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Microbial community functioning at hypoxic sediments revealed by targeted metagenomics and RNA stable isotope probing

Microbial community functioning at hypoxic sediments revealed by targeted metagenomics and RNA stable isotope probing

Identification of microbial communities by RNA stable isotope probing and 16S rRNA sequencing from the Benguela coastal upwelling system (Chapter 4).. Christina Pavloudi, Sa[r]

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Tracing carbon fluxes within two distinct microbial communities in anaerobically methane oxidising mats by stable isotope probing

Tracing carbon fluxes within two distinct microbial communities in anaerobically methane oxidising mats by stable isotope probing

Figure 3.15: Total 13 C-assimilation rates for bacterial lipid biomarker compounds of ANME-1 (left) and -2 (right) dominated communities incubated with different 13 C-labelled subst[r]

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Characterisation of microbial transformation of halogenated organic contaminants using compound-specific stable isotope analysis

Characterisation of microbial transformation of halogenated organic contaminants using compound-specific stable isotope analysis

In recent years, the range of applications involving stable isotope tracers for the analysis of microbial degradation processes has been greatly extended and currently includes the analysis of: i) products and metabolites; ii) phospholipids fatty acids; iii) nucleic acids (RNA or DNA); and iv) proteins (Kästner et al., 2006, Stelzer et al., 2006, Neufeld et al., 2007, Whiteley et al., 2007, Bombach et al., 2010, Jehmlich et al., 2010). These stable isotope probing (SIP) methods have the advantage of providing direct proof for the existence of particular anabolic or catabolic pathways with a specific substrate, or the identity of the microorganisms and enzymes involved in a process. However, as a prerequisite, the substrate must be used as a carbon source. Approaches where a co-substrate for growth e.g. acetate or ammonium have also been used but in such cases the overall activity of the microbial community is identified, but not the specific community responsible for the biodegradation (Kittelmann & Friedrich, 2008a, Kittelmann & Friedrich, 2008b) (Siegert et al., 2013). For example, the involvement of Dehalococcoides- related microorganisms in the dehalogenation of PCE in a tidal flat and river sediments was suggested by incorporation of the carbon derived from 13 C-labeled acetate into the biomass (Kittelmann & Friedrich, 2008a, Kittelmann & Friedrich, 2008b). Substrates investigated using SIP approaches over the last years included common groundwater contaminants such as BTEX and MTBE (Lueders et al., 2004, Bombach et al., 2010, Herrmann et al., 2010, Winderl et al., 2010, Bastida et al., 2011, Bozinovski et al., 2012), (Morasch et al., 2007). In the case of the chlorinated ethenes, which are used as electron acceptors and not as carbon sources, stable isotope tracers are generally not applicable.
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Stabile Cu-Isotope im Boden

Stabile Cu-Isotope im Boden

Kupfer-Isotope werden bei verschiedenen Prozessen wie der Adsorption an Oxy- (hydr)oxide, bei der Reduktion oder Oxi- dation oder beim Transport in der Pflanze fraktioniert (Abb. 1). Viele dieser Prozes- se bestimmen auch das Verhalten von Cu im Boden. Daher wurde erprobt, ob sich die Messung von Cu-Isotopenverhält- nissen zur Untersuchung von biogeo- chemischen Prozessen im Boden eignet. Um die Fraktionierung von Cu-Isotopen im Boden zu erfassen, wurden vier ver- schiedene Bodentypen untersucht. Bei den beprobten Böden handelte es sich um jeweils zwei Braunerden, Podsole, Pseudogleye und Gleye.
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Reassessing Hydrological Processes That Control Stable Isotope Tracers in Groundwater of the Atacama Desert (Northern Chile)

Reassessing Hydrological Processes That Control Stable Isotope Tracers in Groundwater of the Atacama Desert (Northern Chile)

Abstract: A collection of 514 stable isotope water samples from the Atacama Desert is being reassessed geostatistically. The evaluation reveals that adjacent Andean catchments can exhibit distinct δ 18 O and δ 2 H value ranges in meteoric waters, despite similar sample altitudes of up to 4000 m above sea level (a.s.l.). It is proposed that the individual topographic features of each catchment at the western Andean Precordillera either inhibit or facilitate vapor mixing processes of easterly and westerly air masses with different isotopic compositions. This process likely causes catchment-specific isotope value ranges in precipitations (between − 7‰ and − 19‰ δ 18 O) that are being consistently reflected in the isotope values of groundwater and surface waters of these catchments. Further, due to evaporation-driven isotopic fractionation and subsurface water mixing, isotope samples of the regional Pampa del Tamarugal Aquifer plot collectively parallel to the local meteoric water line. Besides, there is no evidence for hydrothermal isotopic water-rock interactions. Overall, the observed catchment-dependent isotope characteristics allow for using δ 18 O and δ 2 H as tracers to delineate regionally distinct groundwater compartments and associated recharge areas. In this context, δ 18 O, δ 2 H and 3 H data of shallow groundwater at three alluvial fans challenge the established idea of recharge from alluvial fans after flash floods.
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Exploring water cycle dynamics by sampling multiple stable water isotope pools in a developed landscape in Germany

Exploring water cycle dynamics by sampling multiple stable water isotope pools in a developed landscape in Germany

A spatially distributed snapshot sampling of soil water iso- topes at two soil depths at 52 sampling points across different land uses (arable land, forest, and grassland) revealed that topsoil isotopic signatures were similar to the precipitation input signal. Preferential water flow paths occurred under forested soils, explaining the isotopic similarities between top- and subsoil isotopic signatures. Due to human-impacted agricultural land use (tilling and compression) of arable and grassland soils, water delivery to the deeper soil layers was reduced, resulting in significant different isotopic signatures. However, the land use influence became less pronounced with depth and soil water approached groundwater δ values. Seasonally tracing stable water isotopes through soil profiles showed that the influence of new percolating soil water de- creased with depth as no remarkable seasonality in soil iso- topic signatures was obvious at depths > 0.9 m and constant values were observed through space and time. Since classic isotope evaluation methods such as transfer-function-based mean transit time calculations did not provide a good fit be- tween the observed and calculated data, we established a hy-
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Construction and specification of a cryogenic vacuum extraction device for application in stable water isotope analysis

Construction and specification of a cryogenic vacuum extraction device for application in stable water isotope analysis

However, to determine the isotopic signature of environmental water, it is necessary to sepa- rate the water from the other components of the sample media (plant material, soil). There- fore, several extraction methods have been developed: Azeotropic distillation, cryogenic vac- uum extraction, and centrifugation. Cryogenic vacuum extraction is one of the most widely used methods to obtain extracts suitable for isotopic water analysis (Peters and Yakir, 2008). Hence, the aim of this thesis was to construct a vacuum-tight, reliable, and user-friendly cryo- genic vacuum extraction device with an extendable modularity and several independently working extraction units for the application in stable water isotope research sciences in order to extract water from soil and plant samples and, thereafter, analyse their stable water isotope composition to quantify hydrological processes in local water cycles.
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Monitoring the Sphingolipid de novo Synthesis by Stable-Isotope Labeling and Liquid Chromatography-Mass Spectrometry

Monitoring the Sphingolipid de novo Synthesis by Stable-Isotope Labeling and Liquid Chromatography-Mass Spectrometry

the amino acid L -serine is catalyzed by serine palmitoyltransferase (SPT). The product, 3-ketosphinganine, is then converted into more complex sphingolipids by additional ER-bound enzymes, resulting in the formation of ceramides. Since sphingolipid homeostasis is crucial to numerous cellular functions, improved assessment of sphingolipid metabolism will be key to better understanding several human diseases. To date, no assay exists capable of monitoring de novo synthesis sphingolipid in its entirety. Here, we have established a cell-free assay utilizing rat liver microsomes containing all the enzymes necessary for bottom-up synthesis of ceramides. Following lipid extraction, we were able to track the different intermediates of the sphingolipid metabolism pathway, namely 3-ketosphinganine, sphinganine, dihydroceramide, and ceramide. This was achieved by chromatographic separation of sphingolipid metabolites followed by detection of their accurate mass and characteristic fragmentations through high-resolution mass spectrometry and tandem-mass spectrometry. We were able to distinguish, unequivocally, between de novo synthesized sphingolipids and intrinsic species, inevitably present in the microsome preparations, through the addition of stable isotope-labeled palmitate-d 3 and L -serine-d 3 . To the best of our knowledge, this is the
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Determination of Thallium in Brain Tissue by Stable Isotope Dilution and Field Desorption Mass Spectrometry 

Determination of Thallium in Brain Tissue by Stable Isotope Dilution and Field Desorption Mass Spectrometry 

F ield desorption mass spectrometry appears to be a reliable, sensitive, and fast method fo r the determ ination o f thallium in b iological samples. In particular, the use o f a stable isotope labelled internal standard and the possibility o f analyzing untreated samples are important advantages o f the method. F inally, the sensitivity o f field desorption fo r thallium appears to be o f the same order as fo r alkali metals, which enables its determination in trace and ultratrace quantities.

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Bias of ostracod stable isotope data caused by drying of sieve residues from water

Bias of ostracod stable isotope data caused by drying of sieve residues from water

Abstract Stable isotope analysis of ostracod shells is used routinely for palaeoenvironmental studies of ostracod-bearing records. Sample treatment usually involves the disaggregation of sediments and sieving; before the sieving residues were washed with water onto petri dishes and oven-dried. In our study, we compared d 18 O and d 13 C values of shells that were oven-dried from water and from ethanol alternatively. Large isotopic differences of up to 3% were deter- mined for d 18 O values, whereas differences in d 13 C values were less pronounced with differences of up to 1.6%. Stable isotope values of shells dried from water were lower for both oxygen and carbon as a result of calcite crystals precipitated on the shell surfaces during the drying process. Therefore, ostra- cod shells for stable isotope analysis should not be prepared by drying from water. Instead, shells should be dried from ethanol to obtain reliable stable isotope data; likewise freeze-drying is expected to provide trustworthy results.
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Nitrogen Cycling in the Past and in the Present Mediterranean Sea and Arabian Sea - Implications from Stable Isotope Studies

Nitrogen Cycling in the Past and in the Present Mediterranean Sea and Arabian Sea - Implications from Stable Isotope Studies

63 New data were raised from 2 Ocean Drilling Program (ODP) Sites (722 B and 724 C) in the western Arabian Sea; additional core data are from cores 111 KL, NAST and EAST in the northern and central Arabian Sea (Suthhof et al., 2001; Ivanova et al., 2003) (Figure 5.1 and Table 5.1). Site 722 is located on the Owen Ridge at a water depth of 2028 m (16°37’N; 059°48’E), i.e. below the oxygen minimum zone of the Arabian Sea. Due to low detrital and biogenic particle fluxes in this offshore setting, the bulk sediment accumulation rates (BAR) calculated from linear sedimentation rates (based on the age model and on determinations of dry-bulk densities given in Prell et al. (1989)) on the Owen Ridge are lower than at the Oman margin Site 724. Site 724 is located on the upper slope of the Oman margin at a water depth of about 600 m (18°17’N; 057°28’E), i.e. within the oxygen minimum layer. Sediments at Site 724 have higher organic carbon contents as well as higher accumulation rates compared to those at Site 722. Age models for Holes 722 B and 724 C are based on oxygen isotope stratigraphies of Clemens and Prell (1991) and Zahn and Pedersen (1991) and have been adjusted to visually fit the high-resolution
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Synthesis of a stable isotope labeled 2-13C-2-fluoro-adenosine building block to study the TROSY properties in RNA

Synthesis of a stable isotope labeled 2-13C-2-fluoro-adenosine building block to study the TROSY properties in RNA

Transverse Relaxation Optimized Spectroscopy (TROSY) ... Results and Discussion ... Synthesis of 2- 13 C-2-fluoro-adenosine triphosphate ... Formation of the Phosphorodichloridate Interm[r]

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Quality evaluation of olive oil by statistical analysis of multicomponent stable isotope dilution assay data of aroma active compounds

Quality evaluation of olive oil by statistical analysis of multicomponent stable isotope dilution assay data of aroma active compounds

Compound identification was performed by comparing the following criteria with the reference substances: RI on FFAP and OV-1701 capillaries, mass spectra obtained by EI-MS, and odor quality perceived at the sniffing port. Auxiliary to the characteristic green and fruity odor notes, several off-flavor- inducing aroma active compounds were found in the olive oils. All of these compounds had been already identified by several authors in olive oil samples of different qualities. 5,10,13,14,19,20,23 Furthermore, the odor active compounds were quantified by HS-SPME-GC-MS with stable isotope labeled internal stan- dards in our study. In addition acetone, ethyl acetate, and ethanol were quantified by dynamic headspace analysis. Figure 1 shows box plots of the quantification results. E-2-Hexenal (8),
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MOnAMi | JTAG-Probing zur Datensicherung von Mobiltelefonen

MOnAMi | JTAG-Probing zur Datensicherung von Mobiltelefonen

Das hier untersuchte Feature der RIFF Box, das Probing, soll es dem Nutzer laut Her- steller ermöglichen, die JTAG Pins eines nicht unterstützten Modells korrekt zuzuord- nen. Auch kann damit festgestellt werden, ob es sich bei einer Anordnung von Pins auf einem Motherboard tatsächlich um eine JTAG Schnittstelle handelt. Dazu wird mit ei- ner Nadel an jedem Pin die Spannung am ADC2 Punkt bei einem PRB_LEVEL Signal beim logischen Null-Level (Probe(0), V1) und einem PRB_LEVEL Signal beim logi- schen Eins-Level (Probe(1), V2) gemessen (siehe Abbildung 4).

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Analysis of bisphenols and bisphenol A diglycidyl ethers by stable isotope dilution assay liquid chromatography-tandem mass spectrometry

Analysis of bisphenols and bisphenol A diglycidyl ethers by stable isotope dilution assay liquid chromatography-tandem mass spectrometry

From an analytical perspective, thermal paper can be regarded as a matrix with only limited complexity, also bisphenols – applied in their native monomeric form – are contained in high amounts. In the next phase of the project, it was aimed to work with more complex matrices that contain fewer concentrations (to be expected) of the target analytes. Canned beer, as fermented beverage, seemed to be an appropriate sample type. Interferences have been shown in GC measurements [86]. Concerning leaching from epoxy can linings, next to BPA also BADGE and its derivatives were considered as analytes of interest. Thus, decision was taken to synthesize three more isotope standards based on BPA-d 4 and develop a LC-MS/MS
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Über die Häufigkeiten der Isotope des Zirkons 

Über die Häufigkeiten der Isotope des Zirkons 

Dieses Werk wurde im Jahr 2013 vom Verlag Zeitschrift für Naturforschung in Zusammenarbeit mit der Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. Nach Abzug dieser Kompone[r]

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Die stellaren Neutroneneinfangquerschnitte der Isotope ¹⁶⁴Er und ¹⁷⁰Er

Die stellaren Neutroneneinfangquerschnitte der Isotope ¹⁶⁴Er und ¹⁷⁰Er

Die Summe beider Ereignisse kann dann als ein Ereignis registriert und der direkten Zerfallslinie zugeschlagen werden (summing-in). Die entsprechenden Korrekturen für diesen systema[r]

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Studies of plant terpenoid biosynthesis using 13C stable isotope labeling techniques (KIT Scientific Reports ; 7583)

Studies of plant terpenoid biosynthesis using 13C stable isotope labeling techniques (KIT Scientific Reports ; 7583)

Diese vorliegende Dissertation trägt wesentlich zu einem vertieften Verständnis über die Terpenoid-Biosynthese der Pflanzen und die Regulierung des MEP-Stoffwechsels unter besonderer Beachtung der Isopren- und Monoterpenbiosynthese bei, ermöglicht durch moderne und neu etablierte Methoden, insbesondere der Verwendung von stabilen Isotopen. Stabile Isotope stellen ein nützliches Werkzeug dar, um spezifische Substanzen, wie organische Stoffe und atmosphärische Gase, zu markieren. Im Gegensatz zu radioaktiven Isotopen haben stabile Isotope den Vorteil, unschädlich zu sein. Die markierten Verbindungen (d.h. angereichert mit schwereren Isotopen) können zurückverfolgt und isoliert werden. Somit können stabile Isotope genutzt werden, um die Terpenoidbiosynthese in Pflanzen zu studieren, um Informationen zu Kohlenstoff-Quellen und -Flüssen innerhalb des MEP-Stoffwechsels in verschiedenem räumlichen und zeitlichen Zusammenhang zu untersuchen, sowie um Einblicke in die Regulierung der Enzyme des MEP-Stoffwechsels zu erhalten.
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Probing stratospheric transport and chemistry with new balloon and aircraft observations of the meridional and vertical N2O isotope distribution

Probing stratospheric transport and chemistry with new balloon and aircraft observations of the meridional and vertical N2O isotope distribution

2 con- tamination (Rahn and Wahlen, 1997). Laboratory studies of isotope fractionation in N 2 O photolysis at 185 nm and dur- ing “photo-oxidation” found only small oxygen isotope ef- fects (Johnston et al., 1995), in apparent contradiction to the stratospheric findings. However, additional high-quality field data from Rahn and Wahlen (1997) were accompanied by theoretical predictions of an increase of the photolytic iso- tope effect towards longer, stratospherically more relevant wavelengths (Yung and Miller, 1997). Laboratory measure- ments of isotope effects between 193 and 208 nm quickly showed that these theoretical predictions were qualitatively correct, but at least a factor of two too small in magnitude (Rahn et al., 1998). Analytical advances in the late 1990s then allowed the position-dependent measurement of the ni- trogen isotope distribution between the terminal and cen- tral nitrogen atoms in N 2 O (Brenninkmeijer and R¨ockmann,
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Stable water isotope tracing through hydrological models for disentangling runoff generation processes at the hillslope scale

Stable water isotope tracing through hydrological models for disentangling runoff generation processes at the hillslope scale

Although the first 1-D process-orientated models to de- scribe the dynamics of stable water isotope profiles for open water bodies (Craig and Gordon, 1965) were devel- oped as early as in the mid-1960s, and a bit later for soils (Zimmermann et al., 1968), fully distributed 2-D to 3-D hy- drological tracer models benefitting from the additional in- formation to be gained by stable water isotopes are still in their early development stages (Davies et al., 2013) or use strong simplifications of the flow processes (e.g., TAC D us- ing a kinematic wave approach; Uhlenbrook et al., 2004). This can be attributed to the high number of interwoven pro- cesses affecting the soil water isotope fluxes not only in the soil’s liquid phase but also in its vapor phase. The more process-based 1-D models (Braud et al., 2005; Haverd and Cuntz, 2010) therefore simultaneously solve the heat balance and the mass balance simultaneously for the liquid and the vapor phase and are thereby describing the
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