Development and application of a GC system for NMHC analyses of air samples from the CARIBIC aircraft project

The subject of this thesis is the development of a Gaschromatography (GC) system for non-methane hydrocarbons (NMHCs) and measurement of samples within the project CARIBIC (Civil Aircraft for the Regular Investigation of the atmosphere Based on an Instrument Container, www.caribic-atmospheric.com). Air samples collected at cruising altitude from the upper troposphere and lowermost stratosphere contain hydrocarbons at low levels (ppt range), which imposes substantial demands on detection limits. Full automation enabled to maintain constant conditions during the sample processing and analyses. Additionally, automation allows overnight operation thus saving time. A gas chromatography using flame ionization detection (FID) together with the dual column approach enables simultaneous detection with almost equal carbon atom response for all hydrocarbons except for ethyne. The first part of this thesis presents the technical descriptions of individual parts of the analytical system. Apart from the sample treatment and calibration procedures, the sample collector is described. The second part deals with analytical performance of the GC system by discussing tests that had been made. Finally, results for measurement flight are assessed in terms of quality of the data and two flights are discussed in detail. Analytical performance is characterized using detection limits for each compound, using uncertainties for each compound, using tests of calibration mixture conditioning and carbon dioxide trap to find out their influence on analyses, and finally by comparing the responses of calibrated substances during period when analyses of the flights were made. Comparison of both systems shows good agreement. However, because of insufficient capacity of the CO2 trap the signal of one column was suppressed due to breakthroughed carbon dioxide so much that its results appeared to be unreliable. Plausibility tests for the internal consistency of the given data sets are based on common patterns exhibited by tropospheric NMHCs. All tests show that samples from the first flights do not comply with the expected pattern. Additionally, detected alkene artefacts suggest potential problems with storing or contamination within all measurement flights. Two last flights # 130-133 and # 166-169 comply with the tests therefore their detailed analysis is made. Samples were analyzed in terms of their origin (troposphere vs. stratosphere, backward trajectories), their aging (NMHCs ratios) and detected plumes were compared to chemical signatures of Asian outflows. In the last chapter a future development of the presented system with focus on separation is drawn. An extensive appendix documents all important aspects of the dissertation from theoretical introduction through illustration of sample treatment to overview diagrams for the measured flights.

Development of two real-time PCR assays for the detection of Mycoplasma hyopneumoniae in clinical samples

In order to improve the diagnosis of enzootic pneumonia (EP) in pigs two real-time polymerase chain reaction (rtPCR) assays for the detection of Mycoplasma hyopneumoniae in bronchial swabs from lung necropsies were established and validated in parallel. As a gold standard, the current "mosaic diagnosis" was taken, including epidemiological tracing, clinical signs, macro- and histopathological lesions of the lungs and immunofluorescence. One rtPCR is targeting a repeated DNA element of the M. hyopneumoniae genome (REP assay), the other a putative ABC transporter gene (ABC assay). Both assays were shown to be specific for M. hyopneumoniae and did not cross react with other bacteria and mollicutes from pig. With material from pigs of defined EP-negative farms the two assays showed to be 100% specific. When testing lungs from pig farms with EP, the REP assay detected 50% and the ABC assay 90% of the farms as positive. Both tests together detected all positive farms. Within a positive herd the two assays tested similarly with on average over 90% of the lung samples analysed from a single farm showing positive scores. A series of samples with suspicion of EP and samples from pigs with diseases other than respiratory taken from current routine diagnostic was assayed. None of the assays showed false positive results. The sensitivities in this sample group were 50% for the REP and 70% for the ABC assays and for both assays together 85%. The two assays run in parallel are therefore a valuable tool for the improvement of the current diagnosis of EP.

Clinical outcomes and molecular genotyping of Staphylococcus aureus isolated from milk samples of dairy primiparous Mediterranean buffaloes (Bubalus bubalis)

Staphylococcus aureus is one of the most important pathogens causing mastitis in dairy cows and in Mediterranean buffaloes. Genotype B (GTB) is contagious in dairy cows and may occur in up to 87% of cows of a dairy herd. It was the aim of this study to evaluate genotypes present, clinical outcomes, and prevalence of Staph. aureus in milk samples of primiparous Mediterranean dairy buffaloes. Two hundred composite milk samples originating from 40 primiparous buffaloes were collected from May to June 2012, at d 10, 30, 60, 90, and 150 d in milk (DIM) to perform somatic cell counts and bacteriological cultures. Daily milk yields were recorded. Before parturition until 40 to 50 DIM, all primiparous animals were housed separated from the pluriparous animals. Milking was performed in the same milking parlor, but the primiparous animals were milked first. After 50 DIM, the primiparous were mixed with the pluriparous animals, including the milking procedure. Individual quarter samples were collected from each animal, and aliquots of 1 mL were mixed and used for molecular identification and genotyping of Staph. aureus. The identification of Staph. aureus was performed verifying the presence of nuc gene by nuc gene PCR. All the nuc-positive isolates were subjected to genotype analysis by means of PCR amplification of the 16S-23S rRNA intergenic spacer region and analyzed by a miniaturized electrophoresis system. Of all 200 composite samples, 41 (20.5%) were positive for Staph. aureus, and no genotype other than GTB was identified. The prevalence of samples positive for Staph. aureus was 0% at 10 DIM and increased to a maximum of 22/40 (55%) at 90 DIM. During the period of interest, 14 buffaloes tested positive for Staph. aureus once, 6 were positive twice, and 5 were positive 3 times, whereas 15 animals were negative at every sampling. At 90 and 150 DIM, 7 (17.5%) and 3 buffaloes (7.5%), respectively, showed clinical mastitis (CM), and only 1 (2.5%) showed CM at both samplings. At 60, 90, and 150 DIM, 1 buffalo was found with subclinical mastitis at each sampling. At 30, 60, 90, and 150 DIM, 2.5 (1/40), 22.5 (9/40), 35 (14/40), and 10% (4/40) were considered affected by intramammary infection, respectively. Buffaloes with CM caused by Staph. aureus had statistically significantly higher mean somatic cell count values (6.06 ± 0.29, Log10 cells/mL ± standard deviation) and statistically significantly lower mean daily milk yields (7.15 ± 1.49, liters/animal per day) than healthy animals (4.69 ± 0.23 and 13.87 ± 2.64, respectively), buffaloes with IMI (4.82 ± 0.23 and 11.16 ± 1.80, respectively), or with subclinical mastitis (5.47 ± 0.10 and 10.33 ± 0.68, respectively). Based on our knowledge, this is the first time that Staph. aureus GTB has been identified in milk samples of dairy Mediterranean buffaloes.

Development of a method for fast and automatic radiocarbon measurement of aerosol samples by online coupling of an elemental analyzer with a MICADAS AMS

A fast and automatic method for radiocarbon analysis of aerosol samples is presented. This type of analysis requires high number of sample measurements of low carbon masses, but accepts precisions lower than for carbon dating analysis. The method is based on online Trapping CO2 and coupling an elemental analyzer with a MICADAS AMS by means of a gas interface. It gives similar results to a previously validated reference method for the same set of samples. This method is fast and automatic and typically provides uncertainties of 1.5–5% for representative aerosol samples. It proves to be robust and reliable and allows for overnight and unattended measurements. A constant and cross contamination correction is included, which indicates a constant contamination of 1.4 ± 0.2 μg C with 70 ± 7 pMC and a cross contamination of (0.2 ± 0.1)% from the previous sample. A Real-time online coupling version of the method was also investigated. It shows promising results for standard materials with slightly higher uncertainties than the Trapping online approach.

The localization and identification of candidate tumor suppressor genes involved in prostate cancer

Frequent loss of heterozygosity (LOH) at specific chromosomal regions are highly associated with the inactivation of tumor suppressor genes (TSGs) (Weinberg, 1991; Bishop, 1989). Chromosome 8p is the most frequently reported site of LOH (∼60%) in prostate cancer (PC), suggesting that there may be inactivated TSG(s) involved in PC on chromosome 8p. (Bergerheim et. al., 1991; Kagan et. al., 1995). In order to identify the smallest common regions of frequent LOH (SCLs) on chromosome 8, we screened 52 PC patient/tumor samples with 39 polymorphic markers in successive screenings. In the course of refining the SCLs, we identified 3 tumors with >6 Mb homozygous deletions (HZDs) at 8p22 and 8p21, suggesting the presence of candidate TSGs at both loci. These HZDs spanned the two SCLs at 8p22 (46%) and 8p21 (45%). The SCLs were narrowed to 3.2 cM at 8p22 and less than 3 cM at 8p21. ^ In order to identify candidate TSGs within the SCLs on 8p, two approaches were used. In the candidate gene approach, thirty genes that mapped to the SCLs were evaluated for expression in normal prostate and in PC cell lines. One of the candidate genes, Clusterin, showed decreased expression in 4/7 (57%) prostate cancer cell lines by Northern blot analysis. Clusterin will be further examined as a candidate TSG. ^ The second approach involved utilizing subtractive hybridization and hybrid affinity capture to generate pools of expressed sequence tags (ESTs) enriched for genes that are downregulated or deleted in PC and that map to specific regions of interest. We took advantage of a prostate cancer cell line (PC3) with a known HZD of a candidate TSG, CTNNA1 on 5q31, to develop and validate a model system. We then developed subtracted libraries enriched for 8p22 and 8p21 ESTs by this method, using two cell lines, MDAPCa-2b and PC3. The ESTs were cloned, and 40 were sequenced and evaluated for expression in normal prostate and PC cell lines. Three ESTs from the subtracted libraries, C2, C17 and F12, showed decreased expression in 29–57% of the prostate tumor cell lines studied, and will be further examined as candidate TSGs. ^

(Table 2) Geochemical composition of suspended matter samples from the northern Dvina River

The results of the analysis of samples of the Northern Dvina River's suspended particulate matter obtained by the sedimentation method from large water volumes in the periods of the spring high water and summer low water are presented. By the method of sequential leaching using different reagents, four fractions have been separated: the F1 is the sorbed complex and carbonates, the F2 is the amorphous hydroxides of Fe and Mn, the F3 is the form connected with the organic matter, and the F4 is the residual or silicate-detrital (inert) form. The data have shown that all ten elements determined were grouped with respect to the ratio of the distinguished forms: F4 is the predominant form for Al and Fe (73-88% of all the forms; however, the summer sample contains only 38% of this form of iron, and F2 is the predominant form for this period with 46.6%). As to Mn, the F1, F2, and F4 are nearly equally distributed in the spring high water samples, and only the F3 form is less important (5.4%). In the summer sample, the manganese sorbed complex is predominant (53.5%); for Cu, Ni, Cr, and Co, the inert F4 form is predominant (60-70%) in the sample of the spring suspended matter. The summer low water suspended matter has a lower F4 contribution (25-45%); for Zn, Pb, and Cd, the equal distribution of the forms in the spring samples is typical, while the summer suspended matter differs by the F2 form's predominance (53-61% for Zn and Pb). The main conclusion from the acquired data is that the geochemical mobility of all the studied elements, except for cadmium, in the summer low water suspended matter is higher than in the spring suspended matter. The more intensive biogeochemical processes in August, the high level of organic matter, and the higher contribution of phytoplankton lead to the intensification of the metals' geochemical activity in the Northern Dvina suspended matter in the end of the summer compared to the spring high water period when the physical processes are predominant over the biogeochemical ones due to the high speeds of the freshened waters flow.

Igneous geochemistry of OP Leg 126 samples

Major element, trace element, and radiogenic isotope compositions of samples collected from Ocean Drilling Program Leg 126 in the Izu-Bonin forearc basin are presented. Lavas from the center of the basin (Site 793) are high-MgO, low-Ti, two-pyroxene basaltic andesites, and represent the products of synrift volcanism in the forearc region. These synrift lavas share many of the geochemical and petrographic characteristics of boninites. In terms of their element abundances, ratios, and isotope systematics they are intermediate between low-Ti arc tholeiites from the active arc and boninites of the outer-arc high. These features suggest a systematic geochemical gradation between volcanics related to trench distance and a variably depleted source. A basement high drilled on the western flank of the basin (Site 792) comprises a series of plagioclase-rich two-pyroxene andesites with calc-alkaline affinities. These lavas are similar to calc-alkaline volcanics from Japan, but have lower contents of Ti, Zr, and low-field-strength elements (LFSE). Lavas from Site 793 show inter-element variations between Zr, Ti, Sr, Ni, and Cr that are consistent with those predicted during crystallization and melting processes. In comparison, concentrations of P, Y, LFSE, and the rare-earth elements (REE) are anomalous. These elements have been redistributed within the lava pile, concentrating particularly in sections of massive and pillowed flows. Relative movement of these two-element groupings can be related to the alteration of interstitial basaltic andesite glass to a clay mineral assemblage by a post-eruptive process. Fluid-rock interaction has produced similar effects in the basement lavas of Site 792. In this sequence, andesites and dacites have undergone a volume change related to silica mobility. As a result of this process, some lithologies have the major element characteristics of basaltic andesite and rhyolite, but can be related to andesitic or dacitic precursors by silica removal or addition.

Minerals of bulk and fine-grained (2 µm) samples from DSDP Leg 60

A bulk-sediment and clay-fraction X-ray diffraction study of samples from Deep Sea Drilling Project Leg 60 shows an abundance of the following minerals: plagioclase feldspar, zeolite, smectite, Fe-Mg chlorite, attapulgite, and serpentine. Amorphous compounds are also abundant. The variations in abundance of the different components correspond to episodes of volcanic activity through time. Deposits from periods of great activity are composed of sediments very rich in amorphous matter and in "primary" minerals (e.g., plagioclase feldspars). During relatively quiet periods, clay minerals and zeolites predominate.

Concentration of trace elements in samples of sea water determined by use of two methods of concentrating

A device and a specific procedure for simultaneous concentration of trace ele¬ments from sea water by co-precipitating them in precipitate of magnesium hydroxide obtained by electrolytic alkalization of samples in a two-chamber electrolyzer are described. Analyses of sea water samples for zinc, iron, copper, nickel and lead demonstrate that the method produces a thousand-fold concentration and gives results that agree well with those obtained by extractive concentration using diethyldithiocarbamate and 8-hydroxyquinoline in chloroform. Extracts were analyzed by flame atomic absorption. Correlation coefficients of results obtained with use of these two methods of concentration were 0.76-0.87 for zinc, iron, and copper at confidence levels of 0.05-0.07. Average zinc and iron concentrations determined by the method differed by less than 10%.

Sulphur geochemistry of whole-rock samples from ODP Hole 176-735B

Sulfide petrography plus whole rock contents and isotope ratios of sulfur were measured in a 1.5 km section of oceanic gabbros in order to understand the geochemistry of sulfur cycling during low-temperature seawater alteration of the lower oceanic crust, and to test whether microbial effects may be present. Most samples have low SO4/Sum S values (<= 0.15), have retained igneous globules of pyrrhotite ± chalcopyrite ± pentlandite, and host secondary aggregates of pyrrhotite and pyrite laths in smectite ± iron-oxyhydroxide ± magnetite ± calcite pseudomorphs of olivine and clinopyroxene. Compared to fresh gabbro containing 100-1800 ppm sulfur our data indicate an overall addition of sulfide to the lower crust. Selection of samples altered only at temperatures <= 110 °C constrains microbial sulfate reduction as the only viable mechanism for the observed sulfide addition, which may have been enabled by the production of H2 from oxidation of associated olivine and pyroxene. The wide range in d34Ssulfide values (-1.5 to + 16.3 per mil) and variable additions of sulfide are explained by variable epsilon sulfate-sulfide under open system pathways, with a possible progression into closed system pathways. Some samples underwent oxidation related to seawater penetration along permeable fault horizons and have lost sulfur, have high SO4/Sum S (>= 0.46) and variable d34Ssulfide (0.7 to 16.9 per mil). Negative d34Ssulfate-d34Ssulfide values for the majority of samples indicate kinetic isotope fractionation during oxidation of sulfide minerals. Depth trends in sulfide-sulfur contents and sulfide mineral assemblages indicate a late-stage downward penetration of seawater into the lower 1 km of Hole 735B. Our results show that under appropriate temperature conditions, a subsurface biosphere can persist in the lower oceanic crust and alter its geochemistry.

(Table 3) Relative content of n-alkane groups in samples from hydrothermal fields of the Mid-Atlantic Ridge

Optimum conditions were selected for chromatographic separation of model mixtures of C12-C40 n-alkanes. For one of samples of hydrothermal deposits extraction conditions of hydrocarbons were studied and a sample preparation procedure was selected. The procedure was proposed to determine n-alkanes in samples of hydrothermal deposits by means of gas chromatography - mass spectrometry (GC-MS). Detection limit for n-alkanes was 3x10**-9 to 10**-8% depending on components. On the basis of the proposed procedure composition of n-alkanes was studied in samples of hydrothermal deposits collected at the Mid-Atlantic Ridge (Broken Spur, Lost City, and Rainbow hydrothermal fields). Analyses showed that samples contained C14-C35 n-alkanes. Concentrations of the n-alkanes were rather low and varied from 0.002 to 0.038 µg/g. Hypotheses concerning genesis of identified n-alkanes were offered.

Molecular basis of fast inactivation in voltage and Ca2+-activated K+ channels: A transmembrane β-subunit homolog

Voltage-dependent and calcium-sensitive K+ (MaxiK) channels are key regulators of neuronal excitability, secretion, and vascular tone because of their ability to sense transmembrane voltage and intracellular Ca2+. In most tissues, their stimulation results in a noninactivating hyperpolarizing K+ current that reduces excitability. In addition to noninactivating MaxiK currents, an inactivating MaxiK channel phenotype is found in cells like chromaffin cells and hippocampal neurons. The molecular determinants underlying inactivating MaxiK channels remain unknown. Herein, we report a transmembrane β subunit (β2) that yields inactivating MaxiK currents on coexpression with the pore-forming α subunit of MaxiK channels. Intracellular application of trypsin as well as deletion of 19 N-terminal amino acids of the β2 subunit abolished inactivation of the α subunit. Conversely, fusion of these N-terminal amino acids to the noninactivating smooth muscle β1 subunit leads to an inactivating phenotype of MaxiK channels. Furthermore, addition of a synthetic N-terminal peptide of the β2 subunit causes inactivation of the MaxiK channel α subunit by occluding its K+-conducting pore resembling the inactivation caused by the “ball” peptide in voltage-dependent K+ channels. Thus, the inactivating phenotype of MaxiK channels in native tissues can result from the association with different β subunits.

Mössbauer and electron paramagnetic resonance studies of chloroperoxidase following mechanism-based inactivation with allylbenzene

We have used Mössbauer and electron paramagnetic resonance (EPR) spectroscopy to study a heme-N-alkylated derivative of chloroperoxidase (CPO) prepared by mechanism-based inactivation with allylbenzene and hydrogen peroxide. The freshly prepared inactivated enzyme (“green CPO”) displayed a nearly pure low-spin ferric EPR signal with g = 1.94, 2.15, 2.31. The Mössbauer spectrum of the same species recorded at 4.2 K showed magnetic hyperfine splittings, which could be simulated in terms of a spin Hamiltonian with a complete set of hyperfine parameters in the slow spin fluctuation limit. The EPR spectrum of green CPO was simulated using a three-term crystal field model including g-strain. The best-fit parameters implied a very strong octahedral field in which the three 2T2 levels of the (3d)5 configuration in green CPO were lowest in energy, followed by a quartet. In native CPO, the 6A1 states follow the 2T2 ground state doublet. The alkene-mediated inactivation of CPO is spontaneously reversible. Warming of a sample of green CPO to 22°C for increasing times before freezing revealed slow conversion of the novel EPR species to two further spin S = ½ ferric species. One of these species displayed g = 1.82, 2.25, 2.60 indistinguishable from native CPO. By subtracting spectral components due to native and green CPO, a third species with g = 1.86, 2.24, 2.50 could be generated. The EPR spectrum of this “quasi-native CPO,” which appears at intermediate times during the reactivation, was simulated using best-fit parameters similar to those used for native CPO.

The N-terminal domain of a K+ channel β subunit increases the rate of C-type inactivation from the cytoplasmic side of the channel

Voltage-gated K+ channels are complexes of membrane-bound, ion-conducting α and cytoplasmic ancillary (β) subunits. The primary physiologic effect of coexpression of α and β subunits is to increase the intrinsic rate of inactivation of the α subunit. For one β subunit, Kvβ1.1, inactivation is enhanced through an N-type mechanism. A second β subunit, Kvβ1.2, has been shown to increase inactivation, but through a distinct mechanism. Here we show that the degree of enhancement of Kvβ1.2 inactivation is dependent on the amino acid composition in the pore mouth of the α subunit and the concentration of extracellular K+. Experimental conditions that promote C-type inactivation also enhance the stimulation of inactivation by Kvβ1.2, showing that this β subunit directly stimulates C-type inactivation. Chimeric constructs containing just the nonconserved N-terminal region of Kvβ1.2 fused with an α subunit behave in a similar fashion to coexpressed Kvβ1.2 and α subunit. This shows that it is the N-terminal domain of Kvβ1.2 that mediates the increase in C-type inactivation from the cytoplasmic side of the pore. We propose a model whereby the N terminus of Kvβ1.2 acts as a weakly binding “ball” domain that associates with the intracellular vestibule of the α subunit to effect a conformational change leading to enhancement of C-type inactivation.

Internal cleavage of the inhibitory 7B2 carboxyl-terminal peptide by PC2: a potential mechanism for its inactivation.

The neuroendocrine protein 7B2 contains two domains, a 21-kDa protein required for prohormone convertase 2 (PC2) maturation and a carboxyl-terminal (CT) peptide that inhibits PC2 at nanomolar concentrations. To determine how the inhibition of PC2 is terminated, we studied the metabolic fate of the 7B2 CT peptide in RinPE-7B2, AtT-20/PC2-7B2, and alphaTC1-6 cells. Extracts obtained from cells labeled for 6 h with [3H]valine were subjected to immunoprecipitation using an antibody raised against the extreme carboxyl terminus of r7B2, and immunoprecipitated peptides were separated by gel filtration. All three cell lines yielded two distinct peaks at about 3.5 kDa and 1.5 kDa, corresponding to the CT peptide and a smaller fragment consistent with cleavage at an interior Lys-Lys site. These results were corroborated using a newly developed RIA against the carboxyl terminus of the CT peptide which showed that the intact CT peptide represented only about half of the stored CT peptide immunoreactivity, with the remainder present as the 1.5-kDa peptide. Both peptides could be released upon phorbol 12-myristate 13-acetate stimulation. We investigated the possibility that PC2 itself could be responsible for this cleavage by performing in vitro experiments. When 125I-labeled CT peptide was incubated with purified recombinant PC2, a smaller peptide was generated. Analysis of CT peptide derivatives for their inhibitory potency revealed that CT peptide 1-18 (containing Lys-Lys at the carboxyl terminus) represented a potent inhibitor, but that peptide 1-16 was inactive. Inclusion of carboxypeptidase E (CPE) in the reaction greatly diminished the inhibitory potency of the CT peptide against PC2, in line with the notion that the CT peptide cleavage product is not inhibitory after the removal of terminal lysines by CPE. In summary, our data support the idea that PC2 cleaves the 7B2 CT peptide at its internal Lys-Lys site within secretory granules; deactivation of the cleavage product is then accomplished by CPE, thus providing an efficient mechanism for intracellular inactivation of the CT peptide.