MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.

MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments-namely MNXref-and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

Type II aromatic polyketide biosynthetic tailoring enzymes: diversity and adaptation in Streptomyces secondary metabolism.

Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

Unambiguous assessments of reaction paths for selected pericyclic reactions

Four commonplace concerted reactions are examined using (i) correlation diagrams, (ii) frontier molecular orbital analyses for transition states, (iii) Zimmerman-Dewar analyses for transition states and (iv) modified Zimmerman-Dewar analyses for transition states. Only the latter approach is consistently satisfactory.

Reactions of Chlorambucil and its main metabolite, Phenylacetic Acid Mustard, with 2’-deoxyribonucleosides and Calf Thymus DNA

Chlorambucil is an anticancer agent used in the treatment of a variety of cancers, especially in chronic lymphocytic leukemia, and autoimmune diseases. Nevertheless, chlorambucil is potentially mutagenic, teratogenic and carcinogenic. The high antitumor activity and high toxicity of chlorambucil and its main metabolite, phenylacetic acid mustard, to normal tissues have been known for a long time. Despite this, no detailed chemical data on their reactions with biomolecules in aqueous media have been available. The aim of the work described in this thesis was to analyze reactions of chlorambucil with 2’-deoxyribonucleosides and calf thymus DNA in aqueous buffered solution, at physiological pH, and to identify and characterize all adducts by using modern analyzing methods. Our research was also focused on the reactions of phenylacetic acid mustard with 2’-deoxynucleosides under similar conditions. A review of the literature consisting of general background of nucleic acids, alkylating agents and ultraviolet spectroscopy used to identify the purine and pyrimidine nucleosides, as well as the results from experimental work are presented and discussed in this doctoral thesis.

HPLC-ESI-MS/MS analysis of oxidized di-caffeoylquinic acids generated by metalloporphyrin-catalyzed reactions

This paper reports an HPLC-ESI-MS/MS investigation on the oxidation of 3,5- and 4,5- dicaffeoylquinic acid using iron(III) tetraphenylporphyrin chloride as catalyst. Two major mono-oxidised products of the quinic acid moiety have been identified for both compounds. However, only the 4,5-derivative afforded two different tri-oxo products. Thus, it seems that the oxidation pattern depends on the number and positions of the caffeic acid moieties present in caffeoylquinic acid molecules.

Gas-phase solvolysis type reactions of SiCl3+ cations

Gas-phase SiCl3+ ions undergo sequential solvolysis type reactions with water, methanol, ammonia, methylamine and propylene. Studies carried out in a Fourier Transform mass spectrometer reveal that these reactions are facile at 10-8 Torr and give rise to substituted chlorosilyl cations. Ab initio and DFT calculations reveal that these reactions proceed by addition of the silyl cation to the oxygen or nitrogen lone pair followed by a 1,3-H migration in the transition state. These transition states are calculated to lie below the energy of the reactants. By comparison, hydrolysis of gaseous CCl3+ is calculated to involve a substantial positive energy barrier.

Retrieval of kinetic rates in reactions with semi batch liquid phase using ill-posed inverse problem theory

A neural network procedure to solve inverse chemical kinetic problems is discussed in this work. Rate constants are calculated from the product concentration of an irreversible consecutive reaction: the hydrogenation of Citral molecule, a process with industrial interest. Simulated and experimental data are considered. Errors in the simulated data, up to 7% in the concentrations, were assumed to investigate the robustness of the inverse procedure. Also, the proposed method is compared with two common methods in nonlinear analysis; the Simplex and Levenberg-Marquardt approaches. In all situations investigated, the neural network approach was numerically stable and robust with respect to deviations in the initial conditions or experimental noises.

H3PW12O40 (HPA), an efficient and reusable catalyst for biodiesel production related reactions: esterification of oleic acid and etherification of glycerol

In esterification of oleic acid with methanol at 25 °C HPA displayed the highest activity. Moreover the HPA could be reused after being transformed into its cesium salt. In the reaction of etherification of glycerol HPA and Amberlyst 35W showed similar initial activity levels. The results of acid properties demonstrate that HPA is a strong protonic acid and that both surface and bulk protons contribute to the acidity. Because of its strong affinity for polar compounds, HPA is also seemingly dissolved in both oleic acid and methanol. The reaction in this case proceeds with the catalyst in the homogenous phase.

Modification of the performance of WO3-ZrO2 catalysts by metal addition in hydrocarbon reactions

A study of the different hydrocarbon reactions over Ni doped WO3-ZrO2 catalysts was performed. Ni was found as NiO at low Ni concentration while at high Ni concentrations a small fraction was present as a metal. For both cases, Ni strongly modified total acidity and concentration of strong acid sites. In the cyclohexane dehydrogenation reaction, Ni addition promotes both benzene and methyl cyclopentane production. The hydroconversion activity (n-butane and n-octane) increases with the augment of total acidity produced by Ni. The selectivity to reaction products is modified according to the acid strength distribution changes produced by Ni addition.

Produção de lipases de Aspergillus niger e Aspergillus fumigatus através de fermentação em estado sólido, avaliação da especificidade do substrato e seu uso em reações de esterificação e alcoólise: evaluation of substrate specificity and use in esterification and alcoholysis reactions

Filamentous fungi were cultured under solid state fermentation of soybean residues to produce lipases. Enzymes produced by Aspergillus niger esterified oleic and butyric acids in the presence of ethanol, while enzymes produced by Aspergillus fumigatus demonstrated no esterification activity toward lauric acid. In case of A. niger, direct lyophilization of fermented bran led to higher esterification activity. The esterification of oleic acid by enzymes of A. fumigatus was neither influenced by pH adjustment nor by the extraction process. Conversions to ethyl esters were higher after pH adjustment with lyophilized liquid extract of A. niger.

AVOIDING FIRST-YEAR UNIVERSITY CHEMISTRY TEXTBOOKS’ MISREPRESENTATIONS IN THE TEACHING OF SPONTANEOUS REACTIONS

This paper summarizes the misrepresentations related to Gibbs energy in general chemistry textbooks. These misrepresentations arise from a problem in the terminology textbooks use. Thus, after reviewing the proper definition of each of the terms analyzed, we present two problems to exemplify the correct treatment of the quantities involved, which may help in the discussion and clarification of the misleading conventions and assumptions reported in this study.

FAST GC-FID METHOD FOR MONITORING ACIDIC AND BASIC CATALYTIC TRANSESTERIFICATION REACTIONS IN VEGETABLE OILS TO METHYL ESTER BIODIESEL PREPARATION

A fast gas chromatography with a flame ionisation detector (GC-FID) method for the simultaneous analysis of methyl palmitate (C16:0), stearate (C18:0), oleate (C18:1), linoleate (C18:2) and linolenate (C18:3) in biodiesel samples was proposed. The analysis was conducted in a customised ionic-liquid stationary-phase capillary, SLB-IL 111, with a length of 14 m, an internal diameter of 0.10 mm, a film thickness of 0.08 µm and operated isothermally at 160 °C using hydrogen as the carrier gas at a rate of 50 cm s-1 in run time about 3 min. Once methyl myristate (C14:0) is present lower than 0.5% m/m in real samples it was used as an internal standard. The method was successful applied to monitoring basic and acidic catalysis transesterification reactions of vegetable oils such as soybean, canola, corn, sunflower and those used in frying process.

About the kinetics and mechanism of the reactions of 4-(2-pyridylazo)-resorcinol, with Zn2+, Cu2+ and Zn2++Cu2+ equimolar mixtures, in aqueous solutions

The kinetics and mechanism of the reactions between 4(2pyridylazo)-resorcinol and Zn2+, Cu2+ and Zn2++Cu2+ equimolar mixtures were studied. The reactions were performed in aqueous solution (pH = 8.5, borate buffer) and monitored spectrophotometrically at 500 nm using stopped-flow technique. Spectral and kinetic data indicate that the Zn2++Cu2+ equimolar mixture behaves as an unique species and it can be attributed to the interactions of Zn2+ and of Cu2+ with water molecules in the aqueous solution. A mechanism is proposed and the rate constants are calculated.

Country Risk and Market Reactions to Earnings Announcements: Evidence from Finnish Stock Markets

The objective of this thesis is to examine the market reaction around earnings announcements in Finnish stock markets. The aim is to find out whether the extreme market conditions during the financial crisis are reflected in stock prices as a stronger reaction. In addition to this, the purpose is to investigate how extensively Finnish listed companies report the country segmentation of revenues in their interim reports and whether the country risk is having a significant impact on perceived market reaction. The sample covers all companies listed in Helsinki stock exchange at 1.1.2010 and these companies’ interim reports from the first quarter of 2008 to last quarter of 2009. Final sample consists of 81 companies and 630 firm-quarter observations. The data sample has been divided in two parts, of which country risk sample contains 17 companies and 127 observations and comparison sample covers 66 companies and 503 observations. Research methodologies applied in this thesis are event study and cross-sectional regression analysis. Empirical results indicate that the market reaction occurs mainly during the announcement day and is slightly stronger in case of positive earnings surprises than the reactions observed in previous studies. In case of negative earnings surprises no significant differences can be observed. In case of country risk sample and negative earnings surprise market reaction is negative already in advance of the disclosure contrary to comparison sample. In case of positive surprise no differences can be observed. Country risk variable developed during this study seems to explain only minor part of the market reaction.

Sensitive spectrophotometric determination of lansoprazole in pharmaceuticals using ceric ammonium sulphate based on redox and complex formation reactions

Two simple sensitive and cost-effective spectrophotometric methods are described for the determination of lansoprazole (LPZ) in bulk drug and in capsules using ceric ammonium sulphate (CAS), iron (II), orthophenanthroline and thiocyanate as reagents. In both methods, an acidic solution of lansoprazole is treated with a measured excess of CAS followed by the determination of unreacted oxidant by two procedures involving different reaction schemes. The first method involves the reduction of residual oxidant by a known amount of iron(II), and the unreacted iron(II) is complexed with orthophenanthroline at a raised pH, and the absorbance of the resulting complex measured at 510 nm (method A). In the second method, the unreacted CAS is reduced by excess of iron (II), and the resulting iron (III) is complexed with thiocyanate in the acid medium and the absorbance of the complex measured at 470 nm (method B). In both methods, the amount CAS reacted corresponds to the amount of LPZ. In method A, the absorbance is found to increase linearly with the concentration of LPZ where as in method B a linear decrease in absorbance occurs. The systems obey Beer's law for 2.5-30 and 2.5-25 µg mL-1 for method A and method B, respectively, and the corresponding molar absorptivity values are 8.1×10³ and 1.5×10(4) L mol-1cm-1 . The methods were successfully applied to the determination of LPZ in capsules and the results tallied well with the label claim. No interference was observed from the concomitant substances normally added to capsules.