Methods and tools for mass spectrometric lipidome analysis

The analysis of lipid compositions from biological samples has become increasingly important. Lipids have a role in cardiovascular disease, metabolic syndrome and diabetes. They also participate in cellular processes such as signalling, inflammatory response, aging and apoptosis. Also, the mechanisms of regulation of cell membrane lipid compositions are poorly understood, partially because a lack of good analytical methods. Mass spectrometry has opened up new possibilities for lipid analysis due to its high resolving power, sensitivity and the possibility to do structural identification by fragment analysis. The introduction of Electrospray ionization (ESI) and the advances in instrumentation revolutionized the analysis of lipid compositions. ESI is a soft ionization method, i.e. it avoids unwanted fragmentation the lipids. Mass spectrometric analysis of lipid compositions is complicated by incomplete separation of the signals, the differences in the instrument response of different lipids and the large amount of data generated by the measurements. These factors necessitate the use of computer software for the analysis of the data. The topic of the thesis is the development of methods for mass spectrometric analysis of lipids. The work includes both computational and experimental aspects of lipid analysis. The first article explores the practical aspects of quantitative mass spectrometric analysis of complex lipid samples and describes how the properties of phospholipids and their concentration affect the response of the mass spectrometer. The second article describes a new algorithm for computing the theoretical mass spectrometric peak distribution, given the elemental isotope composition and the molecular formula of a compound. The third article introduces programs aimed specifically for the analysis of complex lipid samples and discusses different computational methods for separating the overlapping mass spectrometric peaks of closely related lipids. The fourth article applies the methods developed by simultaneously measuring the progress curve of enzymatic hydrolysis for a large number of phospholipids, which are used to determine the substrate specificity of various A-type phospholipases. The data provides evidence that the substrate efflux from bilayer is the key determining factor for the rate of hydrolysis.

Transfer of F- in the reaction of SF6- with SOF4: Implications for SOF4 production in corona discharges

The temperature (T) and electric field-to-gas pressure (E/P) dependences of the rate coefficientk for the reaction SF 6 � +SOF4rarrSOF 5 � +SF5 have been measured. ForT<270>k approaches a constant of 2.1×10�9 cm3/s, and for 433>T>270 K,k decreases withT according tok (cm3/s)=0.124 exp [�3.3 lnT(K)]. ForE/Pk has a constant value of about 2.5×10�10 cm3/s, and for 130 V/cm·torr>E/P>60 V/cm·torr, the rate is approximately given byk (cm3/s)sim7.0×10�10 exp (�0.022E/P). The measured rate coefficient is used to estimate the influence of this reaction on SOF4 production from negative, point-plane, glow-type corona discharges in gas mixtures containing SF6 and at least trace amounts of O2 and H2O. A chemical kinetics model of the ion-drift region in the discharge gap is used to fit experimental data on SOF4 yields assuming that the SF 6 � +SOF4 reaction is the predominant SOF4 loss mechanism. It is found that the contribution of this reaction to SOF4 destruction falls considerably below the estimated maximum effect assuming that SF 6 � is the predominant charge carrier which reacts only with SOF4. The results of this analysis suggest that SF 6 � is efficiently deactivated by other reactions, and the influence of SF 6 � +SOF4 on SOF4 production is not necessarily more significant than that of other slower secondary processes such as gas-phase hydrolysis

Transformations of acetates of citronellol, geraniol, and linalool by Aspergillus niger: regiospecific hydroxylation of citronellol by a cell-free system

Incubation of acetates of geraniol, citronellol and linalool with Aspergillus niger resulted in their hydrolysis to corresponding alcohols which were further hydroxylated to their respective 8-hydroxy derivatives. In the case of linalyl acetate, besides linalool and 8-hydroxylinalool, small amounts of geraniol and agr-terpineol were also formed. Microsomes (105 000xg sediment) prepared from induced cells of A. niger were found to convert (1-3H)citronellol to 8-hydroxy citronellol in the presence of NADPH and O2. The pH optimum for the hydroxylase was found to be 7.6.

Synthetic Modifications of Estrogens and Androgens

Estrogens the female sex hormones have numerous biological actions. Estradiol is the most abundant estrogen in women before menopause. It influences the development, maturation and function of the female reproductive tract. It also plays a role in mammary cancer. Accordingly determinations of estradiol level in body fluids assist in the evaluation of ovarian function and diagnosis for malignancies. Estriol is the primary estrogen in pregnant women and secreted from the fetoplacental unit. Measurement of estriol in maternal body fluids is the basis of fetoplacental monitoring test. Concentration of estrogens in body fluids is determined by immunoassay. Accuracy of this measurement depends on the availability of a specific antibody. As estrogens are not antigenic, their derivatives (haptens) are coupled with a carrier and this hapten-protein conjugate is used to generate antibodies. Specificity of the generated antibody largely depends on the structure of hapten. Therefore the synthesis of a hapten with a right structure is crucial for the accurate measurement of a steroid. We have synthesised new haptens for estradiol and estriol by adding an alkyl or alkoxy side chain at the C-7 of estrane skeleton. The side chains carry a terminal amino group, which can be used for conjugation with a carrier molecule. Estrogens and their biosynthetic precursor androgens both exist as fatty acid esters. They are known to act as hormone storage but their physiological role is not completely known yet. Our collaborator is studying their effect in cardiovascular diseases. We synthesised fatty acid ester derivatives of several steroids in high yield by a very rapid procedure (in 1 min) under microwave irradiation in an ionic liquid (IL). An expedient regioselective hydrolysis at C-3 of estradiol diesters is also reported. 8-Isoestrogens are compounds of pharmaceutical interests, their synthesis, structure, conformation and biological activity studies are ongoing. 7-Hydroxy-8-isoestradiol and 7-alkyl ether of it were synthesised as well. During this study we have developed a selective O-debenzylation method. A mild route for selective removal of benzylic protection on phenol in presence of benzyl protected alcohol was explored.

Accurate mass-based analysis in human sport doping control : Application of liquid chromatography - time-of-flight mass spectrometry

Human sport doping control analysis is a complex and challenging task for anti-doping laboratories. The List of Prohibited Substances and Methods, updated annually by World Anti-Doping Agency (WADA), consists of hundreds of chemically and pharmacologically different low and high molecular weight compounds. This poses a considerable challenge for laboratories to analyze for them all in a limited amount of time from a limited sample aliquot. The continuous expansion of the Prohibited List obliges laboratories to keep their analytical methods updated and to research new available methodologies. In this thesis, an accurate mass-based analysis employing liquid chromatography - time-of-flight mass spectrometry (LC-TOFMS) was developed and validated to improve the power of doping control analysis. New analytical methods were developed utilizing the high mass accuracy and high information content obtained by TOFMS to generate comprehensive and generic screening procedures. The suitability of LC-TOFMS for comprehensive screening was demonstrated for the first time in the field with mass accuracies better than 1 mDa. Further attention was given to generic sample preparation, an essential part of screening analysis, to rationalize the whole work flow and minimize the need for several separate sample preparation methods. Utilizing both positive and negative ionization allowed the detection of almost 200 prohibited substances. Automatic data processing produced a Microsoft Excel based report highlighting the entries fulfilling the criteria of the reverse data base search (retention time (RT), mass accuracy, isotope match). The quantitative performance of LC-TOFMS was demonstrated with morphine, codeine and their intact glucuronide conjugates. After a straightforward sample preparation the compounds were analyzed directly without the need for hydrolysis, solvent transfer, evaporation or reconstitution. The hydrophilic interaction technique (HILIC) provided good chromatographic separation, which was critical for the morphine glucuronide isomers. A wide linear range (50-5000 ng/ml) with good precision (RSD<10%) and accuracy (±10%) was obtained, showing comparable or better performance to other methods used. In-source collision-induced dissociation (ISCID) allowed confirmation analysis with three diagnostic ions with a median mass accuracy of 1.08 mDa and repeatable ion ratios fulfilling WADA s identification criteria. The suitability of LC-TOFMS for screening of high molecular weight doping agents was demonstrated with plasma volume expanders (PVE), namely dextran and hydroxyethylstarch (HES). Specificity of the assay was improved, since interfering matrix compounds were removed by size exclusion chromatography (SEC). ISCID produced three characteristic ions with an excellent mean mass accuracy of 0.82 mDa at physiological concentration levels. In summary, by combining TOFMS with a proper sample preparation and chromatographic separation, the technique can be utilized extensively in doping control laboratories for comprehensive screening of chemically different low and high molecular weight compounds, for quantification of threshold substances and even for confirmation. LC-TOFMS rationalized the work flow in doping control laboratories by simplifying the screening scheme, expediting reporting and minimizing the analysis costs. Therefore LC-TOFMS can be exploited widely in doping control, and the need for several separate analysis techniques is reduced.

The effects of beta-mercaptoethanol and sodium dodecyl sulfate on the Humicola insolens beta-glucosidase

Hydrolysis of p-nitrophenyl-beta-D-glucoside by the beta-glucosidase of a thermophilic and cellulolytic fungus, Humicola insolens was stimulated by two-fold in the presence of high concentrations of beta-mercaptoethanol. This enzyme did not have any free sulfhydryl groups and high concentrations of beta-mercaptoethanol (5% v/v) reduced all of the three disulfide bonds present in the enzyme. In contrast, the hydrolysis of cellobiose and cellulose polymers was inhibited by 50% under the same conditions. Sodium dodecyl sulfate (1% w/v) even in combination with beta-mercaptoethanol did not show any significant effects on this enzyme. These unusual properties suggest that this enzyme may be of significant importance for understanding the structure of the enzyme.

Immunochemical analysis of prolamins in gluten-free foods

People with coeliac disease have to maintain a gluten-free diet, which means excluding wheat, barley and rye prolamin proteins from their diet. Immunochemical methods are used to analyse the harmful proteins and to control the purity of gluten-free foods. In this thesis, the behaviour of prolamins in immunological gluten assays and with different prolamin-specific antibodies was examined. The immunoassays were also used to detect residual rye prolamins in sourdough systems after enzymatic hydrolysis and wheat prolamins after deamidation. The aim was to characterize the ability of the gluten analysis assays to quantify different prolamins in varying matrices in order to improve the accuracy of the assays. Prolamin groups of cereals consist of a complex mixture of proteins that vary in their size and amino acid sequences. Two common characteristics distinguish prolamins from other cereal proteins. Firstly, they are soluble in aqueous alcohols, and secondly, most of the prolamins are mainly formed from repetitive amino acid sequences containing high amounts of proline and glutamine. The diversity among prolamin proteins sets high requirements for their quantification. In the present study, prolamin contents were evaluated using enzyme-linked immunosorbent assays based on ω- and R5 antibodies. In addition, assays based on A1 and G12 antibodies were used to examine the effect of deamidation on prolamin proteins. The prolamin compositions and the cross-reactivity of antibodies with prolamin groups were evaluated with electrophoretic separation and Western blotting. The results of this thesis research demonstrate that the currently used gluten analysis methods are not able to accurately quantify barley prolamins, especially when hydrolysed or mixed in oats. However, more precise results can be obtained when the standard more closely matches the sample proteins, as demonstrated with barley prolamin standards. The study also revealed that all of the harmful prolamins, i.e. wheat, barley and rye prolamins, are most efficiently extracted with 40% 1-propanol containing 1% dithiothreitol at 50 °C. The extractability of barley and rye prolamins was considerably higher with 40% 1-propanol than with 60% ethanol, which is typically used for prolamin extraction. The prolamin levels of rye were lowered by 99.5% from the original levels when an enzyme-active rye-malt sourdough system was used for prolamin degradation. Such extensive degradation of rye prolamins suggest the use of sourdough as a part of gluten-free baking. Deamidation increases the diversity of prolamins and improves their solubility and ability to form structures such as emulsions and foams. Deamidation changes the protein structure, which has consequences for antibody recognition in gluten analysis. According to the resuts of the present work, the analysis methods were not able to quantify wheat gluten after deamidation except at very high concentrations. Consequently, deamidated gluten peptides can exist in food products and remain undetected, and thus cause a risk for people with gluten intolerance. The results of this thesis demonstrate that current gluten analysis methods cannot accurately quantify prolamins in all food matrices. New information on the prolamins of rye and barley in addition to wheat prolamins is also provided in this thesis, which is essential for improving gluten analysis methods so that they can more accurately quantify prolamins from harmful cereals.

Mechanistic Aspects of Nucleophilic Substitution at Half-Sandwich Metal Complexes

The hydrolysis reactions of organometallic ruthenium(II) piano-stool complexes of the type Ru-II(eta(6)-cymene)(L)Cl](0/+) (1-5, where L = kappa(1)- or kappa(2)-1,1-bis(diphenylphosphino)methane,1,1bis-(diphenylphosphino)methane oxide, kappa(1)-mercaptobenzothiazole) have been studied using density functional theory at the B3LYP level. In addition to considering a syn attack in an associative fashion, where the nucleophile approaches from the same side as the leaving group, we have explored alternative paths such as an anti attack in an associative manner, where the nucleophile attacks from the opposite side of the leaving group. During the anti attack, an intermediate is formed and there is a coordination mode change of the arene ring from eta(6) to eta(2) along with its rotation. When the intermediate goes to the product, the arene ring slips back from eta(2) to eta(6) coordination. This coordinated movement of the arene ring makes the associative anti attack an accessible pathway for the substitution process. Our calculations predict very similar activation barriers for both syn and anti attacks. In the dissociative path, the rate-determining step is the generation of a coordinatively unsaturated 16-electron ruthenium species. This turns out to be viable once solvent effects are included. The large size of the ancillary ligands on Ru makes the dissociative process as favorable as the associative process. Activation energy calculations reveal that although the dissociative path is favorable for kappa(1) complexes, both dissociative and associative processes can have significant contribution to the hydrolysis reaction in kappa(2) complexes. Once activated by hydrolysis, these complexes react with guanine and adenine bases of DNA. The thermodynamic stabilities of complexes formed with the nucleobases are also presented.

Acute toxicity of methyl isocyanate in rabbit: In vitro and in vivo effects on rabbit erythrocyte membrane

Methyl isocyanate (MIC) interaction with the rabbit erythrocyte membrane increased the fluidity of the membrane and decreased the osmotic fragility of erythrocytes both in vitro and in vivo in rabbits intoxicated with MIC subcutaneously. MIC inhibited both acetylcholinesterase (AChE) and adenosine triphosphatase (ATPase) activities of erythrocytes dose-dependently in vitro, while in vivo a decreased trend in ATPase activity with unaltered AChE activity was observed. MIC also caused significant decrease in plasma sodium level with corresponding increase in potassium level in rabbits. The observed effects are due to MIC, per se, as the hydrolysis products of MIC, methylamine and N,Nprime-dimethylurea did not affect the erythrocyte fluidity and enzymes activities both in vitro and in vivo while they increased the osmotic fragility of erythrocytes in vivo in rabbits administered subcutaneously in equimolar concentration to MIC dosage. Inhibition of Na+-K+-dependent ATPase with altered permeability to cations and also probably water transport of plasma membrane due to MIC interaction are envisaged.

Lipeäkäsitellyn vehnän vaikutus lypsylehmien syöntiin ja tuotokseen vapaalla seosrehuruokinnalla

Lipeä on vahva emäs, jonka on havaittu lisäävän hemiselluloosan ja ligniinin hydrolyysiä pötsissä. Näin ollen lipeäkäsittelyllä on mahdollista korvata viljan mekaaninen litistys ja jauhatus. Seosrehuruokinnalla, jonka osana on lipeäkäsitelty vilja, on mahdollista vähentää liiallisesta tärkkelyksestä aiheutuvia metabolisia ongelmia pötsissä. Tämän tutkielman tarkoituksena oli selvittää lipeäkäsitellyn vehnän vaikutusta lypsylehmien syöntiin ja tuotokseen ad libitum seosrehuruokinnoilla. Ruokinnoissa korvattiin kuivaa murskattua vehnää asteittain kokonaisella lipeäkäsitellyllä vehnällä. Kontrollina oli perinteisesti käytetty kuiva, murskattu ohra-kaura seos. Koe tehtiin Ruotsin maatalousyliopiston (SLU) maataloustieteiden laitoksella Uumajassa. Koe alkoi syyskuussa ja päättyi joulukuussa 2010. Kokeessa oli 17 useamman kerran poikinutta lehmää ja 6 ensikkoa (Ruotsin punainen -rotu). Lehmät olivat lämpimässä pihattonavetassa, jossa seosrehun syöntiä mitattiin vaakakuppien avulla. Koekäsittelyt olivat murskattu ohra-kaura seos (1:1), murskattu kuiva vehnä (1:0), murskatun kuivan vehnän ja kokonaisen lipeävehnän seos (1:1) ja kokonainen lipeävehnä (1:0). Ruokintojen kuiva-ainepitoisuudeksi asetettiin 370 g/kg ja raakavalkuaispitoisuudeksi 180 g/kg kuiva-ainetta. Näennäinen ravintoaineen sulavuus määritettiin happoon liukenemattoman tuhkan avulla. Typen hyväksikäyttöä arvioitiin laskennallisen typpitaseen avulla. Koe toteutettiin 4x4 latinalaisen neliön koemallin mukaisesti ja käsittelyjen väliset tilastolliset erot testattiin kontrastien avulla. Kuiva-aineen (PQ=0,02) ja orgaanisen aineen (PQ=0,02) syönnit lisääntyivät, samalla kun niiden sulavuudet paranivat korvattaessa puolet kuivasta vehnästä lipeävehnällä. Ruokintojen välillä ei ollut tilastollisesti merkitsevää eroa maitotuotoksessa eikä energiakorjatussa maitotuotoksessa. Maidon rasvatuotos lisääntyi vähän (PQ=0,04) ja rasvapitoisuus selvästi (PQ=0,004), kun kuivasta vehnästä korvattiin puolet lipeävehnällä. Kun kaikki kuiva vehnä korvattiin lipeävehnällä, maidon valkuaispitoisuus väheni (PL<0,001). Samoin kävi maidon ureapitoisuudelle (PL=0,002). Lipeäkäsittely ei tuottanut tässä kokeessa taloudellisesti kannattavaa tulosta, sillä maidon valkuaispitoisuus väheni ja syönti lisääntyi maitotuotoksen pysyessä samana. Vehnäruokinnoista paras tuotosvaste saatiin kuivan vehnän ja lipeävehnän seoksella.

Crystallization and Preliminary X-ray Diffraction Analysis of Crystals of Thermoascus aurantiacus Xylanase

Crystals suitable for high resolution X-ray diffraction analysis have been grown of the 29,774-Da protein, xylanase (1,-4-beta-xylan xylanohydrolase EC 3.2.1.8) from the thermophilic fungus Thermoascus aurantiacus. This protein, an endoxylanase demonstrates the hydrolysis of β-(1-4)-Image -xylose linkage in xylans and crystallizes as monoclinic pinacoids in the presence of ammonium sulphate buffered at pH 6·5, and also with neutral polyethylene glycol 6000. The crystals belong to space group P 21 and have cell dimensions, a = 41·2 Å, b = 67·76 Å, c = 51·8 Å; β = 113·2°.

Purification and characterization of an extracellular β-glucosidase from the thermophilic fungus Sporotrichum thermophile and its influence on cellulase activity

Multiple forms of beta-glucosidase (EC 3.2.1.21) of Sporotrichum thermophile were produced when the fungus was grown in a cellulose medium. One beta-glucosidase was purified 16-fold from 6-d-old culture filtrates by ion-exchange and gel-filtration chromatography. The purified enzyme was free of cellulase activity. It hydrolysed aryl beta-D-glucosides and beta-D-linked diglucosides. It was optimally active at pH 5.4, at 65-degrees-C. The apparent K(m) values for p-nitrophenyl beta-D-glucoside (PNPG) and cellobiose were 0.29 and 0.83 mm, respectively. Glucose, fucose, nojirimycin and gluconolactone inhibited beta-glucosidase competitively. At high (> 1 mm) substrate concentration, beta-glucosidase catalysed a parallel transglycosylation reaction. The transglycosylation product formed from cellobiose appeared to be a beta-linked tetramer of glucose. Admixtures of beta-glucosidase and cellulase components showed that the concept of cellobiose inhibition of cellulases was not valid for all components of the cellulase system of S. thermophile. Beta-Glucosidase supplementation also stimulated cellulose hydrolysis by cellulases when there was no accumulation of cellobiose in reaction mixture.

Solubility of sulfur dioxide at low partial pressures in dilute sulfuric acid solutions

Equilibrium of dissolution of sulfur dioxide at ppm levels in aqueous solutions of dilute sulfuric acid is analyzed, and a general expression is derived relating the total concentration of sulfur dioxide in the liquid phase to the partial pressure of SO2 in the gas and to the concentration of sulfuric acid in the solution. The equation is simplified for zero and high concentrations of the acid. Experiments at high concentrations of sulfuric acid have enabled the direct determination of Henry’s constant and its dependency on temperature. Heat of dissolution is -31.47 kJ/mol. Experiments in the absence of sulfuric acid and the related simplified expression have led to the determination of the equilibrium constant of the hydrolysis of aqueous sulfur dioxide and its temperature dependency.The heat of hydrolysis is 15.69 kJ/mol. The model equation with these parameters predicts the experimental data of the present work as well as the reported data very well.

Synthesis of (±)-thaps-7(15)-ene and (±)-thaps-6-enes

The synthesis of (±)-3a,4,4,7a-tetramethylhydrindan-2-one 8, containing three contiguous quaternary carbons as present in thapsanes, and the total synthesis of thaps-7(15)-ene 6 and thaps-6-ene 7, probable biogenetic precursors of thapsanes, have been achieved. Thus, orthoester Claisen rearrangement of cyclogeraniol 14, followed by hydrolysis of the resultant ester 16 furnished the eneacid 13. Copper sulfate-catalysed intramolecular cyclopropanation of the diazo ketone 18, derived from the acid 13, generated the cyclopropyl ketone 12. Regiospecific reductive cleavage of cyclopropyl ketone 12 furnished the hydrindanone 8, whereas the diazo ketone 26 furnished the hydrindanone 28avia the cyclopropyl ketone 27. Wittig methylenation of the hydrindanone 28a furnished thaps-7(15)-ene 6, which on isomerisation gave thaps-6-ene 7. Allylic oxidation of thaps-6-ene furnished the thapsenone 31, a degradation product of the natural thapsane 1b.

Direct conversion of 13-beta-alkylgonatetraenes into 13-beta-alkylgon-4-en-3-ones

Birch reduction of 8,9-didehydroestradiol-17 beta 3-methyl ether 1 or 9(11)-didehydroestradiol-17 beta 3-methyl ether 2 followed by acid hydrolysis results in a mixture of 19-nortestosterone 8 and 19-nor-9 beta, 10 alpha-testosterone 9 in varying amounts. However, reduction of their acetates with sodium or lithium, tert-butyl alcohol in liquid ammonia and in the presence of aniline affords exclusively 19-nortestosterone. Similarly, 18a-homo-19-nortestosterone 12 is prepared from the acetate of 18a-homoestradiol-17 beta 3-methyl ether, 10.