Sediment and organic matter properties, and molecular formula from sampling locations in the Northern Black Sea

Remineralization of organic matter in reactive marine sediments releases nutrients and dissolved organic matter (DOM) into the ocean. Here we focused on the molecular-level characterization of DOM by high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in sediment pore waters and bottom waters from contrasting redox regimes in the northern Black Sea with particular emphasis on nitrogen-bearing compounds to derive an improved understanding of the molecular transformations involved in nitrogen release. The number of nitrogen-bearing molecules is generally higher in pore waters than in bottom waters. This suggests intensified degradation of nitrogen-bearing precursor molecules such as proteins in anoxic sediments: No significant difference was observed between sediments deposited under oxic vs anoxic conditions (average O/C ratios of 0.55) suggesting that the different organic matter quality induced by contrasting redox conditions does not impact protein diagenesis in the subseafloor. Compounds in the pore waters were on average larger, less oxygenated, and had a higher number of unsaturations. Applying a mathematical model, we could show that the assemblages of nitrogen-bearing molecular formulas are potential products of proteinaceous material that was transformed by the following reactions: (a) hydrolysis and deamination, both reducing the molecular size and nitrogen content of the products and intermediates; (b) oxidation and hydration of the intermediates; and (c) methylation and dehydration.

Dissolved organic carbon concentrations, amino sugar concentrations and highly significantly correlating FT-ICR mass peak magnitudes obtained from solid phase extracted marine dissolved organic matter during POLARSTERN cruise ANT-XXV/1

Dissolved organic matter (DOM) was extracted with solid phase extraction (SPE) from 137 water samples from different climate zones and different depths along an Eastern Atlantic Ocean transect. The extracts were analyzed with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with electrospray ionization (ESI). D14C analyses were performed on subsamples of the SPE-DOM. In addition, the amount of dissolved organic carbon was determined for all water and SPE-DOM samples as well as the yield of amino sugars for selected samples. Linear correlations were observed between the magnitudes of 43% of the FT-ICR mass peaks and the extract D14C values. Decreasing SPE-DOM D14C values went along with a shift in the molecular composition to higher average masses (m/z) and lower hydrogen/carbon (H/C) ratios. The correlation was used to model the SPE-DOM D14C distribution for all 137 samples. Based on single mass peaks a degradation index was developed to compare the degradation state of marine SPE-DOM samples analyzed with FT-ICR MS. A correlation between D14C, degradation index, DOC values and amino sugar yield supports that SPE-DOM analyzed with FT-ICR MS reflects trends of bulk DOM. A relative mass peak magnitude ratio was used to compare aged SPE-DOM and fresh SPE-DOM regarding single mass peaks. The magnitude ratios show a continuum of different reactivities for the single compounds. Only few of the compounds present in the FT-ICR mass spectra are expected to be highly degraded in the oldest water masses of the Pacific Ocean. All other compounds should persist partly thermohaline circulation. Prokaryotic (bacterial) production, transformation and accumulation of this very stable DOM occurs probably primarily in the upper ocean. This DOM is an important contribution to very old DOM, showing that production and degradation are dynamic processes.

Proteomic analysis of a noninvasive human model of acute inflammation and its resolution:the twenty-one day gingivitis model

The 21-day experimental gingivitis model, an established noninvasive model of inflammation in response to increasing bacterial accumulation in humans, is designed to enable the study of both the induction and resolution of inflammation. Here, we have analyzed gingival crevicular fluid, an oral fluid comprising a serum transudate and tissue exudates, by LC-MS/MS using Fourier transform ion cyclotron resonance mass spectrometry and iTRAQ isobaric mass tags, to establish meta-proteomic profiles of inflammation-induced changes in proteins in healthy young volunteers. Across the course of experimentally induced gingivitis, we identified 16 bacterial and 186 human proteins. Although abundances of the bacterial proteins identified did not vary temporally, Fusobacterium outer membrane proteins were detected. Fusobacterium species have previously been associated with periodontal health or disease. The human proteins identified spanned a wide range of compartments (both extracellular and intracellular) and functions, including serum proteins, proteins displaying antibacterial properties, and proteins with functions associated with cellular transcription, DNA binding, the cytoskeleton, cell adhesion, and cilia. PolySNAP3 clustering software was used in a multilayered analytical approach. Clusters of proteins that associated with changes to the clinical parameters included neuronal and synapse associated proteins.

Structure, energetics and reactions of metal cation complexes of dipeptides in the gas phase

Structure, energetics and reactions of ions in the gas phase can be revealed by mass spectrometry techniques coupled to ions activation methods. Ions can gain enough energy for dissociation by absorbing IR light photons introduced by an IR laser to the mass spectrometer. Also collisions with a neutral molecule can increase the internal energy of ions and provide the dissociation threshold energy. Infrared multiple photon dissociation (IRMPD) or sustained off-resonance irradiation collision-induced dissociation (SORI-CID) methods are combined with Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometers where ions can be held at low pressures for a long time. The outcome of ion activation techniques especially when it is compared to the computational methods results is of great importance since it provides useful information about the structure, thermochemistry and reactivity of ions of interest. In this work structure, energetics and reactivity of metal cation complexes with dipeptides are investigated. Effect of metal cation size and charge as well as microsolvation on the structure of these complexes has been studied. Structures of bare and hydrated Na and Ca complexes with isomeric dipeptides AlaGly and GlyAla are characterized by means of IRMPD spectroscopy and computational methods. At the second step unimolecular dissociation reactions of singly charged and doubly charged multimetallic complexes of alkaline earth metal cations with GlyGly are examined by CID method. Also structural features of these complexes are revealed by comparing their IRMPD spectra with calculated IR spectra of possible structures. At last the unimolecular dissociation reactions of Mn complexes are studied. IRMPD spectroscopy along with computational methods is also employed for structural elucidation of Mn complexes. In addition the ion-molecule reactions of Mn complexes with CO and water are explored in the low pressures obtained in the ICR cell.

(Table 1) Salinity and dissolved organic carbon concentration of marine water (ANT-XIX/2) and mangrove porewater (Brazil)

The chemical structure of refractory marine dissolved organic matter (DOM) is still largely unknown. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR-MS) was used to resolve the complex mixtures of DOM and provide valuable information on elemental compositions on a molecular scale. We characterized and compared DOM from two sharply contrasting aquatic environments, algal-derived DOM from the Weddell Sea (Antarctica) and terrigenous DOM from pore water of a tropical mangrove area in northern Brazil. Several thousand molecular formulas in the mass range of 300-600 Da were identified and reproduced in element ratio plots. On the basis of molecular elemental composition and double-bond equivalents (DBE) we calculated an average composition for marine DOM. O/C ratios in the marine samples were lower (0.36 ± 0.01) than in the mangrove pore-water sample (0.42). A small proportion of chemical formulas with higher molecular mass in the marine samples were characterized by very low O/C and H/C ratios probably reflecting amphiphilic properties. The average number of unsaturations in the marine samples was surprisingly high (DBE = 9.9; mangrove pore water: DBE = 9.4) most likely due to a significant contribution of carbonyl carbon. There was no significant difference in elemental composition between surface and deep-water DOM in the Weddell Sea. Although there were some molecules with unique marine elemental composition, there was a conspicuous degree of similarity between the terrigenous and algal-derived end members. Approximately one third of the molecular formulas were present in all marine as well as in the mangrove samples. We infer that different forms of microbial degradation ultimately lead to similar structural features that are intrinsically refractory, independent of the source of the organic matter and the environmental conditions where degradation took place.

Glycerol dialkyl glycerol tetraethers (GDGT) abundance of sediment core GeoB15103-1

Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and utilized in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single sub-mm sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional LC/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-µm resolution (~4-year temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the 200-yr de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and hydrological factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments.

Electrical characterization of amorphous silicon MIS-based structures for HIT solar cell applications

A complete electrical characterization of hydrogenated amorphous silicon layers (a-Si:H) deposited on crystalline silicon (c-Si) substrates by electron cyclotron resonance chemical vapor deposition (ECR-CVD) was carried out. These structures are of interest for photovoltaic applications. Different growth temperatures between 30 and 200 °C were used. A rapid thermal annealing in forming gas atmosphere at 200 °C during 10 min was applied after the metallization process. The evolution of interfacial state density with the deposition temperature indicates a better interface passivation at higher growth temperatures. However, in these cases, an important contribution of slow states is detected as well. Thus, using intermediate growth temperatures (100–150 °C) might be the best choice.

Deposition of Intrinsic a-Si:H by ECR-CVD to Passivate the Crystalline Silicon Heterointerface in HIT Solar Cells

We have deposited intrinsic amorphous silicon (a-Si:H) using the electron cyclotron resonance (ECR) chemical vapor deposition technique in order to analyze the a-Si:H/c-Si heterointerface and assess the possible application in heterojunction with intrinsic thin layer (HIT) solar cells. Physical characterization of the deposited films shows that the hydrogen content is in the 15-30% range, depending on deposition temperature. The optical bandgap value is always comprised within the range 1.9- 2.2 eV. Minority carrier lifetime measurements performed on the heterostructures reach high values up to 1.3 ms, indicating a well-passivated a-Si:H/c-Si heterointerface for deposition temperatures as low as 100°C. In addition, we prove that the metal-oxide- semiconductor conductance method to obtain interface trap distribution can be applied to the a-Si:H/c-Si heterointerface, since the intrinsic a-Si:H layer behaves as an insulator at low or negative bias. Values for the minimum of D_it as low as 8 × 10^10 cm^2 · eV^-1 were obtained for our samples, pointing to good surface passivation properties of ECR-deposited a-Si:H for HIT solar cell applications.

High rate deposition of ta-C:H using an electron cyclotron wave resonance plasma source

A compact electron cyclotron wave resonance (ECWR) source has been developed for the high rate deposition of hydrogenated tetrahedral amorphous carbon (ta-C:H). The ECWR provides growth rates of up to 1.5 nm/s over a 4-inch diameter and an independent control of the deposition rate and ion energy. The ta-C:H was deposited using acetylene as the source gas and was characterized as having an sp3 content of up to 77%, plasmon energy of 27 eV, refractive index of 2.45, hydrogen content of about 30%, optical gap of up to 2.1 eV and RMS surface roughness of 0.04 nm. © 1999 Elsevier Science S.A. All rights reserved.

High rate deposition of Ta-C:H using an electron cyclotron wave resonance plasma source

A compact electron cyclotron wave resonance (ECWR) source has been developed for the high rate deposition of hydrogenated tetrahedral amorphous carbon (ta-C:H). The ECWR provides growth rates of up to 900 angstrom/min and an independent control of the deposition rate and ion energy. The ta-C:H was deposited using acetylene as the source gas and was characterized in terms of its bonding, stress and friction coefficient. The results indicated that the ta-C:H produced using this source fulfills the necessary requirements for applications requiring enhanced tribological performance.

The preparation, characterization and tribological properties of TA-C : H deposited using an electron cyclotron wave resonance plasma beam source

A compact electron cyclotron wave resonance (ECWR) source has been developed for the high rate deposition of hydrogenated tetrahedral amorphous carbon (ta-C:H). The ECWR provides growth rates of up to 900 Å/min over a 4″ diameter and an independent control of the deposition rate and ion energy. The ta-C:H was deposited using acetylene as the source gas and was characterized in terms of its sp3 content, mass density, intrinsic stress, hydrogen content, C-H bonding, Raman spectra, optical gap, surface roughness and friction coefficient. The results obtained indicated that the film properties were maximized at an ion energy of approximately 167 eV, corresponding to an energy per daughter carbon ion of 76 eV. The relationship between the incident ion energy and film densification was also explained in terms of the subsurface implantation of carbon ions into the growing film.

Deposition of carbon nitride films using an electron cyclotron wave resonance plasma source

Hydrogenated amorphous carbon nitride (a-C:N:H) has been synthesized using a high plasma density electron cyclotron wave resonance (ECWR) technique using N2 and C2H2 as source gases, at different ratios and a fixed ion energy (80 eV). The composition, structure and bonding state of the films were investigated and related to their optical and electrical properties. The nitrogen content in the film rises rapidly until the N2/C2H2 gas ratio reaches 2 and then increases more gradually, while the deposition rate decreases steeply, placing an upper limit for the nitrogen incorporation at 30 at%. For nitrogen contents above 20 at%, the band gap and sp3-bonded carbon fraction decrease from 1.7 to 1.1 eV and approximately 65 to 40%, respectively. Films with higher nitrogen content are less dense than the original hydrogenated tetrahedral amorphous carbon (ta-C:H) film but, because they have a relatively high band gap (1.1 eV), high resistivity (109 Ω cm) and moderate sp3-bonded carbon fraction (40%), they should be classed as polymeric in nature.