen, Mark J; Beatson, Scott A; Bailey, Christopher M

    2005-04-01

    We review the biology of non-flagellar type-III secretion systems from a Darwinian perspective, highlighting the themes of evolution, conservation, variation and decay. The presence of these systems in environmental organisms such as Myxococcus, Desulfovibrio and Verrucomicrobium hints at roles beyond virulence. We review newly discovered sequence homologies (e.g., YopN/TyeA and SepL). We discuss synapomorphies that might be useful in formulating a taxonomy of type-III secretion. The problem of information overload is likely to be ameliorated by launch of a web site devoted to the comparative biology of type-III secretion ().

  14. Simulations in evolution. III. Randomness as a generator of opportunities.

    PubMed

    Testa, Bernard; Bojarski, Andrzej J; Mordalski, Stefan

    2013-01-01

    In Neo-Darwinism, variation and natural selection are the two evolutionary mechanisms which propel biological evolution. Our previous reports presented a histogram model to simulate the evolution of populations of individuals classified into bins according to an unspecified, quantifiable phenotypic character, and whose number in each bin changed generation after generation under the influence of fitness, while the total population was maintained constant. The histogram model also allowed Shannon entropy (SE) to be monitored continuously as the information content of the total population decreased or increased. Here, a simple Perl (Practical Extraction and Reporting Language) application was developed to carry out these computations, with the critical feature of an added random factor in the percent of individuals whose offspring moved to a vicinal bin. The results of the simulations demonstrate that the random factor mimicking variation increased considerably the range of values covered by Shannon entropy, especially when the percentage of changed offspring was high. This increase in information content is interpreted as facilitated adaptability of the population.

  15. Pele III, plate tectonics, atmospheric and biotic evolution

    SciTech Connect

    Sloan, R.E. . Dept. of Geology and Geophysics)

    1994-04-01

    This paper is an elaboration of Pele I and II, Landis et al GSA Abstr. V. 25 No.6, and Hengst et al GSA Abstr. V. 25 No.6. The Pele hypothesis is that CO[sub 2] concentration in the atmosphere is directly related to the rate of seafloor spreading and the existence of superplumes. Excess CO[sub 2] favors expansion of plants and is converted to O[sub 2] by photosynthesis and deposition of buried carbon and carbonate. O[sub 2] is removed from the atmosphere by weathering. Resulting major variations in atmospheric CO[sub 2] and O[sub 2] have significant impact on the evolution and extinction of organisms.

  16. The evolution of galaxies. III - Metal-enhanced star formation

    NASA Technical Reports Server (NTRS)

    Talbot, R. J., Jr.; Arnett, W. D.

    1973-01-01

    The problem of the paucity of low-metal-abundance low-mass stars is discussed. One alternative to the variable-initial-mass-function (VIMF) solution is proposed. It is shown that this solution - metal-enhanced star formation - satisfies the classical test which prompted the VIMF hypothesis. Furthermore, with no additional parameters it provides improved fits to other tests - e.g., inhomogeneities in the abundances in young stars, concordance of all nucleo-cosmochronologies, and a required yield of heavy-element production which is consistent with current stellar evolution theory. In this model the age of the Galaxy is 18.6 plus or minus 5.7 b.y.

  17. Biochemical evolution II: origin of life in tubular microstructures on weathered feldspar surfaces.

    PubMed

    Parsons, I; Lee, M R; Smith, J V

    1998-12-22

    Mineral surfaces were important during the emergence of life on Earth because the assembly of the necessary complex biomolecules by random collisions in dilute aqueous solutions is implausible. Most silicate mineral surfaces are hydrophilic and organophobic and unsuitable for catalytic reactions, but some silica-rich surfaces of partly dealuminated feldspars and zeolites are organophilic and potentially catalytic. Weathered alkali feldspar crystals from granitic rocks at Shap, north west England, contain abundant tubular etch pits, typically 0.4-0.6 microm wide, forming an orthogonal honeycomb network in a surface zone 50 microm thick, with 2-3 x 10(6) intersections per mm2 of crystal surface. Surviving metamorphic rocks demonstrate that granites and acidic surface water were present on the Earth's surface by approximately 3.8 Ga. By analogy with Shap granite, honeycombed feldspar has considerable potential as a natural catalytic surface for the start of biochemical evolution. Biomolecules should have become available by catalysis of amino acids, etc. The honeycomb would have provided access to various mineral inclusions in the feldspar, particularly apatite and oxides, which contain phosphorus and transition metals necessary for energetic life. The organized environment would have protected complex molecules from dispersion into dilute solutions, from hydrolysis, and from UV radiation. Sub-micrometer tubes in the honeycomb might have acted as rudimentary cell walls for proto-organisms, which ultimately evolved a lipid lid giving further shelter from the hostile outside environment. A lid would finally have become a complete cell wall permitting detachment and flotation in primordial "soup." Etch features on weathered alkali feldspar from Shap match the shape of overlying soil bacteria.

  18. Biochemical evolution II: Origin of life in tubular microstructures on weathered feldspar surfaces

    PubMed Central

    Parsons, Ian; Lee, Martin R.; Smith, Joseph V.

    1998-01-01

    Mineral surfaces were important during the emergence of life on Earth because the assembly of the necessary complex biomolecules by random collisions in dilute aqueous solutions is implausible. Most silicate mineral surfaces are hydrophilic and organophobic and unsuitable for catalytic reactions, but some silica-rich surfaces of partly dealuminated feldspars and zeolites are organophilic and potentially catalytic. Weathered alkali feldspar crystals from granitic rocks at Shap, north west England, contain abundant tubular etch pits, typically 0.4–0.6 μm wide, forming an orthogonal honeycomb network in a surface zone 50 μm thick, with 2–3 × 106 intersections per mm2 of crystal surface. Surviving metamorphic rocks demonstrate that granites and acidic surface water were present on the Earth’s surface by ∼3.8 Ga. By analogy with Shap granite, honeycombed feldspar has considerable potential as a natural catalytic surface for the start of biochemical evolution. Biomolecules should have become available by catalysis of amino acids, etc. The honeycomb would have provided access to various mineral inclusions in the feldspar, particularly apatite and oxides, which contain phosphorus and transition metals necessary for energetic life. The organized environment would have protected complex molecules from dispersion into dilute solutions, from hydrolysis, and from UV radiation. Sub-micrometer tubes in the honeycomb might have acted as rudimentary cell walls for proto-organisms, which ultimately evolved a lipid lid giving further shelter from the hostile outside environment. A lid would finally have become a complete cell wall permitting detachment and flotation in primordial “soup.” Etch features on weathered alkali feldspar from Shap match the shape of overlying soil bacteria. PMID:9860941

  19. Cell wall-bound cationic and anionic class III isoperoxidases of pea root: biochemical characterization and function in root growth.

    PubMed

    Kukavica, Biljana M; Veljovicc-Jovanovicc, Sonja D; Menckhoff, Ljiljana; Lüthje, Sabine

    2012-07-01

    Cell wall isolated from pea roots was used to separate and characterize two fractions possessing class III peroxidase activity: (i) ionically bound proteins and (ii) covalently bound proteins. Modified SDS-PAGE separated peroxidase isoforms by their apparent molecular weights: four bands of 56, 46, 44, and 41kDa were found in the ionically bound fraction (iPOD) and one band (70kDa) was resolved after treatment of the cell wall with cellulase and pectinase (cPOD). Isoelectric focusing (IEF) patterns for iPODs and cPODs were significantly different: five iPODs with highly cationic pI (9.5-9.2) were detected, whereas the nine cPODs were anionic with pI values between pH 3.7 and 5. iPODs and cPODs showed rather specific substrate affinity and different sensitivity to inhibitors, heat, and deglycosylation treatments. Peroxidase and oxidase activities and their IEF patterns for both fractions were determined in different zones along the root and in roots of different ages. New iPODs with pI 9.34 and 9.5 were induced with root growth, while the activity of cPODs was more related to the formation of the cell wall in non-elongating tissue. Treatment with auxin that inhibits root growth led to suppression of iPOD and induction of cPOD. A similar effect was obtained with the widely used elicitor, chitosan, which also induced cPODs with pI 5.3 and 5.7, which may be specifically related to pathogen defence. The differences reported here between biochemical properties of cPOD and iPOD and their differential induction during development and under specific treatments implicate that they are involved in specific and different physiological processes. PMID:22760472

  20. Adaptative biochemical pathways and regulatory networks in Klebsiella oxytoca BAS-10 producing a biotechnologically relevant exopolysaccharide during Fe(III)-citrate fermentation

    PubMed Central

    2012-01-01

    Background A bacterial strain previously isolated from pyrite mine drainage and named BAS-10 was tentatively identified as Klebsiella oxytoca. Unlikely other enterobacteria, BAS-10 is able to grow on Fe(III)-citrate as sole carbon and energy source, yielding acetic acid and CO2 coupled with Fe(III) reduction to Fe(II) and showing unusual physiological characteristics. In fact, under this growth condition, BAS-10 produces an exopolysaccharide (EPS) having a high rhamnose content and metal-binding properties, whose biotechnological applications were proven as very relevant. Results Further phylogenetic analysis, based on 16S rDNA sequence, definitively confirmed that BAS-10 belongs to K. oxytoca species. In order to rationalize the biochemical peculiarities of this unusual enterobacteriun, combined 2D-Differential Gel Electrophoresis (2D-DIGE) analysis and mass spectrometry procedures were used to investigate its proteomic changes: i) under aerobic or anaerobic cultivation with Fe(III)-citrate as sole carbon source; ii) under anaerobic cultivations using Na(I)-citrate or Fe(III)-citrate as sole carbon source. Combining data from these differential studies peculiar levels of outer membrane proteins, key regulatory factors of carbon and nitrogen metabolism and enzymes involved in TCA cycle and sugar biosynthesis or required for citrate fermentation and stress response during anaerobic growth on Fe(III)-citrate were revealed. The protein differential regulation seems to ensure efficient cell growth coupled with EPS production by adapting metabolic and biochemical processes in order to face iron toxicity and to optimize energy production. Conclusion Differential proteomics provided insights on the molecular mechanisms necessary for anaeorobic utilization of Fe(III)-citrate in a biotechnologically promising enterobacteriun, also revealing genes that can be targeted for the rational design of high-yielding EPS producer strains. PMID:23176641

  1. EVOLUTION OF [O III] {lambda}5007 EMISSION-LINE PROFILES IN NARROW EMISSION-LINE GALAXIES

    SciTech Connect

    Wang, J.; Mao, Y. F.; Wei, J. Y.

    2011-11-01

    The active galactic nucleus (AGN)-host co-evolution issue is investigated here by focusing on the evolution of the [O III] {lambda}5007 emission-line profile. A large sample of narrow emission-line galaxies is selected from the Max-Planck Institute for Astrophysics/Johns Hopkins University Sloan Digital Sky Survey DR7 catalog to simultaneously measure both the [O III] line profile and circumnuclear stellar population in an individual spectrum. By requiring that (1) the [O III] line signal-to-noise ratio is larger than 30 and (2) the [O III] line width is larger than the instrumental resolution by a factor of two, our sample is narrowed down to 2333 Seyfert galaxies/LINERs (AGNs), 793 transition galaxies, and 190 star-forming galaxies. In addition to the commonly used profile parameters (i.e., line centroid, relative velocity shift, and velocity dispersion), two dimensionless shape parameters, skewness and kurtosis, are used to quantify the line shape deviation from a pure Gaussian function. We show that the transition galaxies are systematically associated with narrower line widths and weaker [O III] broad wings than the AGNs, which implies that the kinematics of emission-line gas are different in the two kinds of objects. By combining the measured host properties and line shape parameters, we find that the AGNs with stronger blue asymmetries tend to be associated with younger stellar populations. However, a similar trend is not identified in the transition galaxies. The failure likely results from a selection effect in which the transition galaxies are systematically associated with younger stellar populations than the AGNs. The evolutionary significance revealed here suggests that both narrow-line region kinematics and outflow feedback in AGNs co-evolve with their host galaxies.

  2. Aging as Evolution-Facilitating Program and a Biochemical Approach to Switch It Off

    NASA Astrophysics Data System (ADS)

    Skulachev, Vladimir P.

    A concept is presented considering aging of living organisms as a final step of their ontogenetic program. It is assumed that such an aging program was invented by biological evolution to facilitate the evolutionary process. Indications are summarized suggesting that controlled production of toxic forms of oxygen (so called reactive oxygen species) by respiring intracellular organelles (mitochondria) is an obligatory component of the aging program. First results of a research project devoted to an attempt to interrupt aging program by antioxidants specifically addressed to mitochondria have been described. Within the framework of the project, antioxidants of a new type (SkQ) were synthesized. SkQs are composed of (i) plastoquinone (an antioxidant moiety), (ii) a penetrating cation, and (iii) a decane or pentane linker. Using planar bilayer phospholipid membranes, we selected SkQ derivatives of the highest penetrability, namely plastoquinonyl decyl triphenylphosphonium (SkQ1), plastoquinonyl decyl rhodamine 19 (SkQR1), and methylplastoquinonyl decyl triphenylphosphonium (SkQ3). Anti- and prooxidant properties of these substances and also of ubiquinonyl-decyl-triphenylphosphonium (MitoQ) were tested in isolated mitochondria. Micromolar concentrations of cationic quinones are found to be very strong prooxidants, but in the lower (sub-micromolar) concentrations they display antioxidant activity which decreases in the series SkQ1 = SkQR1 > SkQ3 > MitoQ. Thus, the window between the anti- and prooxidant effects is the smallest for MitoQ and the largest for SkQ1 and SkQR1. SkQ1 is rapidly reduced by complex III of the mitochondrial respiratory chain, i.e. it is a rechargeable antioxidant. Extremely low concentrations of SkQ1 and SkQR1 completely arrest the H2O2-induced apoptosis in human fibroblasts and HeLa cells (for SkQ1, C 1/2 = 8 · 10-9M). Higher concentrations of SkQ1 are required to block necrosis initiated by reactive oxygen species (ROS). In mice, SkQ1

  3. Evolution, biogeography, and systematics of Puriana: evolution and speciation in Ostracoda, III.

    USGS Publications Warehouse

    Cronin, T. M.

    1987-01-01

    Three types of geographic isolation - land barriers, deep water barriers, and climatic barriers - resulted in three distinct evolutionary responses in Neogene and Quaternary species of the epineritic ostracode genus Puriana. Through systematic, paleobiogeographic, and morphologic study of several hundred fossil and Recent populations from the eastern Pacific, western Atlantic, Gulf of Mexico, and the Caribbean, the phylogeny of the genus and the geography of speciation events were determined. Isolation of large populations by the Isthumus of Panama during the Pliocene did not lead to lineage splitting in species known to have existed before the Isthmus formed. Conversely, the establishment of small isolated populations on Caribbean islands by passive dispersal mechanisms frequently led to the evolution of new species or subspecies. Climatic changes along the southeastern United States during the Pliocene also catalyzed possible parapatric speciation as populations that immigrated to the northeastern periphery of the genus' range split to form new species. The results provide evidence that evolutionary models describing the influence of abiotic events on patterns of evolution and speciation can be tested using properly selected tectonic and climatic events and fossil groups amenable to species-level analysis. Two new species, P. bajaensis and P. paikensis, are described. -Author

  4. Evolution of Class III Homeodomain–Leucine Zipper Genes in Streptophytes

    PubMed Central

    Floyd, Sandra K.; Zalewski, Christopher S.; Bowman, John L.

    2006-01-01

    Land plants underwent tremendous evolutionary change following the divergence of the ancestral lineage from algal relatives. Several important developmental innovations appeared as the embryophyte clade diversified, leading to the appearance of new organs and tissue types. To understand how these changes came about, we need to identify the fundamental genetic developmental programs that are responsible for growth, patterning, and differentiation and describe how these programs were modified and elaborated through time to produce novel morphologies. Class III homeodomain–leucine zipper (class III HD–Zip) genes, identified in the model plant Arabidopsis thaliana, provide good candidates for basic land plant patterning genes. We show that these genes may have evolved in a common ancestor of land plants and their algal sister group and that the gene family has diversified as land plant lineages have diversified. Phylogenetic analysis, expression data from nonflowering lineages, and evidence from Arabidopsis and other flowering plants indicate that class III HD–Zip genes acquired new functions in sporophyte apical growth, vascular patterning and differentiation, and leaf development. Modification of expression patterns that accompanied diversification of class III HD–Zip genes likely played an important role in the evolution of land plant form. PMID:16489224

  5. SIM-GC-MS analysis of biochemical evolution in Amanita genus

    NASA Astrophysics Data System (ADS)

    Ristoiu, Dumitru; Kovacs, Emoke Dalma; Cobzac, Codruta; Parvu, Marcel; Ristoiu, Tania; Kovacs, Melinda Haydee

    2010-11-01

    Amanita is one of the most well known basidiomycetes genus throughout the world because some of its species that are acknowledged due to their toxic and/or hallucinogenic properties. Considering these properties in the last decades become more important for scientist to dignify exactly the chemical content of these mushroom species. Latter researches shown that A. phalloides contain two main groups of toxins: the amatoxins and the phallotoxins. As regards A. rubescens there are not so much studies referring to its biochemical "fingerprint". Two species (A. rubescens and A. phalloides) of Amanita genus were studied in order to determine the biochemical hall-mark at nanoscale for these basidiomycete's species. Parts as caps, gills, flesh and stem of these mushrooms were analyzed on quadrupole mass spectrometer engaged with a gas chromatograph (GC-qMS) using selective ion monitoring mode (SIM). The biochemical profiles of these species had shown the presence of compounds like fatty acid methyl esters (FAMEs), alkaloids, and volatile compounds (including alcohol compounds, carbonyl compounds, terpenes). The levels of biochemical compounds from these species were compared between the two types of species and also between young, mature and old samples for the same species as well as between the parts of mushroom. After this comparison were between the two species it was observed that in case of A. phalloides the alkaloid content were higher usually with almost 50 %. As regards presence of volatile compounds they have almost similar level in both mushroom species. Considering the levels of fatty acid methyl esters, their levels were higher with 30 - 40 % in case of A. rubescens.

  6. Comparative biochemical characterization of peroxidases (class III) tightly bound to the maize root cell walls and modulation of the enzyme properties as a result of covalent binding.

    PubMed

    Hadži-Tašković Šukalović, Vesna; Vuletić, Mirjana; Marković, Ksenija; Cvetić Antić, Tijana; Vučinić, Željko

    2015-01-01

    Comparative biochemical characterization of class III peroxidase activity tightly bound to the cell walls of maize roots was performed. Ionically bound proteins were solubilized from isolated walls by salt washing, and the remaining covalently bound peroxidases were released, either by enzymatic digestion or by a novel alkaline extraction procedure that released covalently bound alkali-resistant peroxidase enzyme. Solubilized fractions, as well as the salt-washed cell wall fragments containing covalently bound proteins, were analyzed for peroxidase activity. Peroxidative and oxidative activities indicated that peroxidase enzymes were predominately associated with walls by ionic interactions, and this fraction differs from the covalently bound one according to molecular weight, isozyme patterns, and biochemical parameters. The effect of covalent binding was evaluated by comparison of the catalytic properties of the enzyme bound to the salt-washed cell wall fragments with the corresponding solubilized and released enzyme. Higher thermal stability, improved resistance to KCN, increased susceptibility to H2O2, stimulated capacity of wall-bound enzyme to oxidize indole-3-acetic acid (IAA) as well as the difference in kinetic parameters between free and bound enzymes point to conformational changes due to covalent binding. Differences in biochemical properties of ionically and covalently bound peroxidases, as well as the modulation of the enzyme properties as a result of covalent binding to the walls, indicate that these two fractions of apoplastic peroxidases play different roles.

  7. Modular evolution of glutathione peroxidase genes in association with different biochemical properties of their encoded proteins in invertebrate animals

    PubMed Central

    Bae, Young-An; Cai, Guo-Bin; Kim, Seon-Hee; Zo, Young-Gun; Kong, Yoon

    2009-01-01

    Background Phospholipid hydroperoxide glutathione peroxidases (PHGPx), the most abundant isoforms of GPx families, interfere directly with hydroperoxidation of lipids. Biochemical properties of these proteins vary along with their donor organisms, which has complicated the phylogenetic classification of diverse PHGPx-like proteins. Despite efforts for comprehensive analyses, the evolutionary aspects of GPx genes in invertebrates remain largely unknown. Results We isolated GPx homologs via in silico screening of genomic and/or expressed sequence tag databases of eukaryotic organisms including protostomian species. Genes showing strong similarity to the mammalian PHGPx genes were commonly found in all genomes examined. GPx3- and GPx7-like genes were additionally detected from nematodes and platyhelminths, respectively. The overall distribution of the PHGPx-like proteins with different biochemical properties was biased across taxa; selenium- and glutathione (GSH)-dependent proteins were exclusively detected in platyhelminth and deuterostomian species, whereas selenium-independent and thioredoxin (Trx)-dependent enzymes were isolated in the other taxa. In comparison of genomic organization, the GSH-dependent PHGPx genes showed a conserved architectural pattern, while their Trx-dependent counterparts displayed complex exon-intron structures. A codon for the resolving Cys engaged in reductant binding was found to be substituted in a series of genes. Selection pressure to maintain the selenocysteine codon in GSH-dependent genes also appeared to be relaxed during their evolution. With the dichotomized fashion in genomic organizations, a highly polytomic topology of their phylogenetic trees implied that the GPx genes have multiple evolutionary intermediate forms. Conclusion Comparative analysis of invertebrate GPx genes provides informative evidence to support the modular pathways of GPx evolution, which have been accompanied with sporadic expansion/deletion and exon

  8. Evidence from Biochemical Pathways in Favor of Unfinished Evolution Rather than Intelligent Design

    ERIC Educational Resources Information Center

    Behrman, Edward J.; Marzluf, George A.

    2004-01-01

    An argument is made in favor of imperfect or unfinished evolution based on some metabolic pathways in which it seems that intelligent design would have done better. The case studies noted indicate the absence of highly intelligent design and are not intended as comprehensive collection but as a limited sample of inefficient situations in…

  9. Biochemical investigation of yttrium(III) complex containing 1,10-phenanthroline: DNA binding and antibacterial activity.

    PubMed

    Khorasani-Motlagh, Mozhgan; Noroozifar, Meissam; Moodi, Asieh; Niroomand, Sona

    2013-03-01

    Characterization of the interaction between yttrium(III) complex containing 1,10-phenanthroline as ligand, [Y(phen)2Cl(OH2)3]Cl2⋅H2O, and DNA has been carried out by UV absorption, fluorescence spectra and viscosity measurements in order to investigate binding mode. The experimental results indicate that the yttrium(III) complex binds to DNA and absorption is decreasing in charge transfer band with the increase in amount of DNA. The binding constant (Kb) at different temperatures as well as thermodynamic parameters, enthalpy change (ΔH°) and entropy change (ΔS°), were calculated according to relevant fluorescent data and Vant' Hoff equation. The results of interaction mechanism studies, suggested that groove binding plays a major role in the binding of the complex and DNA. The activity of yttrium(III) complex against some bacteria was tested and antimicrobial screening tests shown growth inhibitory activity in the presence of yttrium(III) complex.

  10. Biochemical investigation of yttrium(III) complex containing 1,10-phenanthroline: DNA binding and antibacterial activity.

    PubMed

    Khorasani-Motlagh, Mozhgan; Noroozifar, Meissam; Moodi, Asieh; Niroomand, Sona

    2013-03-01

    Characterization of the interaction between yttrium(III) complex containing 1,10-phenanthroline as ligand, [Y(phen)2Cl(OH2)3]Cl2⋅H2O, and DNA has been carried out by UV absorption, fluorescence spectra and viscosity measurements in order to investigate binding mode. The experimental results indicate that the yttrium(III) complex binds to DNA and absorption is decreasing in charge transfer band with the increase in amount of DNA. The binding constant (Kb) at different temperatures as well as thermodynamic parameters, enthalpy change (ΔH°) and entropy change (ΔS°), were calculated according to relevant fluorescent data and Vant' Hoff equation. The results of interaction mechanism studies, suggested that groove binding plays a major role in the binding of the complex and DNA. The activity of yttrium(III) complex against some bacteria was tested and antimicrobial screening tests shown growth inhibitory activity in the presence of yttrium(III) complex. PMID:23384614

  11. Redshift evolution of the dynamical properties of massive galaxies from SDSS-III/BOSS

    SciTech Connect

    Beifiori, Alessandra; Saglia, Roberto P.; Bender, Ralf; Senger, Robert; Thomas, Daniel; Maraston, Claudia; Steele, Oliver; Masters, Karen L.; Pforr, Janine; Tojeiro, Rita; Johansson, Jonas; Nichol, Robert C.; Chen, Yan-Mei; Wake, David; Bolton, Adam; Brownstein, Joel R.; Leauthaud, Alexie; Schneider, Donald P.; Skibba, Ramin; Pan, Kaike; and others

    2014-07-10

    We study the redshift evolution of the dynamical properties of ∼180, 000 massive galaxies from SDSS-III/BOSS combined with a local early-type galaxy sample from SDSS-II in the redshift range 0.1 ≤ z ≤ 0.6. The typical stellar mass of this sample is M{sub *} ∼2 × 10{sup 11} M{sub ☉}. We analyze the evolution of the galaxy parameters effective radius, stellar velocity dispersion, and the dynamical to stellar mass ratio with redshift. As the effective radii of BOSS galaxies at these redshifts are not well resolved in the Sloan Digital Sky Survey (SDSS) imaging we calibrate the SDSS size measurements with Hubble Space Telescope/COSMOS photometry for a sub-sample of galaxies. We further apply a correction for progenitor bias to build a sample which consists of a coeval, passively evolving population. Systematic errors due to size correction and the calculation of dynamical mass are assessed through Monte Carlo simulations. At fixed stellar or dynamical mass, we find moderate evolution in galaxy size and stellar velocity dispersion, in agreement with previous studies. We show that this results in a decrease of the dynamical to stellar mass ratio with redshift at >2σ significance. By combining our sample with high-redshift literature data, we find that this evolution of the dynamical to stellar mass ratio continues beyond z ∼ 0.7 up to z > 2 as M{sub dyn}/M{sub *} ∼(1 + z){sup –0.30±0.12}, further strengthening the evidence for an increase of M{sub dyn}/M{sub *} with cosmic time. This result is in line with recent predictions from galaxy formation simulations based on minor merger driven mass growth, in which the dark matter fraction within the half-light radius increases with cosmic time.

  12. Molecular and biochemical studies of the evolution, infection and transmission of insect bunyaviruses.

    PubMed

    Bishop, D H; Beaty, B J

    1988-10-31

    Members of the Bunyaviridae family of RNA viruses (bunyaviruses, hantaviruses, nairoviruses, phleboviruses and uukuviruses) have been studied at the molecular and genetic level to understand the basis of their evolution and infection in vertebrate and invertebrate (arthropod) hosts. With the exception of the hantaviruses, these viruses infect and are transmitted by a variety of blood-sucking arthropods (mosquitoes, phlebotomines, gnats, ticks, etc.). The viruses are responsible for infection of various vertebrate species, occasionally causing human disease, morbidity and mortality (e.g. Rift Valley fever, Crimean-Congo haemorrhagic fever, Korean haemorrhagic fever). Genetic and molecular analyses of bunyaviruses have established the coding assignments of the three viral RNA species and documented which viral gene products determine host range and virulence. Ecological studies, with molecular techniques, have provided evidence for bunyavirus evolution in nature through genetic drift (involving the accumulation of point mutations) and shift (RNA-segment reassortment).

  13. Morphological and biochemical evidence for the evolution of salt glands in snakes.

    PubMed

    Babonis, Leslie S; Evans, David H

    2011-11-01

    Vertebrate salt glands have evolved independently multiple times, yet there are few hypotheses about the processes underlying the convergent evolution of salt glands across taxa. Here, we compare the morphology and molecular biology of specialized salt-secreting glands from a marine snake (Laticauda semifasciata) with the cephalic glands from semi-marine (Nerodia clarkii clarkii) and freshwater (N. fasciata) watersnakes to look for evidence of a salt gland in the former and to develop hypotheses about the evolution of snake salt glands. Like the salt gland of L. semifasciata, the nasal and anterior/posterior sublingual glands in both species of Nerodia exhibit a compound tubular shape, and express basolateral Na(+)/K(+)-ATPase (NKA) and Na(+)/K(+)/2Cl(-)cotransporter (NKCC); however, the abundance of NKA and NKCC in N. fasciata appears lower than in N. c. clarkii. Aquaporin 3 (AQP3) is also basolateral in the sublingual glands of both species of Nerodia, as is abundant neutral mucin; both AQP3 and mucin are absent from the salt gland in L. semifasciata. Thus, we propose that the evolution of the snake salt gland by co-option of an existing gland involved at least two steps: (i) an increase in the abundance of NKA and NKCC in the basolateral membranes of the secretory epithelia, and (ii) loss of AQP3/mucus secretion from these epithelia.

  14. Changing physical conditions in star-forming galaxies between redshifts 0 < z < 4: [O III]/H β evolution

    NASA Astrophysics Data System (ADS)

    Cullen, F.; Cirasuolo, M.; Kewley, L. J.; McLure, R. J.; Dunlop, J. S.; Bowler, R. A. A.

    2016-08-01

    We investigate the redshift evolution of the [O III]/H β nebular emission line ratio for a sample of galaxies spanning the redshift range 0 < z < 4. We compare the observed evolution to a set of theoretical models which account for the independent evolution of chemical abundance, ionization parameter and interstellar medium (ISM) pressure in star-forming galaxies with redshift. Accounting for selection effects in the combined data sets, we show that the evolution to higher [O III]/H β ratios with redshift is a real physical effect which is best accounted for by a model in which the ionization parameter is elevated from the average values typical of local star-forming galaxies, with a possible simultaneous increase in the ISM pressure. We rule out the possibility that the observed [O III]/H β evolution is purely due to metallicity evolution. We discuss the implications of these results for using local empirical metallicity calibrations to measure metallicities at high redshift, and briefly discuss possible theoretical implications of our results.

  15. Structure/Function Analysis of a Type III Polyketide Synthase in the Brown Alga Ectocarpus siliculosus Reveals a Biochemical Pathway in Phlorotannin Monomer Biosynthesis[W

    PubMed Central

    Meslet-Cladière, Laurence; Delage, Ludovic; Leroux, Cédric J.-J.; Goulitquer, Sophie; Leblanc, Catherine; Creis, Emeline; Gall, Erwan Ar; Stiger-Pouvreau, Valérie; Czjzek, Mirjam; Potin, Philippe

    2013-01-01

    Brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. Despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. We found that a predicted type III polyketide synthase in the genome of the brown alga Ectocarpus siliculosus, PKS1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of phloroglucinol monomers from malonyl-CoA). The crystal structure of PKS1 at 2.85-Å resolution provided a good quality electron density map showing a modified Cys residue, likely connected to a long chain acyl group. An additional pocket not found in other known type III PKSs contains a reaction product that might correspond to a phloroglucinol precursor. In vivo, we also found a positive correlation between the phloroglucinol content and the PKS III gene expression level in cells of a strain of Ectocarpus adapted to freshwater during its reacclimation to seawater. The evolution of the type III PKS gene family in Stramenopiles suggests a lateral gene transfer event from an actinobacterium. PMID:23983220

  16. Specificity of protein — Nucleic acid interaction and the biochemical evolution

    NASA Astrophysics Data System (ADS)

    Podder, S. K.; Basu, H. S.

    1984-12-01

    The water soluble carbodiimide mediated condensation of dipeptides of the general form Gly-X was carried out in the presence of mono- and poly-nucleotides. The observed yield of the tetrapeptide was found to be higher for peptide-nucleotide system of higher interaction specificity following mainly the anticodon-amino acid relationship (Basu, H.S. & Podder, S.K., 1981, Ind. J. Biochem. Biophys., 19, 251 253). The yield of the condensation product of L-peptide was more because of its higher interaction specificity. The extent of the racemization during the condensation of Gly-L-Phe, Gly-L-Tyr and Gly-D-Phe was found to be dependent on the specificity of the interaction —the higher the specificity, the lesser the racemization. The product formed was shown to have a catalytic effect on the condensation reaction. These data thus provide a mechanism showing how the specific interaction between amino acids/dipeptides and nucleic acids could lead to the formation of the ‘primitive’ translation machinery.

  17. Structural and Biochemical Characterization of SrcA, a Multi-cargo Type III Secretion Chaperone in Salmonella Required for Pathogenic Association with a Host

    SciTech Connect

    Cooper, C.; Zhang, K; Andres, S; Fnag, Y; Kaniuk, N; Hannemann, M; Brumell, J; Foster, L; Junop, M; Coombes, B

    2010-01-01

    Many Gram-negative bacteria colonize and exploit host niches using a protein apparatus called a type III secretion system (T3SS) that translocates bacterial effector proteins into host cells where their functions are essential for pathogenesis. A suite of T3SS-associated chaperone proteins bind cargo in the bacterial cytosol, establishing protein interaction networks needed for effector translocation into host cells. In Salmonella enterica serovar Typhimurium, a T3SS encoded in a large genomic island (SPI-2) is required for intracellular infection, but the chaperone complement required for effector translocation by this system is not known. Using a reverse genetics approach, we identified a multi-cargo secretion chaperone that is functionally integrated with the SPI-2-encoded T3SS and required for systemic infection in mice. Crystallographic analysis of SrcA at a resolution of 2.5 {angstrom} revealed a dimer similar to the CesT chaperone from enteropathogenic E. coli but lacking a 17-amino acid extension at the carboxyl terminus. Further biochemical and quantitative proteomics data revealed three protein interactions with SrcA, including two effector cargos (SseL and PipB2) and the type III-associated ATPase, SsaN, that increases the efficiency of effector translocation. Using competitive infections in mice we show that SrcA increases bacterial fitness during host infection, highlighting the in vivo importance of effector chaperones for the SPI-2 T3SS.

  18. Local Luminous Infrared Galaxies. III. Co-evolution of Black Hole Growth and Star Formation Activity?

    NASA Astrophysics Data System (ADS)

    Alonso-Herrero, Almudena; Pereira-Santaella, Miguel; Rieke, George H.; Diamond-Stanic, Aleksandar M.; Wang, Yiping; Hernán-Caballero, Antonio; Rigopoulou, Dimitra

    2013-03-01

    Local luminous infrared (IR) galaxies (LIRGs) have both high star formation rates (SFR) and a high AGN (Seyfert and AGN/starburst composite) incidence. Therefore, they are ideal candidates to explore the co-evolution of black hole (BH) growth and star formation (SF) activity, not necessarily associated with major mergers. Here, we use Spitzer/IRS spectroscopy of a complete volume-limited sample of local LIRGs (distances of <78 Mpc). We estimate typical BH masses of 3 × 107 M ⊙ using [Ne III] 15.56 μm and optical [O III] λ5007 gas velocity dispersions and literature stellar velocity dispersions. We find that in a large fraction of local LIRGs, the current SFR is taking place not only in the inner nuclear ~1.5 kpc region, as estimated from the nuclear 11.3 μm PAH luminosities, but also in the host galaxy. We next use the ratios between the SFRs and BH accretion rates (BHAR) to study whether the SF activity and BH growth are contemporaneous in local LIRGs. On average, local LIRGs have SFR to BHAR ratios higher than those of optically selected Seyferts of similar active galactic nucleus (AGN) luminosities. However, the majority of the IR-bright galaxies in the revised-Shapley-Ames Seyfert sample behave like local LIRGs. Moreover, the AGN incidence tends to be higher in local LIRGs with the lowest SFRs. All of this suggests that in local LIRGs there is a distinct IR-bright star-forming phase taking place prior to the bulk of the current BH growth (i.e., AGN phase). The latter is reflected first as a composite and then as a Seyfert, and later as a non-LIRG optically identified Seyfert nucleus with moderate SF in its host galaxy. This work is based on observations made with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under NASA contract 1407.

  19. LOCAL LUMINOUS INFRARED GALAXIES. III. CO-EVOLUTION OF BLACK HOLE GROWTH AND STAR FORMATION ACTIVITY?

    SciTech Connect

    Alonso-Herrero, Almudena; Hernan-Caballero, Antonio; Pereira-Santaella, Miguel; Rieke, George H.; Diamond-Stanic, Aleksandar M.; Wang Yiping; Rigopoulou, Dimitra

    2013-03-10

    Local luminous infrared (IR) galaxies (LIRGs) have both high star formation rates (SFR) and a high AGN (Seyfert and AGN/starburst composite) incidence. Therefore, they are ideal candidates to explore the co-evolution of black hole (BH) growth and star formation (SF) activity, not necessarily associated with major mergers. Here, we use Spitzer/IRS spectroscopy of a complete volume-limited sample of local LIRGs (distances of <78 Mpc). We estimate typical BH masses of 3 Multiplication-Sign 10{sup 7} M{sub Sun} using [Ne III] 15.56 {mu}m and optical [O III] {lambda}5007 gas velocity dispersions and literature stellar velocity dispersions. We find that in a large fraction of local LIRGs, the current SFR is taking place not only in the inner nuclear {approx}1.5 kpc region, as estimated from the nuclear 11.3 {mu}m PAH luminosities, but also in the host galaxy. We next use the ratios between the SFRs and BH accretion rates (BHAR) to study whether the SF activity and BH growth are contemporaneous in local LIRGs. On average, local LIRGs have SFR to BHAR ratios higher than those of optically selected Seyferts of similar active galactic nucleus (AGN) luminosities. However, the majority of the IR-bright galaxies in the revised-Shapley-Ames Seyfert sample behave like local LIRGs. Moreover, the AGN incidence tends to be higher in local LIRGs with the lowest SFRs. All of this suggests that in local LIRGs there is a distinct IR-bright star-forming phase taking place prior to the bulk of the current BH growth (i.e., AGN phase). The latter is reflected first as a composite and then as a Seyfert, and later as a non-LIRG optically identified Seyfert nucleus with moderate SF in its host galaxy.

  20. Chemical, biochemical, and environmental fiber sensors III; Proceedings of the Meeting, Boston, MA, Sept. 4, 5, 1991

    SciTech Connect

    Lieberman, R.A.

    1992-01-01

    Various papers on chemical, biochemical, and environmental fiber sensors are presented. Individual topics addressed include: fiber optic pressure sensor for combustion monitoring and control, viologen-based fiber optic oxygen sensors, renewable-reagent fiber optic sensor for ocean pCO2, transition metal complexes as indicators for a fiber optic oxygen sensor, fiber optic pH measurements using azo indicators, simple reversible fiber optic chemical sensors using solvatochromic dyes, totally integrated optical measuring sensors, integrated optic biosensor for environmental monitoring, radiation dosimetry using planar waveguide sensors, optical and piezoelectric analysis of polymer films for chemical sensor characterization, source polarization effects in an optical fiber fluorosensor, lens-type refractometer for on-line chemical analysis, fiber optic hydrocarbon sensor system, chemical sensors for environmental monitoring, optical fibers for liquid-crystal sensing and logic devices, suitability of single-mode fluoride fibers for evanescent-wave sensing, integrated modules for fiber optic sensors, optoelectronic sensors based on narrowband A3B5 alloys, fiber Bragg grating chemical sensor.

  1. [Toxicological evaluation of colloidal nano-sized silver stabilized polyvinylpyrrolidone. III. Enzymological, biochemical markers, state of antioxidant defense system].

    PubMed

    Gmoshinsky, I V; Shipelin, V A; Vorozhko, I V; Sentsova, T B; Soto, S Kh; Avren'eva, L I; Guseva, G V; Kravchenko, L V; Khotimchenko, S A; Tutelyan, V A

    2016-01-01

    Nanosized colloidal silver (NCS) with primary nanoparticles (NPs) size in the range of 10-80 nm in aqueous suspension was administered to rats with initial weight 80±10 gfor the first 30 day intragastrically and for lasting 62 days with the diet consumed in doses of 0.1; 1.0 and 10 mg/kg of body weight b.w) per day based on silver (Ag). The control animals received deionized water and carrier of NPs - aqueous solution of stabilizer polyvinylpyrrolidone. Activity (Vmax) was determined in liver of microsomal mixed function monooxygenase isoforms CYP 1A1, 1A2 and 2B1 against their specific substrates, the activity of liver conjugating enzymes (glutathione-S-transferase and UDP-glucuronosyltransferase) in the microsomal fraction and a cytosol, and the overall and non-sedimentable activities of lysosomal hydrolases. In blood plasma there were evaluated malonic dialdehyde, PUFA diene conjugates, in erythrocytes - the activity of antioxidant enzymes. A set of standard biochemical indicators of blood serum was also determined. The studies revealed changes in a number of molecular markers of toxic action. Among them - the increase in the activity of key enzymes I and II stages of detoxification of xenobiotics, indicating its functional overvoltage; reducing the activity of glutathione peroxidase (GP), the total arylsulfatase A and B, β-galactosidase (in the absence of changes in their non-sedimentable activity), levels of uric acid, increased alkaline phosphatase activity. These changes occurred mainly at the dose Ag of 10 mg/kg b.w., except for the GP to which the threshold dose was 1 mg/kg b.w. No significant changes in the studied markers in a dose Ag 0,1 mg/kg b.w. were identified. Possible mechanisms of the toxic action of silver NPs are discussed.

  2. [Toxicological evaluation of colloidal nano-sized silver stabilized polyvinylpyrrolidone. III. Enzymological, biochemical markers, state of antioxidant defense system].

    PubMed

    Gmoshinsky, I V; Shipelin, V A; Vorozhko, I V; Sentsova, T B; Soto, S Kh; Avren'eva, L I; Guseva, G V; Kravchenko, L V; Khotimchenko, S A; Tutelyan, V A

    2016-01-01

    Nanosized colloidal silver (NCS) with primary nanoparticles (NPs) size in the range of 10-80 nm in aqueous suspension was administered to rats with initial weight 80±10 gfor the first 30 day intragastrically and for lasting 62 days with the diet consumed in doses of 0.1; 1.0 and 10 mg/kg of body weight b.w) per day based on silver (Ag). The control animals received deionized water and carrier of NPs - aqueous solution of stabilizer polyvinylpyrrolidone. Activity (Vmax) was determined in liver of microsomal mixed function monooxygenase isoforms CYP 1A1, 1A2 and 2B1 against their specific substrates, the activity of liver conjugating enzymes (glutathione-S-transferase and UDP-glucuronosyltransferase) in the microsomal fraction and a cytosol, and the overall and non-sedimentable activities of lysosomal hydrolases. In blood plasma there were evaluated malonic dialdehyde, PUFA diene conjugates, in erythrocytes - the activity of antioxidant enzymes. A set of standard biochemical indicators of blood serum was also determined. The studies revealed changes in a number of molecular markers of toxic action. Among them - the increase in the activity of key enzymes I and II stages of detoxification of xenobiotics, indicating its functional overvoltage; reducing the activity of glutathione peroxidase (GP), the total arylsulfatase A and B, β-galactosidase (in the absence of changes in their non-sedimentable activity), levels of uric acid, increased alkaline phosphatase activity. These changes occurred mainly at the dose Ag of 10 mg/kg b.w., except for the GP to which the threshold dose was 1 mg/kg b.w. No significant changes in the studied markers in a dose Ag 0,1 mg/kg b.w. were identified. Possible mechanisms of the toxic action of silver NPs are discussed. PMID:27455597

  3. Biochemical characterization of a recombinant plant class III chitinase from the pitcher of the carnivorous plant Nepenthes alata.

    PubMed

    Ishisaki, Kana; Arai, Sachiko; Hamada, Tatsuro; Honda, Yuji

    2012-11-01

    A class III chitinase belonging to the GH18 family from Nepenthes alata (NaCHIT3) was expressed in Escherichia coli. The enzyme exhibited hydrolytic activity toward colloidal chitin, ethylene glycol chitin, and (GlcNAc)(n) (n=5 and 6). The enzyme hydrolyzed the fourth glycosidic linkage from the non-reducing end of (GlcNAc)(6). The anomeric form of the products indicated it was a retaining enzyme. The colloidal chitin hydrolytic reaction displayed high activity between pH 3.9 and 6.9, but the pH optimum of the (GlcNAc)(6) hydrolytic reaction was 3.9 at 37 °C. The optimal temperature for activity was 65 °C in 50 mM sodium acetate buffer (pH 3.9). The pH optima of NaCHIT3 and NaCHIT1 might be related to their roles in chitin degradation in the pitcher fluid.

  4. The evolution of increased competitive ability, innate competitive advantages, and novel biochemical weapons act in concert for a tropical invader.

    PubMed

    Qin, Rui-Min; Zheng, Yu-Long; Valiente-Banuet, Alfonso; Callaway, Ragan M; Barclay, Gregor F; Pereyra, Carlos Silva; Feng, Yu-Long

    2013-02-01

    There are many non-mutually exclusive mechanisms for exotic invasions but few studies have concurrently tested more than one hypothesis for the same species. Here, we tested the evolution of increased competitive ability (EICA) hypothesis in two common garden experiments in which Chromolaena odorata plants originating from native and nonnative ranges were grown in competition with natives from each range, and the novel weapons hypothesis in laboratory experiments with leachates from C. odorata. Compared with conspecifics originating from the native range, C. odorata plants from the nonnative range were stronger competitors at high nutrient concentrations in the nonnative range in China and experienced far more herbivore damage in the native range in Mexico. In both China and Mexico, C. odorata was more suppressed by species native to Mexico than by species native to China. Species native to China were much more inhibited by leaf extracts from C. odorata than species from Mexico, and this difference in allelopathic effects may provide a possible explanation for the biogeographic differences in competitive ability. Our results indicate that EICA, innate competitive advantages, and novel biochemical weapons may act in concert to promote invasion by C. odorata, and emphasize the importance of exploring multiple, non-mutually exclusive mechanisms for invasions.

  5. Effects of combined dietary chromium(III) propionate complex and thiamine supplementation on insulin sensitivity, blood biochemical indices, and mineral levels in high-fructose-fed rats.

    PubMed

    Król, Ewelina; Krejpcio, Zbigniew; Michalak, Sławomir; Wójciak, Rafał W; Bogdański, Paweł

    2012-12-01

    Insulin resistance is the first step in glucose intolerance and the development of type 2 diabetes mellitus, thus effective prevention strategies should also include dietary interventions to enhance insulin sensitivity. Nutrients, such as microelement chromium(III) and thiamine, play regulatory roles in carbohydrate metabolism. The objective of this study was to evaluate the insulin-sensitizing potential of the combined supplementary chromium(III) propionate complex (CrProp) and thiamine in insulin resistance animal model (rats fed a high-fructose diet). The experiment was carried out on 40 nine-week-old male Wistar rats divided into five groups (eight animals each). Animals were fed ad libitum: the control diet (AIN-93 M) and high-fructose diets with and without a combination of two levels of CrProp (0.1 and 1 mg Cr/kg body mass/day) and two levels of thiamine (0.5 and 10 mg/kg body mass/day) for 8 weeks. At the end of the experiment rats were sacrificed to collect blood and internal organs for analyses of blood biochemical and hematologic indices as well as tissular microelement levels that were measured using appropriate methods. It was found that both supplementary CrProp and thiamine (given alone) have significant insulin-sensitizing and moderate blood-lipid-lowering properties, while the combined supplementation with these agents does not give synergistic effects in insulin-resistant rats. CrProp given separately increased kidney Cu and Cr levels, while thiamine alone increased hepatic Cu contents and decreased renal Zn and Cu contents.

  6. Interaction of ribonucleotides with metal hexacyanocobaltate(III): a possible role in chemical evolution.

    PubMed

    Ali, Shah Raj; Kamaluddin

    2007-06-01

    It has been proposed that metal cyanide complexes would have acted as effective prebiotic catalysts. Insoluble metal cyanide complexes could have concentrated biomonomers from the dilute prebiotic soup, facilitating certain prebiotic reactions. In the light of the above hypothesis, interaction of four ribonucleotides, namely 5'-AMP, 5'-GMP, 5'-CMP, and 5'-UMP with copper(II)- and cadmium(II) hexacyanocobaltate(III) has been studied. The interaction was found to be maximum at neutral pH. 5'-GMP showed greater interaction with both the metal hexacyanocobaltate(III) while copper(II) hexacyanocobaltate(III) showed greater uptake than cadmium(II) hexacyanocobaltate(III) for all the four ribonucleotides studied. Infrared spectral studies of ribonucleotides, metal hexacyanocobaltate(III) and ribonucleotide - metal hexacyanocobaltate(III) adducts indicated that the nitrogen base and phosphate moiety of ribonucleotides interact with outer divalent metal ion present in the lattice of metal hexacyanocobaltate(III).

  7. The Assembly and Evolution of Eastern Laurentia: Evidence from the QM-III Experiment

    NASA Astrophysics Data System (ADS)

    Darbyshire, F. A.; Levin, V. L.; Menke, W. H.; Bastow, I. D.; Petrescu, L.; Boyce, A.; Klaser, M.; Dunham, B.; Servali, A.; Neitz, T.

    2014-12-01

    Eastern North America is an excellent region to test hypotheses about the evolution through time of tectonic processes, the growth of continental crust and the assembly of continents. Over a spatial scale of just a few hundred kilometres, the surface geology records almost 3 billion years of Earth history, with a transition from the Archean Superior craton through the Proterozoic Grenville orogenic belt to the Phanerozoic Appalachian terranes and the edge of the North American continent. The boundaries between these major tectonic provinces have been mapped at the surface, and crustal-scale geophysical studies (e.g. LITHOPROBE) have been able to trace their complex signatures to the Moho and below in some parts of eastern Canada. Nevertheless, the nature of the boundaries across the region, and their continuation into the lithospheric mantle, remains enigmatic. The high wavespeed lithospheric keel of the Canadian Shield extends beneath the Proterozoic terranes; however it is still unclear whether this material represents a continuation of Archean lithosphere over which the Grenville terranes have been thrust, or whether the Grenville can be associated with its own thick keel. The transition from Proterozoic to Phanerozoic lithosphere beneath the Appalachian Front is likewise ambiguous. To shed new light on the tectonic evolution of the region, and the nature of the major tectonic boundaries, a broadband seismograph network was installed in eastern Canada in 2012-2013 through the QM-III (Quebec-Maine Across Three Sutures) experiment; stations will remain in place for 2-3 years. The network consists of a dense NW-SE profile from the southern tip of Hudson Bay to coastal Maine, supplemented by existing more sparsely-distributed stations, and a 2D deployment across Maritime Canada. Data acquisition is ongoing, but preliminary results from receiver function analysis, travel-time tomography and surface-wave dispersion are already showing some intriguing variations in

  8. Thermotoga maritima ribonuclease III. Characterization of thermostable biochemical behavior and analysis of conserved base pairs that function as reactivity epitopes for the Thermotoga 23S rRNA precursor.

    PubMed

    Nathania, Lilian; Nicholson, Allen W

    2010-08-24

    The cleavage of double-stranded (ds) RNA by ribonuclease III is a conserved early step in bacterial rRNA maturation. Studies on the mechanism of dsRNA cleavage by RNase III have focused mainly on the enzymes from mesophiles such as Escherichia coli. In contrast, neither the catalytic properties of extremophile RNases III nor the structures and reactivities of their cognate substrates have been described. The biochemical behavior of RNase III of the hyperthermophilic bacterium Thermotoga maritima was analyzed using purified recombinant enzyme. T. maritima (Tm) RNase III catalytic activity exhibits a broad optimal temperature range of approximately 40-70 degrees C, with significant activity at 95 degrees C. Tm-RNase III cleavage of substrate is optimally supported by Mg(2+) at >or=1 mM concentrations. Mn(2+), Co(2+), and Ni(2+) also support activity but with reduced efficiencies. The enzyme functions optimally at pH 8 and approximately 50-80 mM salt concentrations. Small RNA hairpins that incorporate the 16S and 23S pre-rRNA stem sequences are efficiently cleaved by Tm-RNase III at sites that are consistent with production in vivo of the immediate precursors to the mature rRNAs. Analysis of pre-23S substrate variants reveals a dependence of reactivity on the base-pair (bp) sequence in the proximal box (pb), a site of protein contact that functions as a positive recognition determinant for Escherichia coli (Ec) RNase III substrates. The dependence of reactivity on the pb sequence is similar to that observed with Ec-RNase III substrates. In fact, Tm-RNase III cleaves an Ec-RNase III substrate with identical specificity and is inhibited by antideterminant bp that also inhibit Ec-RNase III. These results indicate the conservation, across a broad phylogenetic distance, of positive and negative determinants of reactivity of bacterial RNase III substrates.

  9. Animal lectins as self/non-self recognition molecules. Biochemical and genetic approaches to understanding their biological roles and evolution.

    PubMed

    Vasta, G R; Ahmed, H; Fink, N E; Elola, M T; Marsh, A G; Snowden, A; Odom, E W

    1994-04-15

    In recent years, the significant contributions from molecular research studies on animal lectins have elucidated structural aspects and provided clues not only to their evolution but also to their multiple biological functions. The experimental evidence has suggested that distinct, and probably unrelated, groups of molecules are included under the term "lectin." Within the invertebrate taxa, major groups of lectins can be identified: One group would include lectins that show significant homology to membrane-integrated or soluble vertebrate C-type lectins. The second would include those beta-galactosyl-specific lectins homologous to the S-type vertebrate lectins. The third group would be constituted by lectins that show homology to vertebrate pentraxins that exhibit lectin-like properties, such as C-reactive protein and serum amyloid P. Finally, there are examples that do not exhibit similarities to any of the aforementioned categories. Moreover, the vast majority of invertebrate lectins described so far cannot yet be placed in one or another group because of the lack of information regarding their primary structure. (See Table 1.) Animal lectins do not express a recombinatorial diversity like that of antibodies, but a limited diversity in recognition capabilities would be accomplished by the occurrence of multiple lectins with distinct specificities, the presence of more than one binding site, specific for different carbohydrates in a single molecule, and by certain "flexibility" of the binding sites that would allow the recognition of a range of structurally related carbohydrates. In order to identify the lectins' "natural" ligands, we have investigated the interactions between those proteins and the putative endogenous or exogenous glycosylated substances or cells that may be relevant to their biological function. Results from these studies, together with information on the biochemical properties of invertebrate and vertebrate lectins, including their structural

  10. The Apache Point Observatory Galactic Evolution Experiment (APOGEE) in Sloan Digital Sky Survey III (SDSS-III)

    NASA Astrophysics Data System (ADS)

    Majewski, Steven R.; Wilson, John C.; Hearty, Fred; Schiavon, Ricardo R.; Skrutskie, Michael F.

    2010-03-01

    The Apache Point Observatory Galactic Evolution Experiment (APOGEE) is a large-scale, near-infrared (H-band), high-resolution (R ~ 30,000), high S/N (≳100) spectroscopic survey of Milky Way stellar populations. APOGEE will operate from 1.51-1.68μm, a region that includes useful absorption lines from at least fifteen chemical species including α, odd-Z, and iron peak elements. The APOGEE instrument has a novel design featuring 300 science fibers feeding light to a mosaiced VPH grating and a six-element camera encased in a liquid nitrogen-cooled cryostat. A three year bright-time observing campaign will enable APOGEE to observe approximately 100,000 red giants across the Galactic bulge, disk and halo.

  11. Adaptation of a Cyanobacterium to a Biochemically Rich Environment in Experimental Evolution as an Initial Step toward a Chloroplast-Like State

    PubMed Central

    Suzuki, Shingo; Miyazaki, Mikako; Takikawa, Go; Sakurai, Takahiro; Kashiwagi, Akiko; Sueyoshi, Makoto; Matsumoto, Yusuke; Kiuchi, Ayako; Mori, Kotaro; Yomo, Tetsuya

    2014-01-01

    Chloroplasts originated from cyanobacteria through endosymbiosis. The original cyanobacterial endosymbiont evolved to adapt to the biochemically rich intracellular environment of the host cell while maintaining its photosynthetic function; however, no such process has been experimentally demonstrated. Here, we show the adaptation of a model cyanobacterium, Synechocystis sp. PCC 6803, to a biochemically rich environment by experimental evolution. Synechocystis sp. PCC 6803 does not grow in a biochemically rich, chemically defined medium because several amino acids are toxic to the cells at approximately 1 mM. We cultured the cyanobacteria in media with the toxic amino acids at 0.1 mM, then serially transferred the culture, gradually increasing the concentration of the toxic amino acids. The cells evolved to show approximately the same specific growth rate in media with 0 and 1 mM of the toxic amino acid in approximately 84 generations and evolved to grow faster in the media with 1 mM than in the media with 0 mM in approximately 181 generations. We did not detect a statistically significant decrease in the autotrophic growth of the evolved strain in an inorganic medium, indicating the maintenance of the photosynthetic function. Whole-genome resequencing revealed changes in the genes related to the cell membrane and the carboxysome. Moreover, we quantitatively analyzed the evolutionary changes by using simple mathematical models, which evaluated the evolution as an increase in the half-maximal inhibitory concentration (IC50) and estimated quantitative characteristics of the evolutionary process. Our results clearly demonstrate not only the potential of a model cyanobacterium to adapt to a biochemically rich environment without a significant decrease in photosynthetic function but also the properties of its evolutionary process, which sheds light of the evolution of chloroplasts at the initial stage. PMID:24874568

  12. Adaptation of a cyanobacterium to a biochemically rich environment in experimental evolution as an initial step toward a chloroplast-like state.

    PubMed

    Hosoda, Kazufumi; Habuchi, Masumi; Suzuki, Shingo; Miyazaki, Mikako; Takikawa, Go; Sakurai, Takahiro; Kashiwagi, Akiko; Sueyoshi, Makoto; Matsumoto, Yusuke; Kiuchi, Ayako; Mori, Kotaro; Yomo, Tetsuya

    2014-01-01

    Chloroplasts originated from cyanobacteria through endosymbiosis. The original cyanobacterial endosymbiont evolved to adapt to the biochemically rich intracellular environment of the host cell while maintaining its photosynthetic function; however, no such process has been experimentally demonstrated. Here, we show the adaptation of a model cyanobacterium, Synechocystis sp. PCC 6803, to a biochemically rich environment by experimental evolution. Synechocystis sp. PCC 6803 does not grow in a biochemically rich, chemically defined medium because several amino acids are toxic to the cells at approximately 1 mM. We cultured the cyanobacteria in media with the toxic amino acids at 0.1 mM, then serially transferred the culture, gradually increasing the concentration of the toxic amino acids. The cells evolved to show approximately the same specific growth rate in media with 0 and 1 mM of the toxic amino acid in approximately 84 generations and evolved to grow faster in the media with 1 mM than in the media with 0 mM in approximately 181 generations. We did not detect a statistically significant decrease in the autotrophic growth of the evolved strain in an inorganic medium, indicating the maintenance of the photosynthetic function. Whole-genome resequencing revealed changes in the genes related to the cell membrane and the carboxysome. Moreover, we quantitatively analyzed the evolutionary changes by using simple mathematical models, which evaluated the evolution as an increase in the half-maximal inhibitory concentration (IC50) and estimated quantitative characteristics of the evolutionary process. Our results clearly demonstrate not only the potential of a model cyanobacterium to adapt to a biochemically rich environment without a significant decrease in photosynthetic function but also the properties of its evolutionary process, which sheds light of the evolution of chloroplasts at the initial stage.

  13. Coordination polymers of Fe(iii) and Al(iii) ions with TCA ligand: distinctive fluorescence, CO2 uptake, redox-activity and oxygen evolution reaction.

    PubMed

    Dhara, Barun; Sappati, Subrahmanyam; Singh, Santosh K; Kurungot, Sreekumar; Ghosh, Prasenjit; Ballav, Nirmalya

    2016-04-28

    Fe and Al belong to different groups in the periodic table, one from the p-block and the other from the d-block. In spite of their different groups, they have the similarity of exhibiting a stable 3+ oxidation state. Here we have prepared Fe(iii) and Al(iii) based coordination polymers in the form of metal-organic gels with the 4,4',4''-tricarboxyltriphenylamine (TCA) ligand, namely Fe-TCA and Al-TCA, and evaluated some important physicochemical properties. Specifically, the electrical conductivity, redox-activity, porosity, and electrocatalytic activity (oxygen evolution reaction) of the Fe-TCA system were noted to be remarkably higher than those of the Al-TCA system. As for the photophysical properties, almost complete quenching of the fluorescence originating from TCA was observed in case of the Fe-TCA system, whereas for the Al-TCA system a significant retention of fluorescence with red-shifted emission was observed. Quantum mechanical calculations based on density functional theory (DFT) were performed to unravel the origin of such discriminative behaviour of these coordination polymer systems. PMID:26961352

  14. Coordination polymers of Fe(iii) and Al(iii) ions with TCA ligand: distinctive fluorescence, CO2 uptake, redox-activity and oxygen evolution reaction.

    PubMed

    Dhara, Barun; Sappati, Subrahmanyam; Singh, Santosh K; Kurungot, Sreekumar; Ghosh, Prasenjit; Ballav, Nirmalya

    2016-04-28

    Fe and Al belong to different groups in the periodic table, one from the p-block and the other from the d-block. In spite of their different groups, they have the similarity of exhibiting a stable 3+ oxidation state. Here we have prepared Fe(iii) and Al(iii) based coordination polymers in the form of metal-organic gels with the 4,4',4''-tricarboxyltriphenylamine (TCA) ligand, namely Fe-TCA and Al-TCA, and evaluated some important physicochemical properties. Specifically, the electrical conductivity, redox-activity, porosity, and electrocatalytic activity (oxygen evolution reaction) of the Fe-TCA system were noted to be remarkably higher than those of the Al-TCA system. As for the photophysical properties, almost complete quenching of the fluorescence originating from TCA was observed in case of the Fe-TCA system, whereas for the Al-TCA system a significant retention of fluorescence with red-shifted emission was observed. Quantum mechanical calculations based on density functional theory (DFT) were performed to unravel the origin of such discriminative behaviour of these coordination polymer systems.

  15. A prescription and fast code for the long-term evolution of star clusters - III. Unequal masses and stellar evolution

    NASA Astrophysics Data System (ADS)

    Alexander, Poul E. R.; Gieles, Mark; Lamers, Henny J. G. L. M.; Baumgardt, Holger

    2014-08-01

    We present a new version of the fast star cluster evolution code EVOLVE ME A CLUSTER OF STARS (EMACSS). While previous versions of EMACSS reproduced clusters of single-mass stars, this version models clusters with an evolving stellar content. Stellar evolution dominates early evolution, and leads to: (1) reduction of the mean mass of stars due to the mass loss of high-mass stars; (2) expansion of the half-mass radius; (3) for (nearly) Roche Volume filling clusters, the induced escape of stars. Once sufficient relaxation has occurred (≃10 relaxation times-scales), clusters reach a second, `balanced' state whereby the core releases energy as required by the cluster as a whole. In this state: (1) stars escape due to tidal effects faster than before balanced evolution; (2) the half-mass radius expands or contracts depending on the Roche volume filling factor; and (3) the mean mass of stars increases due to the preferential ejection of low-mass stars. We compare the EMACSS results of several cluster properties against N-body simulations of clusters spanning a range of initial number of stars, mass, half-mass radius, and tidal environments, and show that our prescription accurately predicts cluster evolution for this data base. Finally, we consider applications for EMACSS, such as studies of galactic globular cluster populations in cosmological simulations.

  16. Type III polyketide synthase repertoire in Zingiberaceae: computational insights into the sequence, structure and evolution.

    PubMed

    Mallika, Vijayanathan; Aiswarya, Girija; Gincy, Paily Thottathil; Remakanthan, Appukuttan; Soniya, Eppurathu Vasudevan

    2016-07-01

    Zingiberaceae or 'ginger family' is the largest family in the order 'Zingiberales' with more than 1300 species in 52 genera, which are mostly distributed throughout Asia, tropical Africa and the native regions of America with their maximum diversity in Southeast Asia. Many of the members are important spice, medicinal or ornamental plants including ginger, turmeric, cardamom and kaempferia. These plants are distinguished for the highly valuable metabolic products, which are synthesised through phenylpropanoid pathway, where type III polyketide synthase is the key enzyme. In our present study, we used sequence, structural and evolutionary approaches to scrutinise the type III polyketide synthase (PKS) repertoire encoded in the Zingiberaceae family. Highly conserved amino acid residues in the sequence alignment and phylogram suggested strong relationships between the type III PKS members of Zingiberaceae. Sequence and structural level investigation of type III PKSs showed a small number of variations in the substrate binding pocket, leading to functional divergence among these PKS members. Molecular evolutionary studies indicate that type III PKSs within Zingiberaceae evolved under strong purifying selection pressure, and positive selections were rarely detected in the family. Structural modelling and protein-small molecule interaction studies on Zingiber officinale PKS 'a representative from Zingiberaceae' suggested that the protein is comparatively stable without much disorder and exhibited wide substrate acceptance.

  17. Type III polyketide synthase repertoire in Zingiberaceae: computational insights into the sequence, structure and evolution.

    PubMed

    Mallika, Vijayanathan; Aiswarya, Girija; Gincy, Paily Thottathil; Remakanthan, Appukuttan; Soniya, Eppurathu Vasudevan

    2016-07-01

    Zingiberaceae or 'ginger family' is the largest family in the order 'Zingiberales' with more than 1300 species in 52 genera, which are mostly distributed throughout Asia, tropical Africa and the native regions of America with their maximum diversity in Southeast Asia. Many of the members are important spice, medicinal or ornamental plants including ginger, turmeric, cardamom and kaempferia. These plants are distinguished for the highly valuable metabolic products, which are synthesised through phenylpropanoid pathway, where type III polyketide synthase is the key enzyme. In our present study, we used sequence, structural and evolutionary approaches to scrutinise the type III polyketide synthase (PKS) repertoire encoded in the Zingiberaceae family. Highly conserved amino acid residues in the sequence alignment and phylogram suggested strong relationships between the type III PKS members of Zingiberaceae. Sequence and structural level investigation of type III PKSs showed a small number of variations in the substrate binding pocket, leading to functional divergence among these PKS members. Molecular evolutionary studies indicate that type III PKSs within Zingiberaceae evolved under strong purifying selection pressure, and positive selections were rarely detected in the family. Structural modelling and protein-small molecule interaction studies on Zingiber officinale PKS 'a representative from Zingiberaceae' suggested that the protein is comparatively stable without much disorder and exhibited wide substrate acceptance. PMID:27138283

  18. Structure, Evolution, and Functions of Bacterial Type III Toxin-Antitoxin Systems

    PubMed Central

    Goeders, Nathalie; Chai, Ray; Chen, Bihe; Day, Andrew; Salmond, George P. C.

    2016-01-01

    Toxin-antitoxin (TA) systems are small genetic modules that encode a toxin (that targets an essential cellular process) and an antitoxin that neutralises or suppresses the deleterious effect of the toxin. Based on the molecular nature of the toxin and antitoxin components, TA systems are categorised into different types. Type III TA systems, the focus of this review, are composed of a toxic endoribonuclease neutralised by a non-coding RNA antitoxin in a pseudoknotted configuration. Bioinformatic analysis shows that the Type III systems can be classified into subtypes. These TA systems were originally discovered through a phage resistance phenotype arising due to a process akin to an altruistic suicide; the phenomenon of abortive infection. Some Type III TA systems are bifunctional and can stabilise plasmids during vegetative growth and sporulation. Features particular to Type III systems are explored here, emphasising some of the characteristics of the RNA antitoxin and how these may affect the co-evolutionary relationship between toxins and cognate antitoxins in their quaternary structures. Finally, an updated analysis of the distribution and diversity of these systems are presented and discussed. PMID:27690100

  19. Analysis of conifer FLOWERING LOCUS T/TERMINAL FLOWER1-like genes provides evidence for dramatic biochemical evolution in the angiosperm FT lineage.

    PubMed

    Klintenäs, Maria; Pin, Pierre A; Benlloch, Reyes; Ingvarsson, Pär K; Nilsson, Ove

    2012-12-01

    In flowering plants, homologs of the Arabidopsis phosphatidylethanolamine-binding protein (PEBP) FLOWERING LOCUS T (FT) are key components in controlling flowering time. We show here that, although FT homologs are found in all angiosperms with completed genome sequences, there is no evidence to date that FT-like genes exist in other groups of plants. Through phylogeny reconstructions and heterologous expression, we examined the biochemical function of the Picea (spruces) and Pinus (pines) PEBP families - two gymnosperm taxa phylogenetically distant from the angiosperms. We have defined a lineage of gymnosperm PEBP genes, termed the FT/TERMINAL FLOWER1 (TFL1)-like genes, that share sequence characteristics with both the angiosperm FT- and TFL1-like clades. When expressed in Arabidopsis, FT/TFL1-like genes repressed flowering, indicating that the proteins are biochemically more similar to the angiosperm TFL1-like proteins than to the FT-like proteins. This suggests that the regulation of the vegetative-to-reproductive switch might differ in gymnosperms compared with angiosperms. Molecular evolution studies suggest that plasticity at exon 4 contributes to the divergence of FT-like function in floral promotion. In addition, the presence of FT-like genes in basal angiosperms indicates that the FT-like function emerged at an early stage during the evolution of flowering plants as a means to regulate flowering time.

  20. THE CLUSTERING OF GALAXIES IN THE SDSS-III BARYON OSCILLATION SPECTROSCOPIC SURVEY: LUMINOSITY AND COLOR DEPENDENCE AND REDSHIFT EVOLUTION

    SciTech Connect

    Guo Hong; Zehavi, Idit; Zheng Zheng; Weinberg, David H.; Berlind, Andreas A.; Blanton, Michael; Chen Yanmei; Eisenstein, Daniel J.; McBride, Cameron K.; Ho, Shirley; Ross, Nicholas P.; Kazin, Eyal; Manera, Marc; Maraston, Claudia; Percival, Will J.; Ross, Ashley J.; Samushia, Lado; Nuza, Sebastian E.; Padmanabhan, Nikhil; Parejko, John K.; and others

    2013-04-20

    We measure the luminosity and color dependence and the redshift evolution of galaxy clustering in the Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey Ninth Data Release. We focus on the projected two-point correlation function (2PCF) of subsets of its CMASS sample, which includes about 260,000 galaxies over {approx}3300 deg{sup 2} in the redshift range 0.43 < z < 0.7. To minimize the selection effect on galaxy clustering, we construct well-defined luminosity and color subsamples by carefully accounting for the CMASS galaxy selection cuts. The 2PCF of the whole CMASS sample, if approximated by a power-law, has a correlation length of r{sub 0} = 7.93 {+-} 0.06 h {sup -1} Mpc and an index of {gamma} = 1.85 {+-} 0.01. Clear dependences on galaxy luminosity and color are found for the projected 2PCF in all redshift bins, with more luminous and redder galaxies generally exhibiting stronger clustering and steeper 2PCF. The color dependence is also clearly seen for galaxies within the red sequence, consistent with the behavior of SDSS-II main sample galaxies at lower redshifts. At a given luminosity (k + e corrected), no significant evolution of the projected 2PCFs with redshift is detected for red sequence galaxies. We also construct galaxy samples of fixed number density at different redshifts, using redshift-dependent magnitude thresholds. The clustering of these galaxies in the CMASS redshift range is found to be consistent with that predicted by passive evolution. Our measurements of the luminosity and color dependence and redshift evolution of galaxy clustering will allow for detailed modeling of the relation between galaxies and dark matter halos and new constraints on galaxy formation and evolution.

  1. Cerium(III) Complex Modified Gold Electrode: An Efficient Electrocatalyst for the Oxygen Evolution Reaction.

    PubMed

    Garain, Samiran; Barman, Koushik; Sinha, Tridib Kumar; Jasimuddin, Sk; Haeberle, Jörg; Henkel, Karsten; Schmeisser, Dieter; Mandal, Dipankar

    2016-08-24

    Exploring efficient and inexpensive electrocatalysts for the oxidation of water is of great importance for various electrochemical energy storage and conversion technologies. In the present study, a new water-soluble [Ce(III)(DMF) (HSO4)3] complex was synthesized and characterized by UV-vis, photoluminescence, and high-resolution X-ray photoelectron spectroscopy techniques. Owing to classic 5d → 4f transitions, an intense photoluminescence in the UV region was observed from the water-soluble [Ce(III)(DMF) (HSO4)3] complex. A stacking electrode was designed where self-assembled l-cysteine monolayer modified gold was immobilized with the synthesized cerium complex and was characterized by scanning electron microscopy, electrochemical impedance spectroscopy, and cyclic voltammetry. The resulting electrode, i.e., [Ce(III)(DMF) (HSO4)3]-l-cysteine-Au stacks shows high electrocatalytic water oxidation behavior at an overpotential of η ≈ 0.34 V under neutral pH conditions. We also demonstrated a way where the overpotential is possible to decrease upon irradiation of UV light. PMID:27490440

  2. Spectral evolution of galaxies. III - Cosmological predictions for the Space Telescope faint object camera

    NASA Astrophysics Data System (ADS)

    Bruzual A., G.

    1983-10-01

    The galactic spectral evolutionary models of Bruzual A. (1981) are employed to estimate parameters which will be observable by the wide-field camera and faint-object camera of the Space Telescope. The capabilities and bandpasses of the instruments are reviewed, and the results are presented in tables and graphs. Parameters calculated include the amplitude of the Lyman discontinuity at 912 A, stellar and galaxy rest-frame colors, color evolution, two-color diagrams as a function of redshift, luminosity evolution, surface brightness profiles, galaxy counts, and color and redshift distributions. In general, it is predicted that the space measurements will follow the trends noted in round-based observations.

  3. Rotation in the Pleiades with K2. III. Speculations on Origins and Evolution

    NASA Astrophysics Data System (ADS)

    Stauffer, John; Rebull, Luisa; Bouvier, Jerome; Hillenbrand, Lynne A.; Collier-Cameron, Andrew; Pinsonneault, Marc; Aigrain, Suzanne; Barrado, David; Bouy, Herve; Ciardi, David; Cody, Ann Marie; David, Trevor; Micela, Giusi; Soderblom, David; Somers, Garrett; Stassun, Keivan G.; Valenti, Jeff; Vrba, Frederick J.

    2016-11-01

    We use high-quality K2 light curves for hundreds of stars in the Pleiades to better understand the angular momentum evolution and magnetic dynamos of young low-mass stars. The K2 light curves provide not only rotational periods but also detailed information from the shape of the phased light curve that was not available in previous studies. A slowly rotating sequence begins at {(V-{K}{{s}})}0 ∼ 1.1 (spectral type F5) and ends at {(V-{K}{{s}})}0 ∼ 3.7 (spectral type K8), with periods rising from ∼2 to ∼11 days in that interval. A total of 52% of the Pleiades members in that color interval have periods within 30% of a curve defining the slow sequence; the slowly rotating fraction decreases significantly redward of {(V-{K}{{s}})}0 = 2.6. Nearly all of the slow-sequence stars show light curves that evolve significantly on timescales less than the K2 campaign duration. The majority of the FGK Pleiades members identified as photometric binaries are relatively rapidly rotating, perhaps because binarity inhibits star–disk angular momentum loss mechanisms during pre-main-sequence evolution. The fully convective late M dwarf Pleiades members (5.0 < {(V-{K}{{s}})}0 < 6.0) nearly always show stable light curves, with little spot evolution or evidence of differential rotation. During pre-main-sequence evolution from ∼3 Myr (NGC 2264 age) to ∼125 Myr (Pleiades age), stars of 0.3 {M}ȯ shed about half of their angular momentum, with the fractional change in period between 3 and 125 Myr being nearly independent of mass for fully convective stars. Our data also suggest that very low mass binaries form with rotation periods more similar to each other and faster than would be true if drawn at random from the parent population of single stars.

  4. ENTHALPY-BASED THERMAL EVOLUTION OF LOOPS. III. COMPARISON OF ZERO-DIMENSIONAL MODELS

    SciTech Connect

    Cargill, P. J.; Bradshaw, S. J.; Klimchuk, J. A.

    2012-10-10

    Zero-dimensional (0D) hydrodynamic models provide a simple and quick way to study the thermal evolution of coronal loops subjected to time-dependent heating. This paper presents a comparison of a number of 0D models that have been published in the past and is intended to provide a guide for those interested in either using the old models or developing new ones. The principal difference between the models is the way the exchange of mass and energy between corona, transition region, and chromosphere is treated, as plasma cycles into and out of a loop during a heating-cooling cycle. It is shown that models based on the principles of mass and energy conservation can give satisfactory results at some or, in the case of the Enthalpy-based Thermal Evolution of Loops model, all stages of the loop evolution. Empirical models can have significant difficulties in obtaining accurate behavior due to invocation of assumptions incompatible with the correct exchange of mass and energy between corona, transition region, and chromosphere.

  5. The Evolution of Galaxies. III - From Simple Approaches to Self-Consistent Models.

    NASA Astrophysics Data System (ADS)

    Hensler, G.; Stasińska, G.; Harfst, S.; Kroupa, P.; Theis, Chr.

    2003-07-01

    Galaxies have a history. This has become clear from recent sky surveys which have shown that distant galaxies, formed early in the life of the Universe, differ from the nearby ones. New observational windows at ultraviolet, infrared and millimetric wavelengths (provided by ROSAT, IRAM, IUE, IRAS, ISO) have revealed that galaxies contain a wealth of components: very hot gas, atomic hydrogen, molecules, dust, dark matter...A significant advance is expected from the results of new instruments (VLT, FIRST, XMM) which will=0D=0Aallow one to explore the most distant Universe. Three Euroconferences were planned to punctuate this new epoch in galactic research, bringing together specialists in various fields of Astronomy. The first one, held in Granada (Spain) in May 2000, addressed the observational clues. The second one took place in October 2001 in St. Denis de la Réunion (France) and reviewed the basic building blocks and small-scale processes in galaxy evolution. The third conference was held in Kiel (Germany) in July 2002 and addressed the appropriate modelling of galaxy evolution from their cosmological formation to their presently observable structures. This book contains the proceedings of the third conference and presents the actual state-of-the-art of modelling galaxy evolution. Link: http://www.wkap.nl/prod/b/1-4020-1182-2

  6. Enthalpy-Based Thermal Evolution of Loops: III. Comparison of Zero-Dimensional Models

    NASA Technical Reports Server (NTRS)

    Cargill, P. J.; Bradshaw, Stephen J.; Klimchuk, James A.

    2012-01-01

    Zero dimensional (0D) hydrodynamic models, provide a simple and quick way to study the thermal evolution of coronal loops subjected to time-dependent heating. This paper presents a comparison of a number of 0D models that have been published in the past and is intended to provide a guide for those interested in either using the old models or developing new ones. The principal difference between the models is the way the exchange of mass and energy between corona, transition region and chromosphere is treated, as plasma cycles into and out of a loop during a heating-cooling cycle. It is shown that models based on the principles of mass and energy conservation can give satisfactory results at some, or, in the case of the Enthalpy Based Thermal Evolution of Loops (EBTEL) model, all stages of the loop evolution. Empirical models can lead to low coronal densities, spurious delays between the peak density and temperature, and, for short heating pulses, overly short loop lifetimes.

  7. Charge state evolution in the solar wind. III. Model comparison with observations

    SciTech Connect

    Landi, E.; Oran, R.; Lepri, S. T.; Zurbuchen, T. H.; Fisk, L. A.; Van der Holst, B.

    2014-08-01

    We test three theoretical models of the fast solar wind with a set of remote sensing observations and in-situ measurements taken during the minimum of solar cycle 23. First, the model electron density and temperature are compared to SOHO/SUMER spectroscopic measurements. Second, the model electron density, temperature, and wind speed are used to predict the charge state evolution of the wind plasma from the source regions to the freeze-in point. Frozen-in charge states are compared with Ulysses/SWICS measurements at 1 AU, while charge states close to the Sun are combined with the CHIANTI spectral code to calculate the intensities of selected spectral lines, to be compared with SOHO/SUMER observations in the north polar coronal hole. We find that none of the theoretical models are able to completely reproduce all observations; namely, all of them underestimate the charge state distribution of the solar wind everywhere, although the levels of disagreement vary from model to model. We discuss possible causes of the disagreement, namely, uncertainties in the calculation of the charge state evolution and of line intensities, in the atomic data, and in the assumptions on the wind plasma conditions. Last, we discuss the scenario where the wind is accelerated from a region located in the solar corona rather than in the chromosphere as assumed in the three theoretical models, and find that a wind originating from the corona is in much closer agreement with observations.

  8. Charge State Evolution in the Solar Wind. III. Model Comparison with Observations

    NASA Astrophysics Data System (ADS)

    Landi, E.; Oran, R.; Lepri, S. T.; Zurbuchen, T. H.; Fisk, L. A.; van der Holst, B.

    2014-08-01

    We test three theoretical models of the fast solar wind with a set of remote sensing observations and in-situ measurements taken during the minimum of solar cycle 23. First, the model electron density and temperature are compared to SOHO/SUMER spectroscopic measurements. Second, the model electron density, temperature, and wind speed are used to predict the charge state evolution of the wind plasma from the source regions to the freeze-in point. Frozen-in charge states are compared with Ulysses/SWICS measurements at 1 AU, while charge states close to the Sun are combined with the CHIANTI spectral code to calculate the intensities of selected spectral lines, to be compared with SOHO/SUMER observations in the north polar coronal hole. We find that none of the theoretical models are able to completely reproduce all observations; namely, all of them underestimate the charge state distribution of the solar wind everywhere, although the levels of disagreement vary from model to model. We discuss possible causes of the disagreement, namely, uncertainties in the calculation of the charge state evolution and of line intensities, in the atomic data, and in the assumptions on the wind plasma conditions. Last, we discuss the scenario where the wind is accelerated from a region located in the solar corona rather than in the chromosphere as assumed in the three theoretical models, and find that a wind originating from the corona is in much closer agreement with observations.

  9. Concerted evolution at the population level: pupfish HindIII satellite DNA sequences.

    PubMed Central

    Elder, J F; Turner, B J

    1994-01-01

    The canonical monomers (approximately 170 bp) of an abundant (1.9 x 10(6) copies per diploid genome) satellite DNA sequence family in the genome of Cyprinodon variegatus, a "pupfish" that ranges along the Atlantic coast from Cape Cod to central Mexico, are divergent in base sequence in 10 of 12 samples collected from natural populations. The divergence involves substitutions, deletions, and insertions, is marked in scope (mean pairwise sequence similarity = 61.6%; range = 35-95.9%), is largely confined to the 3' half of the monomer, and is not correlated with the distance among collecting sites. Repetitive cloning and direct genomic sequencing experiments failed to detect intrapopulation and intraindividual variation, suggesting high levels of sequence homogeneity within populations. The satellite sequence has therefore undergone "concerted evolution," at the level of the local population. Concerted evolution has previously almost always been discussed in terms of the divergence of species or higher taxa; its intraspecific occurrence apparently has not been reported previously. The generality of the observation is difficult to evaluate, for although satellite DNAs from a large number of organisms have been studied in detail, there appear to be little or no other data on their sequence variation in natural populations. The relationship (if any) between concerted, population level, satellite DNA divergence and the extent of gene flow/genetic isolation among conspecific natural populations remains to be established. Images PMID:8302879

  10. Degradation of connective tissue matrices by macrophages. III. Morphological and biochemical studies on extracellular, pericellular, and intracellular events in matrix proteolysis by macrophages in culture

    SciTech Connect

    Werb, Z.; Bainton, D.F.; Jones, P.A.

    1980-12-01

    The aim of the present study was to determine the localization of macrophage-mediated degradation of matrix proteins. The sites of matrix degradation were examined ultrastructurally, and the effects of modulation of macrophage secretion, endocytosis, and activity of macrophage hydrolases on matrix degradation were monitored biochemically.

  11. Evolution of GITRL Immune Function: Murine GITRL Exhibits Unique Structural and Biochemical Properties Within the TNF Superfamily

    SciTech Connect

    Chattopadhyay,K.; Ramagopal, U.; Brenowitz, M.; Nathenson, S.; Almo, S.

    2008-01-01

    Glucocorticoid-induced TNF receptor ligand (GITRL), a recently identified member of the TNF superfamily, binds to its receptor, GITR, on both effector and regulatory T cells and generates positive costimulatory signals implicated in a wide range of T cell functions. In contrast to all previously characterized homotrimeric TNF family members, the mouse GITRL crystal structure reveals a previously unrecognized dimeric assembly that is stabilized via a unique 'domain-swapping' interaction. Consistent with its crystal structure, mouse GITRL exists as a stable dimer in solution. Structure-guided mutagenesis studies confirmed the determinants responsible for dimerization and support a previously unrecognized receptor-recognition surface for mouse GITRL that has not been observed for any other TNF family members. Taken together, the unique structural and biochemical behavior of mouse GITRL, along with the unusual domain organization of murine GITR, support a previously unrecognized mechanism for signaling within the TNF superfamily.

  12. Extra-solar planetary systems. III - Potential sites for the origin and evolution of technical civilisations

    NASA Astrophysics Data System (ADS)

    Fogg, M. J.

    1986-07-01

    A series of runs of the Silicon Creation' computer model developed by Fogg (1985) has been analyzed in order to evaluate the probable abundance of planets possessing suitable conditions for the evolution of technologically adept forms of life. The evolutionary simulation encompassed 100,000 disk stars of varying mass, metallicity, and age, and focused on civilizations that may have come into existence on planets over the past 10 to the 10th years of planetary disk history. The frequency of such sites is determined to be 0.00292, and the frequency of planets developing a technological civilization is 0.00009; these figures are two orders of magnitude lower than the most optimistic manipulations of the Drake equation, but not low enough to resolve the Fermi paradox, according to which an alien civilization, if existent, should long ago have colonized the entire Galaxy.

  13. Non-spherical core collapse supernovae. III. Evolution towards homology and dependence on the numerical resolution

    NASA Astrophysics Data System (ADS)

    Gawryszczak, A.; Guzman, J.; Plewa, T.; Kifonidis, K.

    2010-10-01

    Aims: We study the hydrodynamic evolution of a non-spherical core-collapse supernova in two spatial dimensions. We begin our study from the moment of shock revival - taking into account neutrino heating and cooling, nucleosynthesis, convection, and the standing accretion shock (SASI) instability of the supernova blast - and continue for the first week after the explosion when the expanding flow becomes homologous and the ejecta enter the early supernova remnant (SNR) phase. We observe the growth and interaction of Richtmyer-Meshkov, Rayleigh-Taylor, and Kelvin-Helmholtz instabilities resulting in an extensive mixing of the heavy elements throughout the ejecta. We obtain a series of models at progressively higher resolution and provide a discussion of numerical convergence. Methods: Different from previous studies, our computations are performed in a single domain. Periodic mesh mapping is avoided. This is made possible by employing cylindrical coordinates, and an adaptive mesh refinement (AMR) strategy in which the computational workload (defined as the product of the total number of computational cells and the length of the time step) is monitored and, if necessary, reduced. Results: Our results are in overall good agreement with the AMR simulations we have reported in the past. We show, however, that numerical convergence is difficult to achieve, due to the strongly non-linear nature of the problem. Even more importantly, we find that our model displays a strong tendency to expand laterally away from the equatorial plane and toward the poles. We demonstrate that this expansion is a physical property of the low-mode, SASI instability. Although the SASI operates only within about the first second of the explosion, it leaves behind a large lateral velocity gradient in the post shock layer which affects the evolution for minutes and hours later. This results in a prolate deformation of the ejecta and a fast advection of the highest-velocity 56Ni-rich material from

  14. Completeness - III. Identifying characteristic systematics and evolution in galaxy redshift surveys

    NASA Astrophysics Data System (ADS)

    Johnston, Russell; Teodoro, Luís.; Hendry, Martin

    2012-03-01

    This paper continues our development of non-parametric tests for analysing the completeness in apparent magnitude of magnitude-redshift surveys. The purpose of this third and final paper in our completeness series is twofold: first, we explore how certain forms of incompleteness for a given flux-limited galaxy redshift survey would manifest themselves in the 'robust'Tc and Tv completeness estimators introduced in our earlier papers; secondly, we provide a comprehensive error propagation for these estimators. This work was initiated by Rauzy and then extended and developed by Johnston, Teodoro & Hendry (Completeness I) and Teodoro, Johnston & Hendry (Completeness II). Here, we seek to consolidate the ideas laid out in these previous papers. In particular, our goal is to provide for the observational community statistical tools that will be more easily applicable to real survey data. By using both real surveys and Monte Carlo mock survey data, we have found distinct, characteristic behaviour of the Tc and Tv estimators which identify incompleteness in the form of e.g. missing objects within a particular magnitude range. Conversely, we have identified signatures of 'over' completeness, in cases where a survey contains a small region in apparent magnitude that may have too many objects relative to the rest of the data set. Identifying regions of incompleteness (in apparent magnitude) in this way provides a powerful means to e.g. improve weighting schemes for estimating luminosity functions, or for more accurately determining the selection function required to employ measures of galaxy clustering as a cosmological probe. We also demonstrate how incompleteness resulting from luminosity evolution can be identified and provide a framework for using our estimators as a robust tool for constraining models of luminosity evolution. Finally, we explore the error propagation for Tc and Tv. This builds on Completeness II by allowing the definition of these estimators, and their

  15. Thermal evolution and sintering of chondritic planetesimals. III. Modelling the heat conductivity of porous chondrite material

    NASA Astrophysics Data System (ADS)

    Henke, Stephan; Gail, Hans-Peter; Trieloff, Mario

    2016-05-01

    Context. The construction of models for the internal constitution and temporal evolution of large planetesimals, which are the parent bodies of chondrites, requires as accurate as possible information on the heat conductivity of the complex mixture of minerals and iron metal found in chondrites. The few empirical data points on the heat conductivity of chondritic material are severely disturbed by impact-induced microcracks modifying the thermal conductivity. Aims: We attempt to evaluate the heat conductivity of chondritic material with theoretical methods. Methods: We derived the average heat conductivity of a multi-component mineral mixture and granular medium from the heat conductivities of its mixture components. We numerically generated random mixtures of solids with chondritic composition and packings of spheres. We solved the heat conduction equation in high spatial resolution for a test cube filled with such matter. We derived the heat conductivity of the mixture from the calculated heat flux through the cube. Results: For H and L chondrites, our results are in accord with empirical thermal conductivity at zero porosity. However, the porosity dependence of heat conductivity of granular material built from chondrules and matrix is at odds with measurements for chondrites, while our calculations are consistent with data for compacted sandstone. The discrepancy is traced back to subsequent shock modification of the currently available meteoritic material resulting from impacts on the parent body over the last 4.5 Ga. This causes a structure of void space made of fractures/cracks, which lowers the thermal conductivity of the medium and acts as a barrier to heat transfer. This structure is different from the structure that probably exists in the pristine material where voids are represented by pores rather than fractures. The results obtained for the heat conductivity of the pristine material are used for calculating models for the evolution of the H chondrite

  16. Evolution of planetary nebulae. III. Position-velocity images of butterfly-type nebulae

    SciTech Connect

    Icke, V.; Preston, H.L.; Balick, B.

    1989-02-01

    Observations of the motions of the shells of the planetary nebulae NGC 2346, NGC 2371-2, NGC 2440, NGC 6058, NGC 6210, IC 1747, IC 5217, J-320, and M2-9 are presented. These are all 'butterfly' type PNs, and show evidence for bipolar shocks. The observations are interpreted in terms of a fast spherical wind, driven by the central star into a quasi-toroidal envelope deposited earlier by the star, during its slow-wind phase on the asymptotic giant branch. It is shown that this model, which is a straightforward extension of a mechanism previously invoked to account for elliptical PNs, reproduces the essential kinematic features of butterfly PNs. It is inferred that the envelopes of butterflies must have a considerable equator-to-pole density gradient, and it is suggested that the origin of this asphericity must be sought in an as yet unknown mechanism during the AGB, Mira, or OH/IR phases of late stellar evolution. 28 references.

  17. Galaxy Assembly and the Evolution of Structure over the First Third of Cosmic Time - III

    NASA Astrophysics Data System (ADS)

    Faber, Sandra

    2011-10-01

    This survey will document the first third of galactic evolution fromz=8 to 1.5 andtest for evolution in the properties of Type Ia supernovae to z 2 byimaging more than 250,000 galaxies with WFC3/IR and ACS. Five premiermulti-wavelength regions are selected from within the Spitzer SEDSsurvey, providing complementaryIRAC data down to 26.5 AB mag, a unique resource forstellar masses at high redshifts. The use of five widely separatedfields mitigates cosmic variance and yields statistically robustsamples of galaxies down to 10^9 M_Sun out to z 8.We adopt a two-tiered strategy with a "Wide" component {roughly 2orbits deep over 0.2 sq. degrees} and a "Deep" component {roughly 12orbits deep over 0.04 sq. degrees}. Combining these with ultra-deepimaging from the Cycle 17 HUDF09 program yields a three-tieredstrategy for efficient sampling of both rare/bright and faint/commonobjects.Three of the Wide-survey fields are located in COSMOS, EGS, andUKIDSS/UDS. Each of these consists of roughly 3x15 WFC3/IR tiles.Each WFC3 tile will be observed for 2 orbits, with single orbitsseparated in time to allow a search for high-redshift Type Ia SNe.The co-added exposure times will be approximately 2/3 orbit in J{F125W} and 4/3 orbit in H {F160W}. ACS parallels overlap most of theWFC3 area and will consist of roughly 2/3 orbits in V {F606W} and4/3 orbit in I {F814W}. Because of the larger area of ACS,this results in effective exposures that are twice as long {4/3 in V,8/3 in I}, making a very significant improvement to existing ACSmosaics in COSMOS and EGS and creating a new ACS mosaic in UDS/UKIDSSwhere none now exists. Other Wide-survey components are located inthe GOODS fields {North and South} surrounding the Deep-survey areas.The Deep-survey fields cover roughly half of each GOODS field, withexact areas and placements to be determined as part of the Phase-2process. Each WFC3/IR tile within the Deep regions will receiveapproximately 12 orbits of exposure time split between Y{F105W}, J

  18. WINGS-SPE. III. Equivalent width measurements, spectral properties, and evolution of local cluster galaxies

    NASA Astrophysics Data System (ADS)

    Fritz, J.; Poggianti, B. M.; Cava, A.; Moretti, A.; Varela, J.; Bettoni, D.; Couch, W. J.; D'Onofrio D'Onofrio, M.; Dressler, A.; Fasano, G.; Kjærgaard, P.; Marziani, P.; Moles, M.; Omizzolo, A.

    2014-06-01

    Context. Cluster galaxies are the ideal sites to look at when studying the influence of the environment on the various aspects of the evolution of galaxies, such as the changes in their stellar content and morphological transformations. In the framework of wings, the WIde-field Nearby Galaxy-cluster Survey, we have obtained optical spectra for ~6000 galaxies selected in fields centred on 48 local (0.04 < z < 0.07) X-ray selected clusters to tackle these issues. Aims: By classifying the spectra based on given spectral lines, we investigate the frequency of the various spectral types as a function of both the clusters' properties and the galaxies' characteristics. In this way, using the same classification criteria adopted for studies at higher redshift, we can consistently compare the properties of the local cluster population to those of their more distant counterparts. Methods: We describe a method that we have developed to automatically measure the equivalent width of spectral lines in a robust way, even in spectra with a non optimal signal-to-noise ratio. This way, we can derive a spectral classification reflecting the stellar content, based on the presence and strength of the [Oii] and Hδ lines. Results: After a quality check, we are able to measure 4381 of the ~6000 originally observed spectra in the fields of 48 clusters, of which 2744 are spectroscopically confirmed cluster members. The spectral classification is then analysed as a function of galaxies' luminosity, stellar mass, morphology, local density, and host cluster's global properties and compared to higher redshift samples (MORPHS and EDisCS). The vast majority of galaxies in the local clusters population are passive objects, being also the most luminous and massive. At a magnitude limit of MV < -18, galaxies in a post-starburst phase represent only ~11% of the cluster population, and this fraction is reduced to ~5% at MV < -19.5, which compares to the 18% at the same magnitude limit for high

  19. Galaxy Assembly and the Evolution of Structure over the First Third of Cosmic Time - III

    NASA Astrophysics Data System (ADS)

    Faber, Sandra

    2011-10-01

    This survey will document the first third of galactic evolution fromz=8 to 1.5 andtest for evolution in the properties of Type Ia supernovae to z 2 byimaging more than 250,000 galaxies with WFC3/IR and ACS. Five premiermulti-wavelength regions are selected from within the Spitzer SEDSsurvey, providing complementaryIRAC data down to 26.5 AB mag, a unique resource forstellar masses at high redshifts. The use of five widely separatedfields mitigates cosmic variance and yields statistically robustsamples of galaxies down to 10^9 M_Sun out to z 8.We adopt a two-tiered strategy with a "Wide" component {roughly 2orbits deep over 0.2 sq. degrees} and a "Deep" component {roughly 12orbits deep over 0.04 sq. degrees}. Combining these with ultra-deepimaging from the Cycle 17 HUDF09 program yields a three-tieredstrategy for efficient sampling of both rare/bright and faint/commonobjects.Three of the Wide-survey fields are located in COSMOS, EGS, andUKIDSS/UDS. Each of these consists of roughly 3x15 WFC3/IR tiles.Each WFC3 tile will be observed for 2 orbits, with single orbitsseparated in time to allow a search for high-redshift Type Ia SNe.The co-added exposure times will be approximately 2/3 orbit in J{F125W} and 4/3 orbit in H {F160W}. ACS parallels overlap most of theWFC3 area and will consist of roughly 2/3 orbits in V {F606W} and4/3 orbit in I {F814W}. Because of the larger area of ACS,this results in effective exposures that are twice as long {4/3 in V,8/3 in I}, making a very significant improvement to existing ACSmosaics in COSMOS and EGS and creating a new ACS mosaic in UDS/UKIDSSwhere none now exists. Other Wide-survey components are located inthe GOODS fields {North and South} surrounding the Deep-survey areas.The Deep-survey fields cover roughly half of each GOODS field, withexact areas and placements to be determined as part of the Phase-2process. Each WFC3/IR tile within the Deep regions will receiveapproximately 12 orbits of exposure time split between Y{F105W}, J

  20. POISSON project. III. Investigating the evolution of the mass accretion rate

    NASA Astrophysics Data System (ADS)

    Antoniucci, S.; García López, R.; Nisini, B.; Caratti o Garatti, A.; Giannini, T.; Lorenzetti, D.

    2014-12-01

    Context. As part of the Protostellar Optical-Infrared Spectral Survey On NTT (POISSON) project, we present the results of the analysis of low-resolution near-IR spectroscopic data (0.9-2.4 μm) of two samples of young stellar objects in the Lupus (52 objects) and Serpens (17 objects) star-forming clouds, with masses in the range of 0.1 to 2.0 M⊙ and ages spanning from 105 to a few 107 yr. Aims: After determining the accretion parameters of the targets by analysing their H i near-IR emission features, we added the results from the Lupus and Serpens clouds to those from previous regions (investigated in POISSON with the same methodology) to obtain a final catalogue (143 objects) of mass accretion rate values (Ṁacc) derived in a homogeneous and consistent fashion. Our final goal is to analyse how Ṁacc correlates with the stellar mass (M∗) and how it evolves in time in the whole POISSON sample. Methods: We derived the accretion luminosity (Lacc) and Ṁacc for Lupus and Serpens objects from the Brγ (Paβ in a few cases) line by using relevant empirical relationships available in the literature that connect the H i line luminosity and Lacc. To minimise the biases that arise from adopting literature data that are based on different evolutionary models and also for self-consistency, we re-derived mass and age for each source of the POISSON samples using the same set of evolutionary tracks. Results: We observe a correlation Ṁacc~M*2.2 between mass accretion rate and stellar mass, similarly to what has previously been observed in several star-forming regions. We find that the time variation of Ṁacc is roughly consistent with the expected evolution of the accretion rate in viscous disks, with an asymptotic decay that behaves as t-1.6. However, Ṁacc values are characterised by a large scatter at similar ages and are on average higher than the predictions of viscous models. Conclusions: Although part of the scattering may be related to systematics due to the

  1. Biochemical and Structural Characterization of Germicidin Synthase: Analysis of a Type III Polyketide Synthase That Employs Acyl-ACP as a Starter Unit Donor

    SciTech Connect

    Chemler, Joseph A.; Buchholz, Tonia J.; Geders, Todd W.; Akey, David L.; Rath, Christopher M.; Chlipala, George E.; Smith, Janet L.; Sherman, David H.

    2012-08-10

    Germicidin synthase (Gcs) from Streptomyces coelicolor is a type III polyketide synthase (PKS) with broad substrate flexibility for acyl groups linked through a thioester bond to either coenzyme A (CoA) or acyl carrier protein (ACP). Germicidin synthesis was reconstituted in vitro by coupling Gcs with fatty acid biosynthesis. Since Gcs has broad substrate flexibility, we directly compared the kinetic properties of Gcs with both acyl-ACP and acyl-CoA. The catalytic efficiency of Gcs for acyl-ACP was 10-fold higher than for acyl-CoA, suggesting a strong preference toward carrier protein starter unit transfer. The 2.9 {angstrom} germicidin synthase crystal structure revealed canonical type III PKS architecture along with an unusual helical bundle of unknown function that appears to extend the dimerization interface. A pair of arginine residues adjacent to the active site affect catalytic activity but not ACP binding. This investigation provides new and surprising information about the interactions between type III PKSs and ACPs that will facilitate the construction of engineered systems for production of novel polyketides.

  2. The evolution of the role of ABA in the regulation of water-use efficiency: From biochemical mechanisms to stomatal conductance.

    PubMed

    Negin, Boaz; Moshelion, Menachem

    2016-10-01

    Abscisic acid is found in a wide variety of organisms. In the plant kingdom, ABA's role in mediating responses to abiotic stress has been conserved and enhanced throughout evolution. The emergence of plants to terrestrial environments required the development of mechanisms to cope with ongoing and severe abiotic stress such as drought and rapid changes in humidity and temperature. The common understanding is that terrestrial plants evolved strategies ranging from desiccation-tolerance mechanisms (mosses) to drought tolerance (CAM plants), to better exploit different ecological niches. In between these divergent water regulation strategies, ABA plays a significant role in managing plants' adaptation to new environments by optimizing water-use efficiency (WUE) under particular environmental conditions. ABA plays some very different roles in the regulation of WUE. ABA's role in the regulation of guard cells and transpiration has yielded a wide variety of WUE-regulation mechanisms, ranging from no sensitivity (ferns) to low sensitivity (anisohydric behavior) to hypersensitivity to ABA (isohydric behavior and putatively CAM plants). ABA also plays a role in the regulation of non-stomatal, biochemical mechanisms of WUE regulation. In angiosperms, this includes the control of osmotic adjustment and morphological changes, including changes in leaf size, stomatal density, stomatal size and root development. Under severe stress, ABA also appears to initiate leaf senescence via transcriptional regulation, to directly inhibit photosynthesis. PMID:27593466

  3. The evolution of the role of ABA in the regulation of water-use efficiency: From biochemical mechanisms to stomatal conductance.

    PubMed

    Negin, Boaz; Moshelion, Menachem

    2016-10-01

    Abscisic acid is found in a wide variety of organisms. In the plant kingdom, ABA's role in mediating responses to abiotic stress has been conserved and enhanced throughout evolution. The emergence of plants to terrestrial environments required the development of mechanisms to cope with ongoing and severe abiotic stress such as drought and rapid changes in humidity and temperature. The common understanding is that terrestrial plants evolved strategies ranging from desiccation-tolerance mechanisms (mosses) to drought tolerance (CAM plants), to better exploit different ecological niches. In between these divergent water regulation strategies, ABA plays a significant role in managing plants' adaptation to new environments by optimizing water-use efficiency (WUE) under particular environmental conditions. ABA plays some very different roles in the regulation of WUE. ABA's role in the regulation of guard cells and transpiration has yielded a wide variety of WUE-regulation mechanisms, ranging from no sensitivity (ferns) to low sensitivity (anisohydric behavior) to hypersensitivity to ABA (isohydric behavior and putatively CAM plants). ABA also plays a role in the regulation of non-stomatal, biochemical mechanisms of WUE regulation. In angiosperms, this includes the control of osmotic adjustment and morphological changes, including changes in leaf size, stomatal density, stomatal size and root development. Under severe stress, ABA also appears to initiate leaf senescence via transcriptional regulation, to directly inhibit photosynthesis.

  4. Evolution.

    ERIC Educational Resources Information Center

    Mayr, Ernst

    1978-01-01

    Traces the history of evolution theory from Lamarck and Darwin to the present. Discusses natural selection in detail. Suggests that, besides biological evolution, there is also a cultural evolution which is more rapid than the former. (MA)

  5. Simultaneous occurrence of the 11778 (ND4) and the 9438 (COX III) mtDNA mutations in Leber hereditary optic neuropathy: Molecular, biochemical, and clinical findings

    SciTech Connect

    Oostra, R.J.; Bleeker-Wagemakers, E.M.; Zwart, R.

    1995-10-01

    Three mtDNA point mutations at nucleotide position (np) 3460, at np 11778 and at np 14484, are thought to be of primary importance in the pathogenesis of Leber hereditary optic neuropathy (LHON), a maternally inherited disease characterized by subacute central vision loss. These mutations are present in genes coding for subunits of complex I (NADH dehydrogenase) of the respiratory chain, occur exclusively in LHON maternal pedigrees, and have never been reported to occur together. Johns and Neufeld postulated that an mtDNA mutation at np 9438, in the gene coding for one of the subunits (COX III) of complex IV (cytochrome c oxidase), was also of primary importance. Johns and Neufeld (1993) found this mutation, which changed a conserved glycine to a serine, in 5 unrelated LHON probands who did not carry one of the presently known primary mutations, but they did not find it in 400 controls. However, the role of this sequence variant has been questioned in the Journal when it has been found to occur in apparently healthy African and Cuban individuals. Subsequently, Johns et al. described this mutation in two Cuban individuals presenting with optic and peripheral neuropathy. 22 refs., 1 fig., 1 tab.

  6. Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond.

    PubMed

    Ge, Hao; Qian, Hong

    2011-01-01

    A theory for an non-equilibrium phase transition in a driven biochemical network is presented. The theory is based on the chemical master equation (CME) formulation of mesoscopic biochemical reactions and the mathematical method of large deviations. The large deviations theory provides an analytical tool connecting the macroscopic multi-stability of an open chemical system with the multi-scale dynamics of its mesoscopic counterpart. It shows a corresponding non-equilibrium phase transition among multiple stochastic attractors. As an example, in the canonical phosphorylation-dephosphorylation system with feedback that exhibits bistability, we show that the non-equilibrium steady-state (NESS) phase transition has all the characteristics of classic equilibrium phase transition: Maxwell construction, a discontinuous first-derivative of the 'free energy function', Lee-Yang's zero for a generating function and a critical point that matches the cusp in nonlinear bifurcation theory. To the biochemical system, the mathematical analysis suggests three distinct timescales and needed levels of description. They are (i) molecular signalling, (ii) biochemical network nonlinear dynamics, and (iii) cellular evolution. For finite mesoscopic systems such as a cell, motions associated with (i) and (iii) are stochastic while that with (ii) is deterministic. Both (ii) and (iii) are emergent properties of a dynamic biochemical network.

  7. Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond

    PubMed Central

    Ge, Hao; Qian, Hong

    2011-01-01

    A theory for an non-equilibrium phase transition in a driven biochemical network is presented. The theory is based on the chemical master equation (CME) formulation of mesoscopic biochemical reactions and the mathematical method of large deviations. The large deviations theory provides an analytical tool connecting the macroscopic multi-stability of an open chemical system with the multi-scale dynamics of its mesoscopic counterpart. It shows a corresponding non-equilibrium phase transition among multiple stochastic attractors. As an example, in the canonical phosphorylation–dephosphorylation system with feedback that exhibits bistability, we show that the non-equilibrium steady-state (NESS) phase transition has all the characteristics of classic equilibrium phase transition: Maxwell construction, a discontinuous first-derivative of the ‘free energy function’, Lee–Yang's zero for a generating function and a critical point that matches the cusp in nonlinear bifurcation theory. To the biochemical system, the mathematical analysis suggests three distinct timescales and needed levels of description. They are (i) molecular signalling, (ii) biochemical network nonlinear dynamics, and (iii) cellular evolution. For finite mesoscopic systems such as a cell, motions associated with (i) and (iii) are stochastic while that with (ii) is deterministic. Both (ii) and (iii) are emergent properties of a dynamic biochemical network. PMID:20466813

  8. Biochemical evolution III: polymerization on organophilic silica-rich surfaces, crystal-chemical modeling, formation of first cells, and geological clues.

    PubMed

    Smith, J V; Arnold, F P; Parsons, I; Lee, M R

    1999-03-30

    Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal-chemical modeling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular sieve silicalite-ZSM-5-(mutinaite). Calculation of binding and activation energies for catalytic assembly into polymers is progressing for a chemical composition with one catalytic Al-OH site per 25 neutral Si tetrahedral sites. Internal channel intersections and external terminations provide special stereochemical features suitable for complex organic species. Polymer migration along nano/micrometer channels of ancient weathered feldspars, plus exploitation of phosphorus and various transition metals in entrapped apatite and other microminerals, might have generated complexes of replicating catalytic biomolecules, leading to primitive cellular organisms. The first cell wall might have been an internal mineral surface, from which the cell developed a protective biological cap emerging into a nutrient-rich "soup." Ultimately, the biological cap might have expanded into a complete cell wall, allowing mobility and colonization of energy-rich challenging environments. Electron microscopy of honeycomb channels inside weathered feldspars of the Shap granite (northwest England) has revealed modern bacteria, perhaps indicative of Archean ones. All known early rocks were metamorphosed too highly during geologic time to permit simple survival of large-pore zeolites, honeycombed feldspar, and encapsulated species. Possible microscopic clues to the proposed mineral adsorbents/catalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments.

  9. Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal–chemical modeling, formation of first cells, and geological clues

    PubMed Central

    Smith, Joseph V.; Arnold, Frederick P.; Parsons, Ian; Lee, Martin R.

    1999-01-01

    Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal–chemical modeling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular sieve silicalite-ZSM-5-(mutinaite). Calculation of binding and activation energies for catalytic assembly into polymers is progressing for a chemical composition with one catalytic Al–OH site per 25 neutral Si tetrahedral sites. Internal channel intersections and external terminations provide special stereochemical features suitable for complex organic species. Polymer migration along nano/micrometer channels of ancient weathered feldspars, plus exploitation of phosphorus and various transition metals in entrapped apatite and other microminerals, might have generated complexes of replicating catalytic biomolecules, leading to primitive cellular organisms. The first cell wall might have been an internal mineral surface, from which the cell developed a protective biological cap emerging into a nutrient-rich “soup.” Ultimately, the biological cap might have expanded into a complete cell wall, allowing mobility and colonization of energy-rich challenging environments. Electron microscopy of honeycomb channels inside weathered feldspars of the Shap granite (northwest England) has revealed modern bacteria, perhaps indicative of Archean ones. All known early rocks were metamorphosed too highly during geologic time to permit simple survival of large-pore zeolites, honeycombed feldspar, and encapsulated species. Possible microscopic clues to the proposed mineral adsorbents/catalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments. PMID:10097060

  10. One-Pot Synthesis of Fe(III)-Polydopamine Complex Nanospheres: Morphological Evolution, Mechanism, and Application of the Carbonized Hybrid Nanospheres in Catalysis and Zn-Air Battery.

    PubMed

    Ang, Jia Ming; Du, Yonghua; Tay, Boon Ying; Zhao, Chenyang; Kong, Junhua; Stubbs, Ludger Paul; Lu, Xuehong

    2016-09-13

    We report one-pot synthesis of Fe(III)-polydopamine (PDA) complex nanospheres, their structures, morphology evolution, and underlying mechanism. The complex nanospheres were synthesized by introducing ferric ions into the reaction mixture used for polymerization of dopamine. It is verified that both the oxidative polymerization of dopamine and Fe(III)-PDA complexation contribute to the "polymerization" process, in which the ferric ions form coordination bonds with both oxygen and nitrogen, as indicated by X-ray absorption fine-structure spectroscopy. In the "polymerization" process, the morphology of the complex nanostructures is gradually transformed from sheetlike to spherical at the feed Fe(III)/dopamine molar ratio of 1/3. The final size of the complex spheres is much smaller than its neat PDA counterpart. At higher feed Fe(III)/dopamine molar ratios, the final morphology of the "polymerization" products is sheetlike. The results suggest that the formation of spherical morphology is likely to be driven by covalent polymerization-induced decrease of hydrophilic functional groups, which causes reself-assembly of the PDA oligomers to reduce surface area. We also demonstrate that this one-pot synthesis route for hybrid nanospheres enables the facile construction of carbonized PDA (C-PDA) nanospheres uniformly embedded with Fe3O4 nanoparticles of only 3-5 nm in size. The C-PDA/Fe3O4 nanospheres exhibit catalytic activity toward oxygen reduction reaction and deliver a stable discharge voltage for over 200 h when utilized as the cathode in a primary Zn-air battery and are also good recyclable catalyst supports.

  11. One-Pot Synthesis of Fe(III)-Polydopamine Complex Nanospheres: Morphological Evolution, Mechanism, and Application of the Carbonized Hybrid Nanospheres in Catalysis and Zn-Air Battery.

    PubMed

    Ang, Jia Ming; Du, Yonghua; Tay, Boon Ying; Zhao, Chenyang; Kong, Junhua; Stubbs, Ludger Paul; Lu, Xuehong

    2016-09-13

    We report one-pot synthesis of Fe(III)-polydopamine (PDA) complex nanospheres, their structures, morphology evolution, and underlying mechanism. The complex nanospheres were synthesized by introducing ferric ions into the reaction mixture used for polymerization of dopamine. It is verified that both the oxidative polymerization of dopamine and Fe(III)-PDA complexation contribute to the "polymerization" process, in which the ferric ions form coordination bonds with both oxygen and nitrogen, as indicated by X-ray absorption fine-structure spectroscopy. In the "polymerization" process, the morphology of the complex nanostructures is gradually transformed from sheetlike to spherical at the feed Fe(III)/dopamine molar ratio of 1/3. The final size of the complex spheres is much smaller than its neat PDA counterpart. At higher feed Fe(III)/dopamine molar ratios, the final morphology of the "polymerization" products is sheetlike. The results suggest that the formation of spherical morphology is likely to be driven by covalent polymerization-induced decrease of hydrophilic functional groups, which causes reself-assembly of the PDA oligomers to reduce surface area. We also demonstrate that this one-pot synthesis route for hybrid nanospheres enables the facile construction of carbonized PDA (C-PDA) nanospheres uniformly embedded with Fe3O4 nanoparticles of only 3-5 nm in size. The C-PDA/Fe3O4 nanospheres exhibit catalytic activity toward oxygen reduction reaction and deliver a stable discharge voltage for over 200 h when utilized as the cathode in a primary Zn-air battery and are also good recyclable catalyst supports. PMID:27550631

  12. Adiabatic Survey of Subdwarf B Star Oscillations. III. Effects of Extreme Horizontal Branch Stellar Evolution on Pulsation Modes

    NASA Astrophysics Data System (ADS)

    Charpinet, S.; Fontaine, G.; Brassard, P.; Dorman, Ben

    2002-06-01

    We present the final results of a large, systematic survey of the adiabatic oscillation properties of models of subdwarf B (sdB) stars. This survey is aimed at providing the minimal theoretical background with which to understand the asteroseismological characteristics of the recently discovered class of pulsating sdB stars (the EC 14026 objects). In this paper, the last of a series of three, we consider the effects of stellar evolution on the pulsation eigenmodes of sdB star models. We specifically analyze the adiabatic properties of 149 equilibrium models culled from seven distinct extreme horizontal branch evolutionary sequences. Those have been chosen in order to span fully the region of parameter space where real sdB stars are found. We primarily focus on the evolution of the pulsation periods (P) and the rates of period change (dP/dt), which are both a priori observable quantities. Both the acoustic and gravity branches of stellar oscillations are considered. In light of the results derived in the first two papers of this series, we discuss how the values of P and dP/dt relate to the various structural adjustments that sdB stars undergo during evolution. We find that the acoustic modes react primarily to the secular variations of the surface gravity. In contrast, we identify three main factors that regulate the period evolution of gravity modes: these are the variations brought about by evolution in both the surface gravity and the effective temperature, as well as the onset and growth of a chemical discontinuity between the C-O-enriched nucleus and the helium-rich mantle. We also find, as expected from our previous results, that the period evolution of the pulsation modes in sdB stars is further complicated by trapping effects (microtrapping in the case of p-modes) and by avoided crossings between modes. The latter occur preferentially in certain regions of parameter space. We provide our final results in the form of extensive tabular data in the appendices

  13. A unified N-body and statistical treatment of stellar dynamics. III - Early postcollapse evolution of globular clusters

    NASA Technical Reports Server (NTRS)

    Mcmillan, S. L. W.

    1986-01-01

    The period immediately following the core collapse phase in the evolution of a globular cluster is studied using a hybrid N-body/Fokker-Planck stellar dynamical code. Several core oscillations of the type predicted in earlier work are seen. The oscillations are driven by the formation, hardening, and ejection of binaries by three-body processes, and appear to decay on a timescale of about 10 to the 7th yr, for the choice of 'typical' cluster parameters made here. There is no evidence that they are gravothermal in nature. The mechanisms responsible for the decay are discussed in some detail. The distribution of hard binaries produced by the oscillations is compared with theoretical expectations and the longer term evolution of the system is considered.

  14. Galaxy evolution in nearby galaxy groups - III. A GALEX view of NGC 5846, the largest group in the local universe

    NASA Astrophysics Data System (ADS)

    Marino, Antonietta; Mazzei, Paola; Rampazzo, Roberto; Bianchi, Luciana

    2016-06-01

    We explore the co-evolution of galaxies in nearby groups (Vhel ≤ 3000 km s-1) with a multiwavelength approach. We analyse GALEX far-UV (FUV) and near-UV (NUV) imaging, and Sloan Digital Sky Survey u, g, r, i, z data of groups spanning a large range of dynamical phases. We characterize the photometric properties of spectroscopically confirmed galaxy members and investigate the global properties of the groups through a dynamical analysis. Here, we focus on NGC 5846, the third most massive association of early-type galaxies (ETGs) after the Virgo and Fornax clusters. The group, composed of 90 members, is dominated by ETGs (about 80 per cent), and among ETGs about 40 per cent are dwarfs. Results are compared with those obtained for three groups in the LeoII cloud, which are radically different both in member-galaxy population and dynamical properties. The FUV-NUV cumulative colour distribution and the normalized UV luminosity function (LF) significantly differ due to the different fraction of late-type galaxy population. The UV LF of NGC 5846 resembles that of the Virgo cluster, however our analysis suggests that star formation episodes are still occurring in most of the group galaxies, including ETGs. The NUV-i colour distribution, the optical-UV colour-colour diagram, and NUV-r versus Mr colour-magnitude relation suggest that the gas contribution cannot be neglected in the evolution of ETG-type group members. Our analysis highlights that NGC 5846 is still in an active phase of its evolution, notwithstanding the dominance of dwarf and bright ETGs and its virialized configuration.

  15. Examining marginal sequence similarities between bacterial type III secretion system components and Trypanosoma cruzi surface proteins: horizontal gene transfer or convergent evolution?

    PubMed Central

    Silva, Danielle C. F.; Silva, Richard C.; Ferreira, Renata C.; Briones, Marcelo R. S.

    2013-01-01

    The cell invasion mechanism of Trypanosoma cruzi has similarities with some intracellular bacterial taxa especially regarding calcium mobilization. This mechanism is not observed in other trypanosomatids, suggesting that the molecules involved in this type of cell invasion were a product of (1) acquisition by horizontal gene transfer (HGT); (2) secondary loss in the other trypanosomatid lineages of the mechanism inherited since the bifurcation Bacteria-Neomura (1.9 billion to 900 million years ago); or (3) de novo evolution from non-homologous proteins via convergent evolution. Similar to T. cruzi, several bacterial genera require increased host cell cytosolic calcium for intracellular invasion. Among intracellular bacteria, the mechanism of host cell invasion of genus Salmonella is the most similar to T. cruzi. The invasion of Salmonella occurs by contact with the host's cell surface and is mediated by the type III secretion system (T3SS) that promotes the contact-dependent translocation of effector proteins directly into host's cell cytoplasm. Here we provide evidence of distant sequence similarities and structurally conserved domains between T. cruzi and Salmonella spp T3SS proteins. Exhaustive database searches were directed to a wide range of intracellular bacteria and trypanosomatids, exploring sequence patterns for comparison of structural similarities and Bayesian phylogenies. Based on our data we hypothesize that T. cruzi acquired genes for calcium mobilization mediated invasion by ancient HGT from ancestral Salmonella lineages. PMID:23967008

  16. Evolution of the dec-1 eggshell locus in Drosophila. III. Sequence comparisons of the simulans complex repeated domain reveal non-concerted evolution.

    PubMed

    Escher, S A; Lambertsson, A

    1996-01-01

    The X-linked female sterile locus dec-1 (defective chorion-1) was examined in the closely related species D. simulans, D. mauritiana, and D. sechellia (the simulans complex). This locus encodes important eggshell proteins produced in the follicle cells during stages 9 and 12 of oogenesis. In D. melanogaster four variant protein forms have been found, differing in 2-3 kDa each. The variation is due to deletions of 1, 2, or 3 units of a 5-times repeated sequence (78 bp long) of the central coding region. The same type of deletions were found in two variants of D. simulans; in this species, however, the maximum number of repeats observed so far is four. The island species D. mauritiana and D. sechellia both have the repeat sequence repeated three times. Sequence comparisons revealed that the repeats in the simulans complex have been less homogenised by the forces of concerted evolution than the repeats in D. melanogaster. Two domains of the repetitive region that evolve at different rates and are subject to different mechanisms of DNA turnover were also defined.

  17. Infrared Spectroscopic Data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE), SDSS-III Data Release 10

    DOE Data Explorer

    Sloan Digital Sky Survey (SDSS) Data Release 10 is the first spectroscopic release from the Apache Point Observatory Galactic Evolution Experiment (APOGEE), including spectra and derived stellar parameters for more than 50,000 stars. APOGEE is an ongoing survey of ~100,000 stars accessing all parts of the Milky Way. By operating in the infrared (H-band) portion of the electromagnetic spectrum, APOGEE is better able to detect light from stars lying in dusty regions of the Milky Way than surveys conducted in the optical, making this survey particularly well-suited for exploring the Galactic disk and bulge. APOGEE's high resolution spectra provide detailed information about the stellar atmospheres; DR10 provides derived effective temperatures, surface gravities, overall metallicities, and information on the abundances of several chemical elements. [copied from http://www.sdss3.org/dr10/irspec/

  18. Decomposition driven interface evolution for layers of binary mixtures. III. Two-dimensional steady films with flat and modulated surfaces

    NASA Astrophysics Data System (ADS)

    Bribesh, Fathi A. M.; Fraštia, Ľubor; Thiele, Uwe

    2012-06-01

    We study two-dimensional steady concentration and film thickness profiles for isothermal free surface films of a binary liquid mixture on a solid substrate employing model-H that couples the diffusive transport of the components of the mixture (convective Cahn-Hilliard equation) and the transport of momentum (Navier-Stokes-Korteweg equations). The analysis is based on minimising the underlying free energy equivalent to solving the static limit of model-H. Additionally, the linear stability (in time) of relevant layered films is analyzed. This allows for a comparison of the position of certain branching points in the bifurcation diagrams of steady solutions with the value predicted as onset of a linear instability. Results are presented for the cases of (i) a flat film without energetic bias at the free surface, (ii) a flat film with energetic bias, (iii) a height-modulated film without energetic bias, and (iv) a height-modulated film with energetic bias. In all cases we discuss symmetries of the various steady solutions allowing us to order them and to infer properties of solution branches and relations between them.

  19. Temporal evolution of neurophysiological and behavioral features of synapsin I/II/III triple knock-out mice.

    PubMed

    Cambiaghi, Marco; Cursi, Marco; Monzani, Elena; Benfenati, Fabio; Comi, Giancarlo; Minicucci, Fabio; Valtorta, Flavia; Leocani, Letizia

    2013-02-01

    Deletion of one or more synapsin genes in mice results in a spontaneous epilepsy. In these animals, seizures can be evoked by opening or moving the cage. Aim of the present study was to characterize the evolution of the epileptic phenotype by neurophysiological examination and behavioral observation in synapsin triple knock-out (Syn-TKO) mice. Syn-TKO mice were studied from 20 postnatal days (PND) up to 6 months of age by video-EEG recording and behavioral observation. Background EEG spectral analysis was performed and data were compared to WT animals. Syn-TKO revealed rare spontaneous seizures and increased susceptibility to evoked seizures in mice from 60 to 100 PND. Spontaneous and evoked seizures presented similar duration and morphology. At times, seizures were followed by a post-ictal phase characterized by a 4 Hz rhythmic activity and immobility of the animal. Spectral analysis of background EEG evidenced a slowing of the theta-alpha peak in Syn-TKO mice compared to WT mice within the period from PND 40 to 100. These data indicate that Syn-TKO mice do not exhibit a linear progression of the epileptic phenotype, with the period corresponding to a higher susceptibility to evoked seizures characterized by background EEG slowing. This aspect might be connected to brain dysfunction often associated to epilepsy in the interictal period.

  20. The MUSIC of Galaxy Clusters - III. Properties, evolution and Y-M scaling relation of protoclusters of galaxies

    NASA Astrophysics Data System (ADS)

    Sembolini, Federico; De Petris, Marco; Yepes, Gustavo; Foschi, Emma; Lamagna, Luca; Gottlöber, Stefan

    2014-06-01

    In this work, we study the properties of protoclusters of galaxies by employing the MultiDark SImulations of galaxy Clusters (MUSIC) set of hydrodynamical simulations, featuring a sample of 282 resimulated clusters with available merger trees up to z = 4. We study the characteristics and redshift evolution of the mass and the spatial distribution for all the protoclusters, which we define as the most massive progenitors of the clusters identified at z = 0. We extend the study of the baryon content to redshifts larger than 1 also in terms of gas and stars budgets: no remarkable variations with redshift are discovered. Furthermore, motivated by the proven potential of Sunyaev-Zel'dovich surveys to blindly search for faint distant objects, we compute the scaling relation between total object mass and integrated Compton y-parameter. We find that the slope of this scaling law is steeper than what expected for a self-similarity assumption among these objects, and it increases with redshift mainly when radiative processes are included. We use three different criteria to account for the dynamical state of the protoclusters, and find no significant dependence of the scaling parameters on the level of relaxation. We exclude the dynamical state as the cause of the observed deviations from self-similarity in protoclusters.

  1. Surface decoration of amine-rich carbon nitride with iron nanoparticles for arsenite (As(III)) uptake: The evolution of the Fe-phases under ambient conditions.

    PubMed

    Georgiou, Y; Mouzourakis, E; Bourlinos, A B; Zboril, R; Karakassides, M A; Douvalis, A P; Bakas, Th; Deligiannakis, Y

    2016-07-15

    A novel hybrid material (gC3N4-rFe) consisting of amine-rich graphitic carbon nitride (gC3N4), decorated with reduced iron nanoparticles (rFe) is presented. XRD and TEM show that gC3N4-rFe bears aggregation-free Fe-nanoparticles (10nm) uniformly dispersed over the gC3N4 surface. In contrast, non-supported iron nanoparticles are strongly aggregated, with non-uniform size distribution (20-100nm). (57)Fe-Mössbauer spectroscopy, dual-mode electron paramagnetic resonance (EPR) and magnetization measurements, allow a detailed mapping of the evolution of the Fe-phases after exposure to ambient O2. The as-prepared gC3N4-rFe bears Fe(2+) and Fe° phases, however only after long exposure to ambient O2, a Fe-oxide layer is formed around the Fe° core. In this [Fe°/Fe-oxide] core-shell configuration, the gC3N4-rFe hybrid shows enhanced As(III) uptake capacity of 76.5mgg(-1), i.e., ca 90% higher than the unmodified carbonaceous support, and 300% higher than the non-supported Fe-nanoparticles. gC3N4-rFe is a superior As(III) sorbent i.e., compared to its single counterparts or vs. graphite/graphite oxide or activated carbon analogues (11-36mgg(-1)). The present results demonstrate that the gC3N4 matrix is not simply a net that holds the particles, but rather an active component that determines particle formation dynamics and ultimately their redox profile, size and surface dispersion homogeneity.

  2. Star formation in the first galaxies - III. Formation, evolution, and characteristics of the first metal-enriched stellar cluster

    NASA Astrophysics Data System (ADS)

    Safranek-Shrader, Chalence; Montgomery, Michael H.; Milosavljević, Miloš; Bromm, Volker

    2016-01-01

    We simulate the formation of a low-metallicity (10-2 Z⊙) stellar cluster at redshift z ˜ 14. Beginning with cosmological initial conditions, the simulation utilizes adaptive mesh refinement and sink particles to follow the collapse and evolution of gas past the opacity limit for fragmentation, thus resolving the formation of individual protostellar cores. A time- and location-dependent protostellar radiation field, which heats the gas by absorption on dust, is computed by integration of protostellar evolutionary tracks. The simulation also includes a robust non-equilibrium chemical network that self-consistently treats gas thermodynamics and dust-gas coupling. The system is evolved for 18 kyr after the first protostellar source has formed. In this time span, 30 sink particles representing protostellar cores form with a total mass of 81 M⊙. Their masses range from ˜0.1 to 14.4 M⊙ with a median mass ˜0.5-1 M⊙. Massive protostars grow by competitive accretion while lower mass protostars are stunted in growth by close encounters and many-body ejections. In the regime explored here, the characteristic mass scale is determined by the cosmic microwave background temperature floor and the onset of efficient dust-gas coupling. It seems unlikely that host galaxies of the first bursts of metal-enriched star formation will be detectable with the James Webb Space Telescope or other next-generation infrared observatories. Instead, the most promising access route to the dawn of cosmic star formation may lie in the scrutiny of metal-poor, ancient stellar populations in the Galactic neighbourhood. The observable targets corresponding to the system simulated here are ultra-faint dwarf satellite galaxies such as Boötes II and Willman I.

  3. Biochemical comparison of major histocompatibility complex molecules from different subspecies of Mus musculus: evidence for trans-specific evolution of alleles.

    PubMed

    Arden, B; Klein, J

    1982-04-01

    H-2 haplotypes were extracted from wild mice of three subspecies, Mus musculus domesticus, M. m. molossinus, and M. m. castaneus, that are known to have been separated from one another for some 1 to 2 million years. Serologically indistinguishable molecules controlled by some of the polymorphic H-2 loci were compared by tryptic peptide mapping, and the maps were found to be identical. In addition, a number of instances of biochemically indistinguishable H-2 molecules were found among wild mice and inbred strains of the M. m. domesticus subspecies. These findings suggest that some of the H-2 alleles have not altered for greater than 1 million years. To reconcile this apparent stability of H-2 genes with their extraordinary polymorphism (some 100 alleles at each of the polymorphic H-2 loci), it is proposed that the H-2 alleles evolve as if they were separate loci.

  4. Chemical weathering rates of a soil chronosequence on granitic alluvium: III. Hydrochemical evolution and contemporary solute fluxes and rates

    USGS Publications Warehouse

    White, A.F.; Schulz, M.S.; Vivit, D.V.; Blum, A.E.; Stonestrom, D.A.; Harden, J.W.

    2005-01-01

    Although long-term changes in solid-state compositions of soil chronosequences have been extensively investigated, this study presents the first detailed description of the concurrent hydrochemical evolution and contemporary weathering rates in such sequences. The most direct linkage between weathering and hydrology over 3 million years of soil development in the Merced chronosequence in Central California relates decreasing permeability and increasing hydrologic heterogeneity to the development of secondary argillic horizons and silica duripans. In a highly permeable, younger soil (40 kyr old), pore water solutes reflect seasonal to decadal-scale variations in rainfall and evapotranspiration (ET). This climate signal is strongly damped in less permeable older soils (250 to 600 kyr old) where solutes increasingly reflect weathering inputs modified by heterogeneous flow. Elemental balances in the soils are described in terms of solid state, exchange and pore water reservoirs and input/output fluxes from precipitation, ET, biomass, solute discharge and weathering. Solute mineral nutrients are strongly dependent on biomass variations as evidenced by an apparent negative K weathering flux reflecting aggradation by grassland plants. The ratios of solute Na to other base cations progressively increase with soil age. Discharge fluxes of Na and Si, when integrated over geologic time, are comparable to solid-state mass losses in the soils, implying similar past weathering conditions. Similarities in solute and sorbed Ca/Mg ratios reflect short-term equilibrium with the exchange reservoir. Long-term consistency in solute ratios, when contrasted against progressive decreases in solid-state Ca/Mg, requires an additional Ca source, probably from dry deposition. Amorphous silica precipitates from thermodynamically-saturated pore waters during periods of high evapotranspiration and result in the formation of duripans in the oldest soils. The degree of feldspar and secondary

  5. Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3).

    PubMed

    Elahi, Montasir; Islam, Monirul M; Noguchi, Keiichi; Yohda, Masafumi; Toh, Hiroyuki; Kuroda, Yutaka

    2014-03-01

    Dengue viruses (DEN) are classified into four serotypes (DEN1-DEN4) exhibiting high sequence and structural similarities, and infections by multiple serotypes can lead to the deadly dengue hemorrhagic fever. Here, we aim at characterizing the thermodynamic stability of DEN envelope protein domain III (ED3) during its evolution, and we report a structural analysis of DEN4wt ED3 combined with a systematic mutational analysis of residues 310 and 387. Molecular modeling based on our DEN3 and DEN4 ED3 structures indicated that the side-chains of residues 310/387, which are Val(310)/Ile(387) and Met(310)/Leu(387) in DEN3wt and DEN4wt, respectively, could be structurally compensated, and that a "size switch type repacking" might have occurred at these sites during the evolution of DEN into its four serotypes. This was experimentally confirmed by a 10°C and 5°C decrease in the thermal stability of, respectively, DEN3 ED3 variants with Met(310)/Ile(387) and Val(310)/Leu(387), whereas the variant with Met(310)/Leu(387), which contains a double mutation, had the same stability as the wild type DEN3. Namely, the Met310Val mutation should have preceded the Leu387Ile mutation in order to maintain the tight internal packing of ED3 and thus its thermodynamic stability. This view was confirmed by a phylogenetic reconstruction indicating that a common DEN ancestor would have Met(310)/Leu(387), and the intermediate node protein, Val(310)/Leu(387), which then mutated to the Val(310)/Ile(387) pair found in the present DEN3. The hypothesis was further confirmed by the observation that all of the present DEN viruses exhibit only stabilizing amino acid pairs at the 310/387 sites.

  6. THE TENTH DATA RELEASE OF THE SLOAN DIGITAL SKY SURVEY: FIRST SPECTROSCOPIC DATA FROM THE SDSS-III APACHE POINT OBSERVATORY GALACTIC EVOLUTION EXPERIMENT

    SciTech Connect

    Ahn, Christopher P.; Anderton, Timothy; Alexandroff, Rachael; Allende Prieto, Carlos; Anderson, Scott F.; Bhardwaj, Vaishali; Andrews, Brett H.; Aubourg, Éric; Bautista, Julian E.; Bastien, Fabienne A.; Berlind, Andreas A.; Bird, Jonathan C.; Beers, Timothy C.; Beifiori, Alessandra; Bender, Chad F.; Bizyaev, Dmitry; Blake, Cullen H.; and others

    2014-04-01

    The Sloan Digital Sky Survey (SDSS) has been in operation since 2000 April. This paper presents the Tenth Public Data Release (DR10) from its current incarnation, SDSS-III. This data release includes the first spectroscopic data from the Apache Point Observatory Galaxy Evolution Experiment (APOGEE), along with spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS) taken through 2012 July. The APOGEE instrument is a near-infrared R ∼ 22,500 300 fiber spectrograph covering 1.514-1.696 μm. The APOGEE survey is studying the chemical abundances and radial velocities of roughly 100,000 red giant star candidates in the bulge, bar, disk, and halo of the Milky Way. DR10 includes 178,397 spectra of 57,454 stars, each typically observed three or more times, from APOGEE. Derived quantities from these spectra (radial velocities, effective temperatures, surface gravities, and metallicities) are also included. DR10 also roughly doubles the number of BOSS spectra over those included in the Ninth Data Release. DR10 includes a total of 1,507,954 BOSS spectra comprising 927,844 galaxy spectra, 182,009 quasar spectra, and 159,327 stellar spectra selected over 6373.2 deg{sup 2}.

  7. The spectroscopic evolution of the recurrent nova T Pyxidis during its 2011 outburst. III. The ultraviolet development from iron curtain through the post-X-ray turnoff

    NASA Astrophysics Data System (ADS)

    De Gennaro Aquino, I.; Shore, S. N.; Schwarz, G. J.; Mason, E.; Starrfield, S.; Sion, E. M.

    2014-02-01

    We continue the analysis of the multiwavelength evolution of the recurrent nova T Pyx during its 2011 outburst, focussing on the spectral development on the 1150-3000 Å region. This extraordinary data set presents the longest temporal baseline high resolution view of the ultraviolet for any nova to date (classical or recurrent). The observations cover the early Fe-curtain stage, when the UV was completely optically thick, to 834 days after discovery when the outburst was effectively over. We present an analysis of dynamics and abundances of the interstellar species whose resonance lines are accessible in the UV. The Lyα profile is consistent with only interstellar absorption at all epochs and agrees with the H I 21 cm column density. The distance obtained to T Pyx is about 5 kpc, based on the ISM analysis. For the ejecta evolution we have been able to follow the changes in ionization and structure with previously unobtained resolution and cadence. The excited state isoelectronic transitions of C III, N IV], and O V displayed the same detached absorption lines as the optical He I transitions during the optical maximum. This is explained as resonance absorption within the ejecta of FUV ground state lines from the 300-1000 Å range. The resonance lines of all species showed absorption components between -1000 and -3000 km s-1 as soon as the Fe-curtain turned transparent (from day 105); these persisted at the same velocities and varied in strength from one ion to another through day 834. The last ultraviolet spectrum, taken more than 800 days after outburst, showed the same absorption lines on N V and C IV as day 105. There was no evidence of circumstellar absorbers. This and the related observations of profile evolution effectively rule out any wind model for the spectrum. The picture that emerges is of ejecta that became optically thin after visual maximum as the X-ray emission became visible following an outwardly propagating ionization front and for which the

  8. Structure and Activity Analyses of Escherichia coli K-12 NagD Provide Insight into the Evolution of Biochemical Function in the Haloakanoic Acid Dehlogenase Superfamily

    SciTech Connect

    Tremblay,L.; Dunaway-Mariano, D.; Allen, K.

    2006-01-01

    The HAD superfamily is a large superfamily of proteins which share a conserved core domain that provides those active site residues responsible for the chemistry common to all family members. The superfamily is further divided into the four subfamilies I, IIA, IIB, and III, based on the topology and insertion site of a cap domain that provides substrate specificity. This structural and functional division implies that members of a given HAD structural subclass may target substrates that have similar structural characteristics. To understand the structure/function relationships in all of the subfamilies, a type IIA subfamily member, NagD from Escherichia coli K-12, was selected (type I, IIB, and III members have been more extensively studied). The structure of the NagD protein was solved to 1.80 Angstroms with R{sub work} = 19.8% and R{sub free} = 21.8%. Substrate screening and kinetic analysis showed NagD to have high specificity for nucleotide monophosphates with kcat/Km = 3.12 x 10{sup 4} and 1.28 x 10{sup 4} {micro}M{sup -1} s{sup -1} for UMP and GMP, respectively. This specificity is consistent with the presence of analogues of NagD that exist as fusion proteins with a nucleotide pyrophosphatase from the Nudix family. Docking of the nucleoside substrate in the active site brings it in contact with conserved residues from the cap domain that can act as a substrate specificity loop (NagD residues 144-149) in the type IIA subfamily. NagD and other subfamily IIA and IIB members show the common trait that substrate specificity and catalytic efficiencies (k{sub cat}/K{sub m}) are low (1 x 10{sup 4} M{sup -1} s{sup -1}) and the boundaries defining physiological substrates are somewhat overlapping. The ability to catabolize other related secondary metabolites indicates that there is regulation at the genetic level.

  9. Biochemical, transcriptomic and proteomic analyses of digestion in the scorpion Tityus serrulatus: insights into function and evolution of digestion in an ancient arthropod.

    PubMed

    Fuzita, Felipe J; Pinkse, Martijn W H; Patane, José S L; Juliano, Maria A; Verhaert, Peter D E M; Lopes, Adriana R

    2015-01-01

    Scorpions are among the oldest terrestrial arthropods and they have passed through small morphological changes during their evolutionary history on land. They are efficient predators capable of capturing and consuming large preys and due to envenomation these animals can become a human health challenge. Understanding the physiology of scorpions can not only lead to evolutionary insights but also is a crucial step in the development of control strategies. However, the digestive process in scorpions has been scarcely studied. In this work, we describe the combinatory use of next generation sequencing, proteomic analysis and biochemical assays in order to investigate the digestive process in the yellow scorpion Tityus serrulatus, mainly focusing in the initial protein digestion. The transcriptome generated database allowed the quantitative identification by mass spectrometry of different enzymes and proteins involved in digestion. All the results suggested that cysteine cathepsins play an important role in protein digestion. Two digestive cysteine cathepsins were isolated and characterized presenting acidic characteristics (pH optima and stability), zymogen conversion to the mature form after acidic activation and a cross-class inhibition by pepstatin. A more elucidative picture of the molecular mechanism of digestion in a scorpion was proposed based on our results from Tityus serrulatus. The midgut and midgut glands (MMG) are composed by secretory and digestive cells. In fasting animals, the secretory granules are ready for the next predation event, containing enzymes needed for alkaline extra-oral digestion which will compose the digestive fluid, such as trypsins, astacins and chitinase. The digestive vacuoles are filled with an acidic proteolytic cocktail to the intracellular digestion composed by cathepsins L, B, F, D and legumain. Other proteins as lipases, carbohydrases, ctenitoxins and a chitolectin with a perithrophin domain were also detected. Evolutionarily

  10. Biochemical, transcriptomic and proteomic analyses of digestion in the scorpion Tityus serrulatus: insights into function and evolution of digestion in an ancient arthropod.

    PubMed

    Fuzita, Felipe J; Pinkse, Martijn W H; Patane, José S L; Juliano, Maria A; Verhaert, Peter D E M; Lopes, Adriana R

    2015-01-01

    Scorpions are among the oldest terrestrial arthropods and they have passed through small morphological changes during their evolutionary history on land. They are efficient predators capable of capturing and consuming large preys and due to envenomation these animals can become a human health challenge. Understanding the physiology of scorpions can not only lead to evolutionary insights but also is a crucial step in the development of control strategies. However, the digestive process in scorpions has been scarcely studied. In this work, we describe the combinatory use of next generation sequencing, proteomic analysis and biochemical assays in order to investigate the digestive process in the yellow scorpion Tityus serrulatus, mainly focusing in the initial protein digestion. The transcriptome generated database allowed the quantitative identification by mass spectrometry of different enzymes and proteins involved in digestion. All the results suggested that cysteine cathepsins play an important role in protein digestion. Two digestive cysteine cathepsins were isolated and characterized presenting acidic characteristics (pH optima and stability), zymogen conversion to the mature form after acidic activation and a cross-class inhibition by pepstatin. A more elucidative picture of the molecular mechanism of digestion in a scorpion was proposed based on our results from Tityus serrulatus. The midgut and midgut glands (MMG) are composed by secretory and digestive cells. In fasting animals, the secretory granules are ready for the next predation event, containing enzymes needed for alkaline extra-oral digestion which will compose the digestive fluid, such as trypsins, astacins and chitinase. The digestive vacuoles are filled with an acidic proteolytic cocktail to the intracellular digestion composed by cathepsins L, B, F, D and legumain. Other proteins as lipases, carbohydrases, ctenitoxins and a chitolectin with a perithrophin domain were also detected. Evolutionarily

  11. Biochemical, Transcriptomic and Proteomic Analyses of Digestion in the Scorpion Tityus serrulatus: Insights into Function and Evolution of Digestion in an Ancient Arthropod

    PubMed Central

    Fuzita, Felipe J.; Pinkse, Martijn W. H.; Patane, José S. L.; Juliano, Maria A.; Verhaert, Peter D. E. M.; Lopes, Adriana R.

    2015-01-01

    Scorpions are among the oldest terrestrial arthropods and they have passed through small morphological changes during their evolutionary history on land. They are efficient predators capable of capturing and consuming large preys and due to envenomation these animals can become a human health challenge. Understanding the physiology of scorpions can not only lead to evolutionary insights but also is a crucial step in the development of control strategies. However, the digestive process in scorpions has been scarcely studied. In this work, we describe the combinatory use of next generation sequencing, proteomic analysis and biochemical assays in order to investigate the digestive process in the yellow scorpion Tityus serrulatus, mainly focusing in the initial protein digestion. The transcriptome generated database allowed the quantitative identification by mass spectrometry of different enzymes and proteins involved in digestion. All the results suggested that cysteine cathepsins play an important role in protein digestion. Two digestive cysteine cathepsins were isolated and characterized presenting acidic characteristics (pH optima and stability), zymogen conversion to the mature form after acidic activation and a cross-class inhibition by pepstatin. A more elucidative picture of the molecular mechanism of digestion in a scorpion was proposed based on our results from Tityus serrulatus. The midgut and midgut glands (MMG) are composed by secretory and digestive cells. In fasting animals, the secretory granules are ready for the next predation event, containing enzymes needed for alkaline extra-oral digestion which will compose the digestive fluid, such as trypsins, astacins and chitinase. The digestive vacuoles are filled with an acidic proteolytic cocktail to the intracellular digestion composed by cathepsins L, B, F, D and legumain. Other proteins as lipases, carbohydrases, ctenitoxins and a chitolectin with a perithrophin domain were also detected. Evolutionarily

  12. Evolution of the H β + [O III] and [O II] luminosity functions and the [O II] star formation history of the Universe up to z ˜ 5 from HiZELS

    NASA Astrophysics Data System (ADS)

    Khostovan, A. A.; Sobral, D.; Mobasher, B.; Best, P. N.; Smail, I.; Stott, J. P.; Hemmati, S.; Nayyeri, H.

    2015-10-01

    We investigate the evolution of the H β + [O III] and [O II] luminosity functions from z ˜ 0.8 to ˜5 in four redshift slices per emission line using data from the High-z Emission Line Survey (HiZELS). This is the first time that the H β + [O III] and [O II] luminosity functions have been studied at these redshifts in a self-consistent analysis. This is also the largest sample of [O II] and H β + [O III] emitters (3475 and 3298 emitters, respectively) in this redshift range, with large comoving volumes ˜1 × 106 Mpc-3 in two independent volumes (COSMOS and UDS), greatly reducing the effects of cosmic variance. The emitters were selected by a combination of photometric redshift and colour-colour selections, as well as spectroscopic follow-up, including recent spectroscopic observations using DEIMOS and MOSFIRE on the Keck Telescopes and FMOS on Subaru. We find a strong increase in L⋆ and a decrease in φ⋆ for both H β + [O III] and [O II] emitters. We derive the [O II] star formation history of the Universe since z ˜ 5 and find that the cosmic star formation rate density (SFRD) rises from z ˜ 5 to ˜3 and then drops towards z ˜ 0. We also find that our star formation history is able to reproduce the evolution of the stellar mass density up to z ˜ 5 based only on a single tracer of star formation. When comparing the H β + [O III] SFRDs to the [O II] and H α SFRD measurements in the literature, we find that there is a remarkable agreement, suggesting that the H β + [O III] sample is dominated by star-forming galaxies at high-z rather than AGNs.

  13. Evolution of TEM-Type Enzymes: Biochemical and Genetic Characterization of Two New Complex Mutant TEM Enzymes, TEM-151 and TEM-152, from a Single Patient▿ †

    PubMed Central

    Robin, Frédéric; Delmas, Julien; Schweitzer, Cédric; Tournilhac, Olivier; Lesens, Olivier; Chanal, Catherine; Bonnet, Richard

    2007-01-01

    Two clinical isolates of Escherichia coli, CF1179 and CF1295, were isolated from a patient hospitalized in the hematology unit of the University Hospital of Clermont-Ferrand, Clermont-Ferrand, France. They were resistant to penicillin-clavulanate combinations and to ceftazidime. The double-disk synergy test was positive only for isolate CF1179. Molecular comparison of the isolates showed that they were clonally related. E. coli recombinant strains exhibiting the resistance phenotype of the clinical strains were obtained by cloning. The clones corresponding to strains CF1179 and CF1295 produced TEM-type beta-lactamases with pI values of 5.7 and 5.3, respectively. Sequencing analysis revealed two novel blaTEM genes encoding closely related complex mutant TEM enzymes, designated TEM-151 (pI 5.3) and TEM-152 (pI 5.7). These two genes also harbored a new promoter region which presented a 9-bp deletion. The two novel β-lactamases differed from the parental enzyme, TEM-1, by the substitution Arg164His, previously observed in extended-spectrum beta-lactamases (ESBLs), and by the substitutions Met69Val and Asn276Asp, previously observed in the inhibitor-resistant penicillinase TEM-36/IRT-7. They differed by two amino acid substitutions: TEM-152 harbored a Glu240Lys ESBL-type substitution and TEM-151 had an Ala284Gly substitution. Functional analysis of TEM-151 and TEM-152 showed that both enzymes had hydrolytic activity against ceftazidime (kcat, 5 and 16 s−1, respectively). TEM-152 was more resistant than TEM-151 to the inhibitor clavulanic acid (50% inhibitory concentrations, 1 versus 0.17 μM). These results confirm the evolution of TEM-type enzymes toward complex enzymes harboring the two kinds of substitutions which confer an extended spectrum of action against beta-lactam antibiotics and resistance to inhibitors. PMID:17220412

  14. Biochemical adaptation to ocean acidification.

    PubMed

    Stillman, Jonathon H; Paganini, Adam W

    2015-06-01

    The change in oceanic carbonate chemistry due to increased atmospheric PCO2  has caused pH to decline in marine surface waters, a phenomenon known as ocean acidification (OA). The effects of OA on organisms have been shown to be widespread among diverse taxa from a wide range of habitats. The majority of studies of organismal response to OA are in short-term exposures to future levels of PCO2 . From such studies, much information has been gathered on plastic responses organisms may make in the future that are beneficial or harmful to fitness. Relatively few studies have examined whether organisms can adapt to negative-fitness consequences of plastic responses to OA. We outline major approaches that have been used to study the adaptive potential for organisms to OA, which include comparative studies and experimental evolution. Organisms that inhabit a range of pH environments (e.g. pH gradients at volcanic CO2 seeps or in upwelling zones) have great potential for studies that identify adaptive shifts that have occurred through evolution. Comparative studies have advanced our understanding of adaptation to OA by linking whole-organism responses with cellular mechanisms. Such optimization of function provides a link between genetic variation and adaptive evolution in tuning optimal function of rate-limiting cellular processes in different pH conditions. For example, in experimental evolution studies of organisms with short generation times (e.g. phytoplankton), hundreds of generations of growth under future conditions has resulted in fixed differences in gene expression related to acid-base regulation. However, biochemical mechanisms for adaptive responses to OA have yet to be fully characterized, and are likely to be more complex than simply changes in gene expression or protein modification. Finally, we present a hypothesis regarding an unexplored area for biochemical adaptation to ocean acidification. In this hypothesis, proteins and membranes exposed to the

  15. THE SPECTRAL EVOLUTION OF THE FIRST GALAXIES. I. JAMES WEBB SPACE TELESCOPE DETECTION LIMITS AND COLOR CRITERIA FOR POPULATION III GALAXIES

    SciTech Connect

    Zackrisson, Erik; Rydberg, Claes-Erik; Oestlin, Goeran; Tuli, Manan; Schaerer, Daniel

    2011-10-10

    The James Webb Space Telescope (JWST) is expected to revolutionize our understanding of the high-redshift universe, and may be able to test the prediction that the first, chemically pristine (Population III) stars are formed with very high characteristic masses. Since isolated Population III stars are likely to be beyond the reach of JWST, small Population III galaxies may offer the best prospects of directly probing the properties of metal-free stars. Here, we present Yggdrasil, a new spectral synthesis code geared toward the first galaxies. Using this model, we explore the JWST imaging detection limits for Population III galaxies and investigate to what extent such objects may be identified based on their JWST colors. We predict that JWST should be able to detect Population III galaxies with stellar population masses as low as {approx}10{sup 5} M{sub sun} at z {approx} 10 in ultra deep exposures. Over limited redshift intervals, it may also be possible to use color criteria to select Population III galaxy candidates for follow-up spectroscopy. The colors of young Population III galaxies dominated by direct starlight can be used to probe the stellar initial mass function (IMF), but this requires almost complete leakage of ionizing photons into the intergalactic medium. The colors of objects dominated by nebular emission show no corresponding IMF sensitivity. We also note that a clean selection of Population III galaxies at z {approx} 7-8 can be achieved by adding two JWST/MIRI filters to the JWST/NIRCam filter sets usually discussed in the context of JWST ultra deep fields.

  16. The Spectral Evolution of the First Galaxies. I. James Webb Space Telescope Detection Limits and Color Criteria for Population III Galaxies

    NASA Astrophysics Data System (ADS)

    Zackrisson, Erik; Rydberg, Claes-Erik; Schaerer, Daniel; Östlin, Göran; Tuli, Manan

    2011-10-01

    The James Webb Space Telescope (JWST) is expected to revolutionize our understanding of the high-redshift universe, and may be able to test the prediction that the first, chemically pristine (Population III) stars are formed with very high characteristic masses. Since isolated Population III stars are likely to be beyond the reach of JWST, small Population III galaxies may offer the best prospects of directly probing the properties of metal-free stars. Here, we present Yggdrasil, a new spectral synthesis code geared toward the first galaxies. Using this model, we explore the JWST imaging detection limits for Population III galaxies and investigate to what extent such objects may be identified based on their JWST colors. We predict that JWST should be able to detect Population III galaxies with stellar population masses as low as ~105 M sun at z ≈ 10 in ultra deep exposures. Over limited redshift intervals, it may also be possible to use color criteria to select Population III galaxy candidates for follow-up spectroscopy. The colors of young Population III galaxies dominated by direct starlight can be used to probe the stellar initial mass function (IMF), but this requires almost complete leakage of ionizing photons into the intergalactic medium. The colors of objects dominated by nebular emission show no corresponding IMF sensitivity. We also note that a clean selection of Population III galaxies at z ≈ 7-8 can be achieved by adding two JWST/MIRI filters to the JWST/NIRCam filter sets usually discussed in the context of JWST ultra deep fields.

  17. Biochemical Education in Thailand: Past, Present, and Future.

    ERIC Educational Resources Information Center

    Svasti, Jisnuson; Surarit, Rudee

    1991-01-01

    Traces the history of Thailand's biochemical education from its initial evolution from medicine to modern day. Discusses the following aspects of Thailand's modern biochemical education: biochemistry teaching at Thai schools, university departments and biochemistry courses, textbooks, degree programs, interplay between research and teaching, and…

  18. Biochemical transformation of coals

    DOEpatents

    Lin, Mow S.; Premuzic, Eugene T.

    1999-03-23

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

  19. Biochemical transformation of coals

    DOEpatents

    Lin, M.S.; Premuzic, E.T.

    1999-03-23

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed. 7 figs.

  20. SAGE III

    Atmospheric Science Data Center

    2016-06-15

    SAGE III Data and Information The Stratospheric Aerosol and Gas ... on the spacecraft. SAGE III produced L1 and L2 scientific data from 5/07/2002 until 12/31/2005. The flight of the second instrument is as ... Guide Documents:  Project Guide Data Products User's Guide  (PDF) Relevant Documents:  ...

  1. Early bioenergetic evolution

    PubMed Central

    Sousa, Filipa L.; Thiergart, Thorsten; Landan, Giddy; Nelson-Sathi, Shijulal; Pereira, Inês A. C.; Allen, John F.; Lane, Nick; Martin, William F.

    2013-01-01

    Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood–Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type ‘reduced iron → reduced carbon’ at the beginning of bioenergetic evolution

  2. Systems biology and the origins of life? part II. Are biochemical networks possible ancestors of living systems? networks of catalysed chemical reactions: non-equilibrium, self-organization and evolution.

    PubMed

    Ricard, Jacques

    2010-01-01

    The present article discusses the possibility that catalysed chemical networks can evolve. Even simple enzyme-catalysed chemical reactions can display this property. The example studied is that of a two-substrate proteinoid, or enzyme, reaction displaying random binding of its substrates A and B. The fundamental property of such a system is to display either emergence or integration depending on the respective values of the probabilities that the enzyme has bound one of its substrate regardless it has bound the other substrate, or, specifically, after it has bound the other substrate. There is emergence of information if p(A)>p(AB) and p(B)>p(BA). Conversely, if p(A)evolution. Defined as open non-equilibrium structures, such biochemical networks possess two remarkable properties: (1) the probability of occurrence of their nodes is dependant upon the input and output of matter

  3. Biochemical Engineering Fundamentals

    ERIC Educational Resources Information Center

    Bailey, J. E.; Ollis, D. F.

    1976-01-01

    Discusses a biochemical engineering course that is offered as part of a chemical engineering curriculum and includes topics that influence the behavior of man-made or natural microbial or enzyme reactors. (MLH)

  4. Biochemical Education in Leisure.

    ERIC Educational Resources Information Center

    Tayyab, Saad

    1994-01-01

    Presents two alternative teaching approaches to ensure that students become active participants of learning in the biochemistry classroom. Diagrams and rules are provided for using educational playing cards and creating a biochemical comic book. (ZWH)

  5. The evolution of the [O II], H β and [O III] emission line luminosity functions over the last nine billions years

    NASA Astrophysics Data System (ADS)

    Comparat, Johan; Zhu, Guangtun; Gonzalez-Perez, Violeta; Norberg, Peder; Newman, Jeffrey; Tresse, Laurence; Richard, Johan; Yepes, Gustavo; Kneib, Jean-Paul; Raichoor, Anand; Prada, Francisco; Maraston, Claudia; Yèche, Christophe; Delubac, Timothée; Jullo, Eric

    2016-09-01

    Emission line galaxies are one of the main tracers of the large-scale structure to be targeted by the next-generation dark energy surveys. To provide a better understanding of the properties and statistics of these galaxies, we have collected spectroscopic data from the VVDS and DEEP2 deep surveys and estimated the galaxy luminosity functions (LFs) of three distinct emission lines, [O II}] (λ λ 3726,3729) (0.5 < z < 1.3), Hβ (λ4861) (0.3 < z < 0.8) and [O {III}] (λ 5007) (0.3 < z < 0.8). Our measurements are based on 35 639 emission line galaxies and cover a volume of ˜107 Mpc3. We present the first measurement of the Hβ LF at these redshifts. We have also compiled LFs from the literature that were based on independent data or covered different redshift ranges, and we fit the entire set over the whole redshift range with analytic Schechter and Saunders models, assuming a natural redshift dependence of the parameters. We find that the characteristic luminosity (L*) and density (φ*) of all LFs increase with redshift. Using the Schechter model over the redshift ranges considered, we find that, for [O {II}] emitters, the characteristic luminosity L*(z = 0.5) = 3.2 × 1041 erg s-1 increases by a factor of 2.7 ± 0.2 from z = 0.5 to 1.3; for Hβ emitters L*(z = 0.3) = 1.3 × 1041 erg s-1 increases by a factor of 2.0 ± 0.2 from z = 0.3 to 0.8; and for [O {III}] emitters L*(z = 0.3) = 7.3 × 1041 erg s-1 increases by a factor of 3.5 ± 0.4 from z = 0.3 to 0.8.

  6. Star formation properties in barred galaxies. III. Statistical study of bar-driven secular evolution using a sample of nearby barred spirals

    SciTech Connect

    Zhou, Zhi-Min; Wu, Hong; Cao, Chen E-mail: hwu@bao.ac.cn

    2015-01-01

    Stellar bars are important internal drivers of secular evolution in disk galaxies. Using a sample of nearby spiral galaxies with weak and strong bars, we explore the relationships between the star formation feature and stellar bars in galaxies. We find that galaxies with weak bars tend coincide with low concentrical star formation activity, while those with strong bars show a large scatter in the distribution of star formation activity. We find enhanced star formation activity in bulges toward stronger bars, although not predominantly, consistent with previous studies. Our results suggest that different stages of the secular process and many other factors may contribute to the complexity of the secular evolution. In addition, barred galaxies with intense star formation in bars tend to have active star formation in their bulges and disks, and bulges have higher star formation densities than bars and disks, indicating the evolutionary effects of bars. We then derived a possible criterion to quantify the different stages of the bar-driven physical process, while future work is needed because of the uncertainties.

  7. Welding III.

    ERIC Educational Resources Information Center

    Allegheny County Community Coll., Pittsburgh, PA.

    Instructional objectives and performance requirements are outlined in this course guide for Welding III, an advanced course in arc welding offered at the Community College of Allegheny County to provide students with the proficiency necessary for industrial certification. The course objectives, which are outlined first, specify that students will…

  8. Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

    NASA Technical Reports Server (NTRS)

    Nakayama, S.; Kretsinger, R. H.

    1993-01-01

    In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

  9. Evolution of long-lived globular cluster stars. III. Effect of the initial helium spread on the position of stars in a synthetic Hertzsprung-Russell diagram

    NASA Astrophysics Data System (ADS)

    Chantereau, W.; Charbonnel, C.; Meynet, G.

    2016-08-01

    Context. Globular clusters host multiple populations of long-lived low-mass stars whose origin remains an open question. Several scenarios have been proposed to explain the associated photometric and spectroscopic peculiarities. They differ, for instance, in the maximum helium enrichment they predict for stars of the second population, which these stars can inherit at birth as the result of the internal pollution of the cluster by different types of stars of the first population. Aims: We present the distribution of helium-rich stars in present-day globular clusters as it is expected in the original framework of the fast-rotating massive stars scenario (FRMS) as first-population polluters. We focus on NGC 6752. Methods: We completed a grid of 330 stellar evolution models for globular cluster low-mass stars computed with different initial chemical compositions corresponding to the predictions of the original FRMS scenario for [Fe/H] = -1.75. Starting from the initial helium-sodium relation that allows reproducing the currently observed distribution of sodium in NGC 6752, we deduce the helium distribution expected in that cluster at ages equal to 9 and 13 Gyr. We distinguish the stars that are moderately enriched in helium from those that are very helium-rich (initial helium mass fraction below and above 0.4, respectively), and compare the predictions of the FRMS framework with other scenarios for globular cluster enrichment. Results: The effect of helium enrichment on the stellar lifetime and evolution reduces the total number of very helium-rich stars that remain in the cluster at 9 and 13 Gyr to only 12% and 10%, respectively, from an initial fraction of 21%. Within this age range, most of the stars still burn their hydrogen in their core, which widens the MS band significantly in effective temperature. The fraction of very helium-rich stars drops in the more advanced evolution phases, where the associated spread in effective temperature strongly decreases. These

  10. A stochastic Monte Carlo approach to modelling real star cluster evolution - III. Direct integration of three- and four-body interactions

    NASA Astrophysics Data System (ADS)

    Giersz, M.; Spurzem, R.

    2003-08-01

    Spherically symmetric equal-mass star clusters containing a large number of primordial binaries are studied using a hybrid method, consisting of a gas dynamical model for single stars and a Monte Carlo treatment for relaxation of binaries and the setup of close resonant and fly-by encounters of single stars with binaries and binaries with each other (three- and four-body encounters). What differs from our previous work is that each encounter is being integrated using a highly accurate direct few-body integrator which uses regularized variables. Hence we can study the systematic evolution of individual binary orbital parameters (eccentricity, semimajor axis) and differential and total cross-sections for hardening, dissolution or merging of binaries (minimum distance) from a sampling of several tens of thousands of scattering events as they occur in real cluster evolution, including mass segregation of binaries, gravothermal collapse and re-expansion, a binary burning phase and ultimately gravothermal oscillations. For the first time we are able to present empirical cross-sections for eccentricity variation of binaries in close three- and four-body encounters. It is found that a large fraction of three- and four-body encounters result in merging. Eccentricities are generally increased in strong three- and four-body encounters and there is a characteristic scaling law ~ exp (4efin) of the differential cross-section for eccentricity changes, where efin is the final eccentricity of the binary, or harder binary for four-body encounters. Despite these findings the overall eccentricity distribution remains thermal for all binding energies of binaries, which is understood from the dominant influence of resonant encounters. Previous cross-sections obtained by Spitzer and Gao for strong encounters can be reproduced, while for weak encounters non-standard processes such as the formation of hierarchical triples occur.

  11. Measures of Biochemical Sociology

    ERIC Educational Resources Information Center

    Snell, Joel; Marsh, Mitchell

    2008-01-01

    In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

  12. Biochemical Education in Brazil.

    ERIC Educational Resources Information Center

    Vella, F.

    1988-01-01

    Described are discussions held concerning the problems of biochemical education in Brazil at a meeting of the Sociedade Brazileira de Bioquimica in April 1988. Also discussed are other visits that were made to universities in Brazil. Three major recommendations to improve the state of biochemistry education in Brazil are presented. (CW)

  13. Biochemical upgrading of oils

    DOEpatents

    Premuzic, E.T.; Lin, M.S.

    1999-01-12

    A process for biochemical conversion of heavy crude oils is provided. The process includes contacting heavy crude oils with adapted biocatalysts. The resulting upgraded oil shows, a relative increase in saturated hydrocarbons, emulsions and oxygenates and a decrease in compounds containing organic sulfur, organic nitrogen and trace metals. Adapted microorganisms which have been modified under challenged growth processes are also disclosed. 121 figs.

  14. Nanoparticles as biochemical sensors

    PubMed Central

    El-Ansary, Afaf; Faddah, Layla M

    2010-01-01

    There is little doubt that nanoparticles offer real and new opportunities in many fields, such as biomedicine and materials science. Such particles are small enough to enter almost all areas of the body, including cells and organelles, potentially leading to new approaches in nanomedicine. Sensors for small molecules of biochemical interest are of critical importance. This review is an attempt to trace the use of nanomaterials in biochemical sensor design. The possibility of using nanoparticles functionalized with antibodies as markers for proteins will be elucidated. Moreover, capabilities and applications for nanoparticles based on gold, silver, magnetic, and semiconductor materials (quantum dots), used in optical (absorbance, luminescence, surface enhanced Raman spectroscopy, surface plasmon resonance), electrochemical, and mass-sensitive sensors will be highlighted. The unique ability of nanosensors to improve the analysis of biochemical fluids is discussed either through considering the use of nanoparticles for in vitro molecular diagnosis, or in the biological/biochemical analysis for in vivo interaction with the human body. PMID:24198472

  15. Tidal evolution of the Uranian satellites. III - Evolution through the Miranda-Umbriel 3:1, Miranda-Ariel 5:3, and Ariel-Umbriel 2:1 mean-motion commensurabilities

    NASA Astrophysics Data System (ADS)

    Tittemore, W. C.; Wisdom, J.

    1990-06-01

    Numerical experiments have been conducted which indicate that the orbital eccentricity of Miranda may have reached a value sufficiently large to have affected its thermal evolution. There is a large chaotic zone associated with the Miranda-Ariel 5:3 mean-motion commensurability, even in the planar approximation; the orbital eccentricities of both satellites may vary chaotically for a considerable period. Since the anomalously high orbital inclination of Miranda is a consequence of passage through the 3:1 commensurability with Umbriel, the requirement that the satellites encountered this resonance places a lower limit on the Uranian specific dissipation function of 39,000.

  16. Tidal evolution of the Uranian satellites. III - Evolution through the Miranda-Umbriel 3:1, Miranda-Ariel 5:3, and Ariel-Umbriel 2:1 mean-motion commensurabilities

    NASA Technical Reports Server (NTRS)

    Tittemore, William C.; Wisdom, Jack

    1990-01-01

    Numerical experiments have been conducted which indicate that the orbital eccentricity of Miranda may have reached a value sufficiently large to have affected its thermal evolution. There is a large chaotic zone associated with the Miranda-Ariel 5:3 mean-motion commensurability, even in the planar approximation; the orbital eccentricities of both satellites may vary chaotically for a considerable period. Since the anomalously high orbital inclination of Miranda is a consequence of passage through the 3:1 commensurability with Umbriel, the requirement that the satellites encountered this resonance places a lower limit on the Uranian specific dissipation function of 39,000.

  17. Formation and evolution of early-type galaxies - III. Dependence of the star formation history on the total mass and initial overdensity

    NASA Astrophysics Data System (ADS)

    Merlin, E.; Chiosi, C.; Piovan, L.; Grassi, T.; Buonomo, U.; Barbera, F. La

    2012-12-01

    We investigate the influence of the initial overdensities and masses of proto-galaxies on their subsequent evolution (the star formation history in particular) to understand whether these key parameters are sufficient to account for the varied properties of the galactic populations. By means of fully hydrodynamical N-body simulations performed with the code EVOL, we produce 12 self-similar models of early-type galaxies of different initial masses and overdensities, and follow their evolution from the early epochs (detachment from the linear regime and Hubble flow at z ≥ 20) down to the stage when mass assembly is complete, i.e. z ≤ 1 (in some cases the models are calculated up to z = 0). The simulations include radiative cooling, star formation, stellar energy feedback, re-ionizing photo-heating background and chemical enrichment of the interstellar medium; we do not consider the possible presence of active nuclei. We find a strong correlation between the initial properties of the proto-haloes and their subsequent star formation histories. Massive (Mtot ≃ 1013 M⊙) haloes experience a single, intense burst of star formation (with rates ≥103 M⊙ yr-1) at early epochs, consistently with observations, with less pronounced dependence on the initial overdensity; intermediate-mass (Mtot ≃ 1011 M⊙) haloes have histories that strongly depend on their initial overdensity, whereas low-mass haloes (Mtot ≃ 109 M⊙) always have erratic, bursting like star-forming histories, due to the 'galactic breathing' phenomenon. The model galaxies have morphological, structural and chemical properties resembling those of real galaxies, even though some disagreement still occurs, likely a consequence of some numerical choices. We conclude that total mass and initial overdensity drive the star formation histories of early-type galaxies. The model galaxies belong to the so-called quasi-monolithic (or early hierarchical) scenario in the sense that the aggregation of lumps of

  18. EVOLUTION, NUCLEOSYNTHESIS, AND YIELDS OF AGB STARS AT DIFFERENT METALLICITIES. III. INTERMEDIATE-MASS MODELS, REVISED LOW-MASS MODELS, AND THE pH-FRUITY INTERFACE

    SciTech Connect

    Cristallo, S.; Straniero, O.; Piersanti, L.; Gobrecht, D.

    2015-08-15

    We present a new set of models for intermediate-mass asymptotic giant branch (AGB) stars (4.0, 5.0, and 6.0 M{sub ⊙}) at different metallicities (−2.15 ≤ [Fe/H] ≤ +0.15). This set integrates the existing models for low-mass AGB stars (1.3 ≤ M/M{sub ⊙} ≤ 3.0) already included in the FRUITY database. We describe the physical and chemical evolution of the computed models from the main sequence up to the end of the AGB phase. Due to less efficient third dredge up episodes, models with large core masses show modest surface enhancements. This effect is due to the fact that the interpulse phases are short and, therefore, thermal pulses (TPs) are weak. Moreover, the high temperature at the base of the convective envelope prevents it from deeply penetrating the underlying radiative layers. Depending on the initial stellar mass, the heavy element nucleosynthesis is dominated by different neutron sources. In particular, the s-process distributions of the more massive models are dominated by the {sup 22}Ne(α,n){sup 25}Mg reaction, which is efficiently activated during TPs. At low metallicities, our models undergo hot bottom burning and hot third dredge up. We compare our theoretical final core masses to available white dwarf observations. Moreover, we quantify the influence intermediate-mass models have on the carbon star luminosity function. Finally, we present the upgrade of the FRUITY web interface, which now also includes the physical quantities of the TP-AGB phase for all of the models included in the database (ph-FRUITY)

  19. Evolution, Nucleosynthesis, and Yields of AGB Stars at Different Metallicities. III. Intermediate-mass Models, Revised Low-mass Models, and the ph-FRUITY Interface

    NASA Astrophysics Data System (ADS)

    Cristallo, S.; Straniero, O.; Piersanti, L.; Gobrecht, D.

    2015-08-01

    We present a new set of models for intermediate-mass asymptotic giant branch (AGB) stars (4.0, 5.0, and 6.0 M⊙) at different metallicities (-2.15 ≤ [Fe/H] ≤ +0.15). This set integrates the existing models for low-mass AGB stars (1.3 ≤ M/M⊙ ≤ 3.0) already included in the FRUITY database. We describe the physical and chemical evolution of the computed models from the main sequence up to the end of the AGB phase. Due to less efficient third dredge up episodes, models with large core masses show modest surface enhancements. This effect is due to the fact that the interpulse phases are short and, therefore, thermal pulses (TPs) are weak. Moreover, the high temperature at the base of the convective envelope prevents it from deeply penetrating the underlying radiative layers. Depending on the initial stellar mass, the heavy element nucleosynthesis is dominated by different neutron sources. In particular, the s-process distributions of the more massive models are dominated by the 22Ne(α,n)25Mg reaction, which is efficiently activated during TPs. At low metallicities, our models undergo hot bottom burning and hot third dredge up. We compare our theoretical final core masses to available white dwarf observations. Moreover, we quantify the influence intermediate-mass models have on the carbon star luminosity function. Finally, we present the upgrade of the FRUITY web interface, which now also includes the physical quantities of the TP-AGB phase for all of the models included in the database (ph-FRUITY).

  20. Progress in biochemical engineering.

    PubMed

    Böing, J T

    1976-07-01

    Biochemical engineering is one of the answers to some of the challenges of the present age: hunger, shortage in raw material and energy supply and contamination of environment. Its contribution to the solution of these problems is the industrial production of protein, the use of raw materials (incl. waste products) not used up to now, the accomplishment of chemical reactions at ambient temperatures as well as the degradation or utilization of widely different waste materials.

  1. ON THE CLUSTER PHYSICS OF SUNYAEV-ZEL'DOVICH AND X-RAY SURVEYS. III. MEASUREMENT BIASES AND COSMOLOGICAL EVOLUTION OF GAS AND STELLAR MASS FRACTIONS

    SciTech Connect

    Battaglia, N.; Bond, J. R.; Pfrommer, C.; Sievers, J. L.

    2013-11-10

    Gas masses tightly correlate with the virial masses of galaxy clusters, allowing for a precise determination of cosmological parameters by means of X-ray surveys. However, the gas mass fractions (f{sub gas}) at the virial radius (R{sub 200}) derived from recent Suzaku observations are considerably larger than the cosmic mean, calling into question the accuracy of cosmological parameters. Here, we use a large suite of cosmological hydrodynamical simulations to study measurement biases of f{sub gas}. We employ different variants of simulated physics, including radiative gas physics, star formation, and thermal feedback by active galactic nuclei, which we show is able to arrest overcooling and to result in constant stellar mass fractions for redshifts z < 1. Computing the mass profiles in 48 angular cones, we find anisotropic gas and total mass distributions that imply an angular variance of f{sub gas} at the level of 30%. This anisotropy originates from the recent formation epoch of clusters and from the strong internal baryon-to-dark-matter density bias. In the most extreme cones, f{sub gas} can be biased high by a factor of two at R{sub 200} in massive clusters (M{sub 200} ∼ 10{sup 15} M{sub ☉}), thereby providing an explanation for high f{sub gas} measurements by Suzaku. While projection lowers this factor, there are other measurement biases that may (partially) compensate. At R{sub 200}, f{sub gas} is biased high by 20% when assuming hydrostatic equilibrium masses, i.e., neglecting the kinetic pressure, and by another ∼10%-20% due to the presence of density clumping. At larger radii, both measurement biases increase dramatically. While the cluster sample variance of the true f{sub gas} decreases to a level of 5% at R{sub 200}, the sample variance that includes both measurement biases remains fairly constant at the level of 10%-20%. The constant redshift evolution of f{sub gas} within R{sub 500} for massive clusters is encouraging for using gas masses to

  2. Molecular evolution of aerobic energy metabolism in primates.

    PubMed

    Grossman, L I; Schmidt, T R; Wildman, D E; Goodman, M

    2001-01-01

    As part of our goal to reconstruct human evolution at the DNA level, we have been examining changes in the biochemical machinery for aerobic energy metabolism. We find that protein subunits of two of the electron transfer complexes, complex III and complex IV, and cytochrome c, the protein carrier that connects them, have all undergone a period of rapid protein evolution in the anthropoid lineage that ultimately led to humans. Indeed, subunit IV of cytochrome c oxidase (COX; complex IV) provides one of the best examples of positively selected changes of any protein studied. The rate of subunit IV evolution accelerated in our catarrhine ancestors in the period between 40 to 18 million years ago and then decelerated in the descendant hominid lineages, a pattern of rate changes indicative of positive selection of adaptive changes followed by purifying selection acting against further changes. Besides clear evidence that adaptive evolution occurred for cytochrome c and subunits of complexes III (e.g., cytochrome c(1)) and IV (e.g., COX2 and COX4), modest rate accelerations in the lineage that led to humans are seen for other subunits of both complexes. In addition the contractile muscle-specific isoform of COX subunit VIII became a pseudogene in an anthropoid ancestor of humans but appears to be a functional gene in the nonanthropoid primates. These changes in the aerobic energy complexes coincide with the expansion of the energy-dependent neocortex during the emergence of the higher primates. Discovering the biochemical adaptations suggested by molecular evolutionary analysis will be an exciting challenge.

  3. Biochemical Reversal of Aging

    NASA Astrophysics Data System (ADS)

    Ely, John T. A.

    2006-03-01

    We cite our progress on biochemical reversal of aging. However, it may be circa 2 years before we have necessary substances at low cost. Meanwhile, without them, a number of measures can be adopted providing marked improvement for the problems of aging in modern societies. For example, enzymes are needed to excrete toxins that accelerate aging; Hg is the ultimate toxin that disables all enzymes (including those needed to excrete Hg itself). Low Hg level in the urine, due to loss of excretory ability, causes the diagnosis of Hg toxicity to almost always be missed. Hg sources must be removed from the body! Another example is excess sugar; hyperglycemia decreases intracellular ascorbic acid (AA) by competitively inhibiting the insulin- mediated active transport of AA into cells. Thus, immunity is impaired by low leucocyte AA. AA is needed for new proteins in aging tissues. Humans must supplement AA; their need same as in AA-synthesizing mammals.

  4. The Origin and Evolution of Viruses

    NASA Astrophysics Data System (ADS)

    Agol, Vadim I.

    The lecture covers three main topics: (i) Viruses: properties, place in the living world, and possible origin; (ii) Molecular basis of viral variability and evolution; and (iii) Evolution of viral pathogenicity and emerging viral infections.

  5. Columnar modelling of nucleation burst evolution in the convective boundary layer - first results from a feasibility study Part III: Preliminary results on physicochemical model performance using two "clean air mass" reference scenarios

    NASA Astrophysics Data System (ADS)

    Hellmuth, O.

    2006-09-01

    In Paper I of four papers, a revised columnar high-order model to investigate gas-aerosol-turbulence interactions in the convective boundary layer (CBL) was proposed. In Paper II, the model capability to predict first-, second- and third-order moments of meteorological variables in the CBL was demonstrated using available observational data. In the present Paper III, the high-order modelling concept is extended to sulphur and ammonia chemistry as well as to aerosol dynamics. Based on the previous CBL simulation, a feasibility study is performed using two "clean air mass" scenarios with an emission source at the ground but low aerosol background concentration. Such scenarios synoptically correspond to the advection of fresh post-frontal air in an anthropogenically influenced region. The aim is to evaluate the time-height evolution of ultrafine condensation nuclei (UCNs) and to elucidate the interactions between meteorological and physicochemical variables in a CBL column. The scenarios differ in the treatment of new particle formation (NPF), whereas homogeneous nucleation according to the classical nucleation theory (CNT) is considered. The first scenario considers nucleation of a binary system consisting of water vapour and sulphuric acid (H2SO4) vapour, the second one nucleation of a ternary system additionally involving ammonia (NH3). Here, the two synthetic scenarios are discussed in detail, whereas special attention is payed to the role of turbulence in the formation of the typical UCN burst behaviour, that can often be observed in the surface layer. The intercomparison of the two scenarios reveals large differences in the evolution of the UCN number concentration in the surface layer as well as in the time-height cross-sections of first-order moments and double correlation terms. Although in both cases the occurrence of NPF bursts could be simulated, the burst characteristics and genesis of the bursts are completely different. It is demonstrated, that

  6. Expression of CA III in rodent models of obesity.

    PubMed

    Stanton, L W; Ponte, P A; Coleman, R T; Snyder, M A

    1991-06-01

    To achieve a better understanding of the biochemical basis of obesity, we have undertaken comparative analyses of adipose tissue of lean and obese mice. By two-dimensional gel analysis, carbonic anhydrase-III (CA III) has been identified as a major constituent of murine adipose tissue. Quantitative comparisons of CA III protein and mRNA levels indicate that this enzyme is expressed at lower levels in adipose tissue from animals that were either genetically obese or had experimentally induced obesity compared to levels in the corresponding lean controls. This decrease in CA III expression was unique to adipose tissue, since other CA III-containing organs and tissues did not show a change when lean and obese animals were compared. Additionally, levels of CA III in adipose tissue from obese animals responded to acute changes in energy balance of the animal. These results are discussed in light of possible metabolic roles for CA III.

  7. Recruitment of RNA polymerase III in vivo.

    PubMed

    Kenneth, Niall S; Marshall, Lynne; White, Robert J

    2008-06-01

    RNA polymerase (pol) III contains a dissociable subcomplex that is required for initiation, but not for elongation or termination of transcription. This subcomplex is composed of subunits RPC3, RPC6 and RPC7, and interacts with TFIIIB, a factor that is necessary and sufficient to support accurate pol III transcription in vitro. Direct binding of TFIIIB to RPC6 is believed to recruit pol III to its genetic templates. However, this has never been tested in vivo. Here we combine chromatin immunoprecipitation with RNA interference to demonstrate that the RPC3/6/7 subcomplex is required for pol III recruitment in mammalian cells. Specific knockdown of RPC6 by RNAi results in post-transcriptional depletion of the other components of the subcomplex, RPC3 and RPC7, without destabilizing core pol III subunits or TFIIIB. The resultant core enzyme is defective in associating with TFIIIB and target genes in vivo. Promoter occupancy by pol II is unaffected, despite sharing five subunits with the pol III core. These observations provide evidence for the validity in vivo of the model for pol III recruitment that was built on biochemical data.

  8. Solar type III radio burst emission process

    SciTech Connect

    Wentzel, D.G.

    1982-05-01

    The interplanetary type III radio emission has been explained by two qualitatively different nonlinear plasma processes, invoking respectively one- and two-dimensional evolution of plasma wave packets. This paper asks: Is solar coronal type III emission consistent with plasma solitons evolving in one dimension. Although the answer is at best a qualified yes, the theory suggests observational questions that have attracted little attention so far.

  9. Alcoholic myopathy: biochemical mechanisms.

    PubMed

    Preedy, V R; Paice, A; Mantle, D; Dhillon, A S; Palmer, T N; Peters, T J

    2001-08-01

    Between one- and two-thirds of all alcohol abusers have impairment of muscle function that may be accompanied by biochemical lesions and/or the presence of a defined myopathy characterised by selective atrophy of Type II fibres. Perturbations in protein metabolism are central to the effects on muscle and account for the reductions in muscle mass and fibre diameter. Ethanol abuse is also associated with abnormalities in carbohydrate (as well as lipid) metabolism in skeletal muscle. Ethanol-mediated insulin resistance is allied with the inhibitory effects of ethanol on insulin-stimulated carbohydrate metabolism. It acutely impairs insulin-stimulated glucose and lipid metabolism, although it is not known whether it has an analogous effect on insulin-stimulated protein synthesis. In alcoholic cirrhosis, insulin resistance occurs with respect to carbohydrate metabolism, although the actions of insulin to suppress protein degradation and stimulate amino acid uptake are unimpaired. In acute alcohol-dosing studies defective rates of protein synthesis occur, particularly in Type II fibre-predominant muscles. The relative amounts of mRNA-encoding contractile proteins do not appear to be adversely affected by chronic alcohol feeding, although subtle changes in muscle protein isoforms may occur. There are also rapid and sustained reductions in total (largely ribosomal) RNA in chronic studies. Loss of RNA appears to be related to increases in the activities of specific muscle RNases in these long-term studies. However, in acute dosing studies (less than 1 day), the reductions in muscle protein synthesis are not due to overt loss of total RNA. These data implicate a role for translational modifications in the initial stages of the myopathy, although changes in transcription and/or protein degradation may also be superimposed. These events have important implications for whole-body metabolism.

  10. Unquiet Evolution: Consideration of a Previous Synthesis

    ERIC Educational Resources Information Center

    Angseesing, J. P. A.

    1972-01-01

    Presents genetical and biochemical data to show that the conclusion presented by Dyer (EJ 036 108) is by no meas settled. Evidence to support the concept: evolution by selectively neutral polymorphisms is inconclusive. (AL)

  11. A Course in... Biochemical Engineering.

    ERIC Educational Resources Information Center

    Ng, Terry K-L.; And Others

    1988-01-01

    Describes a chemical engineering course for senior undergraduates and first year graduate students in biochemical engineering. Discusses five experiments used in the course: aseptic techniques, dissolved oxygen measurement, oxygen uptake by yeast, continuous sterilization, and cultivation of microorganisms. (MVL)

  12. III-Nitride UV Devices

    NASA Astrophysics Data System (ADS)

    Asif Khan, M.; Shatalov, M.; Maruska, H. P.; Wang, H. M.; Kuokstis, E.

    2005-10-01

    The need for efficient, compact and robust solid-state UV optical sources and sensors had stimulated the development of optical devices based on III-nitride material system. Rapid progress in material growth, device fabrication and packaging enabled demonstration of high efficiency visible-blind and solar-blind photodetectors, deep-UV light-emitting diodes with emission from 400 to 250 nm, and UV laser diodes with operation wavelengths ranging from 340 to 350 nm. Applications of these UV optical devices include flame sensing; fluorescence-based biochemical sensing; covert communications; air, water and food purification and disinfection; and biomedical instrumentation. This paper provides a review of recent advances in the development of UV optical devices. Performance of state-of-the-art devices as well as future prospects and challenges are discussed.

  13. Divergent Evolution of the repFII Replicon of IncF Plasmids Carrying Cytotoxic Necrotizing Factor cnf2, Cytolethal Distending Toxin cdtIII, and f17Ae Fimbrial Variant Genes in Type 2 Necrotoxigenic Escherichia coli Isolates from Calves

    PubMed Central

    Bihannic, Morgan; Haenni, Marisa; Oswald, Eric

    2015-01-01

    Among the pathovars of Escherichia coli in cattle, necrotoxigenic E. coli (NTEC) is defined by the production of cytotoxic necrotizing factors (CNFs). In particular, type 2 NTEC (NTEC2) strains are frequent in diarrheic and septicemic calves and usually coproduce CNF type 2 (CNF2), cytolethal distending toxin type III (CDTIII), and fimbrial adhesins of the F17 family, whose genetic determinants have frequently been reported on the same Vir-like plasmid. In this study, we investigated the genetic environment of the cnf2, f17Ae, and cdtIII genes in a collection of fecal E. coli isolates recovered from 484 French and 58 Iranian calves. In particular, we highlighted the spread of cnf2, f17Ae, and cdtIII on similar 150-kb IncF plasmids harboring the newly assigned repFII replicon allele F74 in NTEC2 isolates. Interestingly, this 150-kb IncF plasmid differed from the 140-kb IncF plasmid harboring the newly assigned repFII replicon allele F75 and carrying cnf2 alone. These results suggest two divergent lineages of cnf2-carrying IncF plasmids depending on the presence of the f17Ae and cdtIII genes. This partition was observed in E. coli strains of unrelated backgrounds, suggesting two different evolutionary paths of cnf2-carrying IncF plasmids rather than divergent evolutions of NTEC2 clones. The driving forces for such divergent evolutions are not known, and further studies are required to clarify the selection of plasmid subtypes spreading virulence determinants in E. coli, in particular, plasmids of the IncF family. PMID:26546422

  14. Divergent Evolution of the repFII Replicon of IncF Plasmids Carrying Cytotoxic Necrotizing Factor cnf2, Cytolethal Distending Toxin cdtIII, and f17Ae Fimbrial Variant Genes in Type 2 Necrotoxigenic Escherichia coli Isolates from Calves.

    PubMed

    Bihannic, Morgan; Haenni, Marisa; Oswald, Eric; Madec, Jean-Yves

    2015-11-06

    Among the pathovars of Escherichia coli in cattle, necrotoxigenic E. coli (NTEC) is defined by the production of cytotoxic necrotizing factors (CNFs). In particular, type 2 NTEC (NTEC2) strains are frequent in diarrheic and septicemic calves and usually coproduce CNF type 2 (CNF2), cytolethal distending toxin type III (CDTIII), and fimbrial adhesins of the F17 family, whose genetic determinants have frequently been reported on the same Vir-like plasmid. In this study, we investigated the genetic environment of the cnf2, f17Ae, and cdtIII genes in a collection of fecal E. coli isolates recovered from 484 French and 58 Iranian calves. In particular, we highlighted the spread of cnf2, f17Ae, and cdtIII on similar 150-kb IncF plasmids harboring the newly assigned repFII replicon allele F74 in NTEC2 isolates. Interestingly, this 150-kb IncF plasmid differed from the 140-kb IncF plasmid harboring the newly assigned repFII replicon allele F75 and carrying cnf2 alone. These results suggest two divergent lineages of cnf2-carrying IncF plasmids depending on the presence of the f17Ae and cdtIII genes. This partition was observed in E. coli strains of unrelated backgrounds, suggesting two different evolutionary paths of cnf2-carrying IncF plasmids rather than divergent evolutions of NTEC2 clones. The driving forces for such divergent evolutions are not known, and further studies are required to clarify the selection of plasmid subtypes spreading virulence determinants in E. coli, in particular, plasmids of the IncF family.

  15. BEST: Biochemical Engineering Simulation Technology

    SciTech Connect

    Not Available

    1996-01-01

    The idea of developing a process simulator that can describe biochemical engineering (a relatively new technology area) was formulated at the National Renewable Energy Laboratory (NREL) during the late 1980s. The initial plan was to build a consortium of industrial and U.S. Department of Energy (DOE) partners to enhance a commercial simulator with biochemical unit operations. DOE supported this effort; however, before the consortium was established, the process simulator industry changed considerably. Work on the first phase of implementing various fermentation reactors into the chemical process simulator, ASPEN/SP-BEST, is complete. This report will focus on those developments. Simulation Sciences, Inc. (SimSci) no longer supports ASPEN/SP, and Aspen Technology, Inc. (AspenTech) has developed an add-on to its ASPEN PLUS (also called BioProcess Simulator [BPS]). This report will also explain the similarities and differences between BEST and BPS. ASPEN, developed by the Massachusetts Institute of Technology for DOE in the late 1970s, is still the state-of-the-art chemical process simulator. It was selected as the only simulator with the potential to be easily expanded into the biochemical area. ASPEN/SP, commercially sold by SimSci, was selected for the BEST work. SimSci completed work on batch, fed-batch, and continuous fermentation reactors in 1993, just as it announced it would no longer commercially support the complete ASPEN/SP product. BEST was left without a basic support program. Luckily, during this same time frame, AspenTech was developing a biochemical simulator with its version of ASPEN (ASPEN PLUS), which incorporates most BEST concepts. The future of BEST will involve developing physical property data and models appropriate to biochemical systems that are necessary for good biochemical process design.

  16. Bacterial genomes: evolution of pathogenicity.

    PubMed

    Arnold, Dawn L; Jackson, Robert W

    2011-08-01

    Bacterial pathogens continue to pose a major threat to economically important plant resources. Disease outbreaks can occur through rapid evolution of a pathogen to overcome host defences. The advent of genome sequencing, especially next-generation technologies, has seen a revolution in the study of plant pathogen evolution over the past five years. This review highlights recent developments in understanding bacterial plant pathogen evolution, enabled by genomics and specifically focusing on type III protein effectors. The genotypic changes and mechanisms involved in pathogen evolution are now much better understood. However, there is still much to be learned about the drivers of pathogen evolution, both in terms of plant resistance and bacterial lifestyle.

  17. Circadian Clocks: Unexpected Biochemical Cogs

    PubMed Central

    Mori, Tetsuya; Mchaourab, Hassane; Johnson, Carl Hirschie

    2015-01-01

    A circadian oscillation can be reconstituted in vitro from three proteins that cycles with a period of ~24 h. Two recent studies provide surprising biochemical answers to why this remarkable oscillator has such a long time constant and how it can switch effortlessly between alternating enzymatic modes. PMID:26439342

  18. Metabolism. Part III: Lipids.

    ERIC Educational Resources Information Center

    Bodner, George M.

    1986-01-01

    Describes the metabolic processes of complex lipids, including saponification, activation and transport, and the beta-oxidation spiral. Discusses fatty acid degradation in regard to biochemical energy and ketone bodies. (TW)

  19. Biochemical Engineering. Part II: Process Design

    ERIC Educational Resources Information Center

    Atkinson, B.

    1972-01-01

    Describes types of industrial techniques involving biochemical products, specifying the advantages and disadvantages of batch and continuous processes, and contrasting biochemical and chemical engineering. See SE 506 318 for Part I. (AL)

  20. CITY III Operator's Manual.

    ERIC Educational Resources Information Center

    Envirometrics, Inc., Washington, DC.

    CITY III is a computer-assisted simulation game of an urban system involving player operation of and interaction with economic, social, and government components. The role of operator in the game is to take the handwritten inputs (decisions) from the CITY III participants, process them, and return output which initiates the next round of…

  1. SUPERSTARS III: K-2.

    ERIC Educational Resources Information Center

    North Carolina State Dept. of Public Education, Raleigh.

    SUPERSTARS III is a K-8 program designed as an enrichment opportunity for self-directed learners in mathematics. The basic purpose of SUPERSTARS III is to provide the extra challenge that self-motivated students need in mathematics and to do so in a structured, long-term program that does not impinge on the normal classroom routine or the…

  2. Inactivation of food-borne viruses using natural biochemical substances.

    PubMed

    Li, Dan; Baert, Leen; Uyttendaele, Mieke

    2013-08-01

    Food-borne viruses such as human Noroviruses (NoVs), hepatitis A virus (HAV), Rotaviruses (RoVs) are a public health concern worldwide. Biochemical substances, which occur naturally in plants, animals or microorganisms, might possess considerable antimicrobial properties. In this study, the reported effects of biochemical substances on food-borne viruses are reviewed. The biochemical substances are grouped into several categories including (i) polyphenols and proanthocyanins, (ii) saponin, (iii) polysaccharides, (iv) organic acids, (v) proteins and polypeptides, (vi) essential oils. Although not fully understood, the mechanism of action for the antiviral activity of the natural compounds is presented. Generally, it is thought to be the prevention of the viral attachment to host cells, either by causing damage on the viral capsids or change of the receptors on the cell membranes. It is recommended that further studies are undertaken not only on the wide-range screening for novel antiviral substances, but also on the mechanism in-depth as well as the exploration for their potential application in controlling virus contamination in foods or food processing. PMID:23628607

  3. Population III Stars Around the Milky Way

    NASA Astrophysics Data System (ADS)

    Komiya, Yutaka; Suda, Takuma; Fujimoto, Masayuki Y.

    2016-03-01

    We explore the possibility of observing Population III (Pop III) stars, born of primordial gas. Pop III stars with masses below 0.8 M⊙ should survive to date though are not yet observed, but the existence of stars with low metallicity as [{{Fe}}/{{H}}]\\lt -5 in the Milky Way halo suggests the surface pollution of Pop III stars with accreted metals from the interstellar gas after birth. In this paper, we investigate the runaway of Pop III stars from their host mini-halos, considering the ejection of secondary members from binary systems when their massive primaries explode as supernovae. These stars save them from surface pollution. By computing the star formation and chemical evolution along with the hierarchical structure formation based on the extended Press-Schechter merger trees, we demonstrate that several hundreds to tens of thousands of low-mass Pop III stars escape from the building blocks of the Milky Way. The second and later generations of extremely metal-poor stars also escaped from the mini-halos. We discuss the spatial distributions of these escaped stars by evaluating the distances between the mini-halos in the branches of merger trees under the spherical collapse model of dark matter halos. It is demonstrated that the escaped stars distribute beyond the stellar halo with a density profile close to the dark matter halo, while Pop III stars are slightly more centrally concentrated. 6%-30% of the escaped stars leave the Milky Way and go out into the intergalactic space. Based on the results, we discuss the feasibility of observing the Pop III stars with the pristine surface abundance.

  4. Biochemical Markers of Myocardial Damage

    PubMed Central

    2016-01-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  5. Biochemical Markers of Myocardial Damage.

    PubMed

    Bodor, Geza S

    2016-04-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  6. Biochemical structure of Calendula officinalis.

    PubMed

    Korakhashvili, A; Kacharava, T; Kiknavelidze, N

    2007-01-01

    Calendula officinalis is a well known medicinal herb. It is common knowledge that its medicinal properties are conditioned on biologically active complex substances of Carotin (Provitamin A), Stearin, Triterpiniod, Plavonoid, Kumarin, macro and micro compound elements. Because of constant need in raw material of Calendula officinalis, features of its ontogenetic development agro-biological qualities in various eco regions of Georgia were investigated. The data of biologically active compounds, biochemical structure and the maintenance both in flowers and in others parts of plant is presented; the pharmacological activity and importance in medicine was reviewed. PMID:17921550

  7. Constraining the Statistics of Population III Binaries

    NASA Astrophysics Data System (ADS)

    Stacy, Athena

    2013-01-01

    We perform a cosmological simulation in order to model the growth and evolution of Population III (Pop III) stellar systems in a range of host minihalo environments. A Pop III multiple system forms in each of the ten minihaloes, and the overall mass function is top-heavy compared to the currently observed initial mass function in the Milky Way. Using a sink particle to represent each growing protostar, we examine the binary characteristics of the multiple systems, resolving orbits on scales as small as 20 AU. We find a binary fraction of ~36%, with semi-major axes as large as 3000 AU. The distribution of orbital periods is slightly peaked at ~900 yr, while the distribution of mass ratios is relatively flat. Of all sink particles formed within the ten minihaloes, ~50% are lost to mergers with larger sinks, and ~50% of the remaining sinks are ejected from their star-forming disks. The large binary fraction may have important implications for Pop III evolution and nucleosynthesis, as well as the final fate of the first stars.

  8. Constraining the statistics of Population III binaries

    NASA Astrophysics Data System (ADS)

    Stacy, Athena; Bromm, Volker

    2013-08-01

    We perform a cosmological simulation in order to model the growth and evolution of Population III (Pop III) stellar systems in a range of host minihalo environments. A Pop III multiple system forms in each of the 10 minihaloes, and the overall mass function is top-heavy compared to the currently observed initial mass function in the Milky Way. Using a sink particle to represent each growing protostar, we examine the binary characteristics of the multiple systems, resolving orbits on scales as small as 20 au. We find a binary fraction of ˜35 per cent, with semi-major axes as large as 3000 au. The distribution of orbital periods is slightly peaked at ≲ 900 yr, while the distribution of mass ratios is relatively flat. Of all sink particles formed within the 10 minihaloes, ˜50 per cent are lost to mergers with larger sinks, and ˜50 per cent of the remaining sinks are ejected from their star-forming discs. The large binary fraction may have important implications for Pop III evolution and nucleosynthesis, as well as the final fate of the first stars.

  9. Constraining the Statistics of Population III Binaries

    NASA Technical Reports Server (NTRS)

    Stacy, Athena; Bromm, Volker

    2012-01-01

    We perform a cosmological simulation in order to model the growth and evolution of Population III (Pop III) stellar systems in a range of host minihalo environments. A Pop III multiple system forms in each of the ten minihaloes, and the overall mass function is top-heavy compared to the currently observed initial mass function in the Milky Way. Using a sink particle to represent each growing protostar, we examine the binary characteristics of the multiple systems, resolving orbits on scales as small as 20 AU. We find a binary fraction of approx. 36, with semi-major axes as large as 3000 AU. The distribution of orbital periods is slightly peaked at approx. < 900 yr, while the distribution of mass ratios is relatively flat. Of all sink particles formed within the ten minihaloes, approx. 50 are lost to mergers with larger sinks, and 50 of the remaining sinks are ejected from their star-forming disks. The large binary fraction may have important implications for Pop III evolution and nucleosynthesis, as well as the final fate of the first stars.

  10. Photochemical transformation of an iron(III)-arsenite complex in acidic aqueous solution.

    PubMed

    Pozdnyakov, Ivan P; Ding, Wei; Xu, Jing; Chen, Long; Wu, Feng; Grivin, Vjacheslav P; Plyusnin, Victor F

    2016-03-01

    Surface complexation between arsenious acid anions (As(III)) and ferric (hydr)oxides in water is important for the transformation and transfer of inorganic arsenic species. The mechanisms of formation and the photochemistry of dissolved Fe(III)-As(III) complexes in acidic aqueous solution are still unclear. Here, the photooxidation of As(III) in the presence of Fe(III) ions in acidic media has been investigated by laser flash and steady-state photolysis. At low arsenite concentrations (<1 mM), As(III) is oxidized by the ˙OH radical generated by photolysis of the FeOH(2+) complex. At higher arsenite concentrations (>10 mM), photoactive Fe(III)-As(III) complexes are formed (ϕ≈ 0.012). At all arsenite concentrations, a white FeAsO4 colloid is formed during As(III) photolysis in the presence of Fe(III) ions. Solid Fe(III)-As(III) complexes have been prepared and characterized, and the photochemical transformation of As(III) into As(V) in solid Fe(III)-As(III) complexes has been confirmed. These findings are important for a better understanding of the evolution of As(III) species under environmental conditions and should provide guidance for detoxification of As(III)-polluted water systems.

  11. Co(II)1-xCo(0)x/3Mn(III)2x/3S Nanoparticles Supported on B/N-Codoped Mesoporous Nanocarbon as a Bifunctional Electrocatalyst of Oxygen Reduction/Evolution for High-Performance Zinc-Air Batteries.

    PubMed

    Wang, Zilong; Xiao, Shuang; An, Yiming; Long, Xia; Zheng, Xiaoli; Lu, Xihong; Tong, Yexiang; Yang, Shihe

    2016-06-01

    Rechargeable Zn-air battery is an ideal type of energy storage device due to its high energy and power density, high safety, and economic viability. Its large-scale application rests upon the availability of active, durable, low-cost electrocatalysts for the oxygen reduction reaction (ORR) in the discharge process and oxygen evolution reaction (OER) in the charge process. Herein we developed a novel ORR/OER bifunctional electrocatalyst for rechargeable Zn-air batteries based on the codoping and hybridization strategies. The B/N-codoped mesoporous nanocarbon supported Co(II)1-xCo(0)x/3Mn(III)2x/3S nanoparticles exhibit a superior OER performance compared to that of IrO2 catalyst and comparable Zn-air battery performance to that of the Pt-based battery. The rechargeable Zn-air battery shows high discharge peak power density (over 250 mW cm(-2)) and current density (180 mA cm(-2) at 1 V), specific capacity (∼550 mAh g(-1)), small charge-discharge voltage gap of ∼0.72 V at 20 mA cm(-2) and even higher stability than the Pt-based battery. The advanced performance of the bifunctional catalysts highlights the beneficial role of the simultaneous formation of Mn(III) and Co(0) as well as the dispersed hybridization with the codoped nanocarbon support.

  12. Co(II)1-xCo(0)x/3Mn(III)2x/3S Nanoparticles Supported on B/N-Codoped Mesoporous Nanocarbon as a Bifunctional Electrocatalyst of Oxygen Reduction/Evolution for High-Performance Zinc-Air Batteries.

    PubMed

    Wang, Zilong; Xiao, Shuang; An, Yiming; Long, Xia; Zheng, Xiaoli; Lu, Xihong; Tong, Yexiang; Yang, Shihe

    2016-06-01

    Rechargeable Zn-air battery is an ideal type of energy storage device due to its high energy and power density, high safety, and economic viability. Its large-scale application rests upon the availability of active, durable, low-cost electrocatalysts for the oxygen reduction reaction (ORR) in the discharge process and oxygen evolution reaction (OER) in the charge process. Herein we developed a novel ORR/OER bifunctional electrocatalyst for rechargeable Zn-air batteries based on the codoping and hybridization strategies. The B/N-codoped mesoporous nanocarbon supported Co(II)1-xCo(0)x/3Mn(III)2x/3S nanoparticles exhibit a superior OER performance compared to that of IrO2 catalyst and comparable Zn-air battery performance to that of the Pt-based battery. The rechargeable Zn-air battery shows high discharge peak power density (over 250 mW cm(-2)) and current density (180 mA cm(-2) at 1 V), specific capacity (∼550 mAh g(-1)), small charge-discharge voltage gap of ∼0.72 V at 20 mA cm(-2) and even higher stability than the Pt-based battery. The advanced performance of the bifunctional catalysts highlights the beneficial role of the simultaneous formation of Mn(III) and Co(0) as well as the dispersed hybridization with the codoped nanocarbon support. PMID:27163673

  13. Genetics of eukaryotic RNA polymerases I, II, and III.

    PubMed Central

    Archambault, J; Friesen, J D

    1993-01-01

    The transcription of nucleus-encoded genes in eukaryotes is performed by three distinct RNA polymerases termed I, II, and III, each of which is a complex enzyme composed of more than 10 subunits. The isolation of genes encoding subunits of eukaryotic RNA polymerases from a wide spectrum of organisms has confirmed previous biochemical and immunological data indicating that all three enzymes are closely related in structures that have been conserved in evolution. Each RNA polymerase is an enzyme complex composed of two large subunits that are homologous to the two largest subunits of prokaryotic RNA polymerases and are associated with smaller polypeptides, some of which are common to two or to all three eukaryotic enzymes. This remarkable conservation of structure most probably underlies a conservation of function and emphasizes the likelihood that information gained from the study of RNA polymerases from one organism will be applicable to others. The recent isolation of many mutations affecting the structure and/or function of eukaryotic and prokaryotic RNA polymerases now makes it feasible to begin integrating genetic and biochemical information from various species in order to develop a picture of these enzymes. The picture of eukaryotic RNA polymerases depicted in this article emphasizes the role(s) of different polypeptide regions in interaction with other subunits, cofactors, substrates, inhibitors, or accessory transcription factors, as well as the requirement for these interactions in transcription initiation, elongation, pausing, termination, and/or enzyme assembly. Most mutations described here have been isolated in eukaryotic organisms that have well-developed experimental genetic systems as well as amenable biochemistry, such as Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans. When relevant, mutations affecting regions of Escherichia coli RNA polymerase that are conserved among eukaryotes and prokaryotes are also presented

  14. Vector Encoding in Biochemical Networks

    NASA Astrophysics Data System (ADS)

    Potter, Garrett; Sun, Bo

    Encoding of environmental cues via biochemical signaling pathways is of vital importance in the transmission of information for cells in a network. The current literature assumes a single cell state is used to encode information, however, recent research suggests the optimal strategy utilizes a vector of cell states sampled at various time points. To elucidate the optimal sampling strategy for vector encoding, we take an information theoretic approach and determine the mutual information of the calcium signaling dynamics obtained from fibroblast cells perturbed with different concentrations of ATP. Specifically, we analyze the sampling strategies under the cases of fixed and non-fixed vector dimension as well as the efficiency of these strategies. Our results show that sampling with greater frequency is optimal in the case of non-fixed vector dimension but that, in general, a lower sampling frequency is best from both a fixed vector dimension and efficiency standpoint. Further, we find the use of a simple modified Ornstein-Uhlenbeck process as a model qualitatively captures many of our experimental results suggesting that sampling in biochemical networks is based on a few basic components.

  15. Antithrombin III blood test

    MedlinePlus

    ... be due to: Bone marrow transplant Disseminated intravascular coagulation (DIC) AT III deficiency, an inherited condition Liver ... Schmaier AH, Miller JL. Coagulation and fibrinolysis. In: McPherson ... Management by Laboratory Methods . 22nd ed. Philadelphia, PA: ...

  16. The energy costs of insulators in biochemical networks.

    PubMed

    Barton, John P; Sontag, Eduardo D

    2013-03-19

    Complex networks of biochemical reactions, such as intracellular protein signaling pathways and genetic networks, are often conceptualized in terms of modules--semiindependent collections of components that perform a well-defined function and which may be incorporated in multiple pathways. However, due to sequestration of molecular messengers during interactions and other effects, collectively referred to as retroactivity, real biochemical systems do not exhibit perfect modularity. Biochemical signaling pathways can be insulated from impedance and competition effects, which inhibit modularity, through enzymatic futile cycles that consume energy, typically in the form of ATP. We hypothesize that better insulation necessarily requires higher energy consumption. We test this hypothesis through a combined theoretical and computational analysis of a simplified physical model of covalent cycles, using two innovative measures of insulation, as well as a possible new way to characterize optimal insulation through the balancing of these two measures in a Pareto sense. Our results indicate that indeed better insulation requires more energy. While insulation may facilitate evolution by enabling a modular plug-and-play interconnection architecture, allowing for the creation of new behaviors by adding targets to existing pathways, our work suggests that this potential benefit must be balanced against the metabolic costs of insulation necessarily incurred in not affecting the behavior of existing processes. PMID:23528097

  17. How special is the biochemical function of native proteins?

    PubMed

    Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi

    2016-01-01

    Native proteins perform an amazing variety of biochemical functions, including enzymatic catalysis, and can engage in protein-protein and protein-DNA interactions that are essential for life. A key question is how special are these functional properties of proteins. Are they extremely rare, or are they an intrinsic feature? Comparison to the properties of compact conformations of artificially generated compact protein structures selected for thermodynamic stability but not any type of function, the artificial (ART) protein library, demonstrates that a remarkable number of the properties of native-like proteins are recapitulated. These include the complete set of small molecule ligand-binding pockets and most protein-protein interfaces. ART structures are predicted to be capable of weakly binding metabolites and cover a significant fraction of metabolic pathways, with the most enriched pathways including ancient ones such as glycolysis. Native-like active sites are also found in ART proteins. A small fraction of ART proteins are predicted to have strong protein-protein and protein-DNA interactions. Overall, it appears that biochemical function is an intrinsic feature of proteins which nature has significantly optimized during evolution. These studies raise questions as to the relative roles of specificity and promiscuity in the biochemical function and control of cells that need investigation.

  18. How special is the biochemical function of native proteins?

    PubMed Central

    Skolnick, Jeffrey; Gao, Mu; Zhou, Hongyi

    2016-01-01

    Native proteins perform an amazing variety of biochemical functions, including enzymatic catalysis, and can engage in protein-protein and protein-DNA interactions that are essential for life. A key question is how special are these functional properties of proteins. Are they extremely rare, or are they an intrinsic feature? Comparison to the properties of compact conformations of artificially generated compact protein structures selected for thermodynamic stability but not any type of function, the artificial (ART) protein library, demonstrates that a remarkable number of the properties of native-like proteins are recapitulated. These include the complete set of small molecule ligand-binding pockets and most protein-protein interfaces. ART structures are predicted to be capable of weakly binding metabolites and cover a significant fraction of metabolic pathways, with the most enriched pathways including ancient ones such as glycolysis. Native-like active sites are also found in ART proteins. A small fraction of ART proteins are predicted to have strong protein-protein and protein-DNA interactions. Overall, it appears that biochemical function is an intrinsic feature of proteins which nature has significantly optimized during evolution. These studies raise questions as to the relative roles of specificity and promiscuity in the biochemical function and control of cells that need investigation. PMID:26962440

  19. Impact of volcanism on the evolution of Lake Van (eastern Anatolia) III: Periodic (Nemrut) vs. episodic (Süphan) explosive eruptions and climate forcing reflected in a tephra gap between ca. 14 ka and ca. 30 ka

    NASA Astrophysics Data System (ADS)

    Schmincke, Hans-Ulrich; Sumita, Mari

    2014-09-01

    Fifteen Lateglacial to Holocene rhyolitic, dominantly primary tephra layers piston-cored and drilled (ICDP Paleovan drilling project) in western Lake Van (eastern Anatolia, Turkey) were precisely correlated to either of the two adjacent and active large volcanoes Nemrut and Süphan based on shard textures, mineralogy and mineral and glass compositions. The young peralkaline (comenditic to pantelleritic) primary rhyolitic Nemrut tephras are characterized by anorthoclase, hedenbergitic to augitic clinopyroxene, fayalitic olivine, minor quartz, and rare accessory chevkinite and zircon. Phenocrysts in subalkaline primary rhyolitic Süphan tephras are chiefly oligoclase-labradorite, with minor K-rich sanidine in some, biotite, amphibole, hypersthene, rare augitic clinopyroxene, relatively common allanite and rare zircon. Two contrasting explosive eruptive modes are distinguished from each other: episodic (Süphan) and periodic (Nemrut). The Lateglacial Süphan tephra swarm covers a short time interval of ca. 338 years between ca. 13,078 vy BP and 12,740 vy BP, eruptions having occurred statistically every ca. 42 years with especially short intervals between V-11 (reworked) and V-14. Causes for the strongly episodic Süphan explosive behavior might include seismic triggering of a volcano-magma system unable to erupt explosively without the benefit of external triggering, as reflected in pervasive faulting preceding the Süphan tephra swarm. Seismic triggering may have caused the rise of more mafic ("trachyandesitic") parent magma, heating near-surface pockets of highly evolved magma - that might have formed silicic domes during this stage of volcano evolution - resulting in ascent and finally explosive fragmentation of magma essentially by external factors, probably significantly enhanced by magma-water/ice interaction. Explosive eruptions of the Nemrut volcano system, interpreted to be underlain by a large fractionating magma reservoir, follow a more periodic mode of (a

  20. Biochemical Analysis of Protein SUMOylation

    PubMed Central

    Alontaga, Aileen Y.; Bobkova, Ekaterina; Chen, Yuan

    2012-01-01

    SUMOylation, the covalent attachment of Small Ubiquitin-like MOdifier (SUMO) polypeptides to other proteins, is among the most important post-translational modifications that regulate the functional properties of a large number of proteins. SUMOylation is broadly involved in cellular processes such as gene transcription, hormone response, signal transduction, DNA repair and nuclear transport. SUMO modification has also been implicated in the pathogenesis of human diseases, such as cancer, neurodegenerative disorders and viral infection. Attachment of a SUMO protein to another protein is carried out in multiple steps catalyzed by three enzymes. This unit describes and discusses the in vitro biochemical methods used for investigating each step of the SUMOylation process. In addition, a high throughput screening protocol is included for the identification of inhibitors of SUMOylation. PMID:22870855

  1. Biochemical markers of acute pancreatitis.

    PubMed

    Matull, W R; Pereira, S P; O'Donohue, J W

    2006-04-01

    Serum amylase remains the most commonly used biochemical marker for the diagnosis of acute pancreatitis, but its sensitivity can be reduced by late presentation, hypertriglyceridaemia, and chronic alcoholism. Urinary trypsinogen-2 is convenient, of comparable diagnostic accuracy, and provides greater (99%) negative predictive value. Early prediction of the severity of acute pancreatitis can be made by well validated scoring systems at 48 hours, but the novel serum markers procalcitonin and interleukin 6 allow earlier prediction (12 to 24 hours after admission). Serum alanine transaminase >150 IU/l and jaundice suggest a gallstone aetiology, requiring endoscopic retrograde cholangiopancreatography. For obscure aetiologies, serum calcium and triglycerides should be measured. Genetic polymorphisms may play an important role in "idiopathic" acute recurrent pancreatitis.

  2. Hyponatraemia: biochemical and clinical perspectives.

    PubMed Central

    Gill, G.; Leese, G.

    1998-01-01

    Hyponatraemia is a common bio-chemical abnormality, occurring in about 15% of hospital inpatients. It is often associated with severe illness and relatively poor outcome. Pathophysiologically, hyponatraemia may be spurious, dilutional, depletional or redistributional. Particularly difficult causes and concepts of hyponatraemia are the syndrome of inappropriate antidiuresis and the sick cell syndrome, which are discussed here in detail. Therapy should always be targeted at the underlying disease process. 'Hyponatraemic symptoms' are of doubtful importance, and may be more related to water overload and/or the causative disease, than to hyponatraemia per se. Artificial elevation of plasma sodium by saline infusion carries the risk of induction of osmotic demyelination (central pontine myelinolysis). PMID:10211323

  3. Diagnosis of hyperandrogenism: biochemical criteria.

    PubMed

    Stanczyk, Frank Z

    2006-06-01

    Biochemical derangements in ovarian, adrenal, and peripheral androgen production and metabolism play an important role in underlying causes of hyperandrogenism. Specific diagnostic serum markers such as testosterone (total) and dehydroepiandrosterone sulfate (DHEAS), respectively, may be helpful in the diagnosis of ovarian and adrenal hyperandrogenism, respectively. Validated immunoassays or mass spectrometry assays should be used to quantify testosterone, DHEAS and other principal androgens. Free testosterone measurements, determined by equilibrium dialysis or the calculated method, are advocated for routine evaluation of more subtle forms of hyperandrogenism. The skin, with its pilosebaceous units (PSUs), is an important site of active androgen production. A key regulator in PSUs is 5alpha-reductase, which transforms testosterone or androstenedione to dihydrotestosterone (DHT). DHT in blood is not effective in indicating the presence of hyperandrogenism. However, distal metabolites of DHT have been shown to be good markers of clinical manifestations of hirsutism, acne and alopecia. Assays for these peripheral markers need improvement for routine clinical testing. PMID:16772150

  4. Mechanistic insights into type III restriction enzymes.

    PubMed

    Raghavendra, Nidhanapati K; Bheemanaik, Shivakumara; Rao, Desirazu N

    2012-01-01

    Type III restriction-modification (R-M) enzymes need to interact with two separate unmethylated DNA sequences in indirectly repeated, head-to-head orientations for efficient cleavage to occur at a defined location next to only one of the two sites. However, cleavage of sites that are not in head-to-head orientation have been observed to occur under certain reaction conditions in vitro. ATP hydrolysis is required for the long-distance communication between the sites prior to cleavage. Type III R-M enzymes comprise two subunits, Res and Mod that form a homodimeric Mod2 and a heterotetrameric Res2Mod2 complex. The Mod subunit in M2 or R2M2 complex recognizes and methylates DNA while the Res subunit in R2M2 complex is responsible for ATP hydrolysis, DNA translocation and cleavage. A vast majority of biochemical studies on Type III R-M enzymes have been undertaken using two closely related enzymes, EcoP1I and EcoP15I. Divergent opinions about how the long-distance interaction between the recognition sites exist and at least three mechanistic models based on 1D- diffusion and/or 3D- DNA looping have been proposed.

  5. Comparison of Au(III) and Ga(III) ions' binding to calf thymus DNA: spectroscopic characterization and thermal analysis.

    PubMed

    Sarioglu, Omer Faruk; Tekiner-Gursacli, Refiye; Ozdemir, Ayse; Tekinay, Turgay

    2014-09-01

    Metals have been studied as potential chemotherapeutic agents for cancer therapies due to their high reactivity toward a wide variety of substances. The characterization of metal ion-binding capacities is essential to understand the possible effects of metals on target biomolecules. In the present study, biochemical effects of Au(III) and Ga(III) ions on calf thymus DNA (ctDNA) were studied comparatively via bioanalytical, spectroscopic, and thermal methods. Briefly, UV-Vis absorbance spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and Fourier transform infrared (FT-IR) spectroscopy were utilized for spectroscopic characterization, and isothermal titration calorimetry (ITC) measurements were performed for thermal analysis. Our results reveal that both Au(III) and Ga(III) ions are capable of interacting with ctDNA, and Au(III) ions display a more favorable interaction and a higher binding affinity. ITC analyses indicate that the Au(III)-DNA interaction displays a binding affinity (Ka) around 1.43 × 10(6) M(-1), while a Ka around 1.17 × 10(5) M(-1) was observed for the Ga(III)-DNA binding. It was suggested that both metal ions are unlikely to change the structural B-conformation while interacting with ctDNA.

  6. Pyochelin, a siderophore of Pseudomonas aeruginosa: physicochemical characterization of the iron(III), copper(II) and zinc(II) complexes.

    PubMed

    Brandel, Jérémy; Humbert, Nicolas; Elhabiri, Mourad; Schalk, Isabelle J; Mislin, Gaëtan L A; Albrecht-Gary, Anne-Marie

    2012-03-01

    Pseudomonas aeruginosa is an opportunistic pathogen, synthesizing two major siderophores, pyoverdine (Pvd) and pyochelin (Pch), to cover its needs in iron(III). If the high affinity and specificity of Pvd toward iron(III) (pFe = 27.0) was well described in the literature, the physicochemical and coordination properties of Pch toward biologically relevant metals (Fe(III), Cu(II) or Zn(II)) have been only scarcely investigated. We report a thorough physico-chemical investigation of Pch (potentiometry, spectrophotometries, ESI/MS) that highlighted its moderate but significantly higher affinity for Fe(3+) (pFe = 16.0 at p[H] 7.4) than reported previously. We also demonstrated that Pch strongly chelates divalent metals such as Zn(II) (pZn = 11.8 at p[H] 7.4) and Cu(II) (pCu = 14.9 at p[H] 7.4) and forms predominantly 1 : 2 (M(2+)/Pch) complexes. Kinetic studies revealed that the formation of the ferric Pch complexes proceeds through a Eigen-Wilkins dissociative ligand interchange mechanism involving two protonated species of Pch and the Fe(OH)(2+) species of Fe(III). Our physico-chemical parameters supports the previous biochemical studies which proposed that siderophores are not only devoted to iron(III) shuttling but most likely display other specific biological role in the subtle metals homeostasis in microorganisms. This work also represents a step toward deciphering the role of siderophores throughout evolution. PMID:22261733

  7. Evolution of structure in RNA.

    PubMed

    King, G A

    Evidence is presented that structures formed by RNA and by RNA in association with protein have evolved from simpler structures by successive unions among them. The progressively more complex molecular structures have conferred selective advantage in evolution by progressively enhancing the specificities of the biochemical reactions. Before each union, the RNAs which joined at the time of union belonged to separate reproducing species. The record of unions in RNA therefore reflects unions among species in the biosphere, tracing the evolution of life from quite simple reproducing molecules up to well developed organisms.

  8. Computational optimization and biological evolution.

    PubMed

    Goryanin, Igor

    2010-10-01

    Modelling and optimization principles become a key concept in many biological areas, especially in biochemistry. Definitions of objective function, fitness and co-evolution, although they differ between biology and mathematics, are similar in a general sense. Although successful in fitting models to experimental data, and some biochemical predictions, optimization and evolutionary computations should be developed further to make more accurate real-life predictions, and deal not only with one organism in isolation, but also with communities of symbiotic and competing organisms. One of the future goals will be to explain and predict evolution not only for organisms in shake flasks or fermenters, but for real competitive multispecies environments.

  9. Biochemical and physiological processes associated with the differential ozone response in ozone-tolerant and sensitive soybean genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochemical and physiological traits of two soybean [Glycine max (L.) Merr.] genotypes that differ in sensitivity to ozone (O3) were investigated to determine the possible basis for the differential response. Fiskeby III (O3-tolerant) and Mandarin (Ottawa) (O3-sensitive) were grown in a greenhouse ...

  10. Influence of low-frequency vibration on changes of biochemical parameters of living rats

    NASA Astrophysics Data System (ADS)

    Kasprzak, Cezary; Damijan, Zbigniew; Panuszka, Ryszard

    2001-05-01

    The aim of the research was to investigate how some selected biochemical parameters of living rats depend on exposure of low-frequency vibrations. Experiments were run on 30 Wistar rats randomly segregated into three groups: (I) 20 days old (before puberty), (II) 70th day after; (III) control group. The exposure was repeated seven times, for 3 h, at the same time of day. Vibrations applied during the first tests of the experiment had acceleration 1.22 m/s2 and frequency 20 Hz. At the 135th day the rats' bones were a subject of morphometric/biochemical examination. The results of biochemical tests proved decrease in LDL and HDL cholesterol levels for exposed rats as well as the Ca contents in blood plasma. There was evident increasing of Ca in blood plasma in exposed rats for frequency of exposition.

  11. Biochemical transformation of solid carbonaceous material

    DOEpatents

    Lin, Mow S.; Premuzic, Eugene T.

    2001-09-25

    A method of biochemically transforming macromolecular compounds found in solid carbonaceous materials, such as coal is provided. The preparation of new microorganisms, metabolically weaned through challenge growth processes to biochemically transform solid carbonaceous materials at extreme temperatures, pressures, pH, salt and toxic metal concentrations is also disclosed.

  12. Serum Biochemical Phenotypes in the Domestic Dog.

    PubMed

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  13. Serum Biochemical Phenotypes in the Domestic Dog

    PubMed Central

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  14. Biochemical abnormalities and excitotoxicity in Huntington's disease brain.

    PubMed

    Tabrizi, S J; Cleeter, M W; Xuereb, J; Taanman, J W; Cooper, J M; Schapira, A H

    1999-01-01

    The physiological role of huntingtin and the mechanisms by which the expanded CAG repeat in ITI5 and its polyglutamine stretch in mutant huntingtin induce Huntington's disease (HD) are unknown. Several techniques have now demonstrated abnormal metabolism in HD brain; direct measurement of respiratory chain enzyme activities has shown severe deficiency of complex II/III and a milder defect of complex IV. We confirm that these abnormalities appear to be confined to the striatum within the HD brain. Analysis of complex II/III activity in HD fibroblasts was normal, despite expression of mutant huntingtin. Although glyceraldehyde 3-phosphate dehydrogenase (a huntingtin binding protein) activity was normal in all areas studied, aconitase activity was decreased to 8% in HD caudate, 27% in putamen, and 52% in cerebral cortex, but normal in HD cerebellum and fibroblasts. We have demonstrated that although complexes II and III are those parts of the respiratory chain most vulnerable to inhibition in the presence of a nitric oxide (NO*) generator, aconitase activity was even more sensitive to inhibition. The pattern of these enzyme deficiencies and their parallel to the anatomical distribution of HD pathology support an important role for NO* and excitotoxicity in HD pathogenesis. Furthermore, based on the biochemical defects we have described, we suggest that NO* generation produces a graded response, with aconitase inhibition followed by complex II/III inhibition and the initiation of a self-amplifying cycle of free radical generation and aconitase inhibition, which results in severe ATP depletion. We propose that these events are important in determining neuronal cell death and are critical steps in the pathogenesis of HD. PMID:9894873

  15. I. Thermal evolution of Ganymede and implications for surface features. II. Magnetohydrodynamic constraints on deep zonal flow in the giant planets. III. A fast finite-element algorithm for two-dimensional photoclinometry

    SciTech Connect

    Kirk, R.L.

    1987-01-01

    Thermal evolution of Ganymede from a hot start is modeled. On cooling ice I forms above the liquid H/sub 2/O and dense ices at higher entropy below it. A novel diapiric instability is proposed to occur if the ocean thins enough, mixing these layers and perhaps leading to resurfacing and groove formation. Rising warm-ice diapirs may cause a dramatic heat pulse and fracturing at the surface, and provide material for surface flows. Timing of the pulse depends on ice rheology but could agree with crater-density dates for resurfacing. Origins of the Ganymede-Callisto dichotomy in light of the model are discussed. Based on estimates of the conductivity of H/sub 2/ (Jupiter, Saturn) and H/sub 2/O (Uranus, Neptune), the zonal winds of the giant planets will, if they penetrate below the visible atmosphere, interact with the magnetic field well outside the metallic core. The scaling argument is supported by a model with zonal velocity constant on concentric cylinders, the Lorentz torque on each balanced by viscous stresses. The problem of two-dimensional photoclinometry, i.e. reconstruction of a surface from its image, is formulated in terms of finite elements and a fast algorithm using Newton-SOR iteration accelerated by multigridding is presented.

  16. Evolution of chromospheres and coronae in solar mass stars - A far-ultraviolet and soft X-ray comparison of Arcturus /K2 III/ and Alpha Centauri A /G2 V/

    NASA Technical Reports Server (NTRS)

    Ayres, T. R.; Simon, T.; Linsky, J. L.

    1982-01-01

    IUE far-UV and Einstein Observatory soft X-ray observations for the red giant Arcturus and the nearby yellow dwarf Alpha-Centauri A, which are archetypes of solar mass stars in different stages of evolution, are compared. Evidence is found for neither coronal soft X-ray emission from the red giant, at surface flux levels of only 0.0006 that detected previously for the yellow dwarf, nor C II and IV resonance line emission at surface flux levels of only 0.02 those of the yellow dwarf. The resonance line upper limits and previous detections of the C II intersystem UV multiplet 0.01 near 2325 A provide evidence for an Arcturus outer atmosphere that is geometrically extended, tenuous and cool. The red giant has, in addition, a prominent cool stellar wind. An extensive tabulation of line identifications, widths and fluxes for the IUE far-UV echelle spectra of the two stars is given, and two competing explanations for the Wilson-Bappu effect are discussed.

  17. The chemical master equation approach to nonequilibrium steady-state of open biochemical systems: linear single-molecule enzyme kinetics and nonlinear biochemical reaction networks.

    PubMed

    Qian, Hong; Bishop, Lisa M

    2010-09-20

    We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC) with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a) individual biochemical reactions, (b) nonlinear network dynamics approaching to attractors, and (c) cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a) and (c) are stochastic while that with (b) is dominantly deterministic. Both (b) and (c) are emergent properties of a dynamic biochemical network; We suggest that the (c) is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b) in a "punctuated equilibrium" manner.

  18. The Chemical Master Equation Approach to Nonequilibrium Steady-State of Open Biochemical Systems: Linear Single-Molecule Enzyme Kinetics and Nonlinear Biochemical Reaction Networks

    PubMed Central

    Qian, Hong; Bishop, Lisa M.

    2010-01-01

    We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC) with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a) individual biochemical reactions, (b) nonlinear network dynamics approaching to attractors, and (c) cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a) and (c) are stochastic while that with (b) is dominantly deterministic. Both (b) and (c) are emergent properties of a dynamic biochemical network; We suggest that the (c) is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b) in a “punctuated equilibrium” manner. PMID:20957107

  19. Apolipophorin III: a lipid-triggered molecular switch.

    PubMed

    Weers, Paul M M; Ryan, Robert O

    2003-12-01

    Apolipophorin III (apoLp-III) is a low molecular weight exchangeable apolipoprotein that plays an important role in the enhanced neutral lipid transport during insect flight. The protein exists in lipid-free and lipid-bound states. The lipid-bound state is the active form of the protein and occurs when apoLp-III associates with lipid-enriched lipophorins. ApoLp-III is well characterized in two evolutionally divergent species: Locusta migratoria and Manduca sexta. The two apolipoproteins interact in a similar manner with model phospholipid vesicles, and transform them into discoidal particles. Their low intrinsic stability in the lipid-free state likely facilitates interaction with lipid surfaces. Low solution pH also favors lipid binding interaction through increased exposure of hydrophobic surfaces on apoLp-III. While secondary structure is maintained under acidic conditions, apoLp-III tertiary structure is altered, adopting molten globule-like characteristics. In studies of apoLp-III interaction with natural lipoproteins, we found that apoLp-III is readily displaced from the surface of L. migratoria low-density lipophorin by recombinant apoLp-III proteins from either L. migratoria or M. sexta. Thus, despite important differences between these two apoLp-IIIs (amino acid sequence, presence of carbohydrate), their functional similarity is striking. This similarity is also illustrated by the recently published NMR solution structure of M. sexta apoLp-III wherein its molecular architecture closely parallels that of L. migratoria apoLp-III. PMID:14599497

  20. Chemical Properties And Toxicity of Chromium(III) Nutritional Supplements

    SciTech Connect

    Levina, A.; Lay, P.A.

    2009-05-19

    The status of Cr(III) as an essential micronutrient for humans is currently under question. No functional Cr(III)-containing biomolecules have been definitively described as yet, and accumulated experience in the use of Cr(III) nutritional supplements (such as [Cr(pic){sub 3}], where pic = 2-pyridinecarboxylato) has shown no measurable benefits for nondiabetic people. Although the use of large doses of Cr(III) supplements may lead to improvements in glucose metabolism for type 2 diabetics, there is a growing concern over the possible genotoxicity of these compounds, particularly of [Cr(pic){sub 3}]. The current perspective discusses chemical transformations of Cr(III) nutritional supplements in biological media, with implications for both beneficial and toxic actions of Cr(III) complexes, which are likely to arise from the same biochemical mechanisms, dependent on concentrations of the reactive species. These species include: (1) partial hydrolysis products of Cr(III) nutritional supplements, which are capable of binding to biological macromolecules and altering their functions; and (2) highly reactive Cr(VI/V/IV) species and organic radicals, formed in reactions of Cr(III) with biological oxidants. Low concentrations of these species are likely to cause alterations in cell signaling (including enhancement of insulin signaling) through interactions with the active centers of regulatory enzymes in the cell membrane or in the cytoplasm, while higher concentrations are likely to produce genotoxic DNA lesions in the cell nucleus. These data suggest that the potential for genotoxic side-effects of Cr(III) complexes may outweigh their possible benefits as insulin enhancers, and that recommendations for their use as either nutritional supplements or antidiabetic drugs need to be reconsidered in light of these recent findings.

  1. BES-III distributed computing status

    NASA Astrophysics Data System (ADS)

    Belov, S. D.; Deng, Z. Y.; Korenkov, V. V.; Li, W. D.; Lin, T.; Ma, Z. T.; Nicholson, C.; Pelevanyuk, I. S.; Suo, B.; Trofimov, V. V.; Tsaregorodtsev, A. U.; Uzhinskiy, A. V.; Yan, T.; Yan, X. F.; Zhang, X. M.; Zhemchugov, A. S.

    2016-09-01

    The BES-III experiment at the Institute of High Energy Physics (Beijing, China) is aimed at the precision measurements in e+e- annihilation in the energy range from 2.0 till 4.6 GeV. The world's largest samples of J/psi and psi' events and unique samples of XYZ data have been already collected. The expected increase of the data volume in the coming years required a significant evolution of the computing model, namely shift from a centralized data processing to a distributed one. This report summarizes a current design of the BES-III distributed computing system, some of key decisions and experience gained during 2 years of operations.

  2. Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c

    PubMed Central

    Pierron, Denis; Opazo, Juan C.; Heiske, Margit; Papper, Zack; Uddin, Monica; Chand, Gopi; Wildman, Derek E.; Romero, Roberto; Goodman, Morris; Grossman, Lawrence I.

    2011-01-01

    Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades. PMID:22028846

  3. Biochemical Characterization of Indole Prenyltransferases

    PubMed Central

    Yu, Xia; Liu, Yan; Xie, Xiulan; Zheng, Xiao-Dong; Li, Shu-Ming

    2012-01-01

    The putative prenyltransferase gene ACLA_031240 belonging to the dimethylallyltryptophan synthase superfamily was identified in the genome sequence of Aspergillus clavatus and overexpressed in Escherichia coli. The soluble His-tagged protein EAW08391 was purified to near homogeneity and used for biochemical investigation with diverse aromatic substrates in the presence of different prenyl diphosphates. It has shown that in the presence of dimethylallyl diphosphate (DMAPP), the recombinant enzyme accepted very well simple indole derivatives with l-tryptophan as the best substrate. Product formation was also observed for tryptophan-containing cyclic dipeptides but with much lower conversion yields. In contrast, no product formation was detected in the reaction mixtures of l-tryptophan with geranyl or farnesyl diphosphate. Structure elucidation of the enzyme products by NMR and MS analyses proved unequivocally the highly regiospecific regular prenylation at C-5 of the indole nucleus of the simple indole derivatives. EAW08391 was therefore termed 5-dimethylallyltryptophan synthase, and it filled the last gap in the toolbox of indole prenyltransferases regarding their prenylation positions. Km values of 5-dimethylallyltryptophan synthase were determined for l-tryptophan and DMAPP at 34 and 76 μm, respectively. Average turnover number (kcat) at 1.1 s−1 was calculated from kinetic data of l-tryptophan and DMAPP. Catalytic efficiencies of 5-dimethylallyltryptophan synthase for l-tryptophan at 25,588 s−1·m−1 and for other 11 simple indole derivatives up to 1538 s−1·m−1 provided evidence for its potential usage as a catalyst for chemoenzymatic synthesis. PMID:22123822

  4. Simulation of Biochemical Pathway Adaptability Using Evolutionary Algorithms

    SciTech Connect

    Bosl, W J

    2005-01-26

    The systems approach to genomics seeks quantitative and predictive descriptions of cells and organisms. However, both the theoretical and experimental methods necessary for such studies still need to be developed. We are far from understanding even the simplest collective behavior of biomolecules, cells or organisms. A key aspect to all biological problems, including environmental microbiology, evolution of infectious diseases, and the adaptation of cancer cells is the evolvability of genomes. This is particularly important for Genomes to Life missions, which tend to focus on the prospect of engineering microorganisms to achieve desired goals in environmental remediation and climate change mitigation, and energy production. All of these will require quantitative tools for understanding the evolvability of organisms. Laboratory biodefense goals will need quantitative tools for predicting complicated host-pathogen interactions and finding counter-measures. In this project, we seek to develop methods to simulate how external and internal signals cause the genetic apparatus to adapt and organize to produce complex biochemical systems to achieve survival. This project is specifically directed toward building a computational methodology for simulating the adaptability of genomes. This project investigated the feasibility of using a novel quantitative approach to studying the adaptability of genomes and biochemical pathways. This effort was intended to be the preliminary part of a larger, long-term effort between key leaders in computational and systems biology at Harvard University and LLNL, with Dr. Bosl as the lead PI. Scientific goals for the long-term project include the development and testing of new hypotheses to explain the observed adaptability of yeast biochemical pathways when the myosin-II gene is deleted and the development of a novel data-driven evolutionary computation as a way to connect exploratory computational simulation with hypothesis

  5. Effect of Population III multiplicity on dark star formation

    NASA Astrophysics Data System (ADS)

    Stacy, Athena; Pawlik, Andreas H.; Bromm, Volker; Loeb, Abraham

    2012-03-01

    We numerically study the mutual interaction between dark matter (DM) and Population III (Pop III) stellar systems in order to explore the possibility of Pop III dark stars within this physical scenario. We perform a cosmological simulation, initialized at z˜ 100, which follows the evolution of gas and DM. We analyse the formation of the first minihalo at z˜ 20 and the subsequent collapse of the gas to densities of 1012 cm-3. We then use this simulation to initialize a set of smaller scale 'cut-out' simulations in which we further refine the DM to have spatial resolution similar to that of the gas. We test multiple DM density profiles, and we employ the sink particle method to represent the accreting star-forming region. We find that, for a range of DM configurations, the motion of the Pop III star-disc system serves to separate the positions of the protostars with respect to the DM density peak, such that there is insufficient DM to influence the formation and evolution of the protostars for more than ˜5000 years. In addition, the star-disc system causes gravitational scattering of the central DM to lower densities, further decreasing the influence of DM over time. Any DM-powered phase of Pop III stars will thus be very short-lived for the typical multiple system, and DM will not serve to significantly prolong the life of Pop III stars.

  6. Effect of Population III Multiplicity on Dark Star Formation

    NASA Technical Reports Server (NTRS)

    Stacy, Athena; Pawlik, Andreas H.; Bromm, Volker; Loeb, Abraham

    2012-01-01

    We numerically study the mutual interaction between dark matter (DM) and Population III (Pop III) stellar systems in order to explore the possibility of Pop III dark stars within this physical scenario. We perform a cosmological simulation, initialized at z approx. 100, which follows the evolution of gas and DM. We analyze the formation of the first mini halo at z approx. 20 and the subsequent collapse of the gas to densities of 10(exp 12)/cu cm. We then use this simulation to initialize a set of smaller-scale 'cut-out' simulations in which we further refine the DM to have spatial resolution similar to that of the gas. We test multiple DM density profiles, and we employ the sink particle method to represent the accreting star-forming region. We find that, for a range of DM configurations, the motion of the Pop III star-disk system serves to separate the positions of the protostars with respect to the DM density peak, such that there is insufficient DM to influence the formation and evolution of the protostars for more than approx. 5000 years. In addition, the star-disk system causes gravitational scattering of the central DM to lower densities, further decreasing the influence of DM over time. Any DM-powered phase of Pop III stars will thus be very short-lived for the typical multiple system, and DM will not serve to significantly prolong the life of Pop III stars.

  7. A case study of evolutionary computation of biochemical adaptation

    NASA Astrophysics Data System (ADS)

    François, Paul; Siggia, Eric D.

    2008-06-01

    Simulations of evolution have a long history, but their relation to biology is questioned because of the perceived contingency of evolution. Here we provide an example of a biological process, adaptation, where simulations are argued to approach closer to biology. Adaptation is a common feature of sensory systems, and a plausible component of other biochemical networks because it rescales upstream signals to facilitate downstream processing. We create random gene networks numerically, by linking genes with interactions that model transcription, phosphorylation and protein-protein association. We define a fitness function for adaptation in terms of two functional metrics, and show that any reasonable combination of them will yield the same adaptive networks after repeated rounds of mutation and selection. Convergence to these networks is driven by positive selection and thus fast. There is always a path in parameter space of continuously improving fitness that leads to perfect adaptation, implying that the actual mutation rates we use in the simulation do not bias the results. Our results imply a kinetic view of evolution, i.e., it favors gene networks that can be learned quickly from the random examples supplied by mutation. This formulation allows for deductive predictions of the networks realized in nature.

  8. A Program on Biochemical and Biomedical Engineering.

    ERIC Educational Resources Information Center

    San, Ka-Yiu; McIntire, Larry V.

    1989-01-01

    Presents an introduction to the Biochemical and Biomedical Engineering program at Rice University. Describes the development of the academic and enhancement programs, including organizational structure and research project titles. (YP)

  9. DMPS-arsenic challenge test. II. Modulation of arsenic species, including monomethylarsonous acid (MMA(III)), excreted in human urine.

    PubMed

    Aposhian, H V; Zheng, B; Aposhian, M M; Le, X C; Cebrian, M E; Cullen, W; Zakharyan, R A; Ma, M; Dart, R C; Cheng, Z; Andrewes, P; Yip, L; O'Malley, G F; Maiorino, R M; Van Voorhies, W; Healy, S M; Titcomb, A

    2000-05-15

    The administration of sodium 2,3-dimercapto-1-propane sulfonate (DMPS) to humans chronically exposed to inorganic arsenic in their drinking water resulted in the increased urinary excretion of arsenic, the appearance and identification of monomethylarsonous acid (MMA(III)) in their urine, and a large decrease in the concentration and percentage of urinary dimethylarsinic acid (DMA). This is the first time that MMA(III) has been detected in the urine. In vitro biochemical experiments were then designed and performed to understand the urinary appearance of MMA(III) and decrease of DMA. The DMPS-MMA(III) complex was not active as a substrate for the MMA(III) methyltransferase. The experimental results support the hypothesis that DMPS competes with endogenous ligands for MMA(III), forming a DMPS-MMA complex that is readily excreted in the urine and points out the need for studying the biochemical toxicology of MMA(III). It should be emphasized that MMA(III) was excreted in the urine only after DMPS administration. The results of these studies raise many questions about the potential central role of MMA(III) in the toxicity of inorganic arsenic and to the potential involvement of MMA(III) in the little-understood etiology of hyperkeratosis, hyperpigmentation, and cancer that can result from chronic inorganic arsenic exposure.

  10. [Biochemical diagnostics of fatal opium intoxication].

    PubMed

    Papyshev, I P; Astashkina, O G; Tuchik, E S; Nikolaev, B S; Cherniaev, A L

    2013-01-01

    Biochemical diagnostics of fatal opium intoxication remains a topical problem in forensic medical science and practice. We investigated materials obtained in the course of forensic medical expertise of the cases of fatal opium intoxication. The study revealed significant differences between myoglobin levels in blood, urine, myocardium, and skeletal muscles. The proposed approach to biochemical diagnostics of fatal opium intoxication enhances the accuracy and the level of evidence of expert conclusions.

  11. Plutonium (III) and uranium (III) nitrile complexes

    SciTech Connect

    Enriquez, A. E.; Matonic, J. H.; Scott, B. L.; Neu, M. P.

    2002-01-01

    Iodine oxidation of uranium and plutonium metals in tetrahydrofuran and pyridine form AnI{sub 3}(THF){sub 4} and AnI{sub 3}(py){sub 4} (An = Pu, U). These compounds represent convenient entries Into solution An(III) chemistry in organic solvents. Extensions of the actinide metal oxidation methodology in nitrile solvents by I{sub 2}, AgPF{sub 6}, and TIPF{sub 6} are presented here. Treatment of Pu{sup 0} in acetonitrile with iodine yields a putative PuI{sub 3}(NCMe){sub x} intermediate which can be trapped with the tripodal nitrogen donor ligand tpza (tpza = (tris[(2-pyrazinyl)methyl]amine)) and forms the eight-coordinate complex (tpza)PuI{sub 3}(NCMe). Treatment of excess U{sup 0} metal by iodine in acetonitrile afforded a brown crystalline mixed valence complex, [U(NCMe){sub 9}][UI{sub 6}][I], instead of UI{sub 3}(NCMe){sub 4}. The analogous reaction in bezonitrile forms red crystalline UI{sub 4}(NCPh){sub 4}. In contrast, treatment of UI{sub 3}(THF){sub 4} with excess acetonitrile cleanly generates [U(NCMe){sub 9}][I]{sub 3}. Oxidation of Pu{sup 0} by either TI(I) or Ag(I) hexafluorophosphate salts generates a nine-coordinate homoleptic acetonitrile adduct [Pu(NCMe){sub 9}][PF{sub 6}]{sub 3}. Attempts to oxidize U{sub 0} with these salts were unsuccessful.

  12. Lower glycolysis carries a higher flux than any biochemically possible alternative.

    PubMed

    Court, Steven J; Waclaw, Bartlomiej; Allen, Rosalind J

    2015-01-01

    The universality of many pathways of core metabolism suggests a strong role for evolutionary selection, but it remains unclear whether existing pathways have been selected from a large or small set of biochemical possibilities. To address this question, we construct in silico all possible biochemically feasible alternatives to the trunk pathway of glycolysis and gluconeogenesis, one of the most highly conserved pathways in metabolism. We show that, even though a large number of alternative pathways exist, the alternatives carry lower flux than the real pathway under typical physiological conditions. We also find that if physiological conditions were different, different pathways could outperform those found in nature. Together, our results demonstrate how thermodynamic and biophysical constraints restrict the biochemical alternatives that are open to evolution, and suggest that the existing trunk pathway of glycolysis and gluconeogenesis may represent a maximal flux solution. PMID:26416228

  13. Lower glycolysis carries a higher flux than any biochemically possible alternative

    PubMed Central

    Court, Steven J.; Waclaw, Bartlomiej; Allen, Rosalind J.

    2015-01-01

    The universality of many pathways of core metabolism suggests a strong role for evolutionary selection, but it remains unclear whether existing pathways have been selected from a large or small set of biochemical possibilities. To address this question, we construct in silico all possible biochemically feasible alternatives to the trunk pathway of glycolysis and gluconeogenesis, one of the most highly conserved pathways in metabolism. We show that, even though a large number of alternative pathways exist, the alternatives carry lower flux than the real pathway under typical physiological conditions. We also find that if physiological conditions were different, different pathways could outperform those found in nature. Together, our results demonstrate how thermodynamic and biophysical constraints restrict the biochemical alternatives that are open to evolution, and suggest that the existing trunk pathway of glycolysis and gluconeogenesis may represent a maximal flux solution. PMID:26416228

  14. Lower glycolysis carries a higher flux than any biochemically possible alternative.

    PubMed

    Court, Steven J; Waclaw, Bartlomiej; Allen, Rosalind J

    2015-09-29

    The universality of many pathways of core metabolism suggests a strong role for evolutionary selection, but it remains unclear whether existing pathways have been selected from a large or small set of biochemical possibilities. To address this question, we construct in silico all possible biochemically feasible alternatives to the trunk pathway of glycolysis and gluconeogenesis, one of the most highly conserved pathways in metabolism. We show that, even though a large number of alternative pathways exist, the alternatives carry lower flux than the real pathway under typical physiological conditions. We also find that if physiological conditions were different, different pathways could outperform those found in nature. Together, our results demonstrate how thermodynamic and biophysical constraints restrict the biochemical alternatives that are open to evolution, and suggest that the existing trunk pathway of glycolysis and gluconeogenesis may represent a maximal flux solution.

  15. Cranial mononeuropathy III - diabetic type

    MedlinePlus

    ... gov/ency/article/000692.htm Cranial mononeuropathy III - diabetic type To use the sharing features on this page, please enable JavaScript. Cranial mononeuropathy III -- diabetic type -- is usually a complication of diabetes that causes ...

  16. Exposure of Brassica juncea (L) to arsenic species in hydroponic medium: comparative analysis in accumulation and biochemical and transcriptional alterations.

    PubMed

    Ahmad, Mohd Anwar; Gupta, Meetu

    2013-11-01

    Arsenic (As) contamination in the environment has attracted considerable attention worldwide. The objective of the present study was to see the comparative effect of As species As(III) and As(V) on accumulation, biochemical responses, and gene expression analysis in Brassica juncea var. Pusa Jaganath (PJn). Hydroponically grown 14-day-old seedlings of B. juncea were treated with different concentrations of As(III) and As(V). Accumulation of total As increased with increasing concentration of both As species and exposure time, mainly in roots. Reduction in seed germination, root-shoot length, chlorophyll, and protein content were observed with increasing concentration and exposure time of both As species, being more in As(III)-treated leaves. PJn variety showed that antioxidant enzymes (superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX)) and stress-related parameters (cysteine, proline, and malondialdehyde (MDA)) were stimulated and allows plant to tolerate both As species. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis in leaves showed significant changes in protein profile with more stringent effect with As(III) stress. Semiquantitative RT-PCR analysis showed regulation in expression of phytochelatin synthase (PCS), metallothionine-2 (MT-2), glutathione reductase (GR), and glutathione synthetase (GS) genes under both As(III) and As(V) stresses. Results suggested that accumulation and inhibition on physiological parameters differ according to the As species, while molecular and biochemical parameters showed a combinatorial type of tolerance mechanism against As(III) and As(V) stresses.

  17. A general method for modeling biochemical and biomedical response

    NASA Astrophysics Data System (ADS)

    Ortiz, Roberto; Lerd Ng, Jia; Hughes, Tyler; Abou Ghantous, Michel; Bouhali, Othmane; Arredouani, Abdelilah; Allen, Roland

    2012-10-01

    The impressive achievements of biomedical science have come mostly from experimental research with human subjects, animal models, and sophisticated laboratory techniques. Additionally, theoretical chemistry has been a major aid in designing new drugs. Here we introduce a method which is similar to others already well known in theoretical systems biology, but which specifically addresses biochemical changes as the human body responds to medical interventions. It is common in systems biology to use first-order differential equations to model the time evolution of various chemical concentrations, and we as physicists can make a significant impact through designing realistic models and then solving the resulting equations. Biomedical research is rapidly advancing, and the technique presented in this talk can be applied in arbitrarily large models containing tens, hundreds, or even thousands of interacting species, to determine what beneficial effects and side effects may result from pharmaceuticals or other medical interventions.

  18. Manuscript evolution.

    PubMed

    Howe, C J; Barbrook, A C; Spencer, M; Robinson, P; Bordalejo, B; Mooney, L R

    2001-03-01

    Frequently, letters, words and sentences are used in undergraduate textbooks and the popular press as an analogy for the coding, transfer and corruption of information in DNA. We discuss here how the converse can be exploited, by using programs designed for biological analysis of sequence evolution to uncover the relationships between different manuscript versions of a text. We point out similarities between the evolution of DNA and the evolution of texts.

  19. Manuscript evolution.

    PubMed

    Howe, C J; Barbrook, A C; Spencer, M; Robinson, P; Bordalejo, B; Mooney, L R

    2001-09-01

    Frequently, letters, words and sentences are used in undergraduate textbooks and the popular press as an analogy for the coding, transfer and corruption of information in DNA. We discuss here how the converse can be exploited, by using programs designed for biological analysis of sequence evolution to uncover the relationships between different manuscript versions of a text. We point out similarities between the evolution of DNA and the evolution of texts.

  20. Rotation and internal structure of Population III protostars

    NASA Astrophysics Data System (ADS)

    Stacy, Athena; Greif, Thomas H.; Klessen, Ralf S.; Bromm, Volker; Loeb, Abraham

    2013-05-01

    We analyse the cosmological simulations performed in the recent work of Greif et al., which followed the early growth and merger history of Population III (Pop III) stars while resolving scales as small as 0.05 R⊙. This is the first set of cosmological simulations to self-consistently resolve the rotation and internal structure of Pop III protostars. We find that Pop III stars form under significant rotational support which is maintained for the duration of the simulations. The protostellar surfaces spin from ˜50 per cent to nearly 100 per cent of Keplerian rotational velocity. These rotation rates persist after experiencing multiple stellar merger events. In the brief time period simulated (˜10 yr), the protostars show little indication of convective instability, and their properties furthermore show little correlation with the properties of their host minihaloes. If Pop III protostars within this range of environments generally form with high degrees of rotational support, and if this rotational support is maintained for a sufficient amount of time, this has a number of crucial implications for Pop III evolution and nucleosynthesis, as well as the possibility for Pop III pair-instability supernovae, and the question of whether the first stars produced gamma-ray bursts.

  1. TYPE III RADIO BURSTS PERTURBED BY WEAK CORONAL SHOCKS

    SciTech Connect

    Li, B.; Cairns, Iver H.

    2012-07-10

    Some type III bursts are observed to undergo sudden flux modifications, e.g., reductions and intensifications, when type III beams cross shocks in the upper corona or solar wind. First simulations are presented for type III bursts perturbed by weak coronal shocks, which type III beams traverse. The simulations incorporate spatially localized jumps in plasma density and electron and ion temperatures downstream of a shock. A shock is predicted to produce significant modulations to a type III burst: (1) a broadband flux reduction or frequency gap caused by the shock's density jump, (2) a narrowband flux intensification originating from where the downstream plasma density locally has a small gradient, (3) a possible intensification from the shock front or just upstream, and (4) changes in the frequency drift rate profile and the temporal evolution of radiation flux at frequencies corresponding to the shocked plasma. The modulations are caused primarily by fundamental modifications to the radiation processes in response to the shocked density and temperatures. The predicted intensifications and reductions appear qualitatively consistent with the available small number of reported observations, although it is unclear how representative these observations are. It is demonstrated that a weak shock can cause an otherwise radio-quiet type III beam to produce observable levels of narrowband radio emission. The simulations suggest that type III bursts with frequency-time fine structures may provide a tool to probe shocks in the corona and solar wind, especially for weak shocks that do not radiate by themselves.

  2. Behind the scene with the fathead team: Part III. Molecular, biochemical, and in vitro analyses

    EPA Science Inventory

    As part of a research team focused on aquatic toxicity testing using fathead minnows as a model species, this presentation is the third in the three-part series, giving an overview of the types of field and laboratory studies as well as sample processing our team conducts at the ...

  3. Type III Hyperlipoproteinaemia

    PubMed Central

    Borrie, Peter

    1969-01-01

    Eighteen patients with type III hyperlipoproteinaemia, diagnosed on the basis of skin lesions, serum lipids, and lipoprotein electrophoresis, have been fully investigated over a period of 15 years. The incidence of coronary artery disease was only slightly increased, and was not increased at all among first-degree relatives. Peripheral occlusive arterial disease was probably more common. An increased incidence of carbohydrate intolerance was found in neither the patients nor their relatives. The effects of treatment on the skin were uniformly good. ImagesFig. 1Fig. 2 PMID:5783124

  4. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  5. 40 CFR 158.2010 - Biochemical pesticides data requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides data...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2010 Biochemical pesticides... required to support registration of biochemical pesticides. Sections 158.2080 through 158.2084 identify...

  6. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  7. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  8. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  9. 40 CFR 158.2000 - Biochemical pesticides definition and applicability.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Biochemical pesticides definition and...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2000 Biochemical pesticides definition and applicability. This subpart applies to all biochemical pesticides as defined in paragraphs...

  10. Nonlinear biochemical signal processing via noise propagation

    NASA Astrophysics Data System (ADS)

    Kim, Kyung Hyuk; Qian, Hong; Sauro, Herbert M.

    2013-10-01

    Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance, fluctuations in biochemical activities become significant and such "noise" can propagate through regulatory cascades in terms of biochemical reaction networks. Here we develop an intuitive, yet fully quantitative method for analyzing how noise affects cellular phenotypes based on identifying a system's nonlinearities and noise propagations. We observe that such noise can simultaneously enhance sensitivities in one behavioral region while reducing sensitivities in another. Employing this novel phenomenon we designed three biochemical signal processing modules: (a) A gene regulatory network that acts as a concentration detector with both enhanced amplitude and sensitivity. (b) A non-cooperative positive feedback system, with a graded dose-response in the deterministic case, that serves as a bistable switch due to noise-induced ultra-sensitivity. (c) A noise-induced linear amplifier for gene regulation that requires no feedback. The methods developed in the present work allow one to understand and engineer nonlinear biochemical signal processors based on fluctuation-induced phenotypes.

  11. Nonlinear biochemical signal processing via noise propagation.

    PubMed

    Kim, Kyung Hyuk; Qian, Hong; Sauro, Herbert M

    2013-10-14

    Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance, fluctuations in biochemical activities become significant and such "noise" can propagate through regulatory cascades in terms of biochemical reaction networks. Here we develop an intuitive, yet fully quantitative method for analyzing how noise affects cellular phenotypes based on identifying a system's nonlinearities and noise propagations. We observe that such noise can simultaneously enhance sensitivities in one behavioral region while reducing sensitivities in another. Employing this novel phenomenon we designed three biochemical signal processing modules: (a) A gene regulatory network that acts as a concentration detector with both enhanced amplitude and sensitivity. (b) A non-cooperative positive feedback system, with a graded dose-response in the deterministic case, that serves as a bistable switch due to noise-induced ultra-sensitivity. (c) A noise-induced linear amplifier for gene regulation that requires no feedback. The methods developed in the present work allow one to understand and engineer nonlinear biochemical signal processors based on fluctuation-induced phenotypes.

  12. POPULATION III HYPERNOVAE

    SciTech Connect

    Smidt, Joseph; Whalen, Daniel J.; Wiggins, Brandon K.; Even, Wesley; Fryer, Chris L.; Johnson, Jarrett L.

    2014-12-20

    Population III supernovae have been of growing interest of late for their potential to directly probe the properties of the first stars, particularly the most energetic events that are visible near the edge of the observable universe. Until now, hypernovae, the unusually energetic Type Ib/c supernovae that are sometimes associated with gamma-ray bursts, have been overlooked as cosmic beacons at the highest redshifts. In this, the latest of a series of studies on Population III supernovae, we present numerical simulations of 25-50 M {sub ☉} hypernovae and their light curves done with the Los Alamos RAGE and SPECTRUM codes. We find that they will be visible at z = 10-15 to the James Webb Space Telescope and z = 4-5 to the Wide-Field Infrared Survey Telescope, tracing star formation rates in the first galaxies and at the end of cosmological reionization. If, however, the hypernova crashes into a dense shell ejected by its progenitor, it is expected that a superluminous event will occur that may be seen at z ∼ 20 in the first generation of stars.

  13. Sloan Digital Sky Survey III (SDSS-III), Data Release 8

    DOE Data Explorer

    Building on the legacy of the Sloan Digital Sky Survey (SDSS) and SDSS-II, the SDSS-III Collaboration is working to map the Milky Way, search for extrasolar planets, and solve the mystery of dark energy. SDSS-III's first release, Data Release 8 (DR8), became available in the first half of 2012. DR8 contains all the images ever taken by the SDSS telescope. Together, these images make up the largest color image of the sky ever made. A version of the DR8 image is shown to the right. DR8 also includes measurements for nearly 500 million stars, galaxies, and quasars, and spectra for nearly two million. All of DR8's images, spectra, and measurements are available to anyone online. You can browse through sky images, look up data for individual objects, or search for objects anywhere using any criteria. SDSS-III will collect data from 2008 to 2014, using the 2.5-meter telescope at Apache Point Observatory. SDSS-III consists of four surveys, each focused on a different scientific theme. These four surveys are: 1) Baryon Oscillation Spectroscopic Survey (BOSS); 2) SEGUE-2 (Sloan Extension for Galactic Understanding and Exploration); 3) The APO Galactic Evolution Experiment (APOGEE); and 4) The Multi-object APO Radial Velocity Exoplanet Large-area Survey (MARVELS). [Copied with edits from http://www.sdss3.org/index.php

  14. Teaching Evolution

    ERIC Educational Resources Information Center

    Bryner, Jeanna

    2005-01-01

    Eighty years after the famous 1925 Scopes "monkey trial," which tested a teacher's right to discuss the theory of evolution in the classroom, evolution--and its most recent counterview, called "intelligent design"--are in the headlines again, and just about everyone seems to have an opinion. This past July, President Bush weighed in, telling…

  15. FTS evolution

    NASA Technical Reports Server (NTRS)

    Provost, David E.

    1990-01-01

    Viewgraphs on flight telerobotic servicer evolution are presented. Topics covered include: paths for FTS evolution; frequently performed actions; primary task states; EPS radiator panel installation; generic task definitions; path planning; non-contact alignment; contact planning and control; and human operator interface.

  16. Chemical evolution and the origin of life

    NASA Technical Reports Server (NTRS)

    Oro, J.

    1983-01-01

    A review is presented of recent advances made in the understanding of the formation of carbon compounds in the universe and the occurrence of processes of chemical evolution. Topics discussed include the principle of evolutionary continuity, evolution as a fundamental principle of the physical universe, the nuclear synthesis of biogenic elements, organic cosmochemistry and interstellar molecules, the solar nebula and the solar system in chemical evolution, the giant planets and Titan in chemical evolution, and comets and their interaction with the earth. Also examined are carbonaceous chondrites, environment of the primitive earth, energy sources available on the primitive earth, the synthesis of biochemical monomers and oligomers, the abiotic transcription of nucleotides, unified prebiotic and enzymatic mechanisms, phospholipids and membranes, and protobiological evolution.

  17. Reconfigurable neuromorphic computation in biochemical systems.

    PubMed

    Chiang, Hui-Ju Katherine; Jiang, Jie-Hong R; Fages, Francois

    2015-08-01

    Implementing application-specific computation and control tasks within a biochemical system has been an important pursuit in synthetic biology. Most synthetic designs to date have focused on realizing systems of fixed functions using specifically engineered components, thus lacking flexibility to adapt to uncertain and dynamically-changing environments. To remedy this limitation, an analog and modularized approach to realize reconfigurable neuromorphic computation with biochemical reactions is presented. We propose a biochemical neural network consisting of neuronal modules and interconnects that are both reconfigurable through external or internal control over the concentrations of certain molecular species. Case studies on classification and machine learning applications using the DNA strain displacement technology demonstrate the effectiveness of our design in both reconfiguration and autonomous adaptation. PMID:26736417

  18. Biochemical Removal of HAP Precursors From Coal

    SciTech Connect

    Olson, G.; Tucker, L.; Richards, J.

    1997-07-01

    This project addresses DOE`s interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals.

  19. Testosterone Deficiency - Establishing A Biochemical Diagnosis

    PubMed Central

    Krakowsky, Yonah

    2015-01-01

    Testosterone deficiency is a common and often unrecognized disorder impacting the lives of many men. Symptoms related to low testosterone are relatively non-specific and clinicians must therefore ensure that a patients’ symptomatology is supported by a biochemical profile suggestive of testosterone deficiency. There are many options available to determine a patient’s testosterone level and laboratories will vary in the type of biochemical assessment they provide. In assessing patients with suspected low testosterone, the presence of symptoms and a low total testosterone is usually sufficient to initiate therapy. In equivocal cases, measurement of free or bioavailable testosterone with a reliable assay can further clarify the clinical picture. By understanding the differences between total, free and bioavailable testosterone, and the accuracy and reliability of their measurement, clinicians can better interpret their patients’ biochemical testosterone profile.

  20. Alterations in phenotypic biochemical markers in bladder epithelium during tumorigenesis.

    PubMed

    Rao, J Y; Hemstreet, G P; Hurst, R E; Bonner, R B; Jones, P L; Min, K W; Fradet, Y

    1993-09-01

    Phenotypic biochemical markers of oncogenesis and differentiation were mapped in bladder biopsies to investigate changes that occur in bladder tumorigenesis and to identify markers for increased bladder cancer risk. Touch preparations from biopsy specimens from 30 patients were obtained from tumors, the adjacent bladder epithelium, and random distant bladder epithelium. Markers, including DNA ploidy, epidermal growth factor receptor (EGFR), and oncoproteins, were quantified in individual cells by using quantitative fluorescence image analysis. Cluster analysis revealed the markers fell into three independent groups: (i) G-actin and EGFR; (ii) ploidy, cytology, and p185 (HER-2/neu oncoprotein) (ERBB2); and (iii) p300, a low-grade tumor antigen. Each marker displayed a gradient of abnormality from distant field to adjacent field to tumor. Different patterns for each marker suggested a developmental sequence of bladder cancer oncogenesis; G-actin was altered in 58% of distant biopsies (vs. 0/6 normals, P < 0.001), ploidy and cytology were altered in < 20% of distant fields and approximately 80% of tumors, and the other markers were intermediate. Patterns of EGFR and p185 suggest low-and high-grade tracks diverge early (P < 0.05 by Mann-Whitney U test for EGFR and ANOVA for p185). In conclusion, this study shows that a sequence of phenotypic changes accompanies development and progression of bladder cancers. Biochemical alterations in cells of the bladder field are often detectable before abnormal pathology, and markers previously thought to be limited to tumors were found in the field. The hierarchy of expression may be useful in identifying high-risk patients, assessing completeness of response to therapy, and monitoring and predicting recurrence. PMID:8367495

  1. Biochemical Screening for in utero Drug Exposure.

    PubMed

    Wright, Tricia E

    2015-01-01

    Licit and illicit drug use is a common complication of pregnancy. Accurate information on drug use is difficult to obtain for many reasons as women fear self-disclosure or consenting for drug testing due to stigma, guilt, and fear of social and legal harm. As information about drug use is clinically very important, biochemical testing is an important adjunct to careful maternal history. In addition, research studies depend on accurate measures of exposure when reporting risks of a substance. This paper delineates available matrices for and methods of biochemical drug testing in pregnant women and neonates.

  2. Biochemical computation for spine structural plasticity

    PubMed Central

    Nishiyama, Jun; Yasuda, Ryohei

    2015-01-01

    The structural plasticity of dendritic spines is considered to be essential for various forms of synaptic plasticity, learning and memory. The process is mediated by a complex signaling network consisting of numerous species of molecules. Furthermore, the spatiotemporal dynamics of the biochemical signaling is regulated in a complicated manner due to geometrical restrictions from the unique morphology of the dendritic branches and spines. Recent advances in optical techniques have enabled the exploration of the spatiotemporal aspects of the signal regulations in spines and dendrites and have provided many insights into the principle of the biochemical computation that underlies spine structural plasticity. PMID:26139370

  3. Definition of four HLA-A2 subtypes by CML typing and biochemical analysis.

    PubMed

    van der Poel, J J; Mölders, H; Thompson, A; Ploegh, H L

    1983-01-01

    The population of HLA-A2-positive individuals, currently considered serologically homogeneous, can be divided into three subtypes on the basis of antigen recognition by various HLA-A2-specific cytotoxic T lymphocytes (CTLs). When these three types of HLA-A2 antigens were analyzed biochemically, they were found to be distinct. Isoelectric focusing (IEF) of HLA antigens digested with neuraminidase (NANAse) suggested that the difference(s) reside in the polypeptide backbone of the HLA-A2 heavy chain. Biochemical analysis distinguishes three distinct categories of HLA-A2 antigens: (1) a major subtype, designated HLA-A2.I, (2) a minor subtype, designated HLA-A2.II, possessing a more basic isoelectric point (IEP) and (3) a minor HLA-A2 subtype more acidic in its IEP than HLA-A2.I, designated HLA-A2.III. A fourth HLA-A2 subtype could be defined by discordance between cell-mediated lympholysis (CML) typing and biochemical analysis. The latter HLA-A2 antigen was defined as a variant by CTL, but was biochemically indistinguishable from the major subtype HLA-A2.I. PMID:6407985

  4. Biochemical characterization of predicted Precambrian RuBisCO.

    PubMed

    Shih, Patrick M; Occhialini, Alessandro; Cameron, Jeffrey C; Andralojc, P John; Parry, Martin A J; Kerfeld, Cheryl A

    2016-01-01

    The antiquity and global abundance of the enzyme, RuBisCO, attests to the crucial and longstanding role it has played in the biogeochemical cycles of Earth over billions of years. The counterproductive oxygenase activity of RuBisCO has persisted over billions of years of evolution, despite its competition with the carboxylase activity necessary for carbon fixation, yet hypotheses regarding the selective pressures governing RuBisCO evolution have been limited to speculation. Here we report the resurrection and biochemical characterization of ancestral RuBisCOs, dating back to over one billion years ago (Gyr ago). Our findings provide an ancient point of reference revealing divergent evolutionary paths taken by eukaryotic homologues towards improved specificity for CO2, versus the evolutionary emphasis on increased rates of carboxylation observed in bacterial homologues. Consistent with these distinctions, in vivo analysis reveals the propensity of ancestral RuBisCO to be encapsulated into modern-day carboxysomes, bacterial organelles central to the cyanobacterial CO2 concentrating mechanism.

  5. Biochemical characterization of predicted Precambrian RuBisCO

    PubMed Central

    Shih, Patrick M.; Occhialini, Alessandro; Cameron, Jeffrey C.; Andralojc, P John; Parry, Martin A. J.; Kerfeld, Cheryl A.

    2016-01-01

    The antiquity and global abundance of the enzyme, RuBisCO, attests to the crucial and longstanding role it has played in the biogeochemical cycles of Earth over billions of years. The counterproductive oxygenase activity of RuBisCO has persisted over billions of years of evolution, despite its competition with the carboxylase activity necessary for carbon fixation, yet hypotheses regarding the selective pressures governing RuBisCO evolution have been limited to speculation. Here we report the resurrection and biochemical characterization of ancestral RuBisCOs, dating back to over one billion years ago (Gyr ago). Our findings provide an ancient point of reference revealing divergent evolutionary paths taken by eukaryotic homologues towards improved specificity for CO2, versus the evolutionary emphasis on increased rates of carboxylation observed in bacterial homologues. Consistent with these distinctions, in vivo analysis reveals the propensity of ancestral RuBisCO to be encapsulated into modern-day carboxysomes, bacterial organelles central to the cyanobacterial CO2 concentrating mechanism. PMID:26790750

  6. Biochemical characterization of predicted Precambrian RuBisCO.

    PubMed

    Shih, Patrick M; Occhialini, Alessandro; Cameron, Jeffrey C; Andralojc, P John; Parry, Martin A J; Kerfeld, Cheryl A

    2016-01-01

    The antiquity and global abundance of the enzyme, RuBisCO, attests to the crucial and longstanding role it has played in the biogeochemical cycles of Earth over billions of years. The counterproductive oxygenase activity of RuBisCO has persisted over billions of years of evolution, despite its competition with the carboxylase activity necessary for carbon fixation, yet hypotheses regarding the selective pressures governing RuBisCO evolution have been limited to speculation. Here we report the resurrection and biochemical characterization of ancestral RuBisCOs, dating back to over one billion years ago (Gyr ago). Our findings provide an ancient point of reference revealing divergent evolutionary paths taken by eukaryotic homologues towards improved specificity for CO2, versus the evolutionary emphasis on increased rates of carboxylation observed in bacterial homologues. Consistent with these distinctions, in vivo analysis reveals the propensity of ancestral RuBisCO to be encapsulated into modern-day carboxysomes, bacterial organelles central to the cyanobacterial CO2 concentrating mechanism. PMID:26790750

  7. Pseudo Class III malocclusion

    PubMed Central

    Al-Hummayani, Fadia M.

    2016-01-01

    The treatment of deep anterior crossbite is technically challenging due to the difficulty of placing traditional brackets with fixed appliances. This case report represents a none traditional treatment modality to treat deep anterior crossbite in an adult pseudo class III malocclusion complicated by severely retruded, supraerupted upper and lower incisors. Treatment was carried out in 2 phases. Phase I treatment was performed by removable appliance “modified Hawley appliance with inverted labial bow,” some modifications were carried out to it to suit the presented case. Positive overbite and overjet was accomplished in one month, in this phase with minimal forces exerted on the lower incisors. Whereas, phase II treatment was performed with fixed appliances (braces) to align teeth and have proper over bite and overjet and to close posterior open bite, this phase was accomplished within 11 month. PMID:27052290

  8. Stellar evolution.

    NASA Technical Reports Server (NTRS)

    Chiu, H.-Y. (Editor); Muriel, A.

    1972-01-01

    Aspects of normal stellar evolution are discussed together with evolution near the main sequence, stellar evolution from main sequence to white dwarf or carbon ignition, the structure of massive main-sequence stars, and problems of stellar stability and stellar pulsation. Other subjects considered include variable stars, white dwarfs, close binaries, novae, early supernova luminosity, neutron stars, the photometry of field horizontal-branch stars, and stellar opacity. Transport mechanisms in stars are examined together with thermonuclear reactions and nucleosynthesis, the instability problem in nuclear burning shells, stellar coalescence, and intense magnetic fields in astrophysics. Individual items are announced in this issue.

  9. Geometry Genetics and Evolution

    NASA Astrophysics Data System (ADS)

    Siggia, Eric

    2011-03-01

    Darwin argued that highly perfected organs such as the vertebrate eye could evolve by a series of small changes, each of which conferred a selective advantage. In the context of gene networks, this idea can be recast into a predictive algorithm, namely find networks that can be built by incremental adaptation (gradient search) to perform some task. It embodies a ``kinetic'' view of evolution where a solution that is quick to evolve is preferred over a global optimum. Examples of biochemical kinetic networks were evolved for temporal adaptation, temperature compensated entrainable clocks, explore-exploit trade off in signal discrimination, will be presented as well as networks that model the spatially periodic somites (vertebrae) and HOX gene expression in the vertebrate embryo. These models appear complex by the criterion of 19th century applied mathematics since there is no separation of time or spatial scales, yet they are all derivable by gradient optimization of simple functions (several in the Pareto evolution) often based on the Shannon entropy of the time or spatial response. Joint work with P. Francois, Physics Dept. McGill University. With P. Francois, Physics Dept. McGill University

  10. Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family[W][OPEN

    PubMed Central

    Ren, Lin-Ling; Liu, Yan-Jing; Liu, Hai-Jing; Qian, Ting-Ting; Qi, Li-Wang; Wang, Xiao-Ru; Zeng, Qing-Yin

    2014-01-01

    Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families. PMID:24934172

  11. Populations III.1 and III.2 gamma-ray bursts: constraints on the event rate for future radio and X-ray surveys

    NASA Astrophysics Data System (ADS)

    de Souza, R. S.; Yoshida, N.; Ioka, K.

    2011-09-01

    Aims: We calculate the theoretical event rate of gamma-ray bursts (GRBs) from the collapse of massive first-generation (Population III; Pop III) stars. The Pop III GRBs could be super-energetic with the isotropic energy up to Eiso ≳ 1055-57 erg, providing a unique probe of the high-redshift Universe. Methods: We consider both the so-called Pop III.1 stars (primordial) and Pop III.2 stars (primordial but affected by radiation from other stars). We employ a semi-analytical approach that considers inhomogeneous hydrogen reionization and chemical evolution of the intergalactic medium. Results: We show that Pop III.2 GRBs occur more than 100 times more frequently than Pop III.1 GRBs, and thus should be suitable targets for future GRB missions. Interestingly, our optimistic model predicts an event rate that is already constrained by the current radio transient searches. We expect ~10-104 radio afterglows above ~0.3 mJy on the sky with ~1 year variability and mostly without GRBs (orphans), which are detectable by ALMA, EVLA, LOFAR, and SKA, while we expect to observe maximum of N < 20 GRBs per year integrated over at z > 6 for Pop III.2 and N < 0.08 per year integrated over at z > 10 for Pop III.1 with EXIST, and N < 0.2 for Pop III.2 GRBs per year integrated over at z > 6 with Swift.

  12. A Course in Biochemical Engineering Fundamentals (Revisited).

    ERIC Educational Resources Information Center

    Bailey, J. E.; Ollis, D. F.

    1985-01-01

    Provides: (1) a glossary of terms used in biochemical engineering; (2) a list of key developments in the field; and (3) emphases placed in 15 topic areas in a course restructured on the basis of these developments. Topic areas include enzyme kinetics/applications, genetics and microbial control, transport phenomena, and others. (JN)

  13. Predictive biochemical assays for late radiation effects

    SciTech Connect

    Rubin, P.; Finkelstein, J.N.; Siemann, D.W.; Shapiro, D.L.; Van Houtte, P.; Penney, D.P.

    1986-04-01

    Surfactant precursors or other products of Type II pneumocytes have the potential to be the first biochemical marker for late radiation effects. This is particularly clinically important in the combined modality era because of the frequent occurrence of pneumonitis and pulmonary fibrosis secondary to radiation or chemotherapy. Accordingly, correlative studies have been pursued with the Type II pneumocyte as a beginning point to understand the complex pathophysiology of radiation pneumonitis and fibrosis. From our ultrastructural and biochemical studies, it is evident that Type II pneumocytes are an early target of radiation and the release of surfactant into the alveolus shortly after exposure persists for days and weeks. Through the use of lavaging techniques, alveolar surfactant has been elevated after pulmonary irradiation. In three murine strains and in the rabbit, there is a strong correlation with surfactant release at 7 and/or 28 days in vivo with later lethality in months. In vitro studies using cultures of type II pneumocytes also demonstrate dose response and tolerance factors that are comparable to the in vivo small and large animal diagnostic models. New markers are being developed to serve as a predictive index for later lethal pneumonopathies. With the development of these techniques, the search for early biochemical markers in man has been undertaken. Through the use of biochemical, histological, and ultrastructural techniques, a causal relationship between radiation effects on type II pneumocytes, pulmonary cells, endothelial cells of blood vessels, and their roles in the production of pneumonitis and fibrosis will evolve.

  14. Biochemical Applications in the Analytical Chemistry Lab

    ERIC Educational Resources Information Center

    Strong, Cynthia; Ruttencutter, Jeffrey

    2004-01-01

    An HPLC and a UV-visible spectrophotometer are identified as instruments that helps to incorporate more biologically-relevant experiments into the course, in order to increase the students understanding of selected biochemistry topics and enhances their ability to apply an analytical approach to biochemical problems. The experiment teaches…

  15. 2009 Biochemical Conversion Platform Review Report

    SciTech Connect

    Ferrell, John

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Biochemical Conversion platform review meeting, held on April 14-16, 2009, at the Sheraton Denver Downtown, Denver, Colorado.

  16. Biochemical Thermodynamics under near Physiological Conditions

    ERIC Educational Resources Information Center

    Mendez, Eduardo

    2008-01-01

    The recommendations for nomenclature and tables in Biochemical Thermodynamics approved by IUBMB and IUPAC in 1994 can be easily introduced after the chemical thermodynamic formalism. Substitution of the usual standard thermodynamic properties by the transformed ones in the thermodynamic equations, and the use of appropriate thermodynamic tables…

  17. Survey of Biochemical Education in Japanese Universities.

    ERIC Educational Resources Information Center

    Kagawa, Yasuo

    1995-01-01

    Reports findings of questionnaires sent to faculty in charge of biochemical education in medical schools and other programs from dentistry to agriculture. Total class hours have declined since 1984. New trends include bioethics and computer-assisted learning. Tables show trends in lecture hours, lecture content, laboratory hours, core subject…

  18. Biochemical Approaches to Improved Nitrogen Fixation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving symbiotic nitrogen fixation by legumes has emerged again as an important topic on the world scene due to the energy crisis and lack of access to nitrogen fertilizer in developing countries. We have taken a biochemical genomics approach to improving symbiotic nitrogen fixation in legumes. L...

  19. Simulating Evolution

    ERIC Educational Resources Information Center

    Stebbins, Robert C.; Allen, Brockenbrough

    1975-01-01

    Described are simulations that can be used to illustrate evolution by natural selection. Suggestions for simulating phenomena such as adaptive radiation, color match to background and vision of predators are offered. (BR)

  20. FORMATION CRITERIA AND THE MASS OF SECONDARY POPULATION III STARS

    SciTech Connect

    Susa, Hajime; Umemura, Masayuki; Hasegawa, Kenji E-mail: umemura@ccs.tsukuba.ac.jp

    2009-09-01

    We explore the formation of secondary Population III (Pop III) stars under radiation hydrodynamic (RHD) feedback by a preformed massive star. To properly treat RHD feedback, we perform three-dimensional RHD simulations incorporating the radiative transfer of ionizing photons as well as H{sub 2} dissociating photons from a preformed star. A collapsing gas cloud is settled at a given distance from a 120 M{sub sun} Pop III star, and the evolution of the cloud is pursued including RHD feedback. We derive the threshold density depending on the distance, above which the cloud can keep collapsing owing to the shielding of H{sub 2} dissociating radiation. We find that an H{sub 2} shell formed ahead of an ionizing front works effectively to shield the H{sub 2} dissociating radiation, leading to the positive feedback for the secondary Pop III star formation. Also, near the threshold density, the envelope of gas cloud is stripped significantly by a shock associated with an ionizing front. By comparing the mass accretion timescale with the Kelvin-Helmholtz timescale, we estimate the mass of secondary Pop III stars. It turns out that the stripping by a shock can reduce the mass of secondary Pop III stars down to {approx}20 M{sub sun}.

  1. Tyrosinemia type III: diagnosis and ten-year follow-up.

    PubMed

    Cerone, R; Holme, E; Schiaffino, M C; Caruso, U; Maritano, L; Romano, C

    1997-09-01

    Tyrosinemia type III, caused by deficiency of 4-hydroxyphenylpyruvate dioxygenase, is a rare disorder of tyrosine catabolism. Primary 4-hydroxyphenylpyruvate dioxygenase deficiency has been described in only three patients. The biochemical phenotype shows hypertyrosinemia and elevated urinary excretion of 4-hydroxyphenyl derivatives. We report the clinical and biochemical findings and the results of long-term follow-up in a new patient with this disorder presenting with severe mental retardation and neurological abnormalities. The clinical phenotype is compared with those reported in the three previously described patients.

  2. Type III restriction-modification enzymes: a historical perspective.

    PubMed

    Rao, Desirazu N; Dryden, David T F; Bheemanaik, Shivakumara

    2014-01-01

    Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

  3. SUPERSTARS III: 3-5.

    ERIC Educational Resources Information Center

    North Carolina State Dept. of Public Education, Raleigh.

    SUPERSTARS III is a K-8 program designed as an enrichment opportunity for self-directed learners in mathematics. The basic purpose of SUPERSTARS III is to provide the extra challenge that self-motivated students need in mathematics and to do so in a structured, long-term program that does not impinge on the normal classroom routine or the…

  4. SUPERSTARS III: 6-8.

    ERIC Educational Resources Information Center

    North Carolina State Dept. of Public Education, Raleigh.

    SUPERSTARS III is a K-8 program designed as an enrichment opportunity for self-directed learners in mathematics. The basic purpose of SUPERSTARS III is to provide the extra challenge that self-motivated students need in mathematics and to do so in a structured, long-term program that does not impinge on the normal classroom routine or the…

  5. Using dBase III.

    ERIC Educational Resources Information Center

    Evans, Janet; And Others

    1986-01-01

    Four articles on dBASE III include three on library applications: a photocopy invoicing system for interlibrary loan, a vertical file subject headings list program, and a subject index to statistical resources. Another article explains the differences between interpreters and compilers and the advantages of the Clipper compiler for dBASE III. (EM)

  6. Biochemical transport modeling, estimation, and detection in realistic environments

    NASA Astrophysics Data System (ADS)

    Ortner, Mathias; Nehorai, Arye

    2006-05-01

    Early detection and estimation of the spread of a biochemical contaminant are major issues for homeland security applications. We present an integrated approach combining the measurements given by an array of biochemical sensors with a physical model of the dispersion and statistical analysis to solve these problems and provide system performance measures. We approximate the dispersion model of the contaminant in a realistic environment through numerical simulations of reflected stochastic diffusions describing the microscopic transport phenomena due to wind and chemical diffusion using the Feynman-Kac formula. We consider arbitrary complex geometries and account for wind turbulence. Localizing the dispersive sources is useful for decontamination purposes and estimation of the cloud evolution. To solve the associated inverse problem, we propose a Bayesian framework based on a random field that is particularly powerful for localizing multiple sources with small amounts of measurements. We also develop a sequential detector using the numerical transport model we propose. Sequential detection allows on-line analysis and detecting wether a change has occurred. We first focus on the formulation of a suitable sequential detector that overcomes the presence of unknown parameters (e.g. release time, intensity and location). We compute a bound on the expected delay before false detection in order to decide the threshold of the test. For a fixed false-alarm rate, we obtain the detection probability of a substance release as a function of its location and initial concentration. Numerical examples are presented for two real-world scenarios: an urban area and an indoor ventilation duct.

  7. Systems glycobiology: biochemical reaction networks regulating glycan structure and function

    PubMed Central

    Neelamegham, Sriram; Liu, Gang

    2011-01-01

    There is a growing use of bioinformatics based methods in the field of Glycobiology. These have been used largely to curate glycan structures, organize array-based experimental data and display existing knowledge of glycosylation-related pathways in silico. Although the cataloging of vast amounts of data is beneficial, it is often a challenge to gain meaningful mechanistic insight from this exercise alone. The development of specific analysis tools to query the database is necessary. If these queries can integrate existing knowledge of glycobiology, new insights may be gained. Such queries that couple biochemical knowledge and mathematics have been developed in the field of Systems Biology. The current review summarizes the current state of the art in the application of computational modeling in the field of Glycobiology. It provides (i) an overview of experimental and online resources that can be used to construct glycosylation reaction networks, (ii) mathematical methods to formulate the problem including a description of ordinary differential equation and logic-based reaction networks, (iii) optimization techniques that can be applied to fit experimental data for the purpose of model reconstruction and for evaluating unknown model parameters, (iv) post-simulation analysis methods that yield experimentally testable hypotheses and (v) a summary of available software tools that can be used by non-specialists to perform many of the above functions. PMID:21436236

  8. The diversity challenge in directed protein evolution.

    PubMed

    Wong, Tuck Seng; Zhurina, Daria; Schwaneberg, Ulrich

    2006-05-01

    Over the past decade, we have witnessed a bloom in the field of evolutive protein engineering which is fueled by advances in molecular biology techniques and high-throughput screening technology. Directed protein evolution is a powerful algorithm using iterative cycles of random mutagenesis and screening for tailoring protein properties to our needs in industrial applications and for elucidating proteins' structure function relationships. This review summarizes, categorizes and discusses advantages and disadvantages of random mutagenesis methods used for generating genetic diversity. These random mutagenesis methods have been classified into four main categories depending on the method employed for nucleotide substitutions: enzyme based methods (Category I), synthetic chemistry based methods (Category II), whole cell methods (Category III) and combined methods (Category I-II, I-III and II-III). The basic principle of each method is discussed and varied mutagenic conditions are summarized in Tables and compared (benchmarked) to each other in terms of: mutational bias, controllable mutation frequency, ability to generate consecutive nucleotide substitutions and subset diversity, dependency on gene length, technical simplicity/robustness and cost-effectiveness. The latter comparison shows how highly-biased and limited current diversity creating methods are. Based on these limitations, strategies for generating diverse mutant libraries are proposed and discussed (RaMuS-Flowchart; KISS principle). We hope that this review provides, especially for researchers just entering the field of directed evolution, a guide for developing successful directed evolution strategies by selecting complementary methods for generating diverse mutant libraries.

  9. Kombucha tea fermentation: Microbial and biochemical dynamics.

    PubMed

    Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

    2016-03-01

    Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

  10. Kombucha tea fermentation: Microbial and biochemical dynamics.

    PubMed

    Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

    2016-03-01

    Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

  11. Type III secretion systems and pathogenicity islands.

    PubMed

    Winstanley, C; Hart, C A

    2001-02-01

    Some bacterial pathogens have evolved by acquiring pathogenicity islands (PIs), which are clusters of genes encoding virulence traits. PIs encoding the secretion of effector molecules via type III secretion (TTS) systems have been discovered in several gram-negative pathogens. TTS systems are involved in contact-dependent secretion of virulence factors and can facilitate delivery of toxins directly into target cells. The expanding list of bacteria found to contain clusters of TTS genes includes members of the genera Yersinia, Salmonella, Shigella, Escherichia, Pseudomonas, Bordetella, Burkholderia, Chlamydia and a number of plant pathogens or symbionts. This review discusses the current knowledge of the role of TTS PIs in pathogenicity, the genetic organisation and evolution of such systems,and the potential for using TTS systems as targets for novel treatments.

  12. The Classification and Evolution of Enzyme Function.

    PubMed

    Martínez Cuesta, Sergio; Rahman, Syed Asad; Furnham, Nicholas; Thornton, Janet M

    2015-09-15

    Enzymes are the proteins responsible for the catalysis of life. Enzymes sharing a common ancestor as defined by sequence and structure similarity are grouped into families and superfamilies. The molecular function of enzymes is defined as their ability to catalyze biochemical reactions; it is manually classified by the Enzyme Commission and robust approaches to quantitatively compare catalytic reactions are just beginning to appear. Here, we present an overview of studies at the interface of the evolution and function of enzymes.

  13. The fine details of evolution.

    PubMed

    Laskowski, Roman A; Thornton, Janet M; Sternberg, Michael J E

    2009-08-01

    Charles Darwin's theory of evolution was based on studies of biology at the species level. In the time since his death, studies at the molecular level have confirmed his ideas about the kinship of all life on Earth and have provided a wealth of detail about the evolutionary relationships between different species and a deeper understanding of the finer workings of natural selection. We now have a wealth of data, including the genome sequences of a wide range of organisms, an even larger number of protein sequences, a significant knowledge of the three-dimensional structures of proteins, DNA and other biological molecules, and a huge body of information about the operation of these molecules as systems in the molecular machinery of all living things. This issue of Biochemical Society Transactions contains papers from oral presentations given at a Biochemical Society Focused Meeting to commemorate the 200th Anniversary of Charles Darwin's birth, held on 26-27 January 2009 at the Wellcome Trust Conference Centre, Cambridge. The talks reported on some of the insights into evolution which have been obtained from the study of protein sequences, structures and systems. PMID:19614583

  14. PREFACE: Quantum Optics III

    NASA Astrophysics Data System (ADS)

    Orszag, M.; Retamal, J. C.; Saavedra, C.; Wallentowitz, S.

    2007-06-01

    All the 50 years of conscious pondering did not bring me nearer to an answer to the question `what is light quanta?'. Nowadays, every rascal believes, he knows it, however, he is mistaken. (A Einstein, 1951 in a letter to M Besso) Quantum optics has played a key role in physics in the last several decades. On the other hand, in these early decades of the information age, the flow of information is becoming more and more central to our daily life. Thus, the related fields of quantum information theory as well as Bose-Einstein condensation have acquired tremendous importance in the last couple of decades. In Quantum Optics III, a fusion of these fields appears in a natural way. Quantum Optics III was held in Pucón, Chile, in 27-30 of November, 2006. This beautiful location in the south of Chile is near the lake Villarrica and below the snow covered volcano of the same name. This fantastic environment contributed to a relaxed atmosphere, suitable for informal discussion and for the students to have a chance to meet the key figures in the field. The previous Quantum Optics conferences took place in Santiago, Chile (Quantum Optics I, 2000) and Cozumel, Mexico (Quantum Optics II, 2004). About 115 participants from 19 countries attended and participated in the meeting to discuss a wide variety of topics such as quantum-information processing, experiments related to non-linear optics and squeezing, various aspects of entanglement including its sudden death, correlated twin-photon experiments, light storage, decoherence-free subspaces, Bose-Einstein condensation, discrete Wigner functions and many more. There was a strong Latin-American participation from Argentina, Brazil, Chile, Colombia, Peru, Uruguay, Venezuela and Mexico, as well as from Europe, USA, China, and Australia. New experimental and theoretical results were presented at the conference. In Latin-America a quiet revolution has taken place in the last twenty years. Several groups working in quantum optics and

  15. Chromium(III) Binding Phage Screening for the Selective Adsorption of Cr(III) and Chromium Speciation.

    PubMed

    Yang, Ting; Zhang, Xiao-Yu; Zhang, Xiao-Xiao; Chen, Ming-Li; Wang, Jian-Hua

    2015-09-30

    The screening of suitable sorption medium is the key for highly selective solid phase extraction (SPE) of heavy metals. Herein, we demonstrate a universal protocol for producing selective SPE adsorbent through an evolutional approach based on phage display peptide library. By choosing chromium(III) as the model target, immobilized Cr(III) resins are first prepared using Ni-NTA affinity resins for the interaction with NEB heptapeptide phage library. After three rounds of positive biopanning against target Cr(III) and negative biopanning against foreign metal species, Cr(III) binding phages with high selectivity are obtained. The binding affinity and selectivity are further assessed with ELISA. The phages bearing peptide (YKASLIT) is finally chosen and immobilized on cytopore beads for Cr(III) preconcentration. The retained Cr(III) is efficiently recovered by 0.10 mol L(-1) HNO3 and quantified with ICP-MS. By loading 4000 μL of sample solution at pH 7.0 for 2 h and stripping with 400 μL of 0.10 mol L(-1) HNO3, a linear range of 0.05-0.50 μg L(-1) is achieved along with an enrichment factor of 7.1. The limit of detection is derived to be 15 ng L(-1) (3σ, n = 7) with a RSD of 3.6% (0.25 μg L(-1), n = 7). The procedure is validated by analyzing chromium content in a certified reference material GBW08608 (simulate water). In addition, chromium speciation in real water samples is demonstrated. Cr(VI) is first converted into Cr(III), and the latter subjected to the sorption onto the Cr(III) binding phage, followed by elution and quantification of the total chromium amount, and finally speciation is achieved by difference.

  16. Chromium(III) Binding Phage Screening for the Selective Adsorption of Cr(III) and Chromium Speciation.

    PubMed

    Yang, Ting; Zhang, Xiao-Yu; Zhang, Xiao-Xiao; Chen, Ming-Li; Wang, Jian-Hua

    2015-09-30

    The screening of suitable sorption medium is the key for highly selective solid phase extraction (SPE) of heavy metals. Herein, we demonstrate a universal protocol for producing selective SPE adsorbent through an evolutional approach based on phage display peptide library. By choosing chromium(III) as the model target, immobilized Cr(III) resins are first prepared using Ni-NTA affinity resins for the interaction with NEB heptapeptide phage library. After three rounds of positive biopanning against target Cr(III) and negative biopanning against foreign metal species, Cr(III) binding phages with high selectivity are obtained. The binding affinity and selectivity are further assessed with ELISA. The phages bearing peptide (YKASLIT) is finally chosen and immobilized on cytopore beads for Cr(III) preconcentration. The retained Cr(III) is efficiently recovered by 0.10 mol L(-1) HNO3 and quantified with ICP-MS. By loading 4000 μL of sample solution at pH 7.0 for 2 h and stripping with 400 μL of 0.10 mol L(-1) HNO3, a linear range of 0.05-0.50 μg L(-1) is achieved along with an enrichment factor of 7.1. The limit of detection is derived to be 15 ng L(-1) (3σ, n = 7) with a RSD of 3.6% (0.25 μg L(-1), n = 7). The procedure is validated by analyzing chromium content in a certified reference material GBW08608 (simulate water). In addition, chromium speciation in real water samples is demonstrated. Cr(VI) is first converted into Cr(III), and the latter subjected to the sorption onto the Cr(III) binding phage, followed by elution and quantification of the total chromium amount, and finally speciation is achieved by difference. PMID:26346061

  17. The evolution of transcriptional regulation in eukaryotes

    NASA Technical Reports Server (NTRS)

    Wray, Gregory A.; Hahn, Matthew W.; Abouheif, Ehab; Balhoff, James P.; Pizer, Margaret; Rockman, Matthew V.; Romano, Laura A.

    2003-01-01

    Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.

  18. Structural and biochemical characterization of DSL ribozyme.

    PubMed

    Horie, Souta; Ikawa, Yoshiya; Inoue, Tan

    2006-01-01

    We recently reported on the molecular design and synthesis of a new RNA ligase ribozyme (DSL), whose active site was selected from a sequence library consisting of 30 random nucleotides set on a defined 3D structure of a designed RNA scaffold. In this study, we report on the structural and biochemical analyses of DSL. Structural analysis indicates that the active site, which consists of the selected sequence, attaches to the folded scaffold as designed. To see whether DSL resembles known ribozymes, a biochemical assay was performed. Metal-dependent kinetic studies suggest that the ligase requires Mg2+ ions. The replacement of Mg2+ with Co(NH3)6(3+) prohibits the reaction, indicating that DSL requires innersphere coordination of Mg2+ for a ligation reaction. The results show that DSL has requirements similar to those of previously reported catalytic RNAs.

  19. Thermodynamics of biochemical networks and duality theorems

    NASA Astrophysics Data System (ADS)

    De Martino, Daniele

    2013-05-01

    One interesting yet difficult computational issue has recently been posed in biophysics in regard to the implementation of thermodynamic constraints to complex networks. Biochemical networks of enzymes inside cells are among the most efficient, robust, differentiated, and flexible free-energy transducers in nature. How is the second law of thermodynamics encoded for these complex networks? In this article it is demonstrated that for chemical reaction networks in the steady state the exclusion (presence) of closed reaction cycles makes possible (impossible) the definition of a chemical potential vector. Interestingly, this statement is encoded in one of the key results in combinatorial optimization, i.e., the Gordan theorem of the alternatives. From a computational viewpoint, the theorem reveals that calculating a reaction's free energy and identifying infeasible loops in flux states are dual problems whose solutions are mutually exclusive, and this opens the way for efficient and scalable methods to perform the energy balance analysis of large-scale biochemical networks.

  20. Least squares estimation in stochastic biochemical networks.

    PubMed

    Rempala, Grzegorz A

    2012-08-01

    The paper presents results on the asymptotic properties of the least-squares estimates (LSEs) of the reaction constants in mass-action, stochastic, biochemical network models. LSEs are assumed to be based on the longitudinal data from partially observed trajectories of a stochastic dynamical system, modeled as a continuous-time, pure jump Markov process. Under certain regularity conditions on such a process, it is shown that the vector of LSEs is jointly consistent and asymptotically normal, with the asymptotic covariance structure given in terms of a system of ordinary differential equations (ODE). The derived asymptotic properties hold true as the biochemical network size (the total species number) increases, in which case the stochastic dynamical system converges to the deterministic mass-action ODE. An example is provided, based on synthetic as well as RT-PCR data from the retro-transcription network of the LINE1 gene.

  1. Construction and analysis of biochemical networks

    NASA Astrophysics Data System (ADS)

    Binns, Michael; Theodoropoulos, Constantinos

    2012-09-01

    Bioprocesses are being implemented for a range of different applications including the production of fuels, chemicals and drugs. Hence, it is becoming increasingly important to understand and model how they function and how they can be modified or designed to give the optimal performance. Here we discuss the construction and analysis of biochemical networks which are the first logical steps towards this goal. The construction of a reaction network is possible through reconstruction: extracting information from literature and from databases. This can be supplemented by reaction prediction methods which can identify steps which are missing from the current knowledge base. Analysis of biochemical systems generally requires some experimental input but can be used to identify important reactions and targets for enhancing the performance of the organism involved. Metabolic flux, pathway and metabolic control analysis can be used to determine the limits, capabilities and potential targets for enhancement respectively.

  2. Sources of type III solar microwave bursts

    NASA Astrophysics Data System (ADS)

    Zhdanov, Dmitriy; Lesovoi, Sergey; Tokhchukova, Susanna

    2016-06-01

    Microwave fine structures allow us to study plasma evolution in an energy release region. The Siberian Solar Radio Telescope (SSRT) is a unique instrument designed to examine fine structures at 5.7 GHz. A complex analysis of data from RATAN-600, 4-8 GHz spectropolarimeter, and SSRT, simultaneously with extreme UV data, made it possible to localize sources of III type microwave drift bursts in August 10, 2011 event within the entire frequency band of burst occurrences, as well as to determine the most probable region of primary energy release. To localize sources of III type bursts from RATAN-600 data, an original method for data processing has been worked out. At 5.7 GHz, the source of bursts was determined along two coordinates whereas at 4.5, 4.7, 4.9, 5.1, 5.3, 5.5 and 6.0 GHz, their locations were identified along one coordinate. The size of the burst source at 5.1 GHz was found to be maximum as compared to source sizes at other frequencies.

  3. Catalytic currents of hydrogen evolution by platinum-group metal mercaptoquinolinates in aqueous-organic media

    SciTech Connect

    Ulakhovich, N.A.; Budnikov, G.K.; Medyantseva, E.P.; Romanova, O.N.; Sturis, A.P.

    1986-06-20

    Coordination compounds of Ru(III), Rh(III), Os(III), and Ir(III) with methyl derivatives of 8-mercaptoquinoline catalyze the evolution of hydrogen on mercury and graphite electrodes in a mixture of DMFA and acetate buffer solution. The catalytic activity of the complexes increases with decreasing acidity of the mercapto group. The proposed scheme of the electrode process includes preprotonation of the original complex with the central atom in the 3+ degree of oxidation.

  4. Biochemical alterations during swimming induced stress.

    PubMed

    Aruj, N; Sharafatullah, T; Najam, R; Ahmed, S P; Ahmad, S I

    1994-07-01

    Stress can be defined as any stimulus that creates an imbalance in the internal environment. Hypothalamus has sensors that detect changes produced in the body. Stress can cause diseases by altering immune system, cardiovascular System neurotransmitter and neuroendocrine functions. Present study is designed to evaluate the effect of stress on few biochemical parameters during swimming induced stress. Significant changes have been observed especially in lipid profile. Corticosterone was also evaluated as reliable stress marker.

  5. Biochemical correlates of neurosensory changes in weightlessness

    NASA Technical Reports Server (NTRS)

    Leach, Carolyn S.; Reschke, Millard F.

    1989-01-01

    The possible existence of a relationship between space motion sickness and chemical and biochemical variables measured in body fluids is studied. Clinical chemistry and endocrine measurements from blood and urine samples taken before and after Space Shuttle flights were analyzed along with the occurrence of SMS during flight and provocative testing before flight. Significant positive correlations were observed with serum chloride and significant negative correlations with serum phosphate, serum uric acid, and plasma thyroid stimulating hormone.

  6. Electronic modulation of biochemical signal generation

    NASA Astrophysics Data System (ADS)

    Gordonov, Tanya; Kim, Eunkyoung; Cheng, Yi; Ben-Yoav, Hadar; Ghodssi, Reza; Rubloff, Gary; Yin, Jun-Jie; Payne, Gregory F.; Bentley, William E.

    2014-08-01

    Microelectronic devices that contain biological components are typically used to interrogate biology rather than control biological function. Patterned assemblies of proteins and cells have, however, been used for in vitro metabolic engineering, where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. Such devices form part of technologies that attempt to recreate animal and human physiological functions on a chip and could be used to revolutionize drug development. These ambitious goals will, however, require new biofabrication methodologies that help connect microelectronics and biological systems and yield new approaches to device assembly and communication. Here, we report the electrically mediated assembly, interrogation and control of a multi-domain fusion protein that produces a bacterial signalling molecule. The biological system can be electrically tuned using a natural redox molecule, and its biochemical response is shown to provide the signalling cues to drive bacterial population behaviour. We show that the biochemical output of the system correlates with the electrical input charge, which suggests that electrical inputs could be used to control complex on-chip biological processes.

  7. Electronic modulation of biochemical signal generation.

    PubMed

    Gordonov, Tanya; Kim, Eunkyoung; Cheng, Yi; Ben-Yoav, Hadar; Ghodssi, Reza; Rubloff, Gary; Yin, Jun-Jie; Payne, Gregory F; Bentley, William E

    2014-08-01

    Microelectronic devices that contain biological components are typically used to interrogate biology rather than control biological function. Patterned assemblies of proteins and cells have, however, been used for in vitro metabolic engineering, where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. Such devices form part of technologies that attempt to recreate animal and human physiological functions on a chip and could be used to revolutionize drug development. These ambitious goals will, however, require new biofabrication methodologies that help connect microelectronics and biological systems and yield new approaches to device assembly and communication. Here, we report the electrically mediated assembly, interrogation and control of a multi-domain fusion protein that produces a bacterial signalling molecule. The biological system can be electrically tuned using a natural redox molecule, and its biochemical response is shown to provide the signalling cues to drive bacterial population behaviour. We show that the biochemical output of the system correlates with the electrical input charge, which suggests that electrical inputs could be used to control complex on-chip biological processes.

  8. Stoichiometric network theory for nonequilibrium biochemical systems.

    PubMed

    Qian, Hong; Beard, Daniel A; Liang, Shou-dan

    2003-02-01

    We introduce the basic concepts and develop a theory for nonequilibrium steady-state biochemical systems applicable to analyzing large-scale complex isothermal reaction networks. In terms of the stoichiometric matrix, we demonstrate both Kirchhoff's flux law sigma(l)J(l)=0 over a biochemical species, and potential law sigma(l) mu(l)=0 over a reaction loop. They reflect mass and energy conservation, respectively. For each reaction, its steady-state flux J can be decomposed into forward and backward one-way fluxes J = J+ - J-, with chemical potential difference deltamu = RT ln(J-/J+). The product -Jdeltamu gives the isothermal heat dissipation rate, which is necessarily non-negative according to the second law of thermodynamics. The stoichiometric network theory (SNT) embodies all of the relevant fundamental physics. Knowing J and deltamu of a biochemical reaction, a conductance can be computed which directly reflects the level of gene expression for the particular enzyme. For sufficiently small flux a linear relationship between J and deltamu can be established as the linear flux-force relation in irreversible thermodynamics, analogous to Ohm's law in electrical circuits.

  9. [Biochemical antenatal screening for fetal anomalies.].

    PubMed

    Torfadóttir, G; Jónsson, J J

    2001-05-01

    Biochemical antenatal screening started 30 years ago. Initially, the goal was to detect neural tube defects by measuring a-fetoprotein in maternal serum (MS-AFP) and amniotic fluid (AF-AFP). The serendipitous discovery of an association between low AFP maternal serum concentration and chromosomal anomalies resulted in increased research interest in biochemical screening in pregnancy. Subsequently double, triple or quadruple tests in 2nd trimester of pregnancy became widely used in combination with fetal chromosome determination in at risk individuals. In Iceland, antenatal screening for chromosomal anomalies has essentially been based on fetal chromosome studies offered to pregnant women 35 years or older. This strategy needs to be revised. Recently first trimester biochemical screening based on maternal serum pregnancy associated plasma protein A (MS-PAPP-A) and free b-human chorionic gonadotropin (MS-free b-hCG) and multivariate risk assessment has been developed. This screening test can be improved if done in conjunction with nuchal translucency measurements in an early sonography scan. PMID:17018982

  10. Hydrogel-based piezoresistive biochemical microsensors

    NASA Astrophysics Data System (ADS)

    Guenther, Margarita; Schulz, Volker; Gerlach, Gerald; Wallmersperger, Thomas; Solzbacher, Florian; Magda, Jules J.; Tathireddy, Prashant; Lin, Genyao; Orthner, Michael P.

    2010-04-01

    This work is motivated by a demand for inexpensive, robust and reliable biochemical sensors with high signal reproducibility and long-term-stable sensitivity, especially for medical applications. Micro-fabricated sensors can provide continuous monitoring and on-line control of analyte concentrations in ambient aqueous solutions. The piezoresistive biochemical sensor containing a special biocompatible polymer (hydrogel) with a sharp volume phase transition in the neutral physiological pH range near 7.4 can detect a specific analyte, for example glucose. Thereby the hydrogel-based biochemical sensors are useful for the diagnosis and monitoring of diabetes. The response of the glucosesensitive hydrogel was studied at different regimes of the glucose concentration change and of the solution supply. Sensor response time and accuracy with which a sensor can track gradual changes in glucose was estimated. Additionally, the influence of various recommended sterilization methods on the gel swelling properties and on the mechano-electrical transducer of the pH-sensors has been evaluated in order to choose the most optimal sterilization method for the implantable sensors. It has been shown that there is no negative effect of gamma irradiation with a dose of 25.7 kGy on the hydrogel sensitivity. In order to achieve an optimum between sensor signal amplitude and sensor response time, corresponding calibration and measurement procedures have been proposed and evaluated for the chemical sensors.

  11. Biochemical reaction engineering for redox reactions.

    PubMed

    Wandrey, Christian

    2004-01-01

    Redox reactions are still a challenge for biochemical engineers. A personal view for the development of this field is given. Cofactor regeneration was an obstacle for quite some time. The first technical breakthrough was achieved with the system formate/formate dehydrogenase for the regeneration of NADH2. In cases where the same enzyme could be used for chiral reduction as well as for cofactor regeneration, isopropanol as a hydrogen source proved to be beneficial. The coproduct (acetone) can be removed by pervaporation. Whole-cell reductions (often yeast reductions) can also be used. By proper biochemical reaction engineering, it is possible to apply these systems in a continuous way. By cloning a formate dehydrogenase and an oxidoreductase "designer bug" can be obtained where formate is used instead of glucose as the hydrogen source. Complex sequences of redox reactions can be established by pathway engineering with a focus on gene overexpression or with a focus on establishing non-natural pathways. The success of pathway engineering can be controlled by measuring cytosolic metabolite concentrations. The optimal exploitation of such systems calls for the integrated cooperation of classical and molecular biochemical engineering.

  12. Outcome of tyrosinaemia type III.

    PubMed

    Ellaway, C J; Holme, E; Standing, S; Preece, M A; Green, A; Ploechl, E; Ugarte, M; Trefz, F K; Leonard, J V

    2001-12-01

    Tyrosinaemia type III is a rare disorder caused by a deficiency of 4-hydroxyphenylpyruvate dioxygenase, the second enzyme in the catabolic pathway of tyrosine. The majority of the nine previously reported patients have presented with neurological symptoms after the neonatal period, while others detected by neonatal screening have been asymptomatic. All have had normal liver and renal function and none has skin or eye abnormalities. A further four patients with tyrosinaemia type III are described. It is not clear whether a strict low tyrosine diet alters the natural history of tyrosinaemia type III, although there remains a suspicion that treatment may be important, at least in infancy.

  13. Stellar Evolution Physics 2 Volume Hardback Set

    NASA Astrophysics Data System (ADS)

    Iben, Icko

    2012-12-01

    Volume 1: Part I. Introduction and Overview: 1. Qualitative description of single and binary star evolution; 2. Quantitative foundations of stellar evolution theory; Part II. Basic Physical Processes in Stellar Interiors: 3. Properties of and physical processes in the interiors of main sequence stars - order of magnitude estimates; 4. Statistical physics, thermodynamics, and equations of state; 5. Polytropes and single zone models: elementary tools for understanding some aspects of stellar structure and evolution; 6. Hydrogen-burning nuclear reactions and energy-generation rates; 7. Photon-matter interactions and opacity; 8. Equations of stellar evolution and methods of solution; Part III. Pre-Main Sequence, Main Sequence, and Shell Hydrogen Burning Evolution of Single Stars: 9. Star formation and evolution to the main-sequence; 10. Solar structure and neutrino physics; 11. Evolution during core hydrogen-burning phases up to the onset of helium burning; Volume 2: Part IV. Transport Processes, Weak Interaction Processes and Helium-Burning Reactions: 12. Diffusion and gravitational settling; 13. Heat conduction by electrons; 14. Beta decay and electron capture at high densities in stars; 15. The current-current weak interaction and the production of neutrino-antineutrino pairs; 16. Helium-burning nuclear reactions and energy-generation rates; Part V. Evolution during Helium-Burning Phases: 17. Evolution of a low mass model burning helium and hydrogen; 18. Evolution of an intermediate mass model burning helium and hydrogen; 19. Neutron production and neutron capture in a thermally pulsing asymptotic giant branch star of intermediate mass; 20. Evolution of a massive population I model during helium- and carbon-burning stages; Part VI. Terminal Evolution of Low and Intermediate Mass Stars: 21. Wind mass loss on the AGB and formation of a circumstellar envelope, evolution of the remnant as the central star of a planetary nebula, and white dwarf evolution; Index.

  14. Security Evolution.

    ERIC Educational Resources Information Center

    De Patta, Joe

    2003-01-01

    Examines how to evaluate school security, begin making schools safe, secure schools without turning them into fortresses, and secure schools easily and affordably; the evolution of security systems into information technology systems; using schools' high-speed network lines; how one specific security system was developed; pros and cons of the…

  15. Art & Evolution

    ERIC Educational Resources Information Center

    Terry, Mark

    2005-01-01

    In this article, the author presents a two-week evolution unit for his biology class. He uses Maria Sybilla Merian (1647-1717) as an example of an Enlightenment mind at work--in this case a woman recognized as one of the great artists and natural scientists of her time. Her representations of butterflies, caterpillars and their pupae, and the…

  16. Insertion devices for Doris III

    SciTech Connect

    Pfluger, J.; Heintze, G. ); Baran, W.; Fernow, D.; Kuntze, K. )

    1992-01-01

    In this paper the mechanical and magnetic layout of the first three insertion devices for DORIS III, an upgraded reconstruction of DORIS II, is described and results of the magnetic characterization are given as well.

  17. Experimental evolution in biofilm populations

    PubMed Central

    Steenackers, Hans P.; Parijs, Ilse; Foster, Kevin R.; Vanderleyden, Jozef

    2016-01-01

    Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

  18. Experimental evolution in biofilm populations.

    PubMed

    Steenackers, Hans P; Parijs, Ilse; Foster, Kevin R; Vanderleyden, Jozef

    2016-05-01

    Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

  19. Experimental evolution in biofilm populations.

    PubMed

    Steenackers, Hans P; Parijs, Ilse; Foster, Kevin R; Vanderleyden, Jozef

    2016-05-01

    Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques.

  20. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

    PubMed

    Kuznetsova, Ekaterina; Nocek, Boguslaw; Brown, Greg; Makarova, Kira S; Flick, Robert; Wolf, Yuri I; Khusnutdinova, Anna; Evdokimova, Elena; Jin, Ke; Tan, Kemin; Hanson, Andrew D; Hasnain, Ghulam; Zallot, Rémi; de Crécy-Lagard, Valérie; Babu, Mohan; Savchenko, Alexei; Joachimiak, Andrzej; Edwards, Aled M; Koonin, Eugene V; Yakunin, Alexander F

    2015-07-24

    The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members. PMID:26071590

  1. Cherenkov imaging and biochemical sensing in vivo during radiation therapy

    NASA Astrophysics Data System (ADS)

    Zhang, Rongxiao

    While Cherenkov emission was discovered more than eighty years ago, the potential applications of imaging this during radiation therapy have just recently been explored. With approximately half of all cancer patients being treated by radiation at some point during their cancer management, there is a constant challenge to ensure optimal treatment efficiency is achieved with maximal tumor to normal tissue therapeutic ratio. To achieve this, the treatment process as well as biological information affecting the treatment should ideally be effective and directly derived from the delivery of radiation to the patient. The value of Cherenkov emission imaging was examined here, primarily for visualization of treatment monitoring and then secondarily for Cherenkov-excited luminescence for tissue biochemical sensing within tissue. Through synchronized gating to the short radiation pulses of a linear accelerator (200Hz & 3 micros pulses), and applying a gated intensified camera for imaging, the Cherenkov radiation can be captured near video frame rates (30 frame per sec) with dim ambient room lighting. This procedure, sometimes termed Cherenkoscopy, is readily visualized without affecting the normal process of external beam radiation therapy. With simulation, phantoms and clinical trial data, each application of Cherenkoscopy was examined: i) for treatment monitoring, ii) for patient position monitoring and motion tracking, and iii) for superficial dose imaging. The temporal dynamics of delivered radiation fields can easily be directly imaged on the patient's surface. Image registration and edge detection of Cherenkov images were used to verify patient positioning during treatment. Inter-fraction setup accuracy and intra-fraction patient motion was detectable to better than 1 mm accuracy. Cherenkov emission in tissue opens up a new field of biochemical sensing within the tissue environment, using luminescent agents which can be activated by this light. In the first study of

  2. Mechanism and evolution of hypoxia-tolerance in humans.

    PubMed

    Hochachka, P W

    1998-04-01

    To physiologists, the term 'adaptation' usually refers to any trait that is considered advantageous; evolutionary biologists require a more rigorous definition (restricting it to traits arising and maintained under selection). By their definition, many physiological traits may merely reflect inheritance passed on through lineage. In considering the evolution of tolerance to reduced oxygen availability, we examined the issue (of true adaptations versus simple inheritance) in pinnipeds (the two dominant groups, phocids and otariids, with varying diving capacities) and in human lineages exposed for varying generational periods to hypobaric hypoxia. Basic principles of the evolution of complex physiological systems first emerged from an analysis of the diving response. We then analyzed human responses to hypobaric hypoxia in three different lineages: lowlanders, Andean natives (Quechuas) and Himalayan natives (Sherpas). As in the pinniped example, we found 'conservative' and 'adaptable' physiological characters involved in human responses to hypoxia. Conservative characters are clearly dominant and are too numerous to outline in detail; three examples are haemoglobin oxygen-affinities, the organization of muscle into different fibre types and the brain's almost exclusive preference for glucose as a fuel. Most notably, we also found evidence for 'adaptable' characters at all levels of organization examined. At the whole-body level in Quechuas and Sherpas, we found (i) that maximum aerobic and anaerobic exercise capacities were down-regulated, (ii) that the acute effect of hypoxia (making up the energy deficit due to oxygen lack; i.e. the Pasteur effect) expected from lowlanders was blunted, and (iii) that acclimation effects were also attenuated. The biochemical behaviour of skeletal muscles was consistent with lowered reliance on glycolytic contributions to energy supply, thus improving the yield of ATP per mole of carbon fuel utilized. Heart adaptations also seemed to

  3. Mechanism and evolution of hypoxia-tolerance in humans.

    PubMed

    Hochachka, P W

    1998-04-01

    To physiologists, the term 'adaptation' usually refers to any trait that is considered advantageous; evolutionary biologists require a more rigorous definition (restricting it to traits arising and maintained under selection). By their definition, many physiological traits may merely reflect inheritance passed on through lineage. In considering the evolution of tolerance to reduced oxygen availability, we examined the issue (of true adaptations versus simple inheritance) in pinnipeds (the two dominant groups, phocids and otariids, with varying diving capacities) and in human lineages exposed for varying generational periods to hypobaric hypoxia. Basic principles of the evolution of complex physiological systems first emerged from an analysis of the diving response. We then analyzed human responses to hypobaric hypoxia in three different lineages: lowlanders, Andean natives (Quechuas) and Himalayan natives (Sherpas). As in the pinniped example, we found 'conservative' and 'adaptable' physiological characters involved in human responses to hypoxia. Conservative characters are clearly dominant and are too numerous to outline in detail; three examples are haemoglobin oxygen-affinities, the organization of muscle into different fibre types and the brain's almost exclusive preference for glucose as a fuel. Most notably, we also found evidence for 'adaptable' characters at all levels of organization examined. At the whole-body level in Quechuas and Sherpas, we found (i) that maximum aerobic and anaerobic exercise capacities were down-regulated, (ii) that the acute effect of hypoxia (making up the energy deficit due to oxygen lack; i.e. the Pasteur effect) expected from lowlanders was blunted, and (iii) that acclimation effects were also attenuated. The biochemical behaviour of skeletal muscles was consistent with lowered reliance on glycolytic contributions to energy supply, thus improving the yield of ATP per mole of carbon fuel utilized. Heart adaptations also seemed to

  4. [Metabolic correction: a biochemical option against diseases].

    PubMed

    Miranda-Massari, Jorge R; González, Michael J; Rodriguez-Gomez, José R; Duconge, Jorge; Allende-Vigo, Myriam Z; Jiménez Ramirez, Francisco J; Cintrón, Kenneth; Ricart, Carlos; Zaragoza-Urdaz, Rafael; Berdiel, Miguel Jabbar; Vázquez, Alex

    2015-01-01

    Human development and its physiology depends on a number of complex biochemical body processes, many of which are interactive and codependent. The speed and the degree in which many physiological reactions are completed depend on enzyme activity, which in turn depends on the bioavailability of co-factors and micronutrients such as vitamins and minerals. To achieve a healthy physiological state, organism need that biochemical reactions occur in a controlled and specific way at a particular speed and level or grade fully completed. To achieve this, is required an optimal metabolic balance. Factors such as, a particular genetic composition, inadequate dietary consumption patterns, traumas, diseases, toxins and environmental stress all of these factors rising demands for nutrients in order to obtain optimal metabolic balance. Metabolic correction is a biochemical and physiological concept that explains how improvements in cellular biochemistry of an organism can help the body achieve metabolic and physiological optimization. We summarize the contribution of several pioneers in understanding the role of micronutrients in health management. The concept of metabolic correction is becoming a significant term due to the presence of genetic variants that affect the speed of reactions of enzymes, causing metabolic alterations that enhance or promote the state/development of multiple diseases. Decline in the nutritional value of the food we eat, the increase in demand for certain nutrients caused by normal development, diseases and medications induce, usually, nutrients consumption. These nutritional deficiencies and insufficiencies are causing massive economic costs due to increased morbidity and mortality in our society. In summary, metabolic correction improves the enzymatic function, which favors the physiological normal functions, thus, contributing to improving health and the welfare of the human being. The purpose of this paper is to describe and introduce the concept

  5. Mitochondrial Evolution

    PubMed Central

    Gray, Michael W.

    2012-01-01

    Viewed through the lens of the genome it contains, the mitochondrion is of unquestioned bacterial ancestry, originating from within the bacterial phylum α-Proteobacteria (Alphaproteobacteria). Accordingly, the endosymbiont hypothesis—the idea that the mitochondrion evolved from a bacterial progenitor via symbiosis within an essentially eukaryotic host cell—has assumed the status of a theory. Yet mitochondrial genome evolution has taken radically different pathways in diverse eukaryotic lineages, and the organelle itself is increasingly viewed as a genetic and functional mosaic, with the bulk of the mitochondrial proteome having an evolutionary origin outside Alphaproteobacteria. New data continue to reshape our views regarding mitochondrial evolution, particularly raising the question of whether the mitochondrion originated after the eukaryotic cell arose, as assumed in the classical endosymbiont hypothesis, or whether this organelle had its beginning at the same time as the cell containing it. PMID:22952398

  6. Microfluidic Compartmentalized Directed Evolution

    PubMed Central

    Paegel, Brian M.; Joyce, Gerald F.

    2010-01-01

    Summary Directed evolution studies often make use of water-in-oil compartments, which conventionally are prepared by bulk emulsification, a crude process that generates non-uniform droplets and can damage biochemical reagents. A microfluidic emulsification circuit was devised that generates uniform water-in-oil droplets (21.9 ± 0.8 μm radius) with high throughput (107–108 droplets per hour). The circuit contains a radial array of aqueous flow nozzles that intersect a surrounding oil flow channel. This device was used to evolve RNA enzymes with RNA ligase activity, selecting enzymes that could resist inhibition by neomycin. Each molecule in the population had the opportunity to undergo 108-fold selective amplification within its respective compartment. Then the progeny RNAs were harvested and used to seed new compartments. During five rounds of this procedure, the enzymes acquired mutations that conferred resistance to neomycin and caused some enzymes to become dependent on neomycin for optimal activity. PMID:20659684

  7. Biochemical processing of heavy oils and residuum

    SciTech Connect

    Lin, M.S.; Premuzic, T.; Yablon, J.H.; Zhou, Wei-Min

    1995-05-01

    During the past several decades, the petroleum industry has adjusted gradually to accommodate the changes in market product demands, government regulations, and the quality and cost of feedstock crude oils. For example, the trends show that the demand for distillate fuels, such as diesel, as compared to gasoline are increasing. Air-quality standards have put additional demand on the processing of heavier and higher sulfur feed stocks. Thus, the 1990 Clean Air Act amendments require the industry to produce greater quantities of oxygenated gasoline, and lower sulfur diesel and reformulated gasoline. Biochemical technology may play an important role in responding to these demands on the petroleum industry.

  8. Biochemical Disincentives to Fertilizing Cellulosic Ethanol Crops

    NASA Astrophysics Data System (ADS)

    Gallagher, M. E.; Hockaday, W. C.; Snapp, S.; McSwiney, C.; Baldock, J.

    2010-12-01

    Corn grain biofuel crops produce the highest yields when the cropping ecosystem is not nitrogen (N)-limited, achieved by application of fertilizer. There are environmental consequences for excessive fertilizer application to crops, including greenhouse gas emissions, hypoxic “dead zones,” and health problems from N runoff into groundwater. The increase in corn acreage in response to demand for alternative fuels (i.e. ethanol) could exacerbate these problems, and divert food supplies to fuel production. A potential substitute for grain ethanol that could reduce some of these impacts is cellulosic ethanol. Cellulosic ethanol feedstocks include grasses (switchgrass), hardwoods, and crop residues (e.g. corn stover, wheat straw). It has been assumed that these feedstocks will require similar N fertilization rates to grain biofuel crops to maximize yields, but carbohydrate yield versus N application has not previously been monitored. We report the biochemical stocks (carbohydrate, protein, and lignin in Mg ha-1) of a corn ecosystem grown under varying N levels. We measured biochemical yield in Mg ha-1 within the grain, leaf and stem, and reproductive parts of corn plants grown at seven N fertilization rates (0-202 kg N ha-1), to evaluate the quantity and quality of these feedstocks across a N fertilization gradient. The N fertilization rate study was performed at the Kellogg Biological Station-Long Term Ecological Research Site (KBS-LTER) in Michigan. Biochemical stocks were measured using 13C nuclear magnetic resonance spectroscopy (NMR), combined with a molecular mixing model (Baldock et al. 2004). Carbohydrate and lignin are the main biochemicals of interest in ethanol production since carbohydrate is the ethanol feedstock, and lignin hinders the carbohydrate to ethanol conversion process. We show that corn residue carbohydrate yields respond only weakly to N fertilization compared to grain. Grain carbohydrate yields plateau in response to fertilization at

  9. Noise-induced metastability in biochemical networks.

    PubMed

    Biancalani, Tommaso; Rogers, Tim; McKane, Alan J

    2012-07-01

    Intracellular biochemical reactions exhibit a rich dynamical phenomenology which cannot be explained within the framework of mean-field rate equations and additive noise. Here, we show that the presence of metastable states and radically different time scales are general features of a broad class of autocatalytic reaction networks, and that this fact may be exploited to gain analytical results. The latter point is demonstrated by a treatment of the paradigmatic Togashi-Kaneko reaction, which has resisted theoretical analysis for the last decade.

  10. Thermal lens spectrometry in biochemical analysis.

    PubMed

    Martín-Biosca, Y; García-Alvarez-Coque, M C; Ramis-Ramos, G

    1994-07-01

    The photothermal spectroscopic techniques, with special emphasis on the thermal lens spectrometry (TLS), are introduced to the non-specialist in laser spectroscopy. The following topics are treated on an elementary basis: fundamentals and analytical characteristics, instrumentation, selectivity and multi-wavelength capability, the models describing the signal-concentration relationship, the sensitivity, background noise and limits of detection, the influence of light scattering and flow. Applications related to the fields of clinical and biochemical analysis and organic pollution are given. The thermal lens circular dichroism and the infrared TLS are also briefly outlined.

  11. Impact analysis of Minuteman III Payload Transporter Type III

    SciTech Connect

    Stirbis, P.P.

    1993-12-01

    An analysis of the impact of the Minuteman III Payload Transporter Type III into a nonyielding target at 46 m.p.h. and 30 m.p.h., and into a yielding target at 46 m.p.h. is presented. The analysis considers the structural response of the tiedown system which secures the Minuteman III re-entry system to the floor of the payload transporter. A finite element model of the re-entry system, its tiedown system, which includes tie-rods and shear pins, and the pallet plate which is attached to the transporter floating plate, was constructed. Because accelerations of the payload transporter are not known, acceleration data from one-quarter scale testing of the Safe Secure Trailer was used to investigate the response of the tiedown system. These accelerations were applied to the pallet plate. The ABAQUS computer code was used to predict the forces in the members of the tiedown system.

  12. The problems raised by the use of cost as an efficiency indicator in a biochemical laboratory.

    PubMed

    Mevellec, P

    1985-01-01

    In the field of health, the increasing gap between technical possibilities and financial resources has led us to search for new instruments of control in the evolution of the hospital system. These new criteria, which have an economic basis, raise many problems and are far from being solved. In this paper, we will study the dual quality of cost indicator, i.e. its quality as a scientific instrument of measure and its quality as an instrument capable of influencing the hospital actors' behaviour. The main variants of cost concept are then correlated with management problems in a study carried out inside a biochemical laboratory.

  13. The START III bargaining space

    SciTech Connect

    Karas, T.H.

    1998-08-01

    The declining state of the Russian military and precarious Russian economic condition will give the US considerable advantages at the START III bargaining table. Taking the US-RF asymmetries into account, this paper discusses a menu of START III measures the US could ask for, and measures it could offer in return, in attempting to negotiate an equitable treaty. Measures the US might seek in a START III treaty include: further reductions in deployed strategic nuclear warheads, irreversibility of reductions through warhead dismantlement; beginning to bring theater nuclear weapons under mutual control, and increased transparency into the Russian nuclear weapons complex. The US may, however, wish to apply its bargaining advantages to attempting to achieve the first steps toward two long-range goals that would enhance US security: bringing theater nuclear weapons into the US-RF arms control arena, and increasing transparency into the Russian nuclear weapons complex. In exchange for measures relating to these objectives, the US might consider offering to Russia: Further strategic weapons reductions approaching levels at which the Russians believe they could maintain a degree of parity with the US; Measures to decrease the large disparities in potential deliver-system uploading capabilities that appear likely under current START II/START III scenarios; and Financial assistance in achieving START II/START III reductions as rapidly as is technically possible.

  14. RNA Editing of Cytochrome Oxidase Subunit III in Sunflower Mitochondria 1

    PubMed Central

    Saiardi, Adolfo; Quagliariello, Carla

    1992-01-01

    Direct sequencing of cytochrome oxidase subunit III (coxIII) mRNA with a specific primer confirms RNA editing in sunflower (Helianthus annus) mitochondria. Six instances of mRNA editing could be verified, one of these specific to this species. All the editing events involve C to U transitions in the coxIII mRNA causing codon changes that lead to amino acids better conserved in evolution than those encoded in the genomic DNA. This observation confirms RNA editing to be widespread in higher plant mitochondria. ImagesFigure 1 PMID:16668785

  15. Cellular localization and biochemical characterization of a novel calcium-dependent protein kinase from tobacco.

    PubMed

    Wang, Yun; Zhang, Mei; Ke, Ke; Lu, Ying Tang

    2005-08-01

    By screening tobacco cDNA library with MCK1 as a probe, we isolated a cDNA clone NtCPK5 (accession number AY971376), which encodes a typical calcium-dependent protein kinase. Sequence analyses indicated that NtCPK5 is related to both CPKs and CRKs superfamilies and has all of the three conserved domains of CPKs. The biochemical activity of NtCPK5 was calcium-dependent. NtCPK5 had Vmax and Km of 526 nmol/min/mg and 210 microg/ml respectively with calf thymus histone (fraction III, abbreviated to histone IIIs) as substrate. For substrate syntide-2, NtCPK5 showed a higher Vmax of 2008 nmol/min/mg and a lower Km of 30 microM. The K0.5 of calcium activation was 0.04 microM or 0.06 microM for histone IIIs or syntide-2 respectively. The putative myristoylation and palmitoylation consensus sequence of NtCPK5 suggests that it could be a membrane-anchoring protein. Indeed, our transient expression experiments with wild type and mutant forms of NtCPK5/GFP fusion proteins showed that NtCPK5 was localized to the plasma membrane of onion epidermal cells and that the localization required the N-terminal acylation sites of NtCPK5/GFP. Taking together, our data have demonstrated the biochemical characteristics of a novel protein NtCPK5 and its subcellular localization as a membrane-anchoring protein. PMID:16117850

  16. Biochemical markers of bone metabolism in growing thoroughbreds: a longitudinal study.

    PubMed

    Price, J S; Jackson, B F; Gray, J A; Harris, P A; Wright, I M; Pfeiffer, D U; Robins, S P; Eastell, R; Ricketts, S W

    2001-08-01

    This study describes longitudinal changes in serum levels of biochemical markers of bone cell activity in a group of 24 thoroughbred foals from birth to 18 months of age. The markers of bone formation included the type I collagen carboxy-terminal propeptide (PICP), the bone-specific isoenzyme of alkaline phosphatase (BAP), and osteocalcin (OC). Levels of the cross-linked telopeptide of type I collagen (ICTP), a marker of bone resorption, and the N-terminal propeptide of type III collagen (PNIIIP), a marker of soft tissue turnover, were also measured. Levels of all markers fell significantly between birth and 18 months of age (70-80 per cent); this decrease being most marked between 0 and 6 months. However, a transient increase in levels of the markers then occurred between 6 and 14 months of age. The timing of this increase was specific for each parameter. ICTP and OC concentrations increased between October and December. PICP concentrations increased between December and April whereas the increase in PIIINP was coincident with the peak in weight gain between April and June. Changes in BAP concentration were less distinct at this time. Season was shown to have significant effects on the biochemical markers independent from the effect of age. Concentrations of all markers decreased with increasing body weight and at any given age heavier horses had lower marker levels. These results show that biochemical markers of bone cell activity and soft tissue turnover follow characteristic patterns of change in growing thoroughbreds influenced by age, season and bodyweight. The demonstration that the reference ranges for the biochemical markers change from month to month means that single samples from individuals are of little value for monitoring bone cell activity in growing thoroughbreds.

  17. [Bulimic behaviors. Clinical, biochemical, pharmacologic data].

    PubMed

    Olié, J P; Truffinet, P

    1989-01-01

    Bulimia nervosa has been recently identified. DSM III-R gives more restrictive criteria for the trouble than DSM III. One may doubt it allows to better understand the probable psychopathological heterogeneity of this eating disorder. Biological indexes up to now only led to partial results. Their interpretation is made more difficult because of the small size of the samples of patients, studied in conditions which are often ill-defined. The biological parameters which are investigated are similar to those studied in depression: monoamines, hypothalamic-pituitary-adrenal axis, hypothalamic-pituitary-thyroid axis, hypothalamic-pituitary-gonadal axis, Growth Hormone, prolactin , melatonin, beta-endorphin, EEG mapping. Antidepressants and anticonvulsants remain the most often mentioned drugs. Tryptophane, lithium, opiate antagonists, amphetamines, serotoninergic drugs are currently being studied.

  18. Biochemical Manifestation of HIV Lipodystrophy Syndrome

    PubMed Central

    Ihenetu, Kenneth; Mason, Darius

    2012-01-01

    Objectives Highly active anti-retroviral therapy (HAART), including protease inhibitors (PI) have led to dramatic improvements in the quality and quantity of life in patients with acquired immunodeficiency syndrome (AIDS). However, a significant number of AIDS patients on HAART develop characteristic changes in body fat redistribution referred to as lipodystrophy syndrome (LDS). Features of LDS include hypertrophy in the neck fat pad (buffalo hump), increased fat in the abdominal region (protease paunch), gynecomastia and loss of fat in the mid-face and extremities. Methods The aim of this paper is to review the current knowledge regarding this syndrome. This article reviews the published investigations on biochemical manifestation of HIV lipodystrophy syndrome. Results It is estimated that approximately 64% of patients treated with PI will experience this syndrome. Biochemically, these patients have increased triglycerides (Trig), total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-C) and extremely low high-density lipoprotein-cholesterol (HDL-C). Conclusions and Public Health Implications It is hoped that awareness of this syndrome would aid in early diagnosis and better patient management, possibly leading to a lower incidence of cardiovascular complications among these patients.

  19. Biochemical enzyme analysis in acute leukaemia.

    PubMed Central

    Drexler, H G; Gaedicke, G; Minowada, J

    1985-01-01

    This report summarises the current knowledge regarding the clinical utility of biochemical enzyme markers for both diagnostic and therapeutic purposes in acute leukaemia. The enzymes studied most extensively in this field are terminal deoxynucleotidyl transferase, adenosine deaminase, 5'-nucleotidase, purine nucleoside phosphorylase, and acid phosphatase, esterase, hexosaminidase isoenzymes. For each enzyme, the quantitative and qualitative characteristics in various immunologically defined subclasses of acute leukaemia are described. The quantitative evaluation of enzyme activities represents an adjunctive classification technique which should be incorporated into the multivariate analysis, the "multiple marker analysis." By qualitative characterisation pronounced heterogeneity of leukaemia subsets is uncovered. The application of 2'-deoxycoformycin, a specific inhibitor of adenosine deaminase, and the potential usefulness of two other enzymes as targets for treatment with selective agents is discussed. The concept that gene products expressed at certain developmental stages of normal cells can similarly be detected in leukaemic cells (which therefore seem to be "frozen" or "arrested" at this particular maturation/differentiation stage) is supported by the results obtained in enzyme studies. Besides their practical clinical importance for classification and treatment of acute leukaemias, biochemical enzyme markers constitute a valuable research tool to disclose biological properties of leukaemic cells. PMID:2981904

  20. Biochemical basis for the biological clock

    NASA Technical Reports Server (NTRS)

    Morre, D. James; Chueh, Pin-Ju; Pletcher, Jake; Tang, Xiaoyu; Wu, Lian-Ying; Morre, Dorothy M.

    2002-01-01

    NADH oxidases at the external surface of plant and animal cells (ECTO-NOX proteins) exhibit stable and recurring patterns of oscillations with potentially clock-related, entrainable, and temperature-compensated period lengths of 24 min. To determine if ECTO-NOX proteins might represent the ultradian time keepers (pacemakers) of the biological clock, COS cells were transfected with cDNAs encoding tNOX proteins having a period length of 22 min or with C575A or C558A cysteine to alanine replacements having period lengths of 36 or 42 min. Here we demonstrate that such transfectants exhibited 22, 36, or 40 to 42 h circadian patterns in the activity of glyceraldehyde-3-phosphate dehydrogenase, a common clock-regulated protein, in addition to the endogenous 24 h circadian period length. The fact that the expression of a single oscillatory ECTO-NOX protein determines the period length of a circadian biochemical marker (60 X the ECTO-NOX period length) provides compelling evidence that ECTO-NOX proteins are the biochemical ultradian drivers of the cellular biological clock.

  1. Biochemical responses of the Skylab crewman

    NASA Technical Reports Server (NTRS)

    Leach, C. S.; Rambaut, P. C.

    1974-01-01

    The biochemical investigations of the Skylab crewmen were designed to study the physiological changes that were observed on flight crews returning from previous space flight missions as well as to study those changes expected to result from prolonged weightless exposure. These studies can be divided into two broad categories. One category included routine blood studies similar to those used in clinical medical practice. The second included research-type endocrine analyses used to investigate more thoroughly the metabolic/endocrine responses to the space flight environment. The premission control values indicated that all Skylab crewmen were healthy and were free from biochemical abnormalities. The routine results during and after flight showed slight but significant changes in electrolytes, glucose, total protein, osmolality, uric acid, cholesterol, and creatinine. Plasma hormal changes included adrenocorticotrophic hormone, cortisol, angiotensin I, aldosterone, insulin, and thyroxine. The 24-hour urine analyses results revealed increased excretion of cortisol, catecholamines, antidiuretic hormone, and aldosterone as well as excretion of significant electrolyte and uric acid during the Skylab flights.

  2. Transient absolute robustness in stochastic biochemical networks.

    PubMed

    Enciso, German A

    2016-08-01

    Absolute robustness allows biochemical networks to sustain a consistent steady-state output in the face of protein concentration variability from cell to cell. This property is structural and can be determined from the topology of the network alone regardless of rate parameters. An important question regarding these systems is the effect of discrete biochemical noise in the dynamical behaviour. In this paper, a variable freezing technique is developed to show that under mild hypotheses the corresponding stochastic system has a transiently robust behaviour. Specifically, after finite time the distribution of the output approximates a Poisson distribution, centred around the deterministic mean. The approximation becomes increasingly accurate, and it holds for increasingly long finite times, as the total protein concentrations grow to infinity. In particular, the stochastic system retains a transient, absolutely robust behaviour corresponding to the deterministic case. This result contrasts with the long-term dynamics of the stochastic system, which eventually must undergo an extinction event that eliminates robustness and is completely different from the deterministic dynamics. The transiently robust behaviour may be sufficient to carry out many forms of robust signal transduction and cellular decision-making in cellular organisms. PMID:27581485

  3. III-Nitride nanowire optoelectronics

    NASA Astrophysics Data System (ADS)

    Zhao, Songrui; Nguyen, Hieu P. T.; Kibria, Md. G.; Mi, Zetian

    2015-11-01

    Group-III nitride nanowire structures, including GaN, InN, AlN and their alloys, have been intensively studied in the past decade. Unique to this material system is that its energy bandgap can be tuned from the deep ultraviolet (~6.2 eV for AlN) to the near infrared (~0.65 eV for InN). In this article, we provide an overview on the recent progress made in III-nitride nanowire optoelectronic devices, including light emitting diodes, lasers, photodetectors, single photon sources, intraband devices, solar cells, and artificial photosynthesis. The present challenges and future prospects of III-nitride nanowire optoelectronic devices are also discussed.

  4. Gd(III)-Gd(III) distance measurements with chirp pump pulses

    NASA Astrophysics Data System (ADS)

    Doll, Andrin; Qi, Mian; Wili, Nino; Pribitzer, Stephan; Godt, Adelheid; Jeschke, Gunnar

    2015-10-01

    The broad EPR spectrum of Gd(III) spin labels restricts the dipolar modulation depth in distance measurements between Gd(III) pairs to a few percent. To overcome this limitation, frequency-swept chirp pulses are utilized as pump pulses in the DEER experiment. Using a model system with 3.4 nm Gd-Gd distance, application of one single chirp pump pulse at Q-band frequencies leads to modulation depths beyond 10%. However, the larger modulation depth is counteracted by a reduction of the absolute echo intensity due to the pump pulse. As supported by spin dynamics simulations, this effect is primarily driven by signal loss to double-quantum coherence and specific to the Gd(III) high spin state of S = 7/2. In order to balance modulation depth and echo intensity for optimum sensitivity, a simple experimental procedure is proposed. An additional improvement by 25% in DEER sensitivity is achieved with two consecutive chirp pump pulses. These pulses pump the Gd(III) spectrum symmetrically around the observation position, therefore mutually compensating for dynamical Bloch-Siegert phase shifts at the observer spins. The improved sensitivity of the DEER data with modulation depths on the order of 20% is due to mitigation of the echo reduction effects by the consecutive pump pulses. In particular, the second pump pulse does not lead to additional signal loss if perfect inversion is assumed. Moreover, the compensation of the dynamical Bloch-Siegert phase prevents signal loss due to spatial dependence of the dynamical phase, which is caused by inhomogeneities in the driving field. The new methodology is combined with pre-polarization techniques to measure long distances up to 8.6 nm, where signal intensity and modulation depth become attenuated by long dipolar evolution windows. In addition, the influence of the zero-field splitting parameters on the echo intensity is studied with simulations. Herein, larger sensitivity is anticipated for Gd(III) complexes with zero

  5. A novel mutation in TTC19 associated with isolated complex III deficiency, cerebellar hypoplasia, and bilateral basal ganglia lesions.

    PubMed

    Melchionda, Laura; Damseh, Nadirah S; Abu Libdeh, Bassam Y; Nasca, Alessia; Elpeleg, Orly; Zanolini, Alice; Ghezzi, Daniele

    2014-01-01

    Isolated complex III (cIII) deficiency is a rare biochemical finding in mitochondrial disorders, mainly associated with mutations in mitochondrial DNA MTCYB gene, encoding cytochrome b, or in assembly factor genes (BCS1L, TTC19, UQCC2, and LYRM7), whereas mutations in nuclear genes encoding cIII structural subunits are extremely infrequent. We report here a patient, a 9 year old female born from first cousin related parents, with normal development till 18 months when she showed unsteady gait with frequent falling down, cognitive, and speech worsening. Her course deteriorated progressively. Brain MRI showed cerebellar vermis hypoplasia and bilateral lentiform nucleus high signal lesions. Now she is bed ridden with tetraparesis and severely impaired cognitive and language functions. Biochemical analysis revealed isolated cIII deficiency in muscle, and impaired respiration in fibroblasts. We identified a novel homozygous rearrangement in TTC19 (c.213_229dup), resulting in frameshift with creation of a premature termination codon (p.Gln77Argfs*30). Western blot analysis demonstrated the absence of TTC19 protein in patient's fibroblasts, while Blue-Native Gel Electrophoresis analysis revealed the presence of cIII-specific assembly intermediates. Mutations in TTC19 have been rarely associated with mitochondrial disease to date, being described in about ten patients with heterogeneous clinical presentations, ranging from early onset encephalomyopathy to adult forms with cerebellar ataxia. Contrariwise, the biochemical defect was a common hallmark in TTC19 mutant patients, confirming the importance of TTC19 in cIII assembly/stability. Therefore, we suggest extending the TTC19 mutational screening to all patients with cIII deficiency, independently from their phenotypes. PMID:25452764

  6. Formation of the first galaxies under Population III stellar feedback

    NASA Astrophysics Data System (ADS)

    Jeon, Myoungwon

    2015-01-01

    The first galaxies, which formed a few hundred million years after the big bang, are related to important cosmological questions. Given thatthey are thought to be the basic building blocks of large galaxies seen today, understanding their formation and properties is essentialto studying galaxy formation as a whole. In this dissertation talk, I will present the results of our highly-resolved cosmological ab-initio simulations to understand the assembly process of first galaxies under the feedback from the preceding generations of first stars, the so-called Population III (Pop III). The first stars formed at z≲30 in dark matter (DM) minihalos with M_{vir}=10^5-10^6Msun, predominately via molecular hydrogen (H_2) cooling. Radiation from Pop III stars dramatically altered the gas within their host minihalos, through photoionization, photoheating, and photoevaporation. Once a Pop III star explodes as a supernova (SN), heavy elements are dispersed, enriching the interstellar (ISM) and intergalactic medium (IGM), thus initiating the process of chemical evolution. I will begin by presenting how the SN explosion of the first stars influences early cosmic history, specifically assessing the time delay in further star formation and tracing the evolution of metal-enriched gas until the second episode star formation happens. These results will show the role of Pop III supernovae on the star formation transition from Pop III to Population II. Additionally, the more distant, diffuse IGM was heated by X-rays emitted by accreting black holes (BHs), or high-mass X-ray binaries (HMXBs), both remnants of Pop III stars. I will present results of a series of simulations where we study the impact of X-ray feedback from BHs and HMXBs on the star formation history in the early universe, and discuss the resulting implications on reionization. I will also present the role of X-rays on the early BH growth, providing constraints on models for supermassive black hole formation. Finally, I

  7. The growing need for biochemical bioherbicides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The volume of herbicide use outpaces that of other pesticides. Evolution of resistance to the currently used herbicides has greatly increased the need for new modes of action (MOAs). More than 20 years have passed since the last new herbicide MOA was introduced. Natural products offer a source of...

  8. Characterization of collagen fibrils after equine suspensory ligament injury: an ultrastructural and biochemical approach.

    PubMed

    Shikh Alsook, M K; Gabriel, A; Salouci, M; Piret, J; Alzamel, N; Moula, N; Denoix, J-M; Antoine, N; Baise, E

    2015-04-01

    Suspensory ligament (SL) injuries are an important cause of lameness in horses. The mechanical properties of connective tissue in normal and pathological ligaments are mainly related to fibril morphology, as well as collagen content and types. The purpose of this study was to evaluate, using biochemical and ultrastructural approaches, the alterations in collagen fibrils after injury. Eight Warmblood horses with visible signs of injury in only one forelimb SL were selected and specimens were examined by transmission electron microscope (TEM). Collagen types I, III and V were purified by differential salt precipitation after collagen extraction with acetic acid containing pepsin. TEM revealed abnormal organization as well as alterations in the diameter and shape of fibrils after SL injury. The bands corresponding to types I, III and V collagen were assessed by densitometry after sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Densitometric analysis indicated that the proportions of type III and type V collagen were higher (P < 0.001) in damaged tissues compared with normal tissues with a mean increase of 20.9% and 17.3%, respectively. Concurrently, a decrease (P < 0.001) in type I collagen within damaged tissues was recorded with a mean decrease of 15.2%. These alterations could be the hallmark of a decrease in the tissue quality and mechanical properties of the ligament. The findings provide new insight for subsequent research on tissue regeneration that may lead to the development of future treatment strategies for SL injury.

  9. Type III Secretion: Building and Operating a Remarkable Nanomachine.

    PubMed

    Portaliou, Athina G; Tsolis, Konstantinos C; Loos, Maria S; Zorzini, Valentina; Economou, Anastassios

    2016-02-01

    The Type III secretion system (T3SS) is a protein export pathway that is widespread in Gram-negative bacteria and delivers effector proteins directly into eukaryotic cells. At its core lie the injectisome (a sophisticated transmembrane secretion apparatus) and a complex network of specialized chaperones that target secretory proteins to the antechamber of the injectisome. The assembly of the system, and the subsequent secretion of proteins through it, undergo fine-tuned, hierarchical regulation. Here, we present the current understanding of the injectisome assembly process, secretion hierarchy, and the role of chaperones. We discuss these events in light of available structural and biochemical dissection and propose future directions essential to revealing mechanistic insight into this fascinating nanomachine. PMID:26520801

  10. Interplanetary density models as inferred from solar Type III bursts

    NASA Astrophysics Data System (ADS)

    Oppeneiger, Lucas; Boudjada, Mohammed Y.; Lammer, Helmut; Lichtenegger, Herbert

    2016-04-01

    We report on the density models derived from spectral features of solar Type III bursts. They are generated by beams of electrons travelling outward from the Sun along open magnetic field lines. Electrons generate Langmuir waves at the plasma frequency along their ray paths through the corona and the interplanetary medium. A large frequency band is covered by the Type III bursts from several MHz down to few kHz. In this analysis, we consider the previous empirical density models proposed to describe the electron density in the interplanetary medium. We show that those models are mainly based on the analysis of Type III bursts generated in the interplanetary medium and observed by satellites (e.g. RAE, HELIOS, VOYAGER, ULYSSES,WIND). Those models are confronted to stereoscopic observations of Type III bursts recorded by WIND, ULYSSES and CASSINI spacecraft. We discuss the spatial evolution of the electron beam along the interplanetary medium where the trajectory is an Archimedean spiral. We show that the electron beams and the source locations are depending on the choose of the empirical density models.

  11. Kilometric type III radio bursts and interplanetary transients

    SciTech Connect

    MacDowall, R.J.

    1988-01-01

    The first detailed observations and analysis of interplanetary (IP) type III bursts which undergo sudden intensity changes are presented. Two major even categories are studied: cutoffs in which the type III intensity is abruptly reduced (by a factor of 10 or more) at some frequency and remains at the reduced level for all lower frequencies, and narrowband intensifications which frequently occur on the high-frequency edge of a cutoff. Based on their apparent radial velocities as well as their occurrence at the same frequencies as kilometric type II emission, a subset of the sudden intensity change events are demonstrated to be associated with IP shocks. Consequently, they provide a new tool for shock detection in the inner heliosphere. Two causes proposed for the shock associated type III burst cutoffs are enhanced levels of background electrons and pitch-angle scattering. In the vicinities of IP shocks, the observed background levels of electrons with energies greater than 2 keV are frequently enhanced by up to 2 orders of magnitude over ambient levels. The magnetic field fluctuations observed downstream of many shocks are effective in pitch-angle scattering type III electrons. Either of these mechanisms may reduce the effective height of the bump-on-tail distribution, and thereby influence the Langmuir wave growth and evolution. The pre-cutoff intensifications are shown to arise in regions of radial extent {Delta}R/R {approx} 0.1. Consequently, they are not the result of processes local to the shock.

  12. Photoinduced biochemical activity of fullerene carboxylic acid

    SciTech Connect

    Tokuyama, Hidetoshi; Yamago, Shigeru; Nakamura, Eiichi; Shiraki, Takashi; Sugiura, Yukio

    1993-08-25

    Here we report the preparation of a water-miscible fullerene carboxylic acid (2) and its biological activity-cytotoxicity and G-selective DNA cleaving ability. What is truly remarkable is that the biological activity of C{sub 60} was observed only under irradiation with visible light and not in the dark, suggesting that fullerenes may serve as useful photosensitive biochemical probes. We have found, for the first time, that even low-energy visible light is surfficient to induce biological activity in fullerene derivatives. Among the numerous implications of the present findings, the most exciting prospect includes the use of fullerene derivatives for photodynamic therapy. 18 refs., 2 figs., 1 tab.

  13. Thin membrane sensor with biochemical switch

    NASA Technical Reports Server (NTRS)

    Case, George D. (Inventor); Worley, III, Jennings F. (Inventor)

    1994-01-01

    A modular biosensor system for chemical or biological agent detection utilizes electrochemical measurement of an ion current across a gate membrane triggered by the reaction of the target agent with a recognition protein conjugated to a channel blocker. The sensor system includes a bioresponse simulator or biochemical switch module which contains the recognition protein-channel blocker conjugate, and in which the detection reactions occur, and a transducer module which contains a gate membrane and a measuring electrode, and in which the presence of agent is sensed electrically. In the poised state, ion channels in the gate membrane are blocked by the recognition protein-channel blocker conjugate. Detection reactions remove the recognition protein-channel blocker conjugate from the ion channels, thus eliciting an ion current surge in the gate membrane which subsequently triggers an output alarm. Sufficiently large currents are generated that simple direct current electronics are adequate for the measurements. The biosensor has applications for environmental, medical, and industrial use.

  14. The biochemical basis of hereditary fructose intolerance.

    PubMed

    Bouteldja, Nadia; Timson, David J

    2010-04-01

    Hereditary fructose intolerance is a rare, but potentially lethal, inherited disorder of fructose metabolism, caused by mutation of the aldolase B gene. Treatment currently relies solely on dietary restriction of problematic sugars. Biochemical study of defective aldolase B enzymes is key to revealing the molecular basis of the disease and providing a stronger basis for improved treatment and diagnosis. Such studies have revealed changes in enzyme activity, stability and oligomerisation. However, linking these changes to disease phenotypes has not always been straightforward. This review gives a general overview of the features of hereditary fructose intolerance, then concentrates on the biochemistry of the AP variant (Ala149Pro variant of aldolase B) and molecular pathological consequences of mutation of the aldolase B gene.

  15. Peter Hochachka: adventures in biochemical adaptation.

    PubMed

    Somero, George N; Suarez, Raul K

    2005-01-01

    Peter Hochachka was one of the most creative forces in the field of comparative physiology during the past half-century. His career was truly an exploratory adventure, in both intellectual and geographic senses. His broad comparative studies of metabolism in organisms as diverse as trout, tunas, oysters, squid, turtles, locusts, hummingbirds, seals, and humans revealed the adaptable features of enzymes and metabolic pathways that provide the biochemical bases for diverse lifestyles and environments. In its combined breadth and depth, no other corpus of work better illustrates the principle of "unity in diversity" that marks comparative physiology. Through his publications, his stimulating mentorship, his broad editorial services, and his continuous-and highly infectious-enthusiasm for his field, Peter Hochachka served as one of the most influential leaders in the transformation of comparative physiology.

  16. Biochemical pathways in seed oil synthesis.

    PubMed

    Bates, Philip D; Stymne, Sten; Ohlrogge, John

    2013-06-01

    Oil produced in plant seeds is utilized as a major source of calories for human nutrition, as feedstocks for non-food uses such as soaps and polymers, and can serve as a high-energy biofuel. The biochemical pathways leading to oil (triacylglycerol) synthesis in seeds involve multiple subcellular organelles, requiring extensive lipid trafficking. Phosphatidylcholine plays a central role in these pathways as a substrate for acyl modifications and likely as a carrier for the trafficking of acyl groups between organelles and membrane subdomains. Although much has been clarified regarding the enzymes and pathways responsible for acyl-group flux, there are still major gaps in our understanding. These include the identity of several key enzymes, how flux between alternative pathways is controlled and the specialized cell biology leading to biogenesis of oil bodies that store up to 80% of carbon in seeds.

  17. [Biochemical complications of experimental vesico-sigmoidostomy].

    PubMed

    Nuñez, R; Blesa, E; Ramos, S; Morillo, M; Ortega, L; Requena, F; Cardesa, J J

    1987-03-01

    Three experimental models of vesico-sigmoidostomy are studied (model-1, end to side V-S plus urethral ligation, model-2, end to end V-S, in "Y of Rous" plus urethral ligation and model-3, vesico-sigmoidoplasty), with aim of reproducing chemical imbalance observed in human subjects with ureterosigmoidostomy. Authors have evaluated clinical biochemical (serum acido-base balance, Cl, Na+, K+, BUN, creatinine, ammonia and albumin), and histologic variables in the first, third and fifth month after operation in 225 rats. Animal of model-1 presented more frequently than model-2 and model-3, alterations (hyperchloraemic acidosis, uraemia, hyperammonemia and hypoalbumin) as well as affectation of upper urinary system for acute or chronic pyelonephritis.

  18. Droplet microfluidics in (bio)chemical analysis.

    PubMed

    Basova, Evgenia Yu; Foret, Frantisek

    2015-01-01

    Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation. It can improve not only the analysis scale, possibility for sensitivity improvement, and reduced consumption of chemical and biological reagents, but also the speed of performing a variety of unit operations. At present, microfluidic platforms can reproducibly generate monodisperse droplet populations at kHz or higher rates with droplet sizes suitable for high-throughput experiments, single-cell detection or even single molecule analysis. In addition to being used as microreactors with volume in the micro- to femtoliter range, droplet based systems have also been used to directly synthesize particles and encapsulate biological entities for biomedicine and biotechnology applications. This minireview summarizes various droplet microfluidics operations and applications for (bio)chemical assays described in the literature during the past few years.

  19. Hemoglobin Variants: Biochemical Properties and Clinical Correlates

    PubMed Central

    Thom, Christopher S.; Dickson, Claire F.; Gell, David A.; Weiss, Mitchell J.

    2013-01-01

    Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples. PMID:23388674

  20. Hemoglobin variants: biochemical properties and clinical correlates.

    PubMed

    Thom, Christopher S; Dickson, Claire F; Gell, David A; Weiss, Mitchell J

    2013-03-01

    Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples.

  1. [Biochemical and immunological markers of autoimmune thyroiditis].

    PubMed

    Biktagirova, E M; Sattarova, L I; Vagapova, G R; Skibo, Y V; Chuhlovina, E N; Kravtsova, O A; Abramova, Z I

    2016-05-01

    Correlations between biochemical and immunological markers of programmed cell death (apoptosis), and the functional state of the thyroid gland (hyperthyroidism, euthyroidism, hypothyroidism) have been investigated in autoimmune thyroiditis (AT) (also known as chronic autoimmune thyroiditis). Annexin V, TRAIL and TNF-a, as well as DNA-hydrolyzing antibodies were used as the main markers. Increased levels of TRAIL were found in the serum of AT patients (hyperthyroidism>hypothyroidism>euthyroidism) compared with healthy individuals. The highest frequency of antibodies to denatured DNA (Abs-dDNA) had the highest frequency in AT patients (97%) compared with healthy controls. Among these patients, 75% had hyperthyroidism, 85% had hypothyroidism, and 84.7% had euthyroidism. Abs hydrolyzing activity demonstrated correlation dependence with symptoms of the thyroid dysfunction. PMID:27563001

  2. Biochemical Pharmacology of the Sigma-1 Receptor.

    PubMed

    Chu, Uyen B; Ruoho, Arnold E

    2016-01-01

    The sigma-1 receptor (S1R) is a 223 amino acid two transmembrane (TM) pass protein. It is a non-ATP-binding nonglycosylated ligand-regulated molecular chaperone of unknown three-dimensional structure. The S1R is resident to eukaryotic mitochondrial-associated endoplasmic reticulum and plasma membranes with broad functions that regulate cellular calcium homeostasis and reduce oxidative stress. Several multitasking functions of the S1R are underwritten by chaperone-mediated direct (and indirect) interactions with ion channels, G-protein coupled receptors and cell-signaling molecules involved in the regulation of cell growth. The S1R is a promising drug target for the treatment of several neurodegenerative diseases related to cellular stress. In vitro and in vivo functional and molecular characteristics of the S1R and its interactions with endogenous and synthetic small molecules have been discovered by the use of pharmacologic, biochemical, biophysical, and molecular biology approaches. The S1R exists in monomer, dimer, tetramer, hexamer/octamer, and higher oligomeric forms that may be important determinants in defining the pharmacology and mechanism(s) of action of the S1R. A canonical GXXXG in putative TM2 is important for S1R oligomerization. The ligand-binding regions of S1R have been identified and include portions of TM2 and the TM proximal regions of the C terminus. Some client protein chaperone functions and interactions with the cochaperone 78-kDa glucose-regulated protein (binding immunoglobulin protein) involve the C terminus. Based on its biochemical features and mechanisms of chaperone action the possibility that the S1R is a member of the small heat shock protein family is discussed.

  3. Biochemically enhanced methane production from coal

    NASA Astrophysics Data System (ADS)

    Opara, Aleksandra

    For many years, biogas was connected mostly with the organic matter decomposition in shallow sediments (e.g., wetlands, landfill gas, etc.). Recently, it has been realized that biogenic methane production is ongoing in many hydrocarbon reservoirs. This research examined microbial methane and carbon dioxide generation from coal. As original contributions methane production from various coal materials was examined in classical and electro-biochemical bench-scale reactors using unique, developed facultative microbial consortia that generate methane under anaerobic conditions. Facultative methanogenic populations are important as all known methanogens are strict anaerobes and their application outside laboratory would be problematic. Additional testing examined the influence of environmental conditions, such as pH, salinity, and nutrient amendments on methane and carbon dioxide generation. In 44-day ex-situ bench-scale batch bioreactor tests, up to 300,000 and 250,000 ppm methane was generated from bituminous coal and bituminous coal waste respectively, a significant improvement over 20-40 ppm methane generated from control samples. Chemical degradation of complex hydrocarbons using environmentally benign reagents, prior to microbial biodegradation and methanogenesis, resulted in dissolution of up to 5% bituminous coal and bituminous coal waste and up to 25% lignite in samples tested. Research results confirm that coal waste may be a significant underutilized resource that could be converted to useful fuel. Rapid acidification of lignite samples resulted in low pH (below 4.0), regardless of chemical pretreatment applied, and did not generate significant methane amounts. These results confirmed the importance of monitoring and adjusting in situ and ex situ environmental conditions during methane production. A patented Electro-Biochemical Reactor technology was used to supply electrons and electron acceptor environments, but appeared to influence methane generation in a

  4. Biochemical diagnosis of neuroendocrine GEP tumor.

    PubMed Central

    Oberg, K.

    1997-01-01

    Neuroendocrine gut and pancreatic tumors are known to contain and secret different peptide hormones and amines. During the last two decades, many radioimmunoassays and Elizas have been developed to analyze these substances in blood and urine, which has enabled clinicians to improve the diagnosis and monitoring of patients with various neuroendocrine tumors. Due to cost constraints in medical care, it is important to try to define the most useful biochemical markers from the clinical point of view. The glycoprotein chromogranin A has been shown to be a useful marker for diagnosing various neuroendocrine tumors, both by histopathology and circulating tumor markers. In patients with demonstrable endocrine tumors, about 90 percent of the patients present high circulating levels of chromogranin A. A hundred-fold increase of plasma chromogranin is seen in patients with midgut carcinoid tumors and liver metastases. The plasma levels of chromogranin A reflect the tumor mass and can be used for monitoring the patient during treatment and follow-up, although the day-to-day variation might be 30-40 percent. High circulating levels of the chromogranin A might be an indicator of bad prognosis in patients with malignant carcinoid tumors. Besides analyzing plasma chromogranin A, specific analyses such as urinary 5-HIAA in midgut carcinoid patients, serum gastrin in patients with Zollinger-Ellison syndrome and insulin/proinsulin in patients with hypoglycemia should be performed. In patients with small tumor masses or intermittent symptoms, provocative tests such as a meal stimulation test, secretin test or pentagastrin stimulation of tachykinin release can supplement the basal measurements of peptides and amines. To fully evaluate the growth potential in neuroendocrine tumors, traditional biochemical markers should be supplemented with indicators of growth proliferation (Ki-67, PCNA) and immunohistochemical staining for the adhesion molecule CD44 and the PDGF-alpha receptor

  5. Transcription fluctuation effects on biochemical oscillations.

    PubMed

    Nishino, Ryota; Sakaue, Takahiro; Nakanishi, Hiizu

    2013-01-01

    Some biochemical systems show oscillation. They often consist of feedback loops with repressive transcription regulation. Such biochemical systems have distinctive characteristics in comparison with ordinary chemical systems: i) numbers of molecules involved are small, ii) there are typically only a couple of genes in a cell with a finite regulation time. Due to the fluctuations caused by these features, the system behavior can be quite different from the one by deterministic rate equations, because the rate equations ignore molecular fluctuations and thus are exact only in the infinite molecular number limit. The molecular fluctuations on a free-running circadian system have been studied by Gonze et al. (2002) by introducing a scale parameter [Formula: see text] for the system size. They consider, however, only the first effect, assuming that the gene process is fast enough for the second effect to be ignored, but this has not been examined systematically yet. Here we study fluctuation effects due to the finite gene regulation time by introducing a new scale parameter [Formula: see text], which we take as the unbinding time of a nuclear protein from the gene. We focus on the case where the fluctuations due to small molecular numbers are negligible. In simulations on the same system studied by Gonze et al., we find the system is unexpectedly sensitive to the fluctuation in the transcription regulation; the period of oscillation fluctuates about 30 min even when the regulation time scale [Formula: see text] is around 30 s, that is even smaller than 1/1000 of its circadian period. We also demonstrate that the distribution width for the oscillation period and amplitude scales with [Formula: see text], and the correlation time scales with [Formula: see text] in the small [Formula: see text] regime. The relative fluctuations for the period are about half of that for the amplitude, namely, the periodicity is more stable than the amplitude.

  6. Pattern Selection by Dynamical Biochemical Signals

    PubMed Central

    Palau-Ortin, David; Formosa-Jordan, Pau; Sancho, José M.; Ibañes, Marta

    2015-01-01

    The development of multicellular organisms involves cells to decide their fate upon the action of biochemical signals. This decision is often spatiotemporally coordinated such that a spatial pattern arises. The dynamics that drive pattern formation usually involve genetic nonlinear interactions and positive feedback loops. These complex dynamics may enable multiple stable patterns for the same conditions. Under these circumstances, pattern formation in a developing tissue involves a selection process: why is a certain pattern formed and not another stable one? Herein we computationally address this issue in the context of the Notch signaling pathway. We characterize a dynamical mechanism for developmental selection of a specific pattern through spatiotemporal changes of the control parameters of the dynamics, in contrast to commonly studied situations in which initial conditions and noise determine which pattern is selected among multiple stable ones. This mechanism can be understood as a path along the parameter space driven by a sequence of biochemical signals. We characterize the selection process for three different scenarios of this dynamical mechanism that can take place during development: the signal either 1) acts in all the cells at the same time, 2) acts only within a cluster of cells, or 3) propagates along the tissue. We found that key elements for pattern selection are the destabilization of the initial pattern, the subsequent exploration of other patterns determined by the spatiotemporal symmetry of the parameter changes, and the speeds of the path compared to the timescales of the pattern formation process itself. Each scenario enables the selection of different types of patterns and creates these elements in distinct ways, resulting in different features. Our approach extends the concept of selection involved in cellular decision-making, usually applied to cell-autonomous decisions, to systems that collectively make decisions through cell

  7. Chromium(III), insoluble salts

    Integrated Risk Information System (IRIS)

    Chromium ( III ) , insoluble salts ; CASRN 16065 - 83 - 1 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments

  8. Title III hazardous air pollutants

    SciTech Connect

    Todd, R.

    1995-12-31

    The author presents an overview of the key provisions of Title III of the Clean Air Act Amendments of 1990. The key provisions include the following: 112(b) -- 189 Hazardous Air Pollutants (HAP); 112(a) -- Major Source: 10 TPY/25 TPY; 112(d) -- Application of MACT; 112(g) -- Modifications; 112(I) -- State Program; 112(j) -- The Hammer; and 112(r) -- Accidental Release Provisions.

  9. Organometallic neptunium(III) complexes.

    PubMed

    Dutkiewicz, Michał S; Farnaby, Joy H; Apostolidis, Christos; Colineau, Eric; Walter, Olaf; Magnani, Nicola; Gardiner, Michael G; Love, Jason B; Kaltsoyannis, Nikolas; Caciuffo, Roberto; Arnold, Polly L

    2016-08-01

    Studies of transuranic organometallic complexes provide a particularly valuable insight into covalent contributions to the metal-ligand bonding, in which the subtle differences between the transuranium actinide ions and their lighter lanthanide counterparts are of fundamental importance for the effective remediation of nuclear waste. Unlike the organometallic chemistry of uranium, which has focused strongly on U(III) and has seen some spectacular advances, that of the transuranics is significantly technically more challenging and has remained dormant. In the case of neptunium, it is limited mainly to Np(IV). Here we report the synthesis of three new Np(III) organometallic compounds and the characterization of their molecular and electronic structures. These studies suggest that Np(III) complexes could act as single-molecule magnets, and that the lower oxidation state of Np(II) is chemically accessible. In comparison with lanthanide analogues, significant d- and f-electron contributions to key Np(III) orbitals are observed, which shows that fundamental neptunium organometallic chemistry can provide new insights into the behaviour of f-elements.

  10. Terrain Perception for DEMO III

    NASA Technical Reports Server (NTRS)

    Manduchi, R.; Bellutta, P.; Matthies, L.; Owens, K.; Rankin, A.

    2000-01-01

    The Demo III program has as its primary focus the development of autonomous mobility for a small rugged cross country vehicle. In this paper we report recent progress on both stereo-based obstacle detection and terrain cover color-based classification.

  11. Organometallic neptunium(III) complexes.

    PubMed

    Dutkiewicz, Michał S; Farnaby, Joy H; Apostolidis, Christos; Colineau, Eric; Walter, Olaf; Magnani, Nicola; Gardiner, Michael G; Love, Jason B; Kaltsoyannis, Nikolas; Caciuffo, Roberto; Arnold, Polly L

    2016-08-01

    Studies of transuranic organometallic complexes provide a particularly valuable insight into covalent contributions to the metal-ligand bonding, in which the subtle differences between the transuranium actinide ions and their lighter lanthanide counterparts are of fundamental importance for the effective remediation of nuclear waste. Unlike the organometallic chemistry of uranium, which has focused strongly on U(III) and has seen some spectacular advances, that of the transuranics is significantly technically more challenging and has remained dormant. In the case of neptunium, it is limited mainly to Np(IV). Here we report the synthesis of three new Np(III) organometallic compounds and the characterization of their molecular and electronic structures. These studies suggest that Np(III) complexes could act as single-molecule magnets, and that the lower oxidation state of Np(II) is chemically accessible. In comparison with lanthanide analogues, significant d- and f-electron contributions to key Np(III) orbitals are observed, which shows that fundamental neptunium organometallic chemistry can provide new insights into the behaviour of f-elements. PMID:27442286

  12. The application of biochemical criteria to the assessment of macrofilarial viability.

    PubMed

    Comley, J C; Rees, M J; O'Dowd, A B

    1988-12-01

    Previous attempts to assess nematode viability have been critically reviewed and the need to apply more objective biochemical criteria emphasized. The practicalities of assay development have been discussed with regard to sensitivity, selectivity and methodological considerations. The biochemical basis and assay methology for six assays (adenine leakage, adenine uptake, leucine uptake, 14CO2 evolution, lactate output and MTT reduction) that we have recently evaluated are detailed. The viability of Acanthocheilonema viteae females exposed for 120 h in vitro to 17 standard compounds (at 10 microM) has been assessed using these six assays and compared relative to motility indices from the micromotility meter. It was concluded that, despite the slightly superior sensitivity of the 14CO2 evolution assay, the MTT reduction method was most suitable for field use due to its technical and practical simplicity, and its applicability to fragments of onchocercal tissue. It was suggested that, in the absence of a better in vitro assay, the feasability of using MTT reduction together with histology should be assessed in a validation exercise with Onchocerca gibsoni.

  13. Mitochondrial evolution.

    PubMed

    Gray, M W; Burger, G; Lang, B F

    1999-03-01

    The serial endosymbiosis theory is a favored model for explaining the origin of mitochondria, a defining event in the evolution of eukaryotic cells. As usually described, this theory posits that mitochondria are the direct descendants of a bacterial endosymbiont that became established at an early stage in a nucleus-containing (but amitochondriate) host cell. Gene sequence data strongly support a monophyletic origin of the mitochondrion from a eubacterial ancestor shared with a subgroup of the alpha-Proteobacteria. However, recent studies of unicellular eukaryotes (protists), some of them little known, have provided insights that challenge the traditional serial endosymbiosis-based view of how the eukaryotic cell and its mitochondrion came to be. These data indicate that the mitochondrion arose in a common ancestor of all extant eukaryotes and raise the possibility that this organelle originated at essentially the same time as the nuclear component of the eukaryotic cell rather than in a separate, subsequent event.

  14. Life style and biochemical adaptation in Antarctic fishes

    NASA Astrophysics Data System (ADS)

    di Prisco, Guido

    2000-12-01

    Respiration and metabolism are under investigation in Antarctic fish, in an effort to understand the interplay between ecology and biochemical and physiological processes. Fish of the dominant suborder Notothenioidei are red-blooded, except Channichthyidae (the most phyletically derived family), whose genomes retain transcriptionally inactive DNA sequences closely related to the α-globin gene of red-blooded notothenioids and have lost the β-globin locus. Our structure/function studies on 38 of the 80 red-blooded species are aimed at correlating sequence, multiplicity and oxygen binding with ecological constraints and at obtaining phylogenetic information on evolution. For comparative purposes, this work has been extended to non-Antarctic notothenioids. All sluggish bottom dwellers have a single major hemoglobin (Hb) and often a minor, functionally similar one. Three species of the family Nototheniidae have different life styles. They have uniquely specialised oxygen-transport systems, adjusted to the mode of life of each species. Artedidraconidae have a single Hb, lacking oxygen-binding cooperativity, similar to the ancestral hemoproteins of primitive organisms. The amino acid sequences are currently used in the molecular modelling approach. The study of several enzymes with key roles in metabolism (e.g. glucose-6-phosphate dehydrogenase, L-glutamate dehydrogenase, phosphorylase b, carbonic anhydrase) indicate that some aspects of the molecular structure (e.g. molecular mass, number of subunits, amino acid sequence, temperature of irreversible heat inactivation) have been conserved during development of cold adaptation. However, high catalytic efficiency, possibly due to subtle molecular changes, is observed at low temperature.

  15. Stress-directed adaptive mutations and evolution.

    PubMed

    Wright, Barbara E

    2004-05-01

    Comparative biochemistry demonstrates that the metabolites, complex biochemical networks, enzymes and regulatory mechanisms essential to all living cells are conserved in amazing detail throughout evolution. Thus, in order to evolve, an organism must overcome new adverse conditions without creating different but equally dangerous alterations in its ongoing successful metabolic relationship with its environment. Evidence suggests that stable long-term acquisitive evolution results from minor increases in mutation rates of genes related to a particular stress, with minimal disturbance to the balanced and resilient metabolism critical for responding to an unpredictable environment. Microorganisms have evolved specific biochemical feedback mechanisms that direct mutations to genes derepressed by starvation or other stressors in their environment. Transcription of the activated genes creates localized supercoiling and DNA secondary structures with unpaired bases vulnerable to mutation. The resulting mutants provide appropriate variants for selection by the stress involved, thus accelerating evolution with minimal random damage to the genome. This model has successfully predicted mutation frequencies in genes of E. coli and humans. Stressed cells observed in the laboratory over hundreds of generations accumulate mutations that also arise by this mechanism. When this occurs in repair-deficient mutator strains with high rates of random mutation, the specific stress-directed mutations are also enhanced.

  16. Biochemical and physiological processes associated with the differential ozone response in ozone-tolerant and sensitive soybean genotypes.

    PubMed

    Chutteang, C; Booker, F L; Na-Ngern, P; Burton, A; Aoki, M; Burkey, K O

    2016-01-01

    Biochemical and physiological traits of two soybean [Glycine max (L.) Merr.] genotypes differing in sensitivity to ozone (O3 ) were investigated to determine the possible basis for the differential response. Fiskeby III (O3 -tolerant) and Mandarin (Ottawa) (O3 -sensitive) were grown in a greenhouse with charcoal-filtered air for 4 weeks, then treated with O3 for 7 h·day(-1) in greenhouse chambers. Mandarin (Ottawa) showed significantly more leaf injury and hydrogen peroxide (H2 O2 ) and superoxide (O2 (-) ) production compared with Fiskeby III. Peroxidase activity in Mandarin (Ottawa) was 31% higher with O3 but was not significantly different in Fiskeby III. Ozone did not affect superoxide dismutase or glutathione reductase activities, or leaf concentrations of glutathione or ascorbic acid. Thus, variation in O3 response between Fiskeby III and Mandarin (Ottawa) was not explained by differences in antioxidant enzymes and metabolites tested. Ethylene emission from leaves declined in Fiskeby III following O3 exposure but not in Mandarin (Ottawa). Ozone exposure reduced quantum yield (ΦPSII ), electron transport rate (ETR) and photochemical quenching (qp ) in Mandarin (Ottawa) more than in Fiskeby III, indicating that efficiency of energy conversion of PSII and photosynthetic electron transport was altered differently in the two genotypes. Short-term exposure to O3 had minimal effects on net carbon exchange rates of both soybean cultivars. A trend toward higher stomatal conductance in Mandarin (Ottawa) suggested stomatal exclusion might contribute to differential O3 sensitivity of the two genotypes. Increased sensitivity of Mandarin (Ottawa) to O3 was associated with higher H2 O2 and O2 (-) production compared with Fiskeby III, possibly associated with genotype differences in stomatal function or regulation of ethylene during the initial phases of O3 response.

  17. Fifty years of co-evolution and beyond: integrating co-evolution from molecules to species.

    PubMed

    Carmona, Diego; Fitzpatrick, Connor R; Johnson, Marc T J

    2015-11-01

    Fifty years after Ehrlich and Raven's seminal paper, the idea of co-evolution continues to grow as a key concept in our understanding of organic evolution. This concept has not only provided a compelling synthesis between evolutionary biology and community ecology, but has also inspired research that extends beyond its original scope. In this article, we identify unresolved questions about the co-evolutionary process and advocate for the integration of co-evolutionary research from molecular to interspecific interactions. We address two basic questions: (i) What is co-evolution and how common is it? (ii) What is the unit of co-evolution? Both questions aim to explore the heart of the co-evolutionary process. Despite the claim that co-evolution is ubiquitous, we argue that there is in fact little evidence to support the view that reciprocal natural selection and coadaptation are common in nature. We also challenge the traditional view that co-evolution only occurs between traits of interacting species. Co-evolution has the potential to explain evolutionary processes and patterns that result from intra- and intermolecular biochemical interactions within cells, intergenomic interactions (e.g. nuclear-cytoplasmic) within species, as well as intergenomic interactions mediated by phenotypic traits between species. Research that bridges across these levels of organization will help to advance our understanding of the importance of the co-evolutionary processes in shaping the diversity of life on Earth.

  18. Chemical constraints on the contribution of population III stars to cosmic reionization

    SciTech Connect

    Kulkarni, Girish; Hennawi, Joseph F.; Rollinde, Emmanuel; Vangioni, Elisabeth

    2014-05-20

    Recent studies have highlighted that galaxies at z = 6-8 fall short of producing enough ionizing photons to reionize the intergalactic medium, and suggest that Population III stars could resolve this tension, because their harder spectra can produce ∼10 × more ionizing photons than Population II. We use a semi-analytic model of galaxy formation, which tracks galactic chemical evolution, to gauge the impact of Population III stars on reionization. Population III supernovae produce distinct metal abundances, and we argue that the duration of the Population III era can be constrained by precise relative abundance measurements in high-z damped Lyα absorbers (DLAs), which provide a chemical record of past star formation. We find that a single generation of Population III stars can self-enrich galaxies above the critical metallicity Z {sub crit} = 10{sup –4} Z {sub ☉} for the Population III-to-II transition, on a very short timescale t {sub self-enrich} ∼ 10{sup 6} yr, owing to the large metal yields and short lifetimes of Population III stars. This subsequently terminates the Population III era, so they contribute ≳ 50% of the ionizing photons only for z ≳ 30, and at z = 10 contribute <1%. The Population III contribution can be increased by delaying metal mixing into the interstellar medium. However, comparing the resulting metal abundance pattern to existing measurements in z ≲ 6 DLAs, we show that the observed [O/Si] ratios of absorbers rule out Population III stars being a major contributor to reionization. Future abundance measurements of z ∼ 7-8 QSOs and gamma-ray bursts should probe the era when the chemical vestiges of Population III star formation become detectable.

  19. Biochemical indices associated with meditation practice: a literature review.

    PubMed

    Delmonte, M M

    1985-01-01

    Research findings on biochemical responsivity to meditation are reviewed. Although there are some contradictory and inconclusive outcomes, there is nevertheless sufficient evidence of interest to warrant further investigation of this area. However, in the meantime, there is no compelling basis to conclude that meditation practice is associated with special state or trait effects at the biochemical level.

  20. A Biochemical Approach to the Problem of Dyslexia.

    ERIC Educational Resources Information Center

    Baker, Sidney McDonald

    1985-01-01

    The paper presents the case of a sixth-grade boy, labeled dyslexic, who responded positively to a biochemical approach. Remedy of iron, zinc, and Vitamin B-6 deficiencies as well as an imbalance of fatty acids resulted in improvements in hair and skin and also in reading. A biochemical approach to behavior problems is proposed. (Author/CL)

  1. Simulation studies in biochemical signaling and enzyme reactions

    NASA Astrophysics Data System (ADS)

    Nelatury, Sudarshan R.; Vagula, Mary C.

    2014-06-01

    Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

  2. Origins and Evolution of Life

    NASA Astrophysics Data System (ADS)

    Gargaud, Muriel; López-García, Purificación; Martin, Hervé

    2011-01-01

    Part I. What Is Life?: 1. Problems raised by a definition of life M. Morange; 2. Some remarks about uses of cosmological anthropic 'principles' D. Lambert; 3. Minimal cell: the biologist point of view C. Brochier-Armanet; 4. Minimal cell: the computer scientist point of view H. Bersini; 5. Origins of life: computing and simulation approaches B. Billoud; Part II. Astronomical and Geophysical Context of the Emergence of Life: 6. Organic molecules in interstellar medium C. Ceccarelli and C. Cernicharo; 7. Cosmochemical evolution and the origin of life: insights from meteorites S. Pizzarello; 8. Astronomical constraints on the emergence of life M. Gounelle and T. Montmerle; 9. Formation of habitable planets J. Chambers; 10. The concept of galactic habitable zone N. Prantzos; 11. The young Sun and its influence on planetary atmospheres M. Güdel and J. Kasting; 12. Climates of the Earth G. Ramstein; Part III. Role of Water in the Emergence of Life: 13. Liquid water: a necessary condition to all forms of life K. Bartik, G. Bruylants, E. Locci and J. Reisse; 14. The role of water in the formation and evolution of planets T. Encrenaz; 15. Water on Mars J. P. Bibring; Part IV. From Non-Living Systems to Life: 16. Energetic constraints on prebiotic pathways: application to the emergence of translation R. Pascal and L. Boiteau; 17. Comparative genomics and early cell evolution A. Lazcano; 18. Origin and evolution of metabolisms J. Peretó; Part V. Mechanisms for Life Evolution: 19. Molecular phylogeny: inferring the patterns of evolution E. Douzery; 20. Horizontal gene transfer: mechanisms and evolutionary consequences D. Moreira; 21. The role of symbiosis in eukaryotic evolution A. Latorre, A. Durbán, A. Moya and J. Peretó; Part VI. Life in Extreme Conditions: 22. Life in extreme conditions: Deinococcus radiodurans, an organism able to survive prolonged desiccation and high doses of ionising radiation S. Sommer and M. Toueille; 23. Molecular effects of UV and ionizing

  3. Analysis of arsenic induced physiological and biochemical responses in a medicinal plant, Withania somnifera.

    PubMed

    Siddiqui, Fauzia; Tandon, P K; Srivastava, Sudhakar

    2015-01-01

    Withania somnifera has been an important herb in the Ayurvedic and indigenous medical systems for centuries in India. However, these grow as weeds mostly in the wastelands, which receive contaminated water from municipal and industrial sources. In the present investigation, plants of Withania somnifera were exposed to various concentrations of arsenate (AsV) and arsenite (AsIII) (0, 10, 25, 50, 100 μM) for 10 days and analysed for accumulation of arsenic (As) and physiological and biochemical changes. Plants showed more As accumulation upon exposure to AsIII (320 μg g(-1) DW in roots and 161 μg g(-1) DW in leaves) than to AsV (173 μg g(-1) DW in roots and 100 μg g(-1) DW in leaves) after 10 days of treatment. Consequently, AsIII exposure caused more toxicity to plants as compared to that AsV, as evaluated in terms of the level of photosynthetic pigments and oxidative stress parameters (superoxide, hydrogen peroxide and lipid peroxidation), particularly at higher concentrations and on longer durations. Plants could tolerate low concentrations (variable for AsIII and AsV) until longer durations (10 days) and high concentrations for shorter durations (1-5 days) through increase in antioxidant enzymes and by augmented synthesis of thiols. In conclusion, As tolerance potential of Withania plants on one hand advocates its prospective use for remediation under proper supervision and on the other demonstrates possible threat of As entry into humans due to medicinal uses. PMID:25648550

  4. Model-Based Design of Biochemical Microreactors

    PubMed Central

    Elbinger, Tobias; Gahn, Markus; Neuss-Radu, Maria; Hante, Falk M.; Voll, Lars M.; Leugering, Günter; Knabner, Peter

    2016-01-01

    Mathematical modeling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation, and optimization of metabolic processes in biochemical microreactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first microreactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments of the reactor multienzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions. The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multienzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the microreactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P) was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns, which differ for different experimental arrangements. Furthermore, the total output of G6P

  5. Model-Based Design of Biochemical Microreactors.

    PubMed

    Elbinger, Tobias; Gahn, Markus; Neuss-Radu, Maria; Hante, Falk M; Voll, Lars M; Leugering, Günter; Knabner, Peter

    2016-01-01

    Mathematical modeling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation, and optimization of metabolic processes in biochemical microreactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first microreactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments of the reactor multienzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions. The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multienzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the microreactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P) was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns, which differ for different experimental arrangements. Furthermore, the total output of G6P

  6. NIF Title III engineering plan

    SciTech Connect

    Deis, G

    1998-06-01

    The purpose of this document is to define the work that must be accomplished by the NIF Project during Title III Engineering. This definition is intended to be sufficiently detailed to provide a framework for yearly planning, to clearly identify the specific deliverables so that the Project teams can focus on them, and to provide a common set of objectives and processes across the Project. This plan has been preceded by similar documents for Title I and Title II design and complements the Site Management Plan, the Project Control Manual, the Quality Assurance Program Plan, the RM Parsons NIF Title III Configuration Control Plan, the Integrated Project Schedule, the Preliminary Safety Analysis Report, the Configuration Management Plan, and the Transition Plan.

  7. [Biochemical, clinical and genetic analysis of various aminoacidopathies (non-ketotic hyperglycemia, maple syrup urine disease, histidinemia, tyrosinemia)].

    PubMed

    László, A; Nagy, I; Szücs, L; Havass, Z; Sztriha, L; Svékus, A; Veres, E

    1992-11-29

    The genetical types were classified according to the clinical findings and biochemical results in cases of 13 newborn/children suffering from various aminoacidopathies. The genetical types were: 3 neonatal and 4 infantile types were found out of 7 non-ketotic disease (MSUD) patient was infantile type with 9.1 per cent keto acid decarboxylase activity in leukocyte homogenate. Among the 3 histidinemic patients 1 was severe neonatal type and 2 cases were chronic types. The 2 treated tyrosinemic children proved to be type III. (chronic with rickets).

  8. Microstructures in type III events in the solar wind

    NASA Technical Reports Server (NTRS)

    Melrose, D. B.; Goldman, M. V.

    1987-01-01

    A model is presented for the generation and evolution of bump-in-tail driven Langmuir waves in the solar wind during type III emission which removes a number of apparent inconsistencies between theory and observations. Growth rates and energy densities of Langmuir waves are considerably enhanced, permitting growth to overcome linear scattering losses, and also allowing nonlinear decay into ion-acoustic waves, in line with observations. Estimates are made of the probability distribution p(E), of wave field strengths E, based on linear and nonlinear wave-packet evolution, yielding p(E) approximately equal to E exp -alpha, alpha greater than or equal to 3. This helps explain why very high values of E are rarely found in the measured spiky wave turbulence.

  9. Silver europium(III) polyphosphate

    PubMed Central

    Ayadi, Mounir; Férid, Mokhtar; Moine, Bernard

    2009-01-01

    Europium(III) silver polyphosphate, AgEu(PO3)4, was prepared by the flux method. The atomic arrangement is built up by infinite (PO3)n chains (periodicity of 4) extending along the c axis. These chains are joined to each other by EuO8 dodeca­hedra. The Ag+ cations are located in the voids of this arrangement and are surrounded by five oxygen atoms in a distorted [4+1] coordination. PMID:21582031

  10. Study of interfacial phenomena for bio/chemical sensing applications

    NASA Astrophysics Data System (ADS)

    Min, Hwall

    This work presents the fundamental study of biological and chemical interfacial phenomena and (bio)chemical sensing applications using high frequency resonator arrays. To realize a versatile (bio)chemical sensing system for the fundamental study as well as their practical applications, the following three distinct components were studied and developed: i) detection platforms with high sensitivity, ii) novel innovative sensing materials with high selectivity, iii) analytical model for data interpretation. 8-pixel micromachined quartz crystal resonator (muQCR) arrays with a fundamental resonance frequency of 60 ¡V 90 MHz have been used to provide a reliable detection platform with high sensitivity. Room temperature ionic liquid (RTIL) has been explored and integrated into the sensing system as a smart chemical sensing material. The use of nanoporous gold (np-Au) enables the combination of the resonator and surface-enhanced Raman spectroscopy for both quantitative and qualitative measurement. A statistical model for the characterization of resonator behavior to study the protein adsorption kinetics is developed by random sequential adsorption (RSA) approach with the integration of an effective surface depletion theory. The investigation of the adsorption kinetics of blood proteins is reported as the fundamental study of biological phenomena using the proposed sensing system. The aim of this work is to study different aspects of protein adsorption and kinetics of adsorption process with blood proteins on different surfaces. We specifically focus on surface depletion effect in conjunction with the RSA model to explain the observed adsorption isotherm characteristics. A number of case studies on protein adsorption conducted using the proposed sensing system has been discussed. Effort is specifically made to understand adsorption kinetics, and the effect of surface on the adsorption process as well as the properties of the adsorbed protein layer. The second half of the

  11. Antithrombin III and the nephrotic syndrome.

    PubMed

    Jørgensen, K A; Stoffersen, E

    1979-05-01

    Plasma and urinary antithrombin III (AT-III) was measured in 15 cases of nephrotic syndrome. Plasma AT-III correlated well with serum albumin, but poorly with proteinuria, whereas urinary AT-III correlated well to proteinuria. The plasma AT-III level had a mean similar to 25 healthy controls, but the range was significantly wider. A case with nephrotic syndrome and left renal vein thrombosis is reported. The urinary output of AT-III rose and the plasma level fell with the activity of the disease. Although AT-III and albumin have similar molecule weight, their renal clearance was found to be different. It is suggested that urinary loss of AT-III plays a role in the hypercoagulable state sometimes found in the nephrotic syndrome.

  12. Bursts of Type III and Type V

    NASA Astrophysics Data System (ADS)

    Suzuki, S.; Dulk, G. A.

    The observational database on Types III and V solar radio bursts is summarized and used as a basis for developing analytical models of the observed phenomena. Type III events are characterized by a rapid drift from high to low frequencies, a harmonic structure consisting of F-H pairs, and circular polarization. Type V events last longer than Type III bursts and have a broader bandwidth. Both bursts are thought to arise from the same mechanism. Probable sources of the F-H pairs are characterized, along with the brightness temperature, time profiles, and polarization features typical of Type III and IIIb, structureless Type III and storm Type III bursts. Attention is also given to the interaction between Type III bursts and the coronal magnetic field and to similarities between Type III events and inverted-U and J bursts.

  13. Organometallic neptunium(III) complexes

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, Michał S.; Farnaby, Joy H.; Apostolidis, Christos; Colineau, Eric; Walter, Olaf; Magnani, Nicola; Gardiner, Michael G.; Love, Jason B.; Kaltsoyannis, Nikolas; Caciuffo, Roberto; Arnold, Polly L.

    2016-08-01

    Studies of transuranic organometallic complexes provide a particularly valuable insight into covalent contributions to the metal-ligand bonding, in which the subtle differences between the transuranium actinide ions and their lighter lanthanide counterparts are of fundamental importance for the effective remediation of nuclear waste. Unlike the organometallic chemistry of uranium, which has focused strongly on UIII and has seen some spectacular advances, that of the transuranics is significantly technically more challenging and has remained dormant. In the case of neptunium, it is limited mainly to NpIV. Here we report the synthesis of three new NpIII organometallic compounds and the characterization of their molecular and electronic structures. These studies suggest that NpIII complexes could act as single-molecule magnets, and that the lower oxidation state of NpII is chemically accessible. In comparison with lanthanide analogues, significant d- and f-electron contributions to key NpIII orbitals are observed, which shows that fundamental neptunium organometallic chemistry can provide new insights into the behaviour of f-elements.

  14. Organometallic neptunium(III) complexes

    NASA Astrophysics Data System (ADS)

    Dutkiewicz, Michał S.; Farnaby, Joy H.; Apostolidis, Christos; Colineau, Eric; Walter, Olaf; Magnani, Nicola; Gardiner, Michael G.; Love, Jason B.; Kaltsoyannis, Nikolas; Caciuffo, Roberto; Arnold, Polly L.

    2016-08-01

    Studies of transuranic organometallic complexes provide a particularly valuable insight into covalent contributions to the metal–ligand bonding, in which the subtle differences between the transuranium actinide ions and their lighter lanthanide counterparts are of fundamental importance for the effective remediation of nuclear waste. Unlike the organometallic chemistry of uranium, which has focused strongly on UIII and has seen some spectacular advances, that of the transuranics is significantly technically more challenging and has remained dormant. In the case of neptunium, it is limited mainly to NpIV. Here we report the synthesis of three new NpIII organometallic compounds and the characterization of their molecular and electronic structures. These studies suggest that NpIII complexes could act as single-molecule magnets, and that the lower oxidation state of NpII is chemically accessible. In comparison with lanthanide analogues, significant d- and f-electron contributions to key NpIII orbitals are observed, which shows that fundamental neptunium organometallic chemistry can provide new insights into the behaviour of f-elements.

  15. Evaluation of the sedative effect of fragrance on Filipinas using a biochemical marker.

    PubMed

    Yamaguchi, Masaki; Sakakima, Josaku; Sato, Kimiharu; Nakano, Kimihiro

    2007-03-01

    The purpose of this study is to evaluate the usefulness of salivary amylase activity as an indicator of the acute psychological sedative effects of fragrances used in household products such as clothing softeners. Twenty seven healthy Philippine female subjects in their late 30 s were enrolled (38.7+/-5.2 yr). This study was undertaken to investigate the favorite fragrance of Asian and Pacific Islander women. Our results indicated that (i) a mixed floral fragrance might be a favorite fragrance for Filipinas; (ii) fragrances contained in a softener significantly induced a sedative effect in humans, as assessed by both analysis of the biochemical marker and subjective evaluation; (iii) salivary amylase activity has the potential to be an excellent indicator for the evaluation of the acute psychological sedative effects of fragrance.

  16. Temperature-sensitive mutants of frog virus 3: biochemical and genetic characterization.

    PubMed Central

    Chinchar, V G; Granoff, A

    1986-01-01

    Nineteen frog virus 3 temperature-sensitive mutants were isolated after mutagenesis with nitrosoguanidine and assayed for viral DNA, RNA, and protein synthesis, as well as assembly site formation at permissive (25 degrees C) and nonpermissive (30 degrees C) temperatures. In addition, mutants were characterized for complementation by both quantitative and qualitative assays. Based on the genetic and biochemical data, the 19 mutants, along with 9 mutants isolated earlier, were ordered into four phenotypic classes which define defects in virion morphogenesis (class I), late mRNA synthesis (class II), viral assembly site formation (class III), and viral DNA synthesis (class IV). In addition, we used two-factor crosses to order 11 mutants, comprising 7 complementation groups, onto a linkage map spanning 77 recombination units. Images PMID:3951023

  17. Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria▿ †

    PubMed Central

    Slater, Steven C.; Goldman, Barry S.; Goodner, Brad; Setubal, João C.; Farrand, Stephen K.; Nester, Eugene W.; Burr, Thomas J.; Banta, Lois; Dickerman, Allan W.; Paulsen, Ian; Otten, Leon; Suen, Garret; Welch, Roy; Almeida, Nalvo F.; Arnold, Frank; Burton, Oliver T.; Du, Zijin; Ewing, Adam; Godsy, Eric; Heisel, Sara; Houmiel, Kathryn L.; Jhaveri, Jinal; Lu, Jing; Miller, Nancy M.; Norton, Stacie; Chen, Qiang; Phoolcharoen, Waranyoo; Ohlin, Victoria; Ondrusek, Dan; Pride, Nicole; Stricklin, Shawn L.; Sun, Jian; Wheeler, Cathy; Wilson, Lindsey; Zhu, Huijun; Wood, Derek W.

    2009-01-01

    The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria. PMID:19251847

  18. Insect evolution.

    PubMed

    Engel, Michael S

    2015-10-01

    It goes without saying that insects epitomize diversity, and with over a million documented species they stand out as one of the most remarkable lineages in the 3.5-billion-year history of life on earth (Figure 1). This reality is passé to even the layperson and is taken for granted in the same way none of us think much of our breathing as we go about our day, and yet insects are just as vital to our existence. Insects are simultaneously familiar and foreign to us, and while a small fraction are beloved or reviled, most are simply ignored. These inexorable evolutionary overachievers outnumber us all, their segmented body plan is remarkably labile, they combine a capacity for high rates of speciation with low levels of natural extinction, and their history of successes eclipses those of the more familiar ages of dinosaurs and mammals alike. It is their evolution - persisting over vast expanses of geological time and inextricably implicated in the diversification of other lineages - that stands as one of the most expansive subjects in biology. PMID:26439349

  19. Insect evolution.

    PubMed

    Engel, Michael S

    2015-10-01

    It goes without saying that insects epitomize diversity, and with over a million documented species they stand out as one of the most remarkable lineages in the 3.5-billion-year history of life on earth (Figure 1). This reality is passé to even the layperson and is taken for granted in the same way none of us think much of our breathing as we go about our day, and yet insects are just as vital to our existence. Insects are simultaneously familiar and foreign to us, and while a small fraction are beloved or reviled, most are simply ignored. These inexorable evolutionary overachievers outnumber us all, their segmented body plan is remarkably labile, they combine a capacity for high rates of speciation with low levels of natural extinction, and their history of successes eclipses those of the more familiar ages of dinosaurs and mammals alike. It is their evolution - persisting over vast expanses of geological time and inextricably implicated in the diversification of other lineages - that stands as one of the most expansive subjects in biology.

  20. Viral evolution

    PubMed Central

    Nasir, Arshan; Kim, Kyung Mo; Caetano-Anollés, Gustavo

    2012-01-01

    Explaining the origin of viruses remains an important challenge for evolutionary biology. Previous explanatory frameworks described viruses as founders of cellular life, as parasitic reductive products of ancient cellular organisms or as escapees of modern genomes. Each of these frameworks endow viruses with distinct molecular, cellular, dynamic and emergent properties that carry broad and important implications for many disciplines, including biology, ecology and epidemiology. In a recent genome-wide structural phylogenomic analysis, we have shown that large-to-medium-sized viruses coevolved with cellular ancestors and have chosen the evolutionary reductive route. Here we interpret these results and provide a parsimonious hypothesis for the origin of viruses that is supported by molecular data and objective evolutionary bioinformatic approaches. Results suggest two important phases in the evolution of viruses: (1) origin from primordial cells and coexistence with cellular ancestors, and (2) prolonged pressure of genome reduction and relatively late adaptation to the parasitic lifestyle once virions and diversified cellular life took over the planet. Under this evolutionary model, new viral lineages can evolve from existing cellular parasites and enhance the diversity of the world’s virosphere. PMID:23550145

  1. PHA bioplastics, biochemicals, and energy from crops.

    PubMed

    Somleva, Maria N; Peoples, Oliver P; Snell, Kristi D

    2013-02-01

    Large scale production of polyhydroxyalkanoates (PHAs) in plants can provide a sustainable supply of bioplastics, biochemicals, and energy from sunlight and atmospheric CO(2). PHAs are a class of polymers with various chain lengths that are naturally produced by some microorganisms as storage materials. The properties of these polyesters make them functionally equivalent to many of the petroleum-based plastics that are currently in the market place. However, unlike most petroleum-derived plastics, PHAs can be produced from renewable feedstocks and easily degrade in most biologically active environments. This review highlights research efforts over the last 20 years to engineer the production of PHAs in plants with a focus on polyhydroxybutryrate (PHB) production in bioenergy crops with C(4) photosynthesis. PHB has the potential to be a high volume commercial product with uses not only in the plastics and materials markets, but also in renewable chemicals and feed. The major challenges of improving product yield and plant fitness in high biomass yielding C(4) crops are discussed in detail.

  2. Biochemical analysis of Phytolacca DOPA dioxygenase.

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Yura, Kei; Ashihara, Hiroshi; Sakuta, Masaaki

    2015-05-01

    The biochemical analysis of Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) was carried out. The recombinant protein of PaDOD1 catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. While the reported motif conserved in DODs from betalain-producing plants was found in PaDOD1, a single amino acid residue alteration was detected in PaDOD2. A mutated PaDOD1 protein with a change of 177 Asn to Gly showed reduced specific activity compared with PaDOD1, while DOPA dioxygenase activity was not observed for a mutated PaDOD2 protein which had its conserved motif replaced with that of PaDOD. A three-dimensional (3D) structural model of PaDOD1 and PaDOD2 showed that the conserved motif in DODs was located in the N-terminal side of a loop, which was found close to the putative active site. The difference in stability of the loop may affect the enzymatic activity of PaDOD2. PMID:26058142

  3. Applied spectrophotometry: analysis of a biochemical mixture.

    PubMed

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software. PMID:23625877

  4. Biochemical analysis of Phytolacca DOPA dioxygenase.

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Yura, Kei; Ashihara, Hiroshi; Sakuta, Masaaki

    2015-05-01

    The biochemical analysis of Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) was carried out. The recombinant protein of PaDOD1 catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. While the reported motif conserved in DODs from betalain-producing plants was found in PaDOD1, a single amino acid residue alteration was detected in PaDOD2. A mutated PaDOD1 protein with a change of 177 Asn to Gly showed reduced specific activity compared with PaDOD1, while DOPA dioxygenase activity was not observed for a mutated PaDOD2 protein which had its conserved motif replaced with that of PaDOD. A three-dimensional (3D) structural model of PaDOD1 and PaDOD2 showed that the conserved motif in DODs was located in the N-terminal side of a loop, which was found close to the putative active site. The difference in stability of the loop may affect the enzymatic activity of PaDOD2.

  5. Biochemical studies of the tracheobronchial epithelium

    SciTech Connect

    Mass, M.J.; Kaufman, D.G.

    1984-06-01

    Tracheobronchial epithelium has been a focus of intense investigation in the field of chemical carcinogenesis. We have reviewed some biochemical investigations that have evolved through linkage with carcinogenesis research. These areas of investigation have included kinetics of carcinogen metabolism, identification of carcinogen metabolites, levels of carcinogen binding to DNA, and analysis of carcinogen-DNA adducts. Such studies appear to have provided a reasonable explanation for the susceptibilities of the respiratory tracts of rats and hamsters to carcinogenesis by benzo(a)pyrene. Coinciding with the attempts to understand the initiation of carcinogenesis in the respiratory tract has also been a major thrust aimed at effecting its prevention both in humans and in animal models for human bronchogenic carcinoma. These studies have concerned the effects of derivatives of vitamin A (retinoids) and their influence on normal cell biology and biochemistry of this tissue. Recent investigations have included the effects of retinoid deficiency on the synthesis of RNA and the identification of RNA species associated with this biological state, and also have included the effects of retinoids on the synthesis of mucus-related glycoproteins. Tracheal organ cultures from retinoid-deficient hamsters have been used successfully to indicate the potency of synthetic retinoids by monitoring the reversal of squamous metaplasia. Techniques applied to this tissue have also served to elucidate features of the metabolism of retinoic acid using high pressure liquid chromatography. 94 references, 9 figures, 2 tables.

  6. Biochemical and Proteomic Characterization of Alkaptonuric Chondrocytes

    PubMed Central

    Braconi, Daniela; Bernardini, Giulia; Bianchini, Claretta; Laschi, Marcella; Millucci, Lia; Amato, Loredana; Tinti, Laura; Serchi, Tommaso; Chellini, Federico; Spreafico, Adriano; Santucci, Annalisa

    2012-01-01

    Alkaptonuria (AKU) is a rare genetic disease associated with the accumulation of homogentisic acid (HGA) and its oxidized/polymerized products which leads to the deposition of melanin-like pigments (ochronosis) in connective tissues. Although numerous case reports have described ochronosis in joints, little is known on the molecular mechanisms leading to such a phenomenon. For this reason, we characterized biochemically chondrocytes isolated from the ochronotic cartilage of AKU patients. Based on the macroscopic appearance of the ochronotic cartilage, two sub-populations were identified: cells coming from the black portion of the cartilage were referred to as “black” AKU chondrocytes, while those coming from the white portion were referred to as “white” AKU chondrocytes. Notably, both AKU chondrocytic types were characterized by increased apoptosis, NO release, and levels of pro-inflammatory cytokines. Transmission electron microscopy also revealed that intracellular ochronotic pigment deposition was common to both “white” and “black” AKU cells. We then undertook a proteomic and redox-proteomic analysis of AKU chondrocytes which revealed profound alterations in the levels of proteins involved in cell defence, protein folding, and cell organization. An increased post-translational oxidation of proteins, which also involved high molecular weight protein aggregates, was found to be particularly relevant in “black” AKU chondrocytes. J. Cell. Physiol. 227: 3333–3343, 2012. © 2011 Wiley Periodicals, Inc. PMID:22213341

  7. Biochemical markers in butadiene-exposed workers

    SciTech Connect

    Bechtold, W.E.; Hayes, R.B.; Thornton-Manning, J.R.; Henderson, R.F.

    1994-11-01

    1,3-Butadiene (BD) is used to manufacture a wide range of polymers and copolymers including styrene-butadiene rubber, polybutadiene, and acrylonitrile-butadiene-syrene resins. The carcinogenicity of BD has been determined in life-span inhalation studies in both Sprague-Dawley rats and B6C3F{sub 1} mice. Results suggest a marked species difference in the carcinogenic effects of BD. For example, female mice exposed to as low as 6.25 ppm BD exhibited increased alveolar/bronchiolar neoplasms. In contrast, BD was only a weak carcinogen in Sprague-Dawley rats. Rats were observed to have an increase only in mammary tumors after exposure to 1000 ppm. A biochemical study of highly exposed BD workers and unexposed controls is providing valuable information on BD metabolism in humans, and how this relates to the development of intermediate biologic effects. A group of heavily exposed workers were identified in a BD production facility in China. The purpose of this paper is to report the initial results from the sampling trip in the first quarter of 1994.

  8. Control analysis for autonomously oscillating biochemical networks.

    PubMed

    Reijenga, Karin A; Westerhoff, Hans V; Kholodenko, Boris N; Snoep, Jacky L

    2002-01-01

    It has hitherto not been possible to analyze the control of oscillatory dynamic cellular processes in other than qualitative ways. The control coefficients, used in metabolic control analyses of steady states, cannot be applied directly to dynamic systems. We here illustrate a way out of this limitation that uses Fourier transforms to convert the time domain into the stationary frequency domain, and then analyses the control of limit cycle oscillations. In addition to the already known summation theorems for frequency and amplitude, we reveal summation theorems that apply to the control of average value, waveform, and phase differences of the oscillations. The approach is made fully operational in an analysis of yeast glycolytic oscillations. It follows an experimental approach, sampling from the model output and using discrete Fourier transforms of this data set. It quantifies the control of various aspects of the oscillations by the external glucose concentration and by various internal molecular processes. We show that the control of various oscillatory properties is distributed over the system enzymes in ways that differ among those properties. The models that are described in this paper can be accessed on http://jjj.biochem.sun.ac.za.

  9. PHA bioplastics, biochemicals, and energy from crops.

    PubMed

    Somleva, Maria N; Peoples, Oliver P; Snell, Kristi D

    2013-02-01

    Large scale production of polyhydroxyalkanoates (PHAs) in plants can provide a sustainable supply of bioplastics, biochemicals, and energy from sunlight and atmospheric CO(2). PHAs are a class of polymers with various chain lengths that are naturally produced by some microorganisms as storage materials. The properties of these polyesters make them functionally equivalent to many of the petroleum-based plastics that are currently in the market place. However, unlike most petroleum-derived plastics, PHAs can be produced from renewable feedstocks and easily degrade in most biologically active environments. This review highlights research efforts over the last 20 years to engineer the production of PHAs in plants with a focus on polyhydroxybutryrate (PHB) production in bioenergy crops with C(4) photosynthesis. PHB has the potential to be a high volume commercial product with uses not only in the plastics and materials markets, but also in renewable chemicals and feed. The major challenges of improving product yield and plant fitness in high biomass yielding C(4) crops are discussed in detail. PMID:23294864

  10. Biochemical Plant Responses to Ozone 1

    PubMed Central

    Rosemann, Detlef; Heller, Werner; Sandermann, Heinrich

    1991-01-01

    Formation of the stilbenes pinosylvin and pinosylvin 3-methyl ether, as well as the activity of the biosynthetic enzyme stilbene synthase (pinosylvin-forming), were induced several hundred- to thousandfold in primary needles of 6-week-old pine (Pinus sylvestris L.) seedlings upon exposure to a single pulse of ozone of at least 0.15 microliters per liter. The seedlings required 4 hours of exposure as a minimum for the induction of stilbene biosynthesis when exposed to 0.2 microliters per liter ozone. Both stilbene synthase activity and stilbene accumulation increased with the duration of ozone treatment. The activity of phenylalanine ammonia-lyase and the activity of chalcone synthase, a key enzyme of the flavonoid pathway that uses the same substrates as stilbene synthase, were also stimulated about twofold by ozone. Stilbene biosynthesis appears to represent the first example of a dose-dependent biochemical response to ozone in a conifer species and may serve as a useful biomarker to study stress impacts on pine trees. PMID:16668544

  11. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, Norman J.; Zhang, Jian Z.

    1996-01-01

    A multiple capillary biochemical analyzer for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal to noise ratio.

  12. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, N.J.; Zhang, J.Z.

    1996-10-22

    A multiple capillary biochemical analyzer is disclosed for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal-to-noise ratio. 12 figs.

  13. Applied spectrophotometry: analysis of a biochemical mixture.

    PubMed

    Trumbo, Toni A; Schultz, Emeric; Borland, Michael G; Pugh, Michael Eugene

    2013-01-01

    Spectrophotometric analysis is essential for determining biomolecule concentration of a solution and is employed ubiquitously in biochemistry and molecular biology. The application of the Beer-Lambert-Bouguer Lawis routinely used to determine the concentration of DNA, RNA or protein. There is however a significant difference in determining the concentration of a given species (RNA, DNA, protein) in isolation (a contrived circumstance) as opposed to determining that concentration in the presence of other species (a more realistic situation). To present the student with a more realistic laboratory experience and also to fill a hole that we believe exists in student experience prior to reaching a biochemistry course, we have devised a three week laboratory experience designed so that students learn to: connect laboratory practice with theory, apply the Beer-Lambert-Bougert Law to biochemical analyses, demonstrate the utility and limitations of example quantitative colorimetric assays, demonstrate the utility and limitations of UV analyses for biomolecules, develop strategies for analysis of a solution of unknown biomolecular composition, use digital micropipettors to make accurate and precise measurements, and apply graphing software.

  14. Diagnosis of growth retardation by biochemical methods.

    PubMed

    Klopper, A

    1984-08-01

    The substances in the blood or urine of a pregnant woman which may give an indication of the state of fetal growth are examined. The drawback of measuring such substances is that the values are variable, making it difficult to distinguish between normal and abnormal. Variability arises from technical factors in measurements, from short-term changes of no significance and from the large spread of normal values from one individual to the next. Biochemical parameters of fetal growth can be applied in one of two ways: as screening tests or as control measures by serial assays to guide management. The criteria by which any test should be evaluated--sensitivity, specificity and relative risk--are examined. Particular substances whose measurement may be helpful are considered in terms of the steroids or proteins produced by the fetoplacental unit. The oestrogens, notably oestriol, hold pride of place among the steroids. Dynamic tests of steroid synthesis are also considered. The chief placental proteins of interest are chorionic gonadotrophin, placental lactogen and Schwangerschaftsprotein 1. It is concluded that the method to be recommended is to screen a whole obstetric population with assays of placental lactogen and to follow those with values below the normal limit with serial oestriol assays. PMID:6332704

  15. [Clinical aspects of acquired antithrombin III deficiency].

    PubMed

    von Blohn, G; Hellstern, P; Köhler, M; Scheffler, P; Wenzel, E

    1986-02-01

    The significance of acquired antithrombin III (AT III) deficiency must be interpreted in close relation to the underlying disease process. In patients with acute or chronic liver impairment, the AT III activity is related to a decrease of procoagulatory factors, whereas, in protein loss syndromes such as nephrotic syndrome, the AT III indicates an increased risk of thromboembolic events. The effect of oral contraceptives (OC) on AT III levels in young healthy females (n = 30) was determined prospectively. AT III decreases during OC usage could not be related to the estrogen content of the examined oral contraceptives, and there was no parallel decrease of AT III activity and concentration in each type of OC. In a prospective study, the extent of AT III decrease was determined in patients undergoing cardiopulmonary bypass operations (CPB) receiving different anticoagulant schedules during extracorporeal circulation (n = 49). There was no significant influence on the effectiveness of anticoagulation by the observed AT III decreases. AT III deficiency during CPB was primarily the result of hemodilution. However, the AT III kinetics were significantly influenced by the different protamin dosages and were not affected by the different heparin dosages. Correction of diminished AT III levels by substitution of AT III concentrates is beneficial in cases, in which an interruption of an enhanced coagulatory process such as disseminated intravascular coagulation is necessary or in patients requiring high dosage heparinization as in deep vein thrombosis. In those cases the quality of AT III correction correlates to the course of the disease. However, the potency of concentrates as well as the individual AT III recovery and half-life must be considered for an appropriate treatment with AT III substitution. PMID:3718407

  16. Biochemical and serological characterization of Bacteroides intermedius strains isolated from the deep periodontal pocket.

    PubMed Central

    Dahlén, G; Wikström, M; Renvert, S; Gmür, R; Guggenheim, B

    1990-01-01

    Fifty-one fluorescence-positive black-pigmented Bacteroides strains obtained from 51 patients with deep periodontal pockets (greater than 6 mm) were identified and characterized. Fifty of these strains were presumptively identified as Bacteroides intermedius according to the indole reaction. This was confirmed by further biochemical characterization. The 50 strains from diseased sites were then compared with 16 B. intermedius strains isolated from periodontally healthy individuals with no signs of destructive periodontal disease. Tests for antimicrobial susceptibility showed similar patterns for all 50 pocket-derived strains, except for one beta-lactamase-positive strain that was resistant to penicillin G and ampicillin. Forty-seven strains were tested for binding of three monoclonal antibodies defining three distinct serogroups of B. intermedius. Thirty-one strains belonged to serogroup I, three to serogroup II and thirteen to serogroup III. In comparison to the strains from the shallow periodontal pockets, serogroup I was significantly overrepresented in the patient group with periodontal disease. We conclude that saccharolytic black-pigmented Bacteroides species from deep periodontal pockets constituted, with very rare exceptions, a biochemically homogeneous but antigenically heterogeneous group of B. intermedius and that serogroup I is predominantly found in deep periodontal lesions. PMID:2229351

  17. The effects of anabolic steroids on rat tendon. An ultrastructural, biomechanical, and biochemical analysis.

    PubMed

    Inhofe, P D; Grana, W A; Egle, D; Min, K W; Tomasek, J

    1995-01-01

    Forty-eight male rats were randomly separated into four groups: a control group, a group treated with anabolic steroids, a group treated with daily exercise, and a group treated with both steroids and exercise. At 6 weeks, biomechanical, ultrastructural, and biochemical testing was performed on the Achilles tendons of half of the rats in each group. The remaining rats continued in the experimental protocol, but steroid administration was discontinued. Similar testing was then performed on the remaining rats at 12 weeks. Testing showed anabolic steroids produced a stiffer tendon that absorbs less energy and fails with less elongation; tendon strength was unaffected. Effects were entirely reversible on discontinuation of the steroids. Light microscopic analysis revealed no changes in the appearance of the fibrils. No change in fibril diameter or shape was noted on electron microscopic analysis. Biochemical testing revealed no change in qualitative immunofluorescence staining with Type III collagen or fibronectin. Abuse of anabolic steroids is a widespread problem among competitive athletes; consequently, complications after their use are seen with increasing frequency. Knowledge of the effects of these drugs on tendon and the musculotendinous unit may prove helpful in counseling athletes who use anabolic steroids.

  18. Adaptive evolution of animal toxin multigene families.

    PubMed

    Kordis, D; Gubensek, F

    2000-12-30

    Animal toxins comprise a diverse array of proteins that have a variety of biochemical and pharmacological functions. A large number of animal toxins are encoded by multigene families. From studies of several toxin multigene families at the gene level the picture is emerging that most have been functionally diversified by gene duplication and adaptive evolution. The number of pharmacological activities in most toxin multigene families results from their adaptive evolution. The molecular evolution of animal toxins has been analysed in some multigene families, at both the intraspecies and interspecies levels. In most toxin multigene families, the rate of non-synonymous to synonymous substitutions (dN/dS) is higher than one. Thus natural selection has acted to diversify coding sequences and consequently the toxin functions. The selection pressure for the rapid adaptive evolution of animal toxins is the need for quick immobilization of the prey in classical predator and prey interactions. Currently available evidence for adaptive evolution in animal toxin multigene families will be considered in this review.

  19. Hereditary sensory and autonomic neuropathies: types II, III, and IV.

    PubMed

    Axelrod, Felicia B; Gold-von Simson, Gabrielle

    2007-01-01

    The hereditary sensory and autonomic neuropathies (HSAN) encompass a number of inherited disorders that are associated with sensory dysfunction (depressed reflexes, altered pain and temperature perception) and varying degrees of autonomic dysfunction (gastroesophageal reflux, postural hypotention, excessive sweating). Subsequent to the numerical classification of four distinct forms of HSAN that was proposed by Dyck and Ohta, additional entities continue to be described, so that identification and classification are ongoing. As a group, the HSAN are rare diseases that affect both sexes. HSAN III is almost exclusive to individuals of Eastern European Jewish extraction, with incidence of 1 per 3600 live births. Several hundred cases with HSAN IV have been reported. The worldwide prevalence of HSAN type II is very low. This review focuses on the description of three of the disorders, HSAN II through IV, that are characterized by autosomal recessive inheritance and onset at birth. These three forms of HSAN have been the most intensively studied, especially familial dysautonomia (Riley-Day syndrome or HSAN III), which is often used as a prototype for comparison to the other HSAN. Each HSAN disorder is likely caused by different genetic errors that affect specific aspects of small fiber neurodevelopment, which result in variable phenotypic expression. As genetic tests are routinely used for diagnostic confirmation of HSAN III only, other means of differentiating between the disorders is necessary. Diagnosis is based on the clinical features, the degree of both sensory and autonomic dysfunction, and biochemical evaluations, with pathologic examinations serving to further confirm differences. Treatments for all these disorders are supportive. PMID:17915006

  20. Neurotypic cell attachment and growth on III-nitride lateral polarity structures.

    PubMed

    Bain, L E; Kirste, R; Johnson, C A; Ghashghaei, H T; Collazo, R; Ivanisevic, A

    2016-01-01

    III-nitride materials have recently received increasing levels of attention for their potential to successfully interface with, and sense biochemical interactions in biological systems. Expanding on available sensing schemes (including transistor-based devices,) a III-N lateral polarity structure capable of introducing quasi-phase matching through a periodic polarity grating presents a novel platform for second harmonic generation. This platform constitutes a non-linear optical phenomenon with exquisite sensitivity to the chemical state of a surface or interface. To characterize the response of a biological system to the nanostructured lateral polarity structures, we cultured neurotypic PC12 cells on AlGaN with varying ratios of Al:Ga - 0, 0.4, 0.6, and 1 - and on surfaces of varying pitch to the III-polar vs. N-polar grating - 5, 10, 20 and 50 μm. While some toxicity associated with increasing Al is observed, we documented and quantified trends in cell responses to the local material polarity and nanoscale roughness. The nitrogen-polar material has a significantly higher nanoscale roughness than III-polar regions, and a 80-200 nm step height difference between the III-polar and N-polar materials in the lateral polarity configuration generates adequate changes in topography to influence cell growth, improves cell adhesion and promotes cell migration along the direction of the features. As the designed material configuration is further explored for biochemical sensing, the lateral polarity scheme may provide a route in assessing the non-specific protein adsorption to this varying nano-topography that drives the subsequent cell response.

  1. Increased procollagen type III peptide in serum of rabbits exposed to diesel engine exhaust

    SciTech Connect

    Suzuki, Takahito; Kanoh, Takako )

    1990-05-01

    Lung connective tissue is composed of collagen, elastin and proteoglycans. Collagen is the most abundant protein, comprising approximately 11% of normal adult lung and it has been provided at least five polymorphic types in lung. Collagen-producing cells such as fibroblasts and endothelial cells can synthesize procollagen within the cells. Once procollagen is secreted extracellularly, both amino- and carboxy-terminal peptides of procollagen are cleaved by endopeptidases. These peptides can move from the tissue into the blood stream. Therefore, the released peptides of type III procollagen may reflect the degree of biosynthesis of type III collagen, and increased peptide level in type III collagen, and increased peptide level in serum may suggest inflammation or the beginning of fibrosis. In this work, the authors have studied the changes of procollagen type III peptide (P-III-P) levels in sera and bronchoalveolar lavage fluid (BALF) from rabbits exposed to diesel exhaust in order to find a useful biochemical indicator of the effects of diesel exhaust exposure on human health.

  2. Biochemical genetics of largemouth bass. Final report

    SciTech Connect

    Phillipp, D.P.; Childers, W.F.; Whitt, G.S.

    1982-10-01

    Distinct biochemical genetic differences exist among largemouth bass (Micropterus salmoides) populations from different geographic regions. The level of genetic variation at 28 enzyme loci was determined for 90 bass populations throughout the United States through the use of vertical starch gel electrophoretic analyses. Allelic polymorphism was observed at 17 of these enzyme loci. Marked differences in allele frequencies at six of these loci exist among populations from the different geographic areas studied. Allele frequencies at two of these loci (isocitrate dehydrogenase-B and aspartate aminotransferase-B) can be used to quantitatively determine the contributions by each of the two recognized subspecies, M. s. salmoides and M. s. floridanus to the total gene pool of any population of largemouth bass. The current range of each subspecies and the extent of the range of intergradation has been redescribed. Furthermore, distinct north-south clinal distributions of the alleles at four of these loci (malate dehydrogenase-B, superoxide dismutase-A, isocitrate dehydrogenase-B and aspartate aminotransferase-B) indicate a possible involvement of these enzymes in the determination of the thermal tolerance/preference limits for this species. In vitro analyses of the different allelic isozymes at the malate dehydrogenase-B locus representing the northern and the southern phenotypes have revealed kinetic differences at temperatures which are encountered routinely in the environment, suggesting a possible mechanism for the genetic determination of thermal requirements. The results of these genetic analyses clearly indicate the need for incorporating sound genetic principles into current and future management programs.

  3. Genetically controlled food preference: biochemical mechanisms.

    PubMed Central

    Guarna, M M; Borowsky, R L

    1993-01-01

    Food choice is known to be correlated with genotype in the crustacean Gammarus palustris. Given a choice of Enteromorpha intestinalis (E) over Ulva lactuca (U), individuals homozygous for the Amy II.52 allele have a greater preference for E than do Amy II.55 homozygotes. To account for this correlation, we hypothesized that the proportions of saccharides released by the enzymatic action of Amy II.52 on E or Amy II.55 on U starches differ from and better stimulate feeding than those released by Amy II.52 on U and Amy II.55 on E starches. To test this, the two forms of amylase were purified by glycogen/ethanol precipitation and preparative PAGE. Their product distributions with each of the starches were determined by HPLC. Each amylase/starch combination gave different distributions of the main products: maltose, maltotriose, and maltotetraose. Feeding preference tests using artificial foods containing these sugars showed that the product distributions from Amy II.52/E starch or Amy II.55/U starch were preferred over those from Amy II.52/U or Amy II.55/E. Patterns of preferences for the artificial foods closely matched those observed in earlier experiments in which different genotypes fed on intact algae. Thus, genetic differences in feeding preferences can be understood in terms of variation in biochemical properties of a digestive enzyme. These results highlight a previously unappreciated role for digestive enzymes: in their capacity to modify the chemical nature of environmental stimuli prior to gustation, digestive enzymes can be viewed as having important chemosensory roles. PMID:7685121

  4. Stabilization of the Escherichia coli DNA polymerase III ε subunit by the θ subunit favors in vivo assembly of the Pol III catalytic core.

    PubMed

    Conte, Emanuele; Vincelli, Gabriele; Schaaper, Roel M; Bressanin, Daniela; Stefan, Alessandra; Dal Piaz, Fabrizio; Hochkoeppler, Alejandro

    2012-07-15

    Escherichia coli DNA polymerase III holoenzyme (HE) contains a core polymerase consisting of three subunits: α (polymerase), ε (3'-5' exonuclease), and θ. Genetic experiments suggested that θ subunit stabilizes the intrinsically labile ε subunit and, furthermore, that θ might affect the cellular amounts of Pol III core and HE. Here, we provide biochemical evidence supporting this model by analyzing the amounts of the relevant proteins. First, we show that a ΔholE strain (lacking θ subunit) displays reduced amounts of free ε. We also demonstrate the existence of a dimer of ε, which may be involved in the stabilization of the protein. Second, θ, when overexpressed, dissociates the ε dimer and significantly increases the amount of Pol III core. The stability of ε also depends on cellular chaperones, including DnaK. Here, we report that: (i) temperature shift-up of ΔdnaK strains leads to rapid depletion of ε, and (ii) overproduction of θ overcomes both the depletion of ε and the temperature sensitivity of the strain. Overall, our data suggest that ε is a critical factor in the assembly of Pol III core, and that this is role is strongly influenced by the θ subunit through its prevention of ε degradation.

  5. Optical properties of the Eu(III)-La(III)-complex-doped polyolefine film and rod samples

    NASA Astrophysics Data System (ADS)

    Pogreb, Roman; Popov, Oleg; Lirtsman, Vlad; Pyshkin, Oleg; Kazachkov, Alexander; Musin, Albina; Finkelshtein, Binyamin; Shmukler, Yuri; Davidov, Dan; Bormashenko, Edward

    2005-04-01

    The work is devoted to luminescent properties of trivalent lanthanide complexes dispersed in thermoplastic host matrices. Polyethylene-based film and polypropylene-based rod both doped with these complexes were manufactured using an extrusion technique. Two kinds of dopants were used: Eu(III)-thenoyltrifluoroacetone-1,10-phenanthroline complex (Eu(III)) and Eu(III)-La(III)-1,10-phenanthroline complex (Eu(III)-La(III)). Comparison was made between these samples regarding absorption, excitation, emission and a lifetime of luminescence. Dependence of emission intensity on the excitation energy was determined. Emission spectra of the films were studied at room and helium temperatures. Optical properties of Eu(III) samples are different from Eu(III)-La(III) samples. Significant difference in spectra of these two types of samples may be attributed to the La(III) action.

  6. Development of demographic norms for four new WAIS-III/WMS-III indexes.

    PubMed

    Lange, Rael T; Chelune, Gordon J; Taylor, Michael J; Woodward, Todd S; Heaton, Robert K

    2006-06-01

    Following the publication of the third edition Wechsler scales (i.e., WAIS-III and WMS-III), demographically corrected norms were made available in the form of a computerized scoring program (i.e., WAIS-III/WMS-III/WIAT-II Scoring Assistant). These norms correct for age, gender, ethnicity, and education. Since then, four new indexes have been developed: the WAIS-III General Ability Index, the WMS-III Delayed Memory Index, and the two alternate Immediate and Delayed Memory Indexes. The purpose of this study was to develop demographically corrected norms for the four new indexes using the standardization sample and education oversample from the WAIS-III and WMS-III. These norms were developed using the same methodology as the demographically corrected norms made available in the WAIS-III/WMS-III/WIAT-II Scoring Assistant.

  7. Development of demographic norms for four new WAIS-III/WMS-III indexes.

    PubMed

    Lange, Rael T; Chelune, Gordon J; Taylor, Michael J; Woodward, Todd S; Heaton, Robert K

    2006-06-01

    Following the publication of the third edition Wechsler scales (i.e., WAIS-III and WMS-III), demographically corrected norms were made available in the form of a computerized scoring program (i.e., WAIS-III/WMS-III/WIAT-II Scoring Assistant). These norms correct for age, gender, ethnicity, and education. Since then, four new indexes have been developed: the WAIS-III General Ability Index, the WMS-III Delayed Memory Index, and the two alternate Immediate and Delayed Memory Indexes. The purpose of this study was to develop demographically corrected norms for the four new indexes using the standardization sample and education oversample from the WAIS-III and WMS-III. These norms were developed using the same methodology as the demographically corrected norms made available in the WAIS-III/WMS-III/WIAT-II Scoring Assistant. PMID:16768593

  8. [INVESTIGATION OF BLOOD BIOCHEMICAL INDICES DURING BICYCLE ERGOMETRY].

    PubMed

    Davydov, B V; Stepanova, G P; Krivitsyna, Z A; Vorontsov, A L; Voronkov, Yu I

    2015-01-01

    Our investigations showed that physical work (bicycle ergometry) alters the biochemical status of male volunteers. On the 5th minute of bicycle endometry capillary blood looses significantly glucose and increases magnesium, phosphorus and particularly lactic acid. Creatine phosphokinase activity and trygliceride levels did not deviate much from baseline values. All the changes had a similar trend equally in the supine and sitting position. Therefore, biochemical investigations may complement essentially the physiological and neurophysiological tests of human adaptability to physical loads. The investigation utilized the dry chemistry technology of rapid biochemical diagnostics. PMID:26738302

  9. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  10. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  11. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  12. 40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections...

  13. Structural and photophysical studies on ternary Sm(III), Nd(III), Yb(III), Er(III) complexes containing pyridyltriazole ligands

    PubMed Central

    Gusev, Alexey N.; Shul’gin, Victor F.; Meshkova, Svetlana B.; Hasegawa, Miki; Alexandrov, Grigory G.; Eremenko, Igor L.; Linert, Wolfgang

    2012-01-01

    Two bidentate pyridine-triazole ligands (3-(pyridine-2-yl)-5-phenyl-1,2,4-triazole (L1) and 5-phenyl-2-(2′-pyridyl)-7,8-benzo-6,5-dihydro-1,3,6-triazaindolizine (L2)), have been synthesized and used for Ln(Dbm)3 (Ln = Sm(III), Nd(III), Yb(III) and Er(III)) coordination. The structures of the ligands and resulting Sm(III) complex were determined in the solid state by X-ray diffraction. The title complexes were characterized by UV, fluorescent, IR-spectroscopy and thermogravimetric and elemental analyses. Photophysical studies on the Ln(III) complexes were carried out showing luminescence in the region typical for Ln(III). The effect of various factors on the enhancement luminescence of complexes is discussed. PMID:23470984

  14. Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars

    PubMed Central

    Smith, Joseph V.

    1998-01-01

    Catalysis at mineral surfaces might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and photochemical gas reactions. Many ideas are implausible in detail because the proposed mineral surfaces strongly prefer water and other ionic species to organic ones. The molecular sieve silicalite (Union Carbide; = Al-free Mobil ZSM-5 zeolite) has a three-dimensional, 10-ring channel system whose electrically neutral Si-O surface strongly adsorbs organic species over water. Three -O-Si tetrahedral bonds lie in the surface, and the fourth Si-O points inwards. In contrast, the outward Si-OH of simple quartz and feldspar crystals generates their ionic organophobicity. The ZSM-5-type zeolite mutinaite occurs in Antarctica with boggsite and tschernichite (Al-analog of Mobil Beta). Archean mutinaite might have become de-aluminated toward silicalite during hot/cold/wet/dry cycles. Catalytic activity of silicalite increases linearly with Al-OH substitution for Si, and Al atoms tend to avoid each other. Adjacent organophilic and catalytic Al-OH regions in nanometer channels might have scavenged organic species for catalytic assembly into specific polymers protected from prompt photochemical destruction. Polymer migration along weathered silicic surfaces of micrometer-wide channels of feldspars might have led to assembly of replicating catalytic biomolecules and perhaps primitive cellular organisms. Silica-rich volcanic glasses should have been abundant on the early Earth, ready for crystallization into zeolites and feldspars, as in present continental basins. Abundant chert from weakly metamorphosed Archaean rocks might retain microscopic clues to the proposed mineral adsorbent/catalysts. Other framework silicas are possible, including ones with laevo/dextro one-dimensional channels. Organic molecules, transition-metal ions, and P occur inside modern feldspars. PMID:9520372

  15. The simulated evolution of biochemical guilds: reconciling Gaia theory and natural selection.

    PubMed

    Downing, K; Zvirinsky, P

    1999-01-01

    Gaia theory, which states that organisms both affect and regulate their environment, poses an interesting problem to Neo-Darwinian evolutionary biologists and provides an exciting set of phenomena for artificial-life investigation. The key challenge is to explain the emergence of biotic communities that are capable, via their implicit coordination, of regulating large-scale biogeochemical factors such as the temperature and chemical composition of the biosphere, but to assume no evolutionary mechanisms beyond contemporary natural selection. Along with providing an introduction to Gaia theory, this article presents simulations of Gaian emergence based on an artificial-life model involving genetic algorithms and guilds of simple metabolizing agents. In these simulations, resource competition leads to guild diversity; the ensemble of guilds then manifests life-sustaining nutrient recycling and exerts distributed control over environmental nutrient ratios. These results illustrate that standard individual-based natural selection is sufficient to explain Gaian self-organization, and they help clarify the relationships between two key metrics of Gaian activity: recycling and regulation.

  16. Implementing Title III -- Air toxics

    SciTech Connect

    Shaw, B.W.

    1995-12-31

    The South Coast Air Quality Management District (AQMD) is taking three basic approaches to implementing the new National Emissions Standards for Hazardous Air Pollutants (NESHAPs) from the Title III program: accept and implement, as written, the NESHAPs where few sources are located in the South Coast Air Basin; incorporate with simplification of the NESHAP requirements into AQMD rules when many sources are involved; then seek equivalency by the US EPA; and incorporate with a market-based rule (VOC RECLAIM), part of many NESHAPs which control volatile organic compound as HAPs. Whatever the approach, emphasis will be placed on: streamlining and simplification; helping sources understand requirements and comply; and common sense.

  17. The Mark III vertex chamber

    SciTech Connect

    Adler, J.; Bolton, T.; Bunnell, K.; Cassell, R.; Cheu, E.; Freese, T.; Grab, C.; Mazaheri, G.; Mir, R.; Odian, A.

    1987-07-01

    The design and construction of the new Mark III vertex chamber is described. Initial tests with cosmic rays prove the ability of track reconstruction and yield triplet resolutions below 50 ..mu..m at 3 atm using argon/ethane (50:50). Also performed are studies using a prototype of a pressurized wire vertex chamber with 8 mm diameter straw geometry. Spatial resolution of 35mm was obtained using dimethyl ether (DME) at 1 atm and 30 ..mu..m using argon/ethane (50/50 mixture) at 4 atm. Preliminary studies indicate the DME to adversely affect such materials as aluminized Mylar and Delrin.

  18. Chemical Evolution of a Bacterial Proteome.

    PubMed

    Hoesl, Michael Georg; Oehm, Stefan; Durkin, Patrick; Darmon, Elise; Peil, Lauri; Aerni, Hans-Rudolf; Rappsilber, Juri; Rinehart, Jesse; Leach, David; Söll, Dieter; Budisa, Nediljko

    2015-08-17

    We have changed the amino acid set of the genetic code of Escherichia coli by evolving cultures capable of growing on the synthetic noncanonical amino acid L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa) as a sole surrogate for the canonical amino acid L-tryptophan (Trp). A long-term cultivation experiment in defined synthetic media resulted in the evolution of cells capable of surviving Trp→[3,2]Tpa substitutions in their proteomes in response to the 20,899 TGG codons of the E. coli W3110 genome. These evolved bacteria with new-to-nature amino acid composition showed robust growth in the complete absence of Trp. Our experimental results illustrate an approach for the evolution of synthetic cells with alternative biochemical building blocks.

  19. Role of cryptic genes in microbial evolution.

    PubMed

    Hall, B G; Yokoyama, S; Calhoun, D H

    1983-12-01

    Cryptic genes are phenotypically silent DNA sequences, not normally expressed during the life cycle of an individual. They may, however, be activated in a few individuals of a large population by mutation, recombination, insertion elements, or other genetic mechanisms. A consideration of the microbial literature concerning biochemical evolution, physiology, and taxonomy provides the basis for a hypothesis of microbial adaptation and evolution by mutational activation of cryptic genes. Evidence is presented, and a mathematical model is derived, indicating that powerful and biologically important mechanisms exist to prevent the loss of cryptic genes. We propose that cryptic genes persist as a vital element of the genetic repertoire, ready for recall by mutational activation in future generations. Cryptic genes provide a versatile endogenous genetic reservoir that enhances the adaptive potential of a species by a mechanism that is independent of genetic exchange.

  20. SAGE III on ISS Lessons Learned on Thermal Interface Design

    NASA Technical Reports Server (NTRS)

    Davis, Warren

    2015-01-01

    The Stratospheric Aerosol and Gas Experiment III (SAGE III) instrument - the fifth in a series of instruments developed for monitoring vertical distribution of aerosols, ozone, and other trace gases in the Earth's stratosphere and troposphere - is currently scheduled for delivery to the International Space Station (ISS) via the SpaceX Dragon vehicle in 2016. The Instrument Adapter Module (IAM), one of many SAGE III subsystems, continuously dissipates a considerable amount of thermal energy during mission operations. Although a portion of this energy is transferred via its large radiator surface area, the majority must be conductively transferred to the ExPRESS Payload Adapter (ExPA) to satisfy thermal mitigation requirements. The baseline IAM-ExPA mechanical interface did not afford the thermal conductance necessary to prevent the IAM from overheating in hot on-orbit cases, and high interfacial conductance was difficult to achieve given the large span between mechanical fasteners, less than stringent flatness specifications, and material usage constraints due to strict contamination requirements. This paper will examine the evolution of the IAM-ExPA thermal interface over the course of three design iterations and will include discussion on design challenges, material selection, testing successes and failures, and lessons learned.

  1. Stable Self-Catalyzed Growth of III-V Nanowires.

    PubMed

    Tersoff, J

    2015-10-14

    Nanowire growth has generally relied on an initial particle of a catalyst such as Au to define the wire diameter and stabilize the growth. Self-catalyzed growth of III-V nanowires avoids the need for a foreign element, with the nanowire growing from the vapor via a droplet of the native group-III liquid. However, as suggested by Gibbs' phase rule, the absence of third element has a destabilizing effect. Here we analyze this system theoretically, finding that growth can be dynamically stable at pressures far above the equilibrium vapor pressure. Steady-state growth occurs via kinetic self-regulation of the droplet volume and wire diameter. In particular, for a given temperature and source-gas pressures there is a unique stable wire diameter and droplet volume, both of which decrease with increasing V/III ratio. We also examine the evolution of the droplet size and wire diameter toward the steady state as the wire grows and discuss implications for structural control. PMID:26389697

  2. SIM Configuration Evolution

    NASA Technical Reports Server (NTRS)

    Aaron, Kim M.

    2000-01-01

    The Space Interferometry Mission (SIM) is a space-based 10 m baseline Michelson interferometer. Planned for launch in 2005 aboard a Delta III launch vehicle, or equivalent, its primary objective is to measure the positions of stars and other celestial objects with an unprecedented accuracy of 4 micro arc seconds. With such an instrument, tremendous advancement can be expected in our understanding of stellar and galactic dynamics. Using triangulation from opposite sides of the orbit around the sun (i.e. by using parallax) one can measure the distance to any observable object in our galaxy. By directly measuring the orbital wobble of nearby stars, the mass and orbit of planets can be determined over a wide range of parameters. The distribution of velocity within nearby galaxies will be measurable. Observations of these and other objects will improve the calibration of distance estimators by more than an order of magnitude. This will permit a much better determination of the Hubble Constant as well as improving our overall understanding of the evolution of the universe. SIM has undergone several transformations, especially over the past year and a half since the start of Phase A. During this phase of a project, it is desirable to perform system-level trade studies, so the substantial evolution of the design that has occurred is quite appropriate. Part of the trade-off process has addressed two major underlying architectures: SIM Classic; and Son of SIM. The difference between these two architectures is related to the overall arrangement of the optical elements and the associated metrology system. Several different configurations have been developed for each architecture. Each configuration is the result of design choices that are influenced by many competing considerations. Some of the more important aspects will be discussed. The Space Interferometry Mission has some extremely challenging goals: millikelvin thermal stability, nanometer stabilization of optics

  3. Using chemical kinetics to model biochemical pathways.

    PubMed

    Le Novère, Nicolas; Endler, Lukas

    2013-01-01

    Chemical kinetics is the study of the rate of reactions transforming some chemical entities into other chemical entities. Over the twentieth century it has become one of the cornerstones of biochemistry. When in the second half of the century basic knowledge of cellular processes became sufficient to understand quantitatively metabolic networks, chemical kinetics associated with systems theory led to the development of what would become an important branch of systems biology. In this chapter we introduce basic concepts of chemical and enzyme kinetics, and show how the temporal evolution of a reaction system can be described by ordinary differential equations. Finally we present a method to apply this type of approach to model any regulatory network.

  4. Evolution of feline immunodeficiency virus Gag proteins.

    PubMed

    Burkala, Evan; Poss, Mary

    2007-10-01

    We evaluated the predicted biochemical properties of Gag proteins from a diverse group of feline immunodeficiency viruses (FIV) to determine how different evolutionary histories of virus and host have changed or constrained these important structural proteins. Our data are based on FIV sequences derived from domestic cat (FIVfca), cougar (FIVpco), and lions (FIVple). Analyses consisted of determining the selective forces acting at each position in the protein and the comparing predictions for secondary structure, charge, hydrophobicity and flexibility for matrix, capsid and nucleocapsid, and the C-terminal peptide, which comprise the Gag proteins. We demonstrate that differences among the FIV Gag proteins have largely arisen by neutral evolution, although many neutrally evolving regions have maintained biochemical features. Regions with predicted differences in biochemical features appear to involve intramolecular interactions and structural elements that undergo conformational changes during particle maturation. In contrast, the majority of sites involved in intermolecular contacts on the protein surface are constrained by purifying selection. There is also conservation of sites that interact with host proteins associated with cellular trafficking and particle budding. NC is the only protein with evidence of positive selection, two of which occur in the N-terminal region responsible for RNA binding and interaction with host proteins.

  5. Resonance electron attachment to plant hormones and its likely connection with biochemical processes

    SciTech Connect

    Pshenichnyuk, Stanislav A.; Modelli, Alberto

    2014-01-21

    Gas-phase formation of temporary negative ion states via resonance attachment of low-energy (0–6 eV) electrons into vacant molecular orbitals of salicylic acid (I) and its derivatives 3-hydroxy- (II) and 4-hydroxybenzoic acid (III), 5-cloro salicylic acid (IV) and methyl salicylate (V) was investigated for the first time by electron transmission spectroscopy. The description of their empty-level structures was supported by density functional theory and Hartree-Fock calculations, using empirically calibrated linear equations to scale the calculated virtual orbital energies. Dissociative electron attachment spectroscopy (DEAS) was used to measure the fragment anion yields generated through dissociative decay channels of the parent molecular anions of compounds I–V, detected with a mass filter as a function of the incident electron energy in the 0–14 eV energy range. The most intense negative fragment produced by DEA to isomers I–III is the dehydrogenated molecular anion [M–H]{sup −}, mainly formed at incident electron energies around 1 eV. The vertical and adiabatic electron affinities were evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. The same theoretical method was also used for evaluation of the thermodynamic energy thresholds for production of the negative fragments observed in the DEA spectra. The gas-phase DEAS data can provide support for biochemical reaction mechanisms in vivo.

  6. Resonance electron attachment to plant hormones and its likely connection with biochemical processes.

    PubMed

    Pshenichnyuk, Stanislav A; Modelli, Alberto

    2014-01-21

    Gas-phase formation of temporary negative ion states via resonance attachment of low-energy (0-6 eV) electrons into vacant molecular orbitals of salicylic acid (I) and its derivatives 3-hydroxy- (II) and 4-hydroxybenzoic acid (III), 5-cloro salicylic acid (IV) and methyl salicylate (V) was investigated for the first time by electron transmission spectroscopy. The description of their empty-level structures was supported by density functional theory and Hartree-Fock calculations, using empirically calibrated linear equations to scale the calculated virtual orbital energies. Dissociative electron attachment spectroscopy (DEAS) was used to measure the fragment anion yields generated through dissociative decay channels of the parent molecular anions of compounds I-V, detected with a mass filter as a function of the incident electron energy in the 0-14 eV energy range. The most intense negative fragment produced by DEA to isomers I-III is the dehydrogenated molecular anion [M-H](-), mainly formed at incident electron energies around 1 eV. The vertical and adiabatic electron affinities were evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. The same theoretical method was also used for evaluation of the thermodynamic energy thresholds for production of the negative fragments observed in the DEA spectra. The gas-phase DEAS data can provide support for biochemical reaction mechanisms in vivo. PMID:25669385

  7. Resonance electron attachment to plant hormones and its likely connection with biochemical processes.

    PubMed

    Pshenichnyuk, Stanislav A; Modelli, Alberto

    2014-01-21

    Gas-phase formation of temporary negative ion states via resonance attachment of low-energy (0-6 eV) electrons into vacant molecular orbitals of salicylic acid (I) and its derivatives 3-hydroxy- (II) and 4-hydroxybenzoic acid (III), 5-cloro salicylic acid (IV) and methyl salicylate (V) was investigated for the first time by electron transmission spectroscopy. The description of their empty-level structures was supported by density functional theory and Hartree-Fock calculations, using empirically calibrated linear equations to scale the calculated virtual orbital energies. Dissociative electron attachment spectroscopy (DEAS) was used to measure the fragment anion yields generated through dissociative decay channels of the parent molecular anions of compounds I-V, detected with a mass filter as a function of the incident electron energy in the 0-14 eV energy range. The most intense negative fragment produced by DEA to isomers I-III is the dehydrogenated molecular anion [M-H](-), mainly formed at incident electron energies around 1 eV. The vertical and adiabatic electron affinities were evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. The same theoretical method was also used for evaluation of the thermodynamic energy thresholds for production of the negative fragments observed in the DEA spectra. The gas-phase DEAS data can provide support for biochemical reaction mechanisms in vivo.

  8. Biochemical and immunohistochemical comparison of collagen in granuloma annulare and skin sarcoidosis.

    PubMed

    Oikarinen, A; Kinnunen, T; Kallioinen, M

    1989-01-01

    Collagen was studied by biochemical and immunohistochemical means in 5 patients with granuloma annulare (GA) and 3 with cutaneous sarcoidosis (SA). The solubility of collagen from the lesional skin in acetic acid was higher than that of collagen from unaffected skin from both patients and control subjects. Collagen concentration in the skin lesions, measured in terms of hydroxyproline content, was reduced in 3 patients with granuloma annulare and one with sarcoidosis, but the ratio of type III/I collagen was unchanged vis-à-vis non-affected skin. The collagen concentration in non-affected skin of both GA and SA-patients was also lower than in controls. The most typical immunohistochemical finding was the association of type III procollagen and fibronectin with granulomas in the lesional skin of both GA and SA cases. The activity of prolyl hydroxylase, a key enzyme in collagen biosynthesis, was markedly increased in the lesional skin, indicating that collagen synthesis in vivo was also increased. Surprisingly, collagen synthesis was not increased in cell culture studies. This could be due to cell selection as observed previously in scleroderma. Another possibility could be that various mediators released in vivo from inflammatory cells activate fibroblasts. However, when cells are subcultivated, this effect is not maintained. In conclusion, marked changes in collagen could be observed in granuloma annulare and skin sarcoidosis, reflecting increased turnover of collagen in vivo.

  9. Resonance electron attachment to plant hormones and its likely connection with biochemical processes

    NASA Astrophysics Data System (ADS)

    Pshenichnyuk, Stanislav A.; Modelli, Alberto

    2014-01-01

    Gas-phase formation of temporary negative ion states via resonance attachment of low-energy (0-6 eV) electrons into vacant molecular orbitals of salicylic acid (I) and its derivatives 3-hydroxy- (II) and 4-hydroxybenzoic acid (III), 5-cloro salicylic acid (IV) and methyl salicylate (V) was investigated for the first time by electron transmission spectroscopy. The description of their empty-level structures was supported by density functional theory and Hartree-Fock calculations, using empirically calibrated linear equations to scale the calculated virtual orbital energies. Dissociative electron attachment spectroscopy (DEAS) was used to measure the fragment anion yields generated through dissociative decay channels of the parent molecular anions of compounds I-V, detected with a mass filter as a function of the incident electron energy in the 0-14 eV energy range. The most intense negative fragment produced by DEA to isomers I-III is the dehydrogenated molecular anion [M-H]-, mainly formed at incident electron energies around 1 eV. The vertical and adiabatic electron affinities were evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. The same theoretical method was also used for evaluation of the thermodynamic energy thresholds for production of the negative fragments observed in the DEA spectra. The gas-phase DEAS data can provide support for biochemical reaction mechanisms in vivo.

  10. Colloidal α-Al2O3 Europium(III) and humic substances interactions: a macroscopic and spectroscopic study.

    PubMed

    Janot, Noémie; Benedetti, Marc F; Reiller, Pascal E

    2011-04-15

    Eu(III) sorption onto α-Al(2)O(3) in the presence of purified Aldrich humic acid (PAHA) is studied by batch experiments and time-resolved laser-induced luminescence spectroscopy of Eu(III). Experiments are conducted at varying pH, at 0.1 mol/L NaClO(4), 10(-6) mol/L Eu(III), 1 g/L α-Al(2)O(3) and 28 mg/L PAHA, which assured a complete Eu(III)-PAHA complexation. Adsorption of Eu(III) presents the expected pH-edge at 7, which is modified by addition of PAHA. Presence of Eu(III) slightly increases PAHA sorption throughout the pH range. The evolutions of luminescence spectra and decay times of the binary systems, that is, Eu(III)/α-Al(2)O(3) and Eu(III)/PAHA, indicate a progressive surface- and humic-complexation with increasing pH. The typical biexponential luminescence decay in Eu(III)/PAHA system is also recorded; the fastest deactivation depending barely on pH. In ternary Eu(III)/PAHA/α-Al(2)O(3) system, the existence of a luminescence biexponential decay for all pH means that Eu(III) is always in the direct neighborhood of the humic substance. Below pH 7, the spectra of the ternary system (Eu(III)/PAHA/α-Al(2)O(3)) are not different from the ones of Eu(III)/PAHA system, implying the same complex symmetry. Nevertheless, the increase of luminescence decay time points to a change in PAHA conformation onto the surface.

  11. PopIII signatures in the spectra of PopII/I GRBs

    NASA Astrophysics Data System (ADS)

    Ma, Q.; Maio, U.; Ciardi, B.; Salvaterra, R.

    2015-05-01

    We investigate signatures of Population III (PopIII) stars in the metal-enriched environment of gamma-ray bursts (GRBs) originating from Population II-I (PopII/I) stars by using abundance ratios derived from numerical simulations that follow stellar evolution and chemical enrichment. We find that at z > 10 more than 10 per cent of PopII/I GRBs explode in a medium previously enriched by PopIII stars (we refer to them as GRBII→III). Although the formation of GRBII→III is more frequent than that of pristine PopIII GRBs (GRBIIIs), we find that the expected GRBII→III observed rate is comparable to that of GRBIIIs, due to the usually larger luminosities of the latter. GRBII→III events take place preferentially in small protogalaxies with stellar masses M⋆ ˜ 104.5-107 M⊙, star formation rates SFR ˜ 10^{-3}-10^{-1} M_{⊙} yr^{-1} and metallicities Z ˜ 10- 4-10- 2 Z⊙. On the other hand, galaxies with Z < 10- 2.8 Z⊙ are dominated by metal enrichment from PopIII stars and should preferentially host GRBII→III. Hence, measured GRB metal content below this limit could represent a strong evidence of enrichment by pristine stellar populations. We discuss how to discriminate PopIII metal enrichment on the basis of various abundance ratios observable in the spectra of GRBs' afterglows. By employing such analysis, we conclude that the currently known candidates at redshift z ≃ 6 - i.e. GRB 050904 and GRB 130606A - are likely not originated in environments pre-enriched by PopIII stars. Abundance measurements for GRBs at z ≃ 5 - such as GRB 100219A and GRB 111008A - are still poor to draw definitive conclusions, although their hosts seem to be dominated by PopII/I pollution and do not show evident signatures of massive PopIII pre-enrichment.

  12. Zinc in +III oxidation state

    NASA Astrophysics Data System (ADS)

    Samanta, Devleena; Jena, Puru

    2012-02-01

    The possibility of Group 12 elements, such as Zn, Cd, and Hg existing in an oxidation state of +III or higher has fascinated chemists for decades. Significant efforts have been made in the past to achieve higher oxidation states for the heavier congener mercury (since the 3^rd ionization potential of the elements decrease as we go down the periodic table). It took nearly 20 years before experiment could confirm the theoretical prediction that Hg indeed can exist in an oxidation state of +IV. While this unusual property of Hg is attributed to the relativistic effects, Zn being much lighter than Hg has not been expected to have an oxidation state higher than +II. Using density functional theory we show that an oxidation state of +III for Zn can be realized by choosing specific ligands with large electron affinities i.e. superhalogens. We demonstrate this by a systematic study of the interaction of Zn with F, BO2, and AuF6 ligands whose electron affinities are progressively higher, namely, 3.4 eV, 4.4 eV, and 8.4 eV, respectively. Discovery of higher oxidation states of elements can help in the formulation of new reactions and hence in the development of new chemistry.

  13. Biochemical observation during 28 days of space flight

    NASA Technical Reports Server (NTRS)

    Leach, C. S.; Kambaut, P. C.

    1975-01-01

    With the completion of the 28-day flight of Skylab 2, the sum of biochemical data on human reaction to the weightless environment was significantly extended both quantitatively and qualitatively. The biochemical studies were divided into two broad categories. One group included the more routine blood studies similar to those used in everyday medical practice. The second category encompassed those analyses used to investigate more thoroughly the endocrinological and fluid changes first seen in the crewmembers following the Gemini, Apollo, and Soviet missions. Significant biochemical changes were observed that varied in magnitude and direction, but all disappeared shortly after return to earth. Most of changes indicate successful adaptation by the body to the combined stresses of weightlessness. Results of the biochemical observation are presented in the form of data tables and graphs.

  14. Pleural, peritoneal and pericardial effusions – a biochemical approach

    PubMed Central

    Kopcinovic, Lara Milevoj; Culej, Jelena

    2014-01-01

    The pathological accumulation of serous fluids in the pleural, peritoneal and pericardial space occurs in a variety of conditions. Since patient management depends on right and timely diagnosis, biochemical analysis of extravascular body fluids is considered a valuable tool in the patient management process. The biochemical evaluation of serous fluids includes the determination of gross appearance, differentiation of transudative from exudative effusions and additional specific biochemical testing to assess the effusion etiology. This article summarized data from the most relevant literature concerning practice with special emphasis on usefulness of biochemical tests used for the investigation of pleural, peritoneal and pericardial effusions. Additionally, preanalytical issues concerning serous fluid analysis were addressed and recommendations concerning acceptable analytical practice in serous fluid analysis were presented. PMID:24627721

  15. 2011 Biomass Program Platform Peer Review: Biochemical Conversion

    SciTech Connect

    Pezzullo, Leslie

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Biochemical Conversion Platform Review meeting.

  16. Rethinking glycolysis: on the biochemical logic of metabolic pathways.

    PubMed

    Bar-Even, Arren; Flamholz, Avi; Noor, Elad; Milo, Ron

    2012-05-17

    Metabolic pathways may seem arbitrary and unnecessarily complex. In many cases, a chemist might devise a simpler route for the biochemical transformation, so why has nature chosen such complex solutions? In this review, we distill lessons from a century of metabolic research and introduce new observations suggesting that the intricate structure of metabolic pathways can be explained by a small set of biochemical principles. Using glycolysis as an example, we demonstrate how three key biochemical constraints--thermodynamic favorability, availability of enzymatic mechanisms and the physicochemical properties of pathway intermediates--eliminate otherwise plausible metabolic strategies. Considering these constraints, glycolysis contains no unnecessary steps and represents one of the very few pathway structures that meet cellular demands. The analysis presented here can be applied to metabolic engineering efforts for the rational design of pathways that produce a desired product while satisfying biochemical constraints.

  17. CELLULAR, BIOCHEMICAL, AND MOLECULAR TECHNIQUES IN DEVELOPMENTAL TOXICOLOGY

    EPA Science Inventory

    Cellular, molecular and biochemical approaches vastly expand the possibilities for revealing the underlying mechanisms of developmental toxicity. The increasing interest in embryonic development as a model system for the study of gene expression has resulted in a cornucopia of i...

  18. Alternative end joining, clonal evolution, and escape from a telomere-driven crisis.

    PubMed

    Hendrickson, Eric A; Baird, Duncan M

    2015-01-01

    Telomere dysfunction and fusion play key roles in driving genomic instability and clonal evolution in many tumor types. We have recently described a role for DNA ligase III (LIG3) in facilitating the escape of cells from crisis induced by telomere dysfunction. Our data indicate that LIG3-mediated telomere fusion is important in facilitating clonal evolution.

  19. Evolution: Help for the Confused.

    ERIC Educational Resources Information Center

    Scheer, Bradley T.

    1979-01-01

    Written in response to an earlier article questioning certain aspects of evolution theory. Discusses ontogeny and phylogeny, the basis of evolution, chance or purpose in evolution, micro and macro-evolution, reversibility, and the evolution processes today. (MA)

  20. Evolution of genetic switch complexity

    PubMed Central

    Broussard, Gregory W.; Hatfull, Graham F.

    2013-01-01

    The circuitry of the phage λ genetic switch determining the outcome of lytic or lysogenic growth is well-integrated and complex, raising the question as to how it evolved. It is plausible that it arose from a simpler ancestral switch with fewer components that underwent various additions and refinements, as it adapted to vast numbers of different hosts and conditions. We have recently identified a new class of genetic switches found in mycobacteriophages and other prophages, in which immunity is dependent on integration. These switches contain only three genes (integrase, repressor and cro) and represent a major departure from the λ-like circuitry, lacking many features such as xis, cII and cIII. These small self-contained switches represent an unrealized, elegant circuitry for controlling infection outcome. In this addendum, we propose a model of possible events in the evolution of a complex λ-like switch from a simpler integration-dependent switch. PMID:23819104

  1. Discriminating model for diagnosis of basal cell carcinoma and melanoma in vitro based on the Raman spectra of selected biochemicals

    NASA Astrophysics Data System (ADS)

    Silveira, Landulfo; Silveira, Fabrício Luiz; Bodanese, Benito; Zângaro, Renato Amaro; Pacheco, Marcos Tadeu T.

    2012-07-01

    Raman spectroscopy has been employed to identify differences in the biochemical constitution of malignant [basal cell carcinoma (BCC) and melanoma (MEL)] cells compared to normal skin tissues, with the goal of skin cancer diagnosis. We collected Raman spectra from compounds such as proteins, lipids, and nucleic acids, which are expected to be represented in human skin spectra, and developed a linear least-squares fitting model to estimate the contributions of these compounds to the tissue spectra. We used a set of 145 spectra from biopsy fragments of normal (30 spectra), BCC (96 spectra), and MEL (19 spectra) skin tissues, collected using a near-infrared Raman spectrometer (830 nm, 50 to 200 mW, and 20 s exposure time) coupled to a Raman probe. We applied the best-fitting model to the spectra of biochemicals and tissues, hypothesizing that the relative spectral contribution of each compound to the tissue Raman spectrum changes according to the disease. We verified that actin, collagen, elastin, and triolein were the most important biochemicals representing the spectral features of skin tissues. A classification model applied to the relative contribution of collagen III, elastin, and melanin using Euclidean distance as a discriminator could differentiate normal from BCC and MEL.

  2. Principles of Adaptive Sorting Revealed by In Silico Evolution

    NASA Astrophysics Data System (ADS)

    Lalanne, Jean-Benoît; François, Paul

    2013-05-01

    Many biological networks have to filter out useful information from a vast excess of spurious interactions. In this Letter, we use computational evolution to predict design features of networks processing ligand categorization. The important problem of early immune response is considered as a case study. Rounds of evolution with different constraints uncover elaborations of the same network motif we name “adaptive sorting.” Corresponding network substructures can be identified in current models of immune recognition. Our work draws a deep analogy between immune recognition and biochemical adaptation.

  3. Energy-based analysis of biochemical cycles using bond graphs

    PubMed Central

    Gawthrop, Peter J.; Crampin, Edmund J.

    2014-01-01

    Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks. PMID:25383030

  4. [Fifty years of cooperation--FEBS and Polish Biochemical Society].

    PubMed

    Barańska, Jolanta

    2014-01-01

    This year, the Federation of European Biochemical Societies (FEBS) celebrates its 50th anniversary. The Polish Biochemical Society, represented by the Society's President, Kazimierz Zakrzewski, was a founding member of the organization. The text presents a history of collaboration between FEBS and Polish Biochemical Society, the participation of Polish Biochemical Society members in different FEBS activities, as well as the role they played in running the Federation. Author describes FEBS Congresses which taken place in Warsaw, the first 3rd FEBS Meeting in 1966 and then 29th Congress in 2004. The profiles of Jakub Karol Parnas, the founding father of the Polish biochemistry and some crucial Presidents of the Society, are also presented. The text describes Parnas Conferences, organized jointly by Polish and Ukrainian Biochemical Societies from 1996, and growing from 2011 into three-nation event with participation of Ukrainian, Israeli and Polish scientists, largely due to significant help from FEBS. Summarizing the last few years, author judge the cooperation between the Federation and the Polish Biochemical Society as optimal.

  5. Energy-based analysis of biochemical cycles using bond graphs.

    PubMed

    Gawthrop, Peter J; Crampin, Edmund J

    2014-11-01

    Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks. PMID:25383030

  6. Effects of Khaya senegalensis leaves on performance, carcass traits, hemtological and biochemical parameters in rabbits

    PubMed Central

    Abdel-Wareth, A. A. A.; Hammad, Seddik; Ahmed, Hassan

    2014-01-01

    One of the challenges facing farmers today is to ensure adequate integration of natural resources into animal feeds. The aim of the present study is to evaluate the effects of Khaya senegalensis (KS) leaves on the performance of growing male rabbits, carcass traits and biochemical as well as hematological parameters. Thirty New Zealand White male growing rabbits were randomly divided into 3 groups (10 rabbits per group). Group I (control) received standard rabbit diet. Rabbits in group II and group III were fed standard rabbit diet supplemented with 35 % and 65 % KS leaves, respectively. All rabbits were fed daily for 25 days. The performance parameters and carcass criteria, including daily body weight gain, final body weight, and the percentage of dressing, were increased in rabbits fed 35 % KS when compared to the control group. Kidney and liver weight ratios increased significantly in group II but dropped in group III. Furthermore, liver enzymes - alanine aminotransferase and aspartate transaminase and kidney function parameters - urea, and creatinine - increased in both group II (significant P<0.05) and in group III (significant P<0.01) when compared to the control group. Moreover, KS leaves induced a significant increase (P<0.05) in the total white blood cell count, the percentage of granulocytes and the platelet count; whereas, the percentage of lymphocytes, red blood cell count, hemoglobin content, mean corpuscular hemoglobin, mean corpuscular volume and mean corpuscular hemoglobin concentration were not statistically significantly changed. This study demonstrates that the performance parameters and carcass traits are improved by the replacement of rabbit's diet with KS leaves. However, KS leaves may adversely affect liver and kidney function in a dose-dependent manner. Therefore, further studies are required to elucidate the maximum tolerable and toxic, as well as lethal doses, and to isolate the pharmacologically active components from KS leaves. PMID

  7. Effect of nonsurgical periodontal therapy on salivary myeloperoxidase levels: A biochemical study

    PubMed Central

    Dagar, Mona; Deepa, Dhruv Kumar; Molly, Madan; Sharma, Anamika; Khattak, Braham Prakash

    2015-01-01

    Background: Myeloperoxidase (MPO), the most abundant protein in neutrophils, is the focus of inflammatory pathologies. MPO could participate in the initiation and progression of periodontal disease. Materials and Methods: A total of 60 patients with healthy gingiva, gingivitis, periodontitis between age group of 20–55 years were selected. Group I - 20 Patients with healthy gingiva, Group II - 20 Patients with generalized gingivitis, Group III - 20 Patients with generalized chronic periodontitis, Group IV - 20 Patients of Group III after 1-month of scaling and root planning. The following parameters were recorded: Gingival index, plaque index, bleeding on probing index, probing pocket depth, clinical attachment level, salivary MPO levels. All the parameters were then statistically analyzed. Results: The mean MPO levels in Group I recorded was - 0.320 + 0.06, Group II was - 0.183 + 0.04, Group III was - 0.814 + 0.08 and Group IV was - 0.386 + 0.08 respectively. All these values were statistically significant when compared between the four groups (P < 0.05). A significantly elevated salivary MPO levels were found in subjects with chronic periodontitis as compared to the gingivitis group and the healthy group (P < 0.05). However, moderate but statistically significant increase in the MPO levels were observed in the gingivitis group as compared to the healthy group (P < 0.05). Furthermore, significant reduction in MPO levels were observed in Group IV after 1-month of nonsurgical periodontal therapy. Conclusion: The activities of MPO enzyme were significantly increased in the saliva of patients with periodontal disease in comparison to healthy individuals. Furthermore, nonsurgical periodontal therapy was found to be effective in improving clinical parameters and in reducing MPO levels. Salivary enzymes like MPO could be considered as a biochemical marker of periodontal disease activity. PMID:26644720

  8. Evolution of plant senescence

    PubMed Central

    Thomas, Howard; Huang, Lin; Young, Mike; Ougham, Helen

    2009-01-01

    -related genes allow a framework to be constructed of decisive events in the evolution of the senescence syndrome of modern land-plants. Combining phylogenetic, comparative sequence, gene expression and morphogenetic information leads to the conclusion that biochemical, cellular, integrative and adaptive systems were progressively added to the ancient primary core process of senescence as the evolving plant encountered new environmental and developmental contexts. PMID:19602260

  9. III-Nitride Nanowire Lasers

    SciTech Connect

    Wright, Jeremy Benjamin

    2014-07-01

    In recent years there has been a tremendous interest in nanoscale optoelectronic devices. Among these devices are semiconductor nanowires whose diameters range from 10-100 nm. To date, nanowires have been grown using many semiconducting material systems and have been utilized as light emitting diodes, photodetectors, and solar cells. Nanowires possess a relatively large index contrast relative to their dielectric environment and can be used as lasers. A key gure of merit that allows for nanowire lasing is the relatively high optical con nement factor. In this work, I discuss the optical characterization of 3 types of III-nitride nanowire laser devices. Two devices were designed to reduce the number of lasing modes to achieve singlemode operation. The third device implements low-group velocity mode lasing with a photonic crystal constructed of an array of nanowires. Single-mode operation is necessary in any application where high beam quality and single frequency operation is required. III-Nitride nanowire lasers typically operate in a combined multi-longitudinal and multi-transverse mode state. Two schemes are introduced here for controlling the optical modes and achieving single-mode op eration. The rst method involves reducing the diameter of individual nanowires to the cut-o condition, where only one optical mode propagates in the wire. The second method employs distributed feedback (DFB) to achieve single-mode lasing by placing individual GaN nanowires onto substrates with etched gratings. The nanowire-grating substrate acted as a distributed feedback mirror producing single mode operation at 370 nm with a mode suppression ratio (MSR) of 17 dB. The usage of lasers for solid state lighting has the potential to further reduce U.S. lighting energy usage through an increase in emitter e ciency. Advances in nanowire fabrication, speci cally a two-step top-down approach, have allowed for the demonstration of a multi-color array of lasers on a single chip that emit

  10. III-nitride nanowire lasers

    NASA Astrophysics Data System (ADS)

    Wright, Jeremy Benjamin

    In recent years there has been a tremendous interest in nanoscale optoelectronic devices. Among these devices are semiconductor nanowires whose diameters range from 10-100 nm. To date, nanowires have been grown using many semiconducting material systems and have been utilized as light emitting diodes, photodetectors, and solar cells. Nanowires possess a relatively large index contrast relative to their dielectric environment and can be used as lasers. A key figure of merit that allows for nanowire lasing is the relatively high optical confinement factor. In this work, I discuss the optical characterization of 3 types of III-nitride nanowire laser devices. Two devices were designed to reduce the number of lasing modes to achieve single-mode operation. The third device implements low-group velocity mode lasing with a photonic crystal constructed of an array of nanowires. Single-mode operation is necessary in any application where high beam quality and single frequency operation is required. III-Nitride nanowire lasers typically operate in a combined multi-longitudinal and multi-transverse mode state. Two schemes are introduced here for controlling the optical modes and achieving single-mode operation. The first method involves reducing the diameter of individual nanowires to the cut-off condition, where only one optical mode propagates in the wire. The second method employs distributed feedback (DFB) to achieve single-mode lasing by placing individual GaN nanowires onto substrates with etched gratings. The nanowire-grating substrate acted as a distributed feedback mirror producing single mode operation at 370 nm with a mode suppression ratio (MSR) of 17 dB. The usage of lasers for solid state lighting has the potential to further reduce U.S. lighting energy usage through an increase in emitter efficiency. Advances in nanowire fabrication, specifically a two-step top-down approach, have allowed for the demonstration of a multi-color array of lasers on a single chip

  11. Spectroscopic identification of type 2 quasars at z < 1 in SDSS-III/BOSS

    NASA Astrophysics Data System (ADS)

    Yuan, Sihan; Strauss, Michael A.; Zakamska, Nadia L.

    2016-10-01

    The physics and demographics of type 2 quasars remain poorly understood, and new samples of such objects selected in a variety of ways can give insight into their physical properties, evolution, and relationship to their host galaxies. We present a sample of 2758 type 2 quasars at z ≲ 1 from the Sloan Digital Sky Survey-III (SDSS-III)/Baryon Oscillation Spectroscopic Survey (BOSS) spectroscopic data base, selected on the basis of their emission-line properties. We probe the luminous end of the population by requiring the rest-frame equivalent width of [O III] to be >100 Å. We distinguish our objects from star-forming galaxies and type 1 quasars using line widths, standard emission line ratio diagnostic diagrams at z < 0.52 and detection of [Ne V]λ3426 Å at z > 0.52. The majority of our objects have [O III] luminosities in the range 1.2 × 1042-3.8 × 1043 erg s-1 and redshifts between 0.4 and 0.65. Our sample includes over 400 type 2 quasars with incorrectly measured redshifts in the BOSS data base; such objects often show kinematic substructure or outflows in the [O III] line. The majority of the sample has counterparts in the Wide-field Infrared Survey Explorer survey, with median infrared luminosity νLν[12 μm] = 4.2 × 1044 erg s- 1. Only 34 per cent of the newly identified type 2 quasars would be selected by infrared colour cuts designed to identify obscured active nuclei, highlighting the difficulty of identifying complete samples of type 2 quasars. We make public the multi-Gaussian decompositions of all [O III] profiles for the new sample and for 568 type 2 quasars from SDSS I/II, together with non-parametric measures of the [O III] line profile shapes. We also identify over 600 candidate double-peaked [O III] profiles.

  12. Type III Protein Secretion Systems in Bacterial Pathogens of Animals and Plants

    PubMed Central

    Hueck, Christoph J.

    1998-01-01

    Various gram-negative animal and plant pathogens use a novel, sec-independent protein secretion system as a basic virulence mechanism. It is becoming increasingly clear that these so-called type III secretion systems inject (translocate) proteins into the cytosol of eukaryotic cells, where the translocated proteins facilitate bacterial pathogenesis by specifically interfering with host cell signal transduction and other cellular processes. Accordingly, some type III secretion systems are activated by bacterial contact with host cell surfaces. Individual type III secretion systems direct the secretion and translocation of a variety of unrelated proteins, which account for species-specific pathogenesis phenotypes. In contrast to the secreted virulence factors, most of the 15 to 20 membrane-associated proteins which constitute the type III secretion apparatus are conserved among different pathogens. Most of the inner membrane components of the type III secretion apparatus show additional homologies to flagellar biosynthetic proteins, while a conserved outer membrane factor is similar to secretins from type II and other secretion pathways. Structurally conserved chaperones which specifically bind to individual secreted proteins play an important role in type III protein secretion, apparently by preventing premature interactions of the secreted factors with other proteins. The genes encoding type III secretion systems are clustered, and various pieces of evidence suggest that these systems have been acquired by horizontal genetic transfer during evolution. Expression of type III secretion systems is coordinately regulated in response to host environmental stimuli by networks of transcription factors. This review comprises a comparison of the structure, function, regulation, and impact on host cells of the type III secretion systems in the animal pathogens Yersinia spp., Pseudomonas aeruginosa, Shigella flexneri, Salmonella typhimurium, enteropathogenic Escherichia coli

  13. Genetic and biochemical diversity among Valeriana jatamansi populations from Himachal Pradesh.

    PubMed

    Singh, Sunil Kumar; Katoch, Rajan; Kapila, Rakesh Kumar

    2015-01-01

    Valeriana jatamansi Jones is an important medicinal plant that grows wild in Himachal Pradesh, India. Molecular and biochemical diversity among 13 natural populations from Himachal Pradesh was assessed using RAPD and GC-MS to know the extent of existing variation. A total of seven genetically diverse groups have been identified based on RAPD analysis which corroborated well with the analysis based on chemical constituents. The essential oil yield ranged from 0.6% to 1.66% (v/w). A negative correlation between patchouli alcohol and viridiflorol, the two major valued constituents, limits the scope of their simultaneous improvement. However, other few populations like Chamba-II and Kandi-I were found promising for viridiflorol and patchouli alcohol, respectively. The analysis of chemical constitution of oil of the populations from a specific region revealed predominance of specific constituents indicating possibility of their collection/selection for specific end uses like phytomedicines. The prevalence of genetically diverse groups along with sufficient chemical diversity in a defined region clearly indicates the role of ecology in the maintenance of evolution of this species. Sufficient molecular and biochemical diversity detected among natural populations of this species will form basis for the future improvement. PMID:25741533

  14. Genetic and Biochemical Diversity among Valeriana jatamansi Populations from Himachal Pradesh

    PubMed Central

    Singh, Sunil Kumar; Katoch, Rajan; Kapila, Rakesh Kumar

    2015-01-01

    Valeriana jatamansi Jones is an important medicinal plant that grows wild in Himachal Pradesh, India. Molecular and biochemical diversity among 13 natural populations from Himachal Pradesh was assessed using RAPD and GC-MS to know the extent of existing variation. A total of seven genetically diverse groups have been identified based on RAPD analysis which corroborated well with the analysis based on chemical constituents. The essential oil yield ranged from 0.6% to 1.66% (v/w). A negative correlation between patchouli alcohol and viridiflorol, the two major valued constituents, limits the scope of their simultaneous improvement. However, other few populations like Chamba-II and Kandi-I were found promising for viridiflorol and patchouli alcohol, respectively. The analysis of chemical constitution of oil of the populations from a specific region revealed predominance of specific constituents indicating possibility of their collection/selection for specific end uses like phytomedicines. The prevalence of genetically diverse groups along with sufficient chemical diversity in a defined region clearly indicates the role of ecology in the maintenance of evolution of this species. Sufficient molecular and biochemical diversity detected among natural populations of this species will form basis for the future improvement. PMID:25741533

  15. Nonprevalence of biochemical fossils in kerogen from pre-Phanerozoic sediments

    PubMed Central

    Leventhal, Joel; Suess, Stephen E.; Cloud, Preston

    1975-01-01

    Evidence of biochemical and geochemical evolution was sought in insoluble carbonaceous matter from 30 selected pre-Phanerozoic sediments ranging in age from about 3.8 to about 0.7 × 109 years. The carbon isotope ratios observed were in the range of -20 to -32 per mil with reference to the Peedee belemnite standard, similar to those previously reported. No systematic trends are obvious to us. Stepwise pyrolysis-gas-chromatography showed only molecules with fewer than 8 carbon atoms at the level of sensitivity of 10-9 g of organics in a 10 mg rock sample. Carbon, hydrogen, and nitrogen analyses showed noncarbonate carbon from less than 0.1% to more than 3%, with very small amounts of N. The H/C (atomic) ratios on HCl-leached and HF-treated samples were generally less than 0.3. Evidence of low pyrolysis yields (micro-analysis) and low H/C atomic ratios (macro-analysis) implies that the carbonaceous solids in even the least metamorphosed of these ancient sediments have evolved far toward amorphous carbon or graphite and do not yield useful “biochemical fossils.” PMID:16592291

  16. DOE/NNSA perspective safeguard by design: GEN III/III+ light water reactors and beyond

    SciTech Connect

    Pan, Paul Y

    2010-12-10

    An overview of key issues relevant to safeguards by design (SBD) for GEN III/IV nuclear reactors is provided. Lessons learned from construction of typical GEN III+ water reactors with respect to SBD are highlighted. Details of SBD for safeguards guidance development for GEN III/III+ light water reactors are developed and reported. This paper also identifies technical challenges to extend SBD including proliferation resistance methodologies to other GEN III/III+ reactors (except HWRs) and GEN IV reactors because of their immaturity in designs.

  17. The type III secretion injectisome.

    PubMed

    Cornelis, Guy R

    2006-11-01

    The type III secretion injectisome is a complex nanomachine that allows bacteria to deliver protein effectors across eukaryotic cellular membranes. In recent years, significant progress has been made in our understanding of its structure, assembly and mode of operation. The principal structural components of the injectisome, from the base located in the bacterial cytosol to the tip of the needle protruding from the cell surface, have been investigated in detail. The structures of several constituent proteins were solved at the atomic level and important insights into the assembly process have been gained. However, despite the ongoing concerted efforts of molecular and structural biologists, the role of many of the constituent components of this nanomachine remain unknown. PMID:17041629

  18. A molecular description of the evolution of resistance

    NASA Technical Reports Server (NTRS)

    Ordoukhanian, P.; Joyce, G. F.

    1999-01-01

    BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.

  19. DSM-III-R and religion.

    PubMed

    Post, S G

    1992-07-01

    The interpretation of religion in DSM-III-R contains considerable negative bias and contributes to unfair stereotypes of religious persons. Particularly new religious movements and religious conversion are unfairly interpreted under the DSM-III-R heading, 'Dissociative Disorder Not Otherwise Specified'. It is suggested that a more balanced and respectful interpretation of religion is needed in DSM-III-R, since psychiatry through its official nomenclature should not contribute to social intolerance of religious nonconformity.

  20. On Type III plessite in chondrites

    NASA Astrophysics Data System (ADS)

    Knox, R., Jr.

    1980-03-01

    Questions are raised concerning the possible sources of heat necessary for converting martensite to coarse Type III plessite in ordinary chondrites. It is suggested that the unusual Type III plesite in the Kingfisher, Oklahoma black chondrite was formed by partial homogenization of preexisting Type III plessite as a result of shock reheating of the metal into the gamma field of the Fe-Ni phase diagram, rather than by decomposition of shock reheated prior martensite in the alpha + gamma field, as originally proposed by Taylor and Heymann. Because martensite is sporadically distributed within Kingfisher plessite it is suggested that microstructures of this kind be called Type II-III plessite.

  1. Spectrofluorimetric determination of Er (III) with diantipyrylmethane.

    PubMed

    Sungur, S

    2001-02-01

    The optimum fluorescence conditions for erbium (III) are obtained by irradiating this lanthanide at 435 nm in 0.04 microg ml(-1) diantipyrylmethane solution at pH = 8 (lambdaem = 510 nm). The method proposed is satisfactory for the determination of erbium (III) in the range of 0.001 to 1 microg ml(-1). The relative standard deviation 0.02 microg ml(-1) Er (III) in 0.04 microg ml(-1) diantipyrylmethane solution is 1.1%. The effect of other rare earths upon the intensity of the fluorescence emitted by erbium (III) is discussed. PMID:11206569

  2. M(III)Dy(III)3 (M = Fe(III), Co(III)) complexes: three-blade propellers exhibiting slow relaxation of magnetization.

    PubMed

    Xu, Gong-Feng; Gamez, Patrick; Tang, Jinkui; Clérac, Rodolphe; Guo, Yun-Nan; Guo, Yang

    2012-05-21

    [Dy(III)(HBpz(3))(2)](2+) moieties (HBpz(3)(-) = hydrotris(pyrazolyl)borate) and a 3d transition-metal ion (Fe(III) or Co(III)) have been rationally assembled using an dithiooxalato dianion ligand into 3d-4f [MDy(3)(HBpz(3))(6)(dto)(3)]·4CH(3)CN·2CH(2)Cl(2) (M = Fe (1), Co (2) complexes. Single-crystal X-ray studies reveal that three eight-coordinated Dy(III) centers in a square antiprismatic coordination environment are connecting to a central octahedral trivalent Fe or Co ion forming a propeller-type complex. The dynamics of the magnetization in the two isostructural compounds, modulated by the nature of the central M(III) metal ion, are remarkably different despite their analogous direct current (dc) magnetic properties. The slow relaxation of the magnetization observed for 2 mainly originates from isolated Dy ions, since a diamagnetic Co(III) metal ion links the magnetic Dy(III) ions. In the case of 1, the magnetic interaction between S = 1/2 Fe(III) ion and the three Dy(III) magnetic centers, although weak, generates a complex energy spectrum of magnetic states with low-lying excited states that induce a smaller energy gap than for 2 and thus a faster relaxation of the magnetization.

  3. Comparative adsorption of Eu(III) and Am(III) on TPD.

    PubMed

    Fan, Q H; Zhao, X L; Ma, X X; Yang, Y B; Wu, W S; Zheng, G D; Wang, D L

    2015-09-01

    Comparative adsorption behaviors of Eu(III) and Am(III) on thorium phosphate diphosphate (TPD), i.e., Th4(PO4)4P2O7, have been studied using a batch approach and surface complexation model (SCM) in this study. The results showed that Eu(III) and Am(III) adsorption increased to a large extent with the increase in TPD dose. Strong pH-dependence was observed in both Eu(III) and Am(III) adsorption processes, suggesting that inner-sphere complexes (ISCs) were possibly responsible for the adsorption of Eu(III) and Am(III). Meanwhile, the adsorption of Eu(III) and Am(III) decreased to a different extent with the increase in ion strength, which was possibly related to outer-sphere complexes and/or ion exchange. In the presence of fulvic acid (FA), the adsorption of Eu(III) and Am(III) showed high enhancement mainly due to the ternary surface complexes of TPD-FA-Eu(3+) and TPD-FA-Am(3+). The SCM showed that one ion exchange (≡S3Am/Eu) and two ISCs (≡(XO)2Am/EuNO3 and ≡(YO)2Am/EuNO3) seemed more reasonable to quantitatively describe the adsorption edges of both Eu(III) and Am(III). Our findings obviously showed that Eu(III) could be a good analogue to study actinide behaviors in practical terms. However, it should be kept in mind that there are still obvious differences between the characteristics of Eu(III) and Am(III) in some special cases, for instance, the complex ability with organic matter and adsorption affinity to a solid surface. PMID:26198355

  4. A method for zooming of nonlinear models of biochemical systems

    PubMed Central

    2011-01-01

    Background Models of biochemical systems are typically complex, which may complicate the discovery of cardinal biochemical principles. It is therefore important to single out the parts of a model that are essential for the function of the system, so that the remaining non-essential parts can be eliminated. However, each component of a mechanistic model has a clear biochemical interpretation, and it is desirable to conserve as much of this interpretability as possible in the reduction process. Furthermore, it is of great advantage if we can translate predictions from the reduced model to the original model. Results In this paper we present a novel method for model reduction that generates reduced models with a clear biochemical interpretation. Unlike conventional methods for model reduction our method enables the mapping of predictions by the reduced model to the corresponding detailed predictions by the original model. The method is based on proper lumping of state variables interacting on short time scales and on the computation of fraction parameters, which serve as the link between the reduced model and the original model. We illustrate the advantages of the proposed method by applying it to two biochemical models. The first model is of modest size and is commonly occurring as a part of larger models. The second model describes glucose transport across the cell membrane in baker's yeast. Both models can be significantly reduced with the proposed method, at the same time as the interpretability is conserved. Conclusions We introduce a novel method for reduction of biochemical models that is compatible with the concept of zooming. Zooming allows the modeler to work on different levels of model granularity, and enables a direct interpretation of how modifications to the model on one level affect the model on other levels in the hierarchy. The method extends the applicability of the method that was previously developed for zooming of linear biochemical models to

  5. [Biochemical selenocysteine synthesis and the phylogenic study].

    PubMed

    Mizutani, Takaharu; Osaka, Takashi; Fujiwara, Toshinobu; Shahidzzman, M

    2008-07-01

    Selenium (Se) is an essential trace element. Se is found as selenocysteine (Sec) in Se-proteins. Sec is the 21(st) amino acid, because Sec has its tRNA, the codon UGA and those components in its translational machinery. Sec UGA codon shares with major stop codon UGA. We purified Sec synthesizing enzymes, such as seryl-tRNA synthetase (SerRS), Sec synthetase (SecS) and selenophosphate synthetase (SePS). I described the procedures to prepare Sec tRNA, SerRS, SecS, SePS and [(75)Se]H(2)Se in detail. We clarified that SecS composed of two proteins, SecSalpha and SecSbeta. Sec synthesizing and incorporating systems present in Monela, Animalia and Protoctista but not in Plantae and Fungi. We showed that protozoa had Sec tRNA on which Sec was synthesized from Ser-tRNA by bovine and protozoa SecS. Some worms, such as Caenorhabditis elegans and Fasiola gigantica, also had Sec tRNA on which Sec was synthesized by bovine liver SecS or C. elegans enzymes. We showed recognition sites of mammalian Sec tRNA by SecS. The identity units of Sec tRNA are 9 bp aminoacyl- and 6 bp D-stems. This recognition is not the base-specific manner but the length-specific manner. From comparison of the phylogeny trees of Sec synthesizing system and translation system, we concluded that the evolution of Sec synthesizing system is older than that of the translation system.

  6. [Biochemical selenocysteine synthesis and the phylogenic study].

    PubMed

    Mizutani, Takaharu; Osaka, Takashi; Fujiwara, Toshinobu; Shahidzzman, M

    2008-07-01

    Selenium (Se) is an essential trace element. Se is found as selenocysteine (Sec) in Se-proteins. Sec is the 21(st) amino acid, because Sec has its tRNA, the codon UGA and those components in its translational machinery. Sec UGA codon shares with major stop codon UGA. We purified Sec synthesizing enzymes, such as seryl-tRNA synthetase (SerRS), Sec synthetase (SecS) and selenophosphate synthetase (SePS). I described the procedures to prepare Sec tRNA, SerRS, SecS, SePS and [(75)Se]H(2)Se in detail. We clarified that SecS composed of two proteins, SecSalpha and SecSbeta. Sec synthesizing and incorporating systems present in Monela, Animalia and Protoctista but not in Plantae and Fungi. We showed that protozoa had Sec tRNA on which Sec was synthesized from Ser-tRNA by bovine and protozoa SecS. Some worms, such as Caenorhabditis elegans and Fasiola gigantica, also had Sec tRNA on which Sec was synthesized by bovine liver SecS or C. elegans enzymes. We showed recognition sites of mammalian Sec tRNA by SecS. The identity units of Sec tRNA are 9 bp aminoacyl- and 6 bp D-stems. This recognition is not the base-specific manner but the length-specific manner. From comparison of the phylogeny trees of Sec synthesizing system and translation system, we concluded that the evolution of Sec synthesizing system is older than that of the translation system. PMID:18591866

  7. Understanding Evolution: An Evolution Website for Teachers

    ERIC Educational Resources Information Center

    Scotchmoor, Judy; Janulaw, Al

    2005-01-01

    While many states are facing challenges to the teaching of evolution in their science classrooms, the University of California Museum of Paleontology, working with the National Center for Science Education, has developed a useful web-based resource for science teachers of all grade- and experience-levels. Understanding Evolution (UE) was developed…

  8. Epidermal growth factor induces biphasic activation of ornithine decarboxylase in human stomach-derived KATO-III cells.

    PubMed

    Ishikawa, T; Mitsuhashi, M; Ichikawa, Y; Tarnawski, A

    1994-01-01

    Effect of epidermal growth factor (EGF) on ornithine decarboxylase (ODC) was examined in human gastric cancer-derived KATO-III cells, because 125I-EGF binding studies indicated a presence of specific binding sites for EGF on these cells. Upon stimulation with EGF, both ODC mRNA expression and ODC enzyme activity were significantly increased in KATO-III cells. However, unlike in other cellular systems, both EGF-induced ODC mRNA expression and ODC enzyme activation were biphasic with the peaks at 15 +/- 10 min and 2.1 +/- 1.5 hrs (mean +/- SE) for mRNA, and 3.1 +/- 1.5 and 7.7 +/- 1.8 hrs (mean +/- SE) for enzyme activity, respectively. Therefore, KATO-III cell line may provide a unique model for the biochemical analysis of EGF action on ODC activation. PMID:8190004

  9. Near-Infrared Photoluminescence and Electroluminescence of Neodymium(III), Erbium(III), and Ytterbium(III) Complexes

    NASA Astrophysics Data System (ADS)

    Kawamura, Yuichiro; Wada, Yuji; Yanagida, Shozo

    2001-01-01

    Tris(dibenzoylmethanato)(monobathophenanthroline)lanthanide(III) complex [Ln(DBM)3 bath (Ln: Nd, Er and Yb)] both in solutions and thin films at room temperature showed narrow band photoluminescence (PL) due to the f-f transitions in the near-IR region: 890, 1070 and 1350 nm for Nd(III), 980 and 1540 nm for Er(III), and 985 nm for Yb(III). The PL efficiencies in solution were determined [φPL=3.3× 10-3 for Nd(III), 7.0× 10-5 for Er(III), and 1.4× 10-2 for Yb(III)]. Organic electroluminescent (EL) devices having the structure of glass substrate/indium-tin oxide/N,N\\prime-diphenyl-N,N\\prime-di(m-tolyl)benzidine{\\slash}Ln(DBM)3bath(Ln: Nd, Er and Yb)/bathocuproine/Mg:Ag/Ag were fabricated, giving the EL bands around 900-1600 nm at room temperature. The external near-IR EL efficiencies at low current density were estimated by comparing with that of the Eu(III) device having the same structure. The saturation of near-IR EL intensity observed at the high current density suggested that the near-IR EL should suffer the T-T annihilation.

  10. Heterotrimetallic coordination polymers: {Cu(II)Ln(III)Fe(III)} chains and {Ni(II)Ln(III)Fe(III)} layers: synthesis, crystal structures, and magnetic properties.

    PubMed

    Alexandru, Maria-Gabriela; Visinescu, Diana; Andruh, Marius; Marino, Nadia; Armentano, Donatella; Cano, Joan; Lloret, Francesc; Julve, Miguel

    2015-03-27

    The use of the [Fe(III) (AA)(CN)4](-) complex anion as metalloligand towards the preformed [Cu(II) (valpn)Ln(III)](3+) or [Ni(II) (valpn)Ln(III) ](3+) heterometallic complex cations (AA=2,2'-bipyridine (bipy) and 1,10-phenathroline (phen); H2 valpn=1,3-propanediyl-bis(2-iminomethylene-6-methoxyphenol)) allowed the preparation of two families of heterotrimetallic complexes: three isostructural 1D coordination polymers of general formula {[Cu(II) (valpn)Ln(III) (H2O)3 (μ-NC)2 Fe(III) (phen)(CN)2 {(μ-NC)Fe(III) (phen)(CN)3}]NO3 ⋅7 H2O}n (Ln=Gd (1), Tb (2), and Dy (3)) and the trinuclear complex [Cu(II) (valpn)La(III) (OH2 )3 (O2 NO)(μ-NC)Fe(III) (phen)(CN)3 ]⋅NO3 ⋅H2O⋅CH3 CN (4) were obtained with the [Cu(II) (valpn)Ln(III)](3+) assembling unit, whereas three isostructural heterotrimetallic 2D networks, {[Ni(II) (valpn)Ln(III) (ONO2 )2 (H2 O)(μ-NC)3 Fe(III) (bipy)(CN)]⋅2 H2 O⋅2 CH3 CN}n (Ln=Gd (5), Tb (6), and Dy (7)) resulted with the related [Ni(II) (valpn)Ln(III) ](3+) precursor. The crystal structure of compound 4 consists of discrete heterotrimetallic complex cations, [Cu(II) (valpn)La(III) (OH2)3 (O2 NO)(μ-NC)Fe(III) (phen)(CN)3 ](+), nitrate counterions, and non-coordinate water and acetonitrile molecules. The heteroleptic {Fe(III) (bipy)(CN)4} moiety in 5-7 acts as a tris-monodentate ligand towards three {Ni(II) (valpn)Ln(III)} binuclear nodes leading to heterotrimetallic 2D networks. The ferromagnetic interaction through the diphenoxo bridge in the Cu(II)-Ln(III) (1-3) and Ni(II)-Ln(III) (5-7) units, as well as through the single cyanide bridge between the Fe(III) and either Ni(II) (5-7) or Cu(II) (4) account for the overall ferromagnetic behavior observed in 1-7. DFT-type calculations were performed to substantiate the magnetic interactions in 1, 4, and 5. Interestingly, compound 6 exhibits slow relaxation of the magnetization with maxima of the out-of-phase ac signals below 4.0 K in the lack of a dc field, the values of the pre

  11. Influence of organic matters on AsIII oxidation by the microflora of polluted soils.

    PubMed

    Lescure, T; Moreau, J; Charles, C; Ben Ali Saanda, T; Thouin, H; Pillas, N; Bauda, P; Lamy, I; Battaglia-Brunet, F

    2016-06-01

    The global AsIII-oxidizing activity of microorganisms in eight surface soils from polluted sites was quantified with and without addition of organic substrates. The organic substances provided differed by their nature: either yeast extract, commonly used in microbiological culture media, or a synthetic mixture of defined organic matters (SMOM) presenting some common features with natural soil organic matter. Correlations were sought between soil characteristics and both the AsIII-oxidizing rate constants and their evolution in accordance with inputs of organic substrates. In the absence of added substrate, the global AsIII oxidation rate constant correlated positively with the concentration of intrinsic organic matter in the soil, suggesting that AsIII-oxidizing activity was limited by organic substrate availability in nutrient-poor soils. This limitation was, however, removed by 0.08 g/L of added organic carbon. In most conditions, the AsIII oxidation rate constant decreased as organic carbon input increased from 0.08 to 0.4 g/L. Incubations of polluted soils in aerobic conditions, amended or not with SMOM, resulted in short-term As mobilization in the presence of SMOM and active microorganisms. In contrast, microbial AsIII oxidation seemed to stabilize As when no organic substrate was added. Results suggest that microbial speciation of arsenic driven by nature and concentration of organic matter exerts a major influence on the fate of this toxic element in surface soils.

  12. Improvement of thermostability and activity of Trichoderma reesei endo-xylanase Xyn III on insoluble substrates.

    PubMed

    Matsuzawa, Tomohiko; Kaneko, Satoshi; Yaoi, Katsuro

    2016-09-01

    Trichoderma reesei Xyn III, an endo-β-1,4-xylanase belonging to glycoside hydrolase family 10 (GH10), is vital for the saccharification of xylans in plant biomass. However, its enzymatic thermostability and hydrolytic activity on insoluble substrates are low. To overcome these difficulties, the thermostability of Xyn III was improved using random mutagenesis and directed evolution, and its hydrolytic activity on insoluble substrates was improved by creating a chimeric protein. In the screening of thermostable Xyn III mutants from a random mutagenesis library, we identified two amino acid residues, Gln286 and Asn340, which are important for the thermostability of Xyn III. The Xyn III Gln286Ala/Asn340Tyr mutant showed xylanase activity even after heat treatment at 60 °C for 30 min or 50 °C for 96 h, indicating a dramatic enhancement in thermostability. In addition, we found that the addition of a xylan-binding domain (XBD) to the C-terminal of Xyn III improved its hydrolytic activity on insoluble xylan. PMID:27138202

  13. Methanogenesis affected by the co-occurrence of iron(III) oxides and humic substances.

    PubMed

    Zhou, Shungui; Xu, Jielong; Yang, Guiqin; Zhuang, Li

    2014-04-01

    Iron oxides and humic substances (humics) have substantial effects on biochemical processes, such as methanogenesis, due to their redox reactivity and ubiquitous presence. This study aimed to investigate how methanogenesis is affected by the common occurrence of these compounds, which has not been considered to date. The experiment was conducted with anoxic paddy soil microcosms receiving a humics surrogate compound (anthraquinone-2,6-disulfonate, AQDS) and three iron(III) oxides (ferrihydrite, hematite, and magnetite) differing in crystallinity and conductivity. Ferrihydrite suppressed methanogenesis, whereas AQDS, hematite, and magnetite facilitated methanogenesis. CH4 production in co-occurring ferrihydrite + AQDS, hematite + AQDS, and magnetite + AQDS cultures was 4.1, 1.3, and 0.9 times greater than the corresponding cultures without AQDS, respectively. Syntrophic cooperation between Geobacter and Methanosarcina occurred in the methanogenesis-facilitated cultures. Experimental results suggested that the conductive characteristics of iron(III) oxides was an important factor determining the methanogenic response to the co-occurrence of iron(III) oxides and humics in anaerobic paddy soil. This work indicated that the type of iron(III) oxides may significantly affect carbon cycling under anoxic conditions in natural wetlands.

  14. Propolis Modifies Collagen Types I and III Accumulation in the Matrix of Burnt Tissue

    PubMed Central

    Olczyk, Pawel; Wisowski, Grzegorz; Komosinska-Vassev, Katarzyna; Stojko, Jerzy; Klimek, Katarzyna; Olczyk, Monika; Kozma, Ewa M.

    2013-01-01

    Wound healing represents an interactive process which requires highly organized activity of various cells, synthesizing cytokines, growth factors, and collagen. Collagen types I and III, serving as structural and regulatory molecules, play pivotal roles during wound healing. The aim of this study was to compare the propolis and silver sulfadiazine therapeutic efficacy throughout the quantitative and qualitative assessment of collagen types I and III accumulation in the matrix of burnt tissues. Burn wounds were inflicted on pigs, chosen for the evaluation of wound repair because of many similarities between pig and human skin. Isolated collagen types I and III were estimated by the surface plasmon resonance method with a subsequent collagenous quantification using electrophoretic and densitometric analyses. Propolis burn treatment led to enhanced collagens and its components expression, especially during the initial stage of the study. Less expressed changes were observed after silver sulfadiazine (AgSD) application. AgSD and, with a smaller intensity, propolis stimulated accumulation of collagenous degradation products. The assessed propolis therapeutic efficacy, throughout quantitatively and qualitatively analyses of collagen types I and III expression and degradation in wounds matrix, may indicate that apitherapeutic agent can generate favorable biochemical environment supporting reepithelization. PMID:23781260

  15. Propolis Modifies Collagen Types I and III Accumulation in the Matrix of Burnt Tissue.

    PubMed

    Olczyk, Pawel; Wisowski, Grzegorz; Komosinska-Vassev, Katarzyna; Stojko, Jerzy; Klimek, Katarzyna; Olczyk, Monika; Kozma, Ewa M

    2013-01-01

    Wound healing represents an interactive process which requires highly organized activity of various cells, synthesizing cytokines, growth factors, and collagen. Collagen types I and III, serving as structural and regulatory molecules, play pivotal roles during wound healing. The aim of this study was to compare the propolis and silver sulfadiazine therapeutic efficacy throughout the quantitative and qualitative assessment of collagen types I and III accumulation in the matrix of burnt tissues. Burn wounds were inflicted on pigs, chosen for the evaluation of wound repair because of many similarities between pig and human skin. Isolated collagen types I and III were estimated by the surface plasmon resonance method with a subsequent collagenous quantification using electrophoretic and densitometric analyses. Propolis burn treatment led to enhanced collagens and its components expression, especially during the initial stage of the study. Less expressed changes were observed after silver sulfadiazine (AgSD) application. AgSD and, with a smaller intensity, propolis stimulated accumulation of collagenous degradation products. The assessed propolis therapeutic efficacy, throughout quantitatively and qualitatively analyses of collagen types I and III expression and degradation in wounds matrix, may indicate that apitherapeutic agent can generate favorable biochemical environment supporting reepithelization.

  16. Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments

    PubMed Central

    Tang, Shaogeng; Henne, W Mike; Borbat, Peter P; Buchkovich, Nicholas J; Freed, Jack H; Mao, Yuxin; Fromme, J Christopher; Emr, Scott D

    2015-01-01

    The endosomal sorting complexes required for transport (ESCRTs) constitute hetero-oligomeric machines that catalyze multiple topologically similar membrane-remodeling processes. Although ESCRT-III subunits polymerize into spirals, how individual ESCRT-III subunits are activated and assembled together into a membrane-deforming filament remains unknown. Here, we determine X-ray crystal structures of the most abundant ESCRT-III subunit Snf7 in its active conformation. Using pulsed dipolar electron spin resonance spectroscopy (PDS), we show that Snf7 activation requires a prominent conformational rearrangement to expose protein-membrane and protein-protein interfaces. This promotes the assembly of Snf7 arrays with ~30 Å periodicity into a membrane-sculpting filament. Using a combination of biochemical and genetic approaches, both in vitro and in vivo, we demonstrate that mutations on these protein interfaces halt Snf7 assembly and block ESCRT function. The architecture of the activated and membrane-bound Snf7 polymer provides crucial insights into the spatially unique ESCRT-III-mediated membrane remodeling. DOI: http://dx.doi.org/10.7554/eLife.12548.001 PMID:26670543

  17. Bacterially expressed and refolded envelope protein (domain III) of dengue virus type-4 binds heparan sulfate.

    PubMed

    Pattnaik, Priyabrata; Babu, J Pradeep; Verma, Shailendra Kumar; Tak, Vijay; Rao, P V Lakshmana

    2007-02-01

    An arboviral infection like dengue fever/dengue hemorrhagic fever (DHF) with high morbidity and mortality rate are extensively prevalent in several parts of the world. Global efforts have been directed towards development of vaccine for prevention of dengue. However, lack of thorough understanding about biology and pathogenesis of dengue virus restricts us from development of an effective vaccine. Here we report molecular interaction of domain III of envelope protein of dengue virus type-4 with heparan sulfate. A codon optimized synthetic gene encoding domain III of dengue virus type-4 envelope protein was expressed in Escherichia coli and purified under denaturing conditions, refolded and purified to homogeneity. Refolded Den4-DIII was characterized using biochemical and biophysical methods and shown to be pure and homogeneous. The purified protein was recognized in Western analyses by monoclonal antibody specific for the 6x His tag as well as the H241 monoclonal antibody. The in vitro refolded recombinant protein preparation was biologically functional and found to bind cell free heparan sulfate. This is the first report providing molecular evidence on binding of dengue-4 envelope protein to heparan sulfate. We developed a homology model of dengue-4 envelope protein (domain III) and mapped the possible amino acid residues critical for binding to heparan sulfate. Domain III envelope protein of dengue virus is a lead vaccine candidate. Our findings further the understanding on biology of dengue virus and will help in development of bioassay for the proposed vaccine candidate.

  18. Structure-function analysis of hRPC62 provides insights into RNA polymerase III transcription initiation.

    PubMed

    Lefèvre, Stéphane; Dumay-Odelot, Hélène; El-Ayoubi, Leyla; Budd, Aidan; Legrand, Pierre; Pinaud, Noël; Teichmann, Martin; Fribourg, Sébastien

    2011-03-01

    The 17-subunit human RNA polymerase III (hPol III) transcribes small, untranslated RNA genes that are involved in the regulation of transcription, splicing and translation. hPol III subunits hRPC62, hRPC39 and hRPC32 form a stable ternary subcomplex required for promoter-specific transcription initiation by hPol III. Here, we report the crystal structure of hRPC62. This subunit folds as a four-tandem extended winged helix (eWH) protein that is structurally related to the transcription factor TFIIEα N terminus. Through biochemical analyses, we mapped the protein-protein interactions of hRPC62, hRPC32 and hRPC39. In addition, we demonstrated that hRPC62 and hRPC39 bind single-stranded and duplex DNA, respectively, in a sequence-independent manner. Overall, we shed light on structural similarities between the hPol III-specific subunit hRPC62 and TFIIEα and propose specific functions for hRPC39 and hRPC62 in transcription initiation by hPol III. PMID:21358628

  19. Early Umbilical Cord Blood-Derived Stem Cell Transplantation Does Not Prevent Neurological Deterioration in Mucopolysaccharidosis Type III.

    PubMed

    Welling, Lindsey; Marchal, Jan Pieter; van Hasselt, Peter; van der Ploeg, Ans T; Wijburg, Frits A; Boelens, Jaap Jan

    2015-01-01

    Mucopolysaccharidosis type III (MPS III), or Sanfilippo disease, is a neurodegenerative lysosomal storage disease (LSD) caused by defective lysosomal degradation of heparan sulfate (HS). No effective disease-modifying therapy is yet available. In contrast to some other neuronopathic LSDs, bone marrow-derived hematopoietic stem cell transplantation (HSCT) fails to prevent neurological deterioration in MPS III patients. We report on the 5-year outcome of early transplantation, i.e., before onset of clinical neurological disease, in combination with the use of umbilical cord blood-derived hematopoietic stem cells (UCBT), in two MPS III patients. Both patients had a normal developmental quotient at the time of UCBT. One patient had a combination of mutations predicting a classical severe phenotype (MPS IIIA), and one patient (MPS IIIB) had mutations predicting a very attenuated phenotype. Transplantation was uncomplicated with full engraftment of donor cells in both.Both patients showed progressive neurological deterioration with regression of cognitive skills and behavioral disturbances during 5 years after successful UCBT, comparable to the natural history of patients with the same combination of mutations. The concentration of HS in CSF in the patient with the attenuated phenotype of MPS IIIB 2 years after UCBT was very high and in the range of untreated MPS III patients.We conclude that the course of cognitive development, behavioral problems, and absence of biochemical correction in CSF demonstrate the absence of relevant effect of UCBT in MPS III patients, even when performed before clinical onset of CNS disease. PMID:25256447

  20. Mechanisms of Sb(III) Photooxidation by the Excitation of Organic Fe(III) Complexes.

    PubMed

    Kong, Linghao; He, Mengchang

    2016-07-01

    Organic Fe(III) complexes are widely distributed in the aqueous environment, which can efficiently generate free radicals under light illumination, playing a significant role in heavy metal speciation. However, the potential importance of the photooxidation of Sb(III) by organic Fe(III) complexes remains unclear. Therefore, the photooxidation mechanisms of Sb(III) were comprehensively investigated in Fe(III)-oxalate, Fe(III)-citrate and Fe(III)-fulvic acid (FA) solutions by kinetic measurements and modeling. Rapid photooxidation of Sb(III) was observed in an Fe(III)-oxalate solution over the pH range of 3 to 7. The addition of tert-butyl alcohol (TBA) as an ·OH scavenger quenched the Sb(III) oxidation, suggesting that ·OH is an important oxidant for Sb(III). However, the incomplete quenching of Sb(III) oxidation indicated the existence of other oxidants, presumably an Fe(IV) species in irradiated Fe(III)-oxalate solution. In acidic solutions, ·OH may be formed by the reaction of Fe(II)(C2O4) with H2O2, but a hypothetical Fe(IV) species may be generated by the reaction of Fe(II)(C2O4)2(2-) with H2O2 at higher pH. Kinetic modeling provides a quantitative explanation of the results. Evidence for the existence of ·OH and hypothetical Fe(IV) was also observed in an irradiated Fe(III)-citrate and Fe(III)-FA system. This study demonstrated an important pathway of Sb(III) oxidation in surface waters. PMID:27267512

  1. Mistakes and Molecular Evolution.

    ERIC Educational Resources Information Center

    Trevors, J. T.

    1998-01-01

    Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

  2. The Evolution of Design

    ERIC Educational Resources Information Center

    Stebbins, G. Ledyard

    1973-01-01

    Describes the basic logic behind the modern view of evolution theory. Despite gaps in fossil records, evidence is indicative of the origin of life from nonliving molecules and evolution of higher forms of life from simpler forms. (PS)

  3. Oxygen and Biological Evolution.

    ERIC Educational Resources Information Center

    Baugh, Mark A.

    1990-01-01

    Discussed is the evolution of aerobic organisms from anaerobic organisms and the accompanying biochemistry that developed to motivate and enable this evolution. Uses of oxygen by aerobic organisms are described. (CW)

  4. Biochemical characterisation during seed development of oil palm (Elaeis guineensis).

    PubMed

    Kok, Sau-Yee; Namasivayam, Parameswari; Ee, Gwendoline Cheng-Lian; Ong-Abdullah, Meilina

    2013-07-01

    Developmental biochemical information is a vital base for the elucidation of seed physiology and metabolism. However, no data regarding the biochemical profile of oil palm (Elaeis guineensis Jacq.) seed development has been reported thus far. In this study, the biochemical changes in the developing oil palm seed were investigated to study their developmental pattern. The biochemical composition found in the seed differed significantly among the developmental stages. During early seed development, the water, hexose (glucose and fructose), calcium and manganese contents were present in significantly high levels compared to the late developmental stage. Remarkable changes in the biochemical composition were observed at 10 weeks after anthesis (WAA): the dry weight and sucrose content increased significantly, whereas the water content and hexose content declined. The switch from a high to low hexose/sucrose ratio could be used to identify the onset of the maturation phase. At the late stage, dramatic water loss occurred, whereas the content of storage reserves increased progressively. Lauric acid was the most abundant fatty acid found in oil palm seed starting from 10 WAA. PMID:23575803

  5. Maximizing the biochemical resolving power of fluorescence microscopy.

    PubMed

    Esposito, Alessandro; Popleteeva, Marina; Venkitaraman, Ashok R

    2013-01-01

    Most recent advances in fluorescence microscopy have focused on achieving spatial resolutions below the diffraction limit. However, the inherent capability of fluorescence microscopy to non-invasively resolve different biochemical or physical environments in biological samples has not yet been formally described, because an adequate and general theoretical framework is lacking. Here, we develop a mathematical characterization of the biochemical resolution in fluorescence detection with Fisher information analysis. To improve the precision and the resolution of quantitative imaging methods, we demonstrate strategies for the optimization of fluorescence lifetime, fluorescence anisotropy and hyperspectral detection, as well as different multi-dimensional techniques. We describe optimized imaging protocols, provide optimization algorithms and describe precision and resolving power in biochemical imaging thanks to the analysis of the general properties of Fisher information in fluorescence detection. These strategies enable the optimal use of the information content available within the limited photon-budget typically available in fluorescence microscopy. This theoretical foundation leads to a generalized strategy for the optimization of multi-dimensional optical detection, and demonstrates how the parallel detection of all properties of fluorescence can maximize the biochemical resolving power of fluorescence microscopy, an approach we term Hyper Dimensional Imaging Microscopy (HDIM). Our work provides a theoretical framework for the description of the biochemical resolution in fluorescence microscopy, irrespective of spatial resolution, and for the development of a new class of microscopes that exploit multi-parametric detection systems. PMID:24204821

  6. Maximizing the Biochemical Resolving Power of Fluorescence Microscopy

    PubMed Central

    Esposito, Alessandro; Popleteeva, Marina; Venkitaraman, Ashok R.

    2013-01-01

    Most recent advances in fluorescence microscopy have focused on achieving spatial resolutions below the diffraction limit. However, the inherent capability of fluorescence microscopy to non-invasively resolve different biochemical or physical environments in biological samples has not yet been formally described, because an adequate and general theoretical framework is lacking. Here, we develop a mathematical characterization of the biochemical resolution in fluorescence detection with Fisher information analysis. To improve the precision and the resolution of quantitative imaging methods, we demonstrate strategies for the optimization of fluorescence lifetime, fluorescence anisotropy and hyperspectral detection, as well as different multi-dimensional techniques. We describe optimized imaging protocols, provide optimization algorithms and describe precision and resolving power in biochemical imaging thanks to the analysis of the general properties of Fisher information in fluorescence detection. These strategies enable the optimal use of the information content available within the limited photon-budget typically available in fluorescence microscopy. This theoretical foundation leads to a generalized strategy for the optimization of multi-dimensional optical detection, and demonstrates how the parallel detection of all properties of fluorescence can maximize the biochemical resolving power of fluorescence microscopy, an approach we term Hyper Dimensional Imaging Microscopy (HDIM). Our work provides a theoretical framework for the description of the biochemical resolution in fluorescence microscopy, irrespective of spatial resolution, and for the development of a new class of microscopes that exploit multi-parametric detection systems. PMID:24204821

  7. Biochemical diagnosis in 3040 kidney stone formers in Argentina.

    PubMed

    Spivacow, Francisco Rodolfo; del Valle, Elisa Elena; Negri, Armando Luis; Fradinger, Erich; Abib, Anabella; Rey, Paula

    2015-08-01

    Nephrolithiasis is a frequent condition in urology that has an important recurrence and high impact in health economy. Knowing the biochemical abnormalities implicated in its pathogenesis is mandatory to establish therapeutic aims. Our objectives are to present the results in 3040 kidney stone formers in Argentina. All patients were selected after completing an ambulatory metabolic protocol with diagnostic purposes. There were 1717 men, (56.48%), with a mean age of 45±12 years, and 1323 women, (43.52%), mean age 44±12 years. 2781 patients had biochemical abnormalities, (91.49%), and were arbitrarily divided in two groups: those who had only one (single) biochemical abnormality (n=2156) and those who had associated abnormalities (n=625). No biochemical abnormalities were found in 259 patients (8.51%). The abnormalities present, single and associated, in order of frequency, were idiopathic hypercalciuria, (56.88%), hyperuricosuria (21.08%), unduly acidic urine (10.95%), hypocitraturia (10.55%), hypomagnesuria (7.9%), primary hyperparathyroidism (3.01%), hyperoxaluria (2.6%), and cystinuria (0.32%). We performed in 484 patient's stone composition and found calcium oxalate stones related to idiopathic hypercalciuria predominantly while uric acid stones to unduly acidic urine. In conclusion, the biochemical abnormalities described are similar to those found in a previous series of our own and to those reported in the literature. Its diagnosis is important to therapeutic purposes to avoid eventual recurrence.

  8. Microstereolithography and its application to biochemical IC chip

    NASA Astrophysics Data System (ADS)

    Ikuta, Koji; Maruo, Shoji; Hasegawa, Tadahiro; Adachi, Takao

    2001-06-01

    The world's first micro stereo lithography, named IH process, was proposed and developed by the speaker in 1992. By now, several types of micro stereo lithography systems have been developed. Three-dimensional resolution of solidification has reached to 0.2 micron at present. These 3D micro fabrication processes using UV curable polymer gave a big impact on not only MEMS but also optics. The latest version of IH process enables us to make a movable micro mechanism without assemble process or sacrificial layer technique often used in silicon process. It is well known that the IH process is the mother of two-photon micro stereo lithography and its applications. Recently new micro chemical device named Biochemical IC Chip was proposed and developed by the speaker. This chip is based on the module IC chip-set like today's TTL family. IH process enable to make the biochemical IC including real three-dimensional micro fluid channels. Various kinds of Biochemical IC chips such as micro pump, switching valve, reactor, concentrator and detector have already been fabricated successfully. Basic performance of micro chemical devices constructed by the biochemical IC chips were demonstrated. The biochemical IC chips will open new bioscience and medicine based on innovative technology.

  9. Biochemical characterisation during seed development of oil palm (Elaeis guineensis).

    PubMed

    Kok, Sau-Yee; Namasivayam, Parameswari; Ee, Gwendoline Cheng-Lian; Ong-Abdullah, Meilina

    2013-07-01

    Developmental biochemical information is a vital base for the elucidation of seed physiology and metabolism. However, no data regarding the biochemical profile of oil palm (Elaeis guineensis Jacq.) seed development has been reported thus far. In this study, the biochemical changes in the developing oil palm seed were investigated to study their developmental pattern. The biochemical composition found in the seed differed significantly among the developmental stages. During early seed development, the water, hexose (glucose and fructose), calcium and manganese contents were present in significantly high levels compared to the late developmental stage. Remarkable changes in the biochemical composition were observed at 10 weeks after anthesis (WAA): the dry weight and sucrose content increased significantly, whereas the water content and hexose content declined. The switch from a high to low hexose/sucrose ratio could be used to identify the onset of the maturation phase. At the late stage, dramatic water loss occurred, whereas the content of storage reserves increased progressively. Lauric acid was the most abundant fatty acid found in oil palm seed starting from 10 WAA.

  10. Preparation of III-V semiconductor nanocrystals

    DOEpatents

    Alivisatos, A. Paul; Olshavsky, Michael A.

    1996-01-01

    Nanometer-scale crystals of III-V semiconductors are disclosed, They are prepared by reacting a group III metal source with a group V anion source in a liquid phase at elevated temperature in the presence of a crystallite growth terminator such as pyridine or quinoline.

  11. Preparation of III-V semiconductor nanocrystals

    SciTech Connect

    Alivisatos, A.P.; Olshavsky, M.A.

    1996-04-09

    Nanometer-scale crystals of III-V semiconductors are disclosed. They are prepared by reacting a group III metal source with a group V anion source in a liquid phase at elevated temperature in the presence of a crystallite growth terminator such as pyridine or quinoline. 4 figs.

  12. Synthesis, spectroscopic and antimicrobial studies of La(III), Ce(III), Sm(III) and Y(III) Metformin HCl chelates.

    PubMed

    Refat, Moamen S; Al-Azab, Fathi M; Al-Maydama, Hussein M A; Amin, Ragab R; Jamil, Yasmin M S; Kobeasy, Mohamed I

    2015-05-01

    Metal complexes of Metformin hydrochloride were prepared using La(III), Ce(III), Sm(III) and Y(III). The resulting complexes were discussed and synthesized to serve as potential insulin-mimetic. Some physical properties and analytical data of the four complexes were checked. The elemental analysis shows that La(III), Ce(III) Sm(III) and Y(III) formed complexes with Metformin in 1:3 (metal:MF) molar ratio. All the synthesized complexes are white and possess high melting points. These complexes are soluble in dimethylsulfoxide and dimethylformamide, partially soluble in hot methanol and insoluble in water and some other organic solvents. From the spectroscopic (infrared, UV-vis and florescence), effective magnetic moment and elemental analyses data, the formula structures are suggested. The results obtained suggested that Metformin reacted with metal ions as a bidentate ligand through its two imino groups. The molar conductance measurements proved that the Metformin complexes are slightly electrolytic in nature. The kinetic thermodynamic parameters such as: E(∗), ΔH(∗), ΔS(∗) and ΔG(∗) were estimated from the DTG curves. The antibacterial evaluations of the Metformin and their complexes were also performed against some gram positive, negative bacteria as well as fungi.

  13. Synthesis and in vitro microbial evaluation of La(III), Ce(III), Sm(III) and Y(III) metal complexes of vitamin B6 drug.

    PubMed

    Refat, Moamen S; Al-Azab, Fathi M; Al-Maydama, Hussein M A; Amin, Ragab R; Jamil, Yasmin M S

    2014-06-01

    Metal complexes of pyridoxine mono hydrochloride (vitamin B6) are prepared using La(III), Ce(III), Sm(III) and Y(III). The resulting complexes are investigated. Some physical properties, conductivity, analytical data and the composition of the four pyridoxine complexes are discussed. The elemental analysis shows that the formed complexes of La(III), Ce(III), Sm(III) and Y(III) with pyridoxine are of 1:2 (metal:PN) molar ratio. All the synthesized complexes are brown in color and possess high melting points. These complexes are partially soluble in hot methanol, dimethylsulfoxide and dimethylformamide and insoluble in water and some other organic solvents. Elemental analysis data, spectroscopic (IR, UV-vis. and florescence), effective magnetic moment in Bohr magnetons and the proton NMR suggest the structures. However, definite particle size is determined by invoking the X-ray powder diffraction and scanning electron microscopy data. The results obtained suggested that pyridoxine reacted with metal ions as a bidentate ligand through its phenolate oxygen and the oxygen of the adjacent group at the 4'-position. The molar conductance measurements proved that the pyridoxine complexes are electrolytic in nature. The kinetic and thermodynamic parameters such as: Ea, ΔH(*), ΔS(*) and ΔG(*) were estimated from the DTG curves. The antibacterial evaluation of the pyridoxine and their complexes were also performed against some gram positive, negative bacteria as well as fungi.

  14. Modal Profiles for the WISC-III.

    ERIC Educational Resources Information Center

    Pritchard, David A.; Livingston, Ronald B.; Reynolds, Cecil R.; Moses, James A., Jr.

    2000-01-01

    Presents a normative typology for classifying the Wechsler Intelligence Scale for Children-Third Edition (WISC-III) factor index profiles according to profile shape. Current analyses indicate that overall profile level accounted for a majority of the variance in WISC-III index scores, but a considerable proportion of the variance was because of…

  15. Synthesis, spectroscopic and antimicrobial studies of La(III), Ce(III), Sm(III) and Y(III) Metformin HCl chelates

    NASA Astrophysics Data System (ADS)

    Refat, Moamen S.; Al-Azab, Fathi M.; Al-Maydama, Hussein M. A.; Amin, Ragab R.; Jamil, Yasmin M. S.; Kobeasy, Mohamed I.

    2015-05-01

    Metal complexes of Metformin hydrochloride were prepared using La(III), Ce(III), Sm(III) and Y(III). The resulting complexes were discussed and synthesized to serve as potential insulin-mimetic. Some physical properties and analytical data of the four complexes were checked. The elemental analysis shows that La(III), Ce(III) Sm(III) and Y(III) formed complexes with Metformin in 1:3 (metal:MF) molar ratio. All the synthesized complexes are white and possess high melting points. These complexes are soluble in dimethylsulfoxide and dimethylformamide, partially soluble in hot methanol and insoluble in water and some other organic solvents. From the spectroscopic (infrared, UV-vis and florescence), effective magnetic moment and elemental analyses data, the formula structures are suggested. The results obtained suggested that Metformin reacted with metal ions as a bidentate ligand through its two imino groups. The molar conductance measurements proved that the Metformin complexes are slightly electrolytic in nature. The kinetic thermodynamic parameters such as: E∗, ΔH∗, ΔS∗ and ΔG∗ were estimated from the DTG curves. The antibacterial evaluations of the Metformin and their complexes were also performed against some gram positive, negative bacteria as well as fungi.

  16. Synthesis and in vitro microbial evaluation of La(III), Ce(III), Sm(III) and Y(III) metal complexes of vitamin B6 drug

    NASA Astrophysics Data System (ADS)

    Refat, Moamen S.; Al-Azab, Fathi M.; Al-Maydama, Hussein M. A.; Amin, Ragab R.; Jamil, Yasmin M. S.

    2014-06-01

    Metal complexes of pyridoxine mono hydrochloride (vitamin B6) are prepared using La(III), Ce(III), Sm(III) and Y(III). The resulting complexes are investigated. Some physical properties, conductivity, analytical data and the composition of the four pyridoxine complexes are discussed. The elemental analysis shows that the formed complexes of La(III), Ce(III), Sm(III) and Y(III) with pyridoxine are of 1:2 (metal:PN) molar ratio. All the synthesized complexes are brown in color and possess high melting points. These complexes are partially soluble in hot methanol, dimethylsulfoxide and dimethylformamide and insoluble in water and some other organic solvents. Elemental analysis data, spectroscopic (IR, UV-vis. and florescence), effective magnetic moment in Bohr magnetons and the proton NMR suggest the structures. However, definite particle size is determined by invoking the X-ray powder diffraction and scanning electron microscopy data. The results obtained suggested that pyridoxine reacted with metal ions as a bidentate ligand through its phenolate oxygen and the oxygen of the adjacent group at the 4‧-position. The molar conductance measurements proved that the pyridoxine complexes are electrolytic in nature. The kinetic and thermodynamic parameters such as: Ea, ΔH*, ΔS* and ΔG* were estimated from the DTG curves. The antibacterial evaluation of the pyridoxine and their complexes were also performed against some gram positive, negative bacteria as well as fungi.

  17. Old Perspectives on Evolution

    ERIC Educational Resources Information Center

    De Blacquiere-Clarkson, John

    1976-01-01

    Presents a perspective on evolution which includes an explanation of the textbook theory of evolution, a review of evolutionary theory before Darwin, and an outline of Darwin's early theories. Describes a rethinking of evolutionary theory to include natural selection, conservative selection, discontinous evolution, catastrophism, and the…

  18. Evolution & Diversity in Plants.

    ERIC Educational Resources Information Center

    Pearson, Lorentz C.

    1988-01-01

    Summarizes recent findings that help in understanding how evolution has brought about the diversity of plant life that presently exists. Discusses basic concepts of evolution, diversity and classification, the three-line hypothesis of plant evolution, the origin of fungi, and the geologic time table. Included are 31 references. (CW)

  19. Evolution for Young Victorians

    NASA Astrophysics Data System (ADS)

    Lightman, Bernard

    2012-07-01

    Evolution was a difficult topic to tackle when writing books for the young in the wake of the controversies over Darwin's Origin of Species. Authors who wrote about evolution for the young experimented with different ways of making the complex concepts of evolutionary theory accessible and less controversial. Many authors depicted presented evolution in a non-Darwinian form amenable to religious interpretation.

  20. A Shuttle evolution strategy

    NASA Technical Reports Server (NTRS)

    Teixeira, Charles; Mallini, Charles

    1989-01-01

    An overview of a potential Space Shuttle evolution strategy is presented. A Shuttle development study which reviews past and ongoing studies, implements a Shuttle Enhancement Data Base, and develops a methodology and a strawman evolution strategy is discussed. The long-term goals of a Shuttle evolution strategy, including increased reliability, lower cost, robustness, resiliency, increased capability, and assured access are addressed.