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Objectives Changes in protein glycosylation are a hallmark of immune-mediated diseases. Glycans are master regulators of the inflammatory response being important molecules for the discrimination between "self"/"non-self". We here explored whether lupus nephritis (LN) exhibit an altered cellular glycosylation aiming to identify a unique glycosignature that characterizes LN pathogenesis. Methods A comprehensive tissue glycomics characterization was performed in a cohort of human biopsy-proven LN clinical samples from SLE patients. A combination of advanced tissue mass spectrometry imaging (MSI); in situ glyco-characterization and ex vivo glycophenotyping of human kidney biopsies were performed to structurally map the N-glycans repertoire in LN samples. Results LN revealed a unique glycan signature characterized by an increased abundance and spatial distribution of unusual mannose-enriched glycans that are typically found in lower microorganisms; this glycosignature was specific of LN as it was not observed in other kidney diseases. Exposure of mannosylated glycans in LN was found to occur at the cell surface of kidney cells promoting an increased recognition by specific glycans-recognizing receptors, expressed by immune cells. This abnormal glyco-signature of LN was demonstrated to be due to a deficient complex N-glycosylation and a proficient O-mannosylation pathway. Moreover, levels of mannosylation detected in kidney biopsies from LN patients at diagnosis were demonstrated to predict the development of chronic kidney disease (CKD) with 93% of specificity. Conclusions Cellular mannosylation is a marker of LN, predicting the development of CKD, and thus constituting a potential glycobiomarker to be included in the diagnostic and prognostic algorithm of LN.

Matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) of intact proteins is mostly performed using time-of-flight (TOF) based mass spectrometers, operated in linear mode. Linear MALDI-TOF systems provide limited mass resolving power and mass accuracy, which complicates assigning identities to the peaks in the MSI datasets. In this work we report ultra-high mass resolution MALDI-MSI based on 15T Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for the analysis of intact proteins directly from non-embedded and OCT-embedded mouse and human (control and type 2 diabetes) pancreas so that small endocrine compartments (islets of Langerhans) may be analyzed in control and pathological tissues. Sample preparation methods, in terms of increased sensitivity while limiting lateral diffusion of analytes, have been investigated. By combining protein localization, high mass accuracy, and the clearly resolved isotope patterns we were able to assign protein identities with additional confidence, including proteins of similar average mass and with interspersed isotopomers. These capabilities allowed us to ascertain the presence of many protein adducts that, with a low resolving power instrument, could be misinterpreted as distinct protein ions. (C) 2017 Published by Elsevier B.V

Contains fulltext : 229584.pdf (Publisher’s version ) (Open Access) Sjögren-Larsson syndrome (SLS) is a rare neurometabolic syndrome caused by deficient fatty aldehyde dehydrogenase. Patients exhibit intellectual disability, spastic paraplegia, and ichthyosis. The accumulation of fatty alcohols and fatty aldehydes has been demonstrated in plasma and skin but never in brain. Brain magnetic resonance imaging and spectroscopy studies, however, have shown an abundant lipid peak in the white matter of patients with SLS, suggesting lipid accumulation in the brain as well. Using histopathology, mass spectrometry imaging, and lipidomics, we studied the morphology and the lipidome of a postmortem brain of a 65-year-old female patient with genetically confirmed SLS and compared the results with a matched control brain. Histopathological analyses revealed structural white matter abnormalities with the presence of small lipid droplets, deficient myelin, and astrogliosis. Biochemically, severely disturbed lipid profiles were found in both white and gray matter of the SLS brain, with accumulation of fatty alcohols and ether lipids. Particularly, long-chain unsaturated ether lipid species accumulated, most prominently in white matter. Also, there was a striking accumulation of odd-chain fatty alcohols and odd-chain ether(phospho)lipids. Our results suggest that the central nervous system involvement in SLS is caused by the accumulation of fatty alcohols leading to a disbalance between ether lipid and glycero(phospho)lipid metabolism resulting in a profoundly disrupted brain lipidome. Our data show that SLS is not a pure leukoencephalopathy, but also a gray matter disease. Additionally, the histopathological abnormalities suggest that astrocytes and microglia might play a pivotal role in the underlying disease mechanism, possibly contributing to the impairment of myelin maintenance.

Prostate cancer is initially treated via androgen deprivation therapy (ADT), a highly successful treatment in the initial pursuit of tumour regression, but commonly restricted by the eventual emergence of a more lethal 'castrate resistant' (CRPC) form of the disease. Intracrine pathways that utilize dehydroepiandrosterone (DHEA) or other circulatory precursor steroids are thought to generate relevant levels of growth-stimulating androgens such as testosterone (T) and dihydrotestosterone (DHT). Decoding this tissue-specific metabolic pathway is key for the development of novel therapeutic treatments. Mass spectrometry imaging (MSI) is an analytical technique that allows the visualization of the distribution of numerous classes of biomolecules within tissue sections. The analysis of androgens by liquid chromatography mass spectrometry (LC/MS)-based methods however presents a challenge due to their generally poor ionization efficiency and low physiological endogenous levels. In MSI, on-tissue chemical derivatization (OTCD) has enabled the limits of steroids to be imaged within tissues to be pushed by overcoming poor ionization performance. However, isobaric interference of key androgen derivatives such as T and DHEA can severely hamper studying the intracrinology in several diseases. Here, we have evaluated the use of laser induced post-ionization (MALDI-2) combined with trapped ion mobility separation (TIMS) and orthogonal time-of-flight (QTOF) MS for the visualization of isobaric derivatized androgens in murine tumour xenograft at about 50 mu m spatial resolution. With this combination, isobaric T and DHEA were separated in tissue sections and the signals of derivatized steroids enhanced by about 20 times. The combination of TIMS and MALDI-2 thus shows unique potential to study tissue intracrinology within target tissues. This could offer the opportunity for many novel insights into tissue-specific androgen biology.

Carotid atherosclerosis is a risk factor for ischemic stroke, one of the main causes of mortality and disability worldwide. The disease is characterized by plaques, heterogeneous deposits of lipids, and necrotic debris in the vascular wall, which grow gradually and may remain asymptomatic for decades. However, at some point a plaque can evolve to a high-risk plaque phenotype, which may trigger a cerebrovascular event. Lipids play a key role in the development and progression of atherosclerosis, but the nature of their involvement is not fully understood. Using matrix-assisted laser desorption/ionization mass spectrometry imaging, we visualized the distribution of approximately 200 different lipid signals, originating of >90 uniquely assigned species, in 106 tissue sections of 12 human carotid atherosclerotic plaques. We performed unsupervised classification of the mass spectrometry dataset, as well as a histology-directed multivariate analysis. These data allowed us to extract the spatial lipid patterns associated with morphological plaque features in advanced plaques from a symptomatic population, revealing spatial lipid patterns in atherosclerosis and their relation to histological tissue type. The abundances of sphingomyelin and oxidized cholesteryl ester species were elevated specifically in necrotic intima areas, whereas diacylglycerols and triacylglycerols were spatially correlated to areas containing the coagulation protein fibrin. These results demonstrate a clear colocalization between plaque features and specific lipid classes, as well as individual lipid species in high-risk atherosclerotic plaques.

Matrix-assisted laser desorption/ionization combined with laser-induced postionization (MALDI-2) is a recently introduced method for enhanced mass spectrometry imaging of numerous classes of biomolecules, including phospho- and glycolipids in tissue sections at high lateral resolution. Here we describe the first adaptation of the technology to a Bruker timsTOF fleX mass spectrometer. Upon use of a 1 kHz postionization laser, MALDI-2 produces a sizable increase in the number of detected features as well as in ion signal intensities. This enhancement is similar to that described previously for low repetition rate MALDI-2 systems, but now enables substantially enhanced measurement speeds. In our proof-of-concept study, we furthermore demonstrate, on examples of rat brain and testis tissue sections, that the combination of MALDI-2 with the trapped ion mobility spectrometry (TIMS) functionality of the instrument can crucially support unravelling the complex molecular composition of the lipidome. Numerous isomeric/isobaric ion species are successfully separated upon using the collisional cross section (CCS) as additional specific physical property. With the possibilities of high data acquisition speed or high separation powers in combination with the increased sensitivity of MALDI-2 available in one instrument, the described methodology could be a valuable tool in many areas of biological and medical research.

Carotid atherosclerosis is one of the main causes of stroke, mortality and disability worldwide. The disease is characterized by plaques, heterogeneous depositions of lipids and necrotic debris in the vascular wall, which grow gradually and may remain asymptomatic for decades. However, at some point a plaque can evolve to a high-risk plaque phenotype, which may trigger a cerebrovascular event. Lipids play a key role in the development and progression of atherosclerosis. Using matrix-assisted laser desorption/ionization mass spectrometry imaging, we visualized the distribution of approximately 200 lipids in 106 tissue sections of 12 human carotid atherosclerotic plaques. We performed unsupervised classification of the mass spectrometry dataset, as well as a histology-driven multivariate analysis. These data allowed us to compare the spatial lipid patterns with morphological plaque features that have been associated with enhanced risk of symptoms. The abundances of sphingomyelin and oxidized cholesteryl ester species were elevated specifically in necrotic intima areas, while diacylglycerols and triacylglycerols were spatially correlated to areas containing the coagulation protein fibrin. This is the first study to systematically investigate spatial lipid patterns in atherosclerosis, analyze their relation to histological tissue type, and to demonstrate a clear co-localization between plaque features and specific lipid classes and individual lipid molecules in high-risk atherosclerotic plaques.

Mass spectrometry imaging (MSI) has provided many results with translational character, which still have to be proven robust in large patient cohorts and across different centers. Although formalin-fixed paraffin-embedded (FFPE) specimens are most common in clinical practice, no MSI multicenter study has been reported for FFPE samples. Here, we report the results of the first round robin MSI study on FFPE tissues with the goal to investigate the consequences of inter- and intracenter technical variation on masking biological effects. A total of four centers were involved with similar MSI instrumentation and sample preparation equipment. A FFPE multi-organ tissue microarray containing eight different types of tissue was analyzed on a peptide and metabolite level, which enabled investigating different molecular and biological differences. Statistical analyses revealed that peptide intercenter variation was significantly lower and metabolite intercenter variation was significantly higher than the respective intracenter variations. When looking at relative univariate effects of mass signals with statistical discriminatory power, the metabolite data was more reproducible across centers compared to the peptide data. With respect to absolute effects (cross-center common intensity scale), multivariate classifiers were able to reach on average > 90% accuracy for peptides and > 80% for metabolites if trained with sufficient amount of cross-center data. Overall, our study showed that MSI data from FFPE samples could be reproduced to a high degree across centers. While metabolite data exhibited more reproducibility with respect to relative effects, peptide data-based classifiers were more directly transferable between centers and therefore more robust than expected. Graphical abstractᅟ Electronic supplementary material The online version of this article (10.1007/s00216-018-1216-2) contains supplementary material, which is available to authorized users.

Three-dimensional (3D) cell culture is a rapidly emerging field, which mimics some of the physiological conditions of human tissues. In cancer biology, it is considered a useful tool in predicting in vivo chemotherapy responses, compared with conventional two-dimensional (2D) cell culture. We have developed a novel 3D cell culture model of osteosarcoma composed of aggregated proliferative tumour spheroids, which shows regions of tumour heterogeneity formed by aggregated spheroids of polyclonal tumour cells. Aggregated spheroids show local necrotic and apoptotic regions and have sizes suitable for the study of spatial distribution of metabolites by mass spectrometry imaging (MSI). We have used this model to perform a proof-of-principle study showing a heterogeneous distribution of endogenous metabolites that colocalise with the necrotic core and apoptotic regions in this model. Cytotoxic chemotherapy (doxorubicin) responses were significantly attenuated in our 3D cell culture model compared with those of standard cell culture, as determined by resazurin assay, despite sufficient doxorubicin diffusion demonstrated by localisation throughout the 3D constructs. Finally, changes to the distribution of endogenous metabolites in response to doxorubicin were readily detected by MSI. Principal component analysis identified 50 metabolites which differed most in their abundance between treatment groups, and of these, 10 were identified by both in-software t test and mixed-effects analysis of variance (ANOVA). Subsequent independent MSIs of identified species were consistent with principle component analysis findings. This proof-of-principle study shows for the first time that chemotherapy-induced changes in metabolite abundance and distribution may be determined in 3D cell culture by MSI, highlighting this method as a potentially useful tool in the elucidation of chemotherapy responses as an alternative to in vivo testing.

A reliable animal model that captures the key features of human cancer is essential to bring new insights for oncology research. In this context, spontaneously occurring canine cancers are excellent models to study tumor development and progression, since dogs share the same environment as humans and present many similarities regarding anatomic, histological, molecular and clinical features. Here, we aimed to identify and characterize intratumor heterogeneity using mass spectrometry imaging (MSI) of proteolytic peptides in order to simultaneously detect morphological and molecular alterations whilst preserving tissue integrity, directing the search for cancer biomarkers. Samples were obtained from five dogs diagnosed with metastatic disease, and MALDI-FT-ICR-MSI data of 17 primary tumors were co-registered to hematoxylin and eosin stained slides. Unsupervised clustering of tumor spectra was performed using the bisecting k-means method in SCiLS Lab (Bruker Daltonics, DE) and two molecularly distinct clusters (CL1 and CL2) were selected regardless morphological presentation. We also performed a supervised analysis, by annotating (FlexImagingTM, Bruker Daltonics, DE) and classifying tumor regions of interest into low- and high-grade populations according to previously established morphological criteria. LC/MS-MS of extracted peptides was used for protein identity assignment based on mass matching, and functional enrichment was performed using a human protein-coding database. Discriminative peaks were identified using ROC and Wilcoxon methods. M/z signals presenting AUC > 0.7 and FDR < 0.05, and biological functions with FDR < 0.05 were considered significant. We found 266 features discriminating low- and high-grade tumor populations, resulting in 44 protein IDs, and 185 features significantly different between CL1 and CL2, with 35 IDs retrieved. CANX, RSPA5 and PDIA3, found down-regulated in high-grade compared to low-grade regions, enriched for protein folding in endoplasmic reticulum process, suggesting that morphology changes may have arisen from protein misfolding due to reticular stress. Both protein sets enriched for cell adhesion molecule binding, cadherin binding and structural molecule activity. HMGN3, HNRNPC and histones H2AFY and HIST1H1C, resulting from the comparison of clusters CL1 and CL2, also enriched for nucleosome binding and chromatin DNA binding, alterations that could have not been detected only by conventional histopathological evaluation. Ongoing analyses aim to further characterize the intratumor molecular heterogeneity of microscopically indistinct populations and its association to cancer progression and metastasis. Citation Format: Yonara G. Cordeiro, Bram P.A.M Heijs, Leandra M. Mulder, René J. van Zeijl, Peter van Veelen, Arnoud de Ru, Ricardo F. Strefezzi, Heidge Fukumasu. Mass spectrometry imaging for the assessment of intratumor molecular heterogeneity in canine metastatic mammary carcinomas: A comparative approach for biomarker discovery [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2709.

Mass spectrometry imaging (MSI) is a molecular imaging technique that maps the distribution of molecules in biological tissues with high spatial resolution. The most widely used MSI modality is matrix-assisted laser desorption/ionization (MALDI), mainly due to the large variety of analyte classes amenable for MALDI analysis. However, the organic matrices used in classical MALDI may impact the quality of the molecular images due to limited lateral resolution and strong background noise in the low mass range, hindering its use in metabolomics. Here we present a matrix-free laser desorption/ionization (LDI) technique based on the deposition of gold nanolayers on tissue sections by means of sputter-coating. This gold coating method is quick, fully automated, reproducible, and allows growing highly controlled gold nanolayers, necessary for high quality and high resolution MS image acquisition. The performance of the developed method has been tested through the acquisition of MS images of brain tissues. The obtained spectra showed a high number of MS peaks in the low mass region (m/z below 1000 Da) with few background peaks, demonstrating the ability of the sputtered gold nanolayers of promoting the desorption/ionization of a wide range of metabolites. These results, together with the reliable MS spectrum calibration using gold peaks, make the developed method a valuable alternative for MSI applications.

Patients with leukemia who receive a T cell–depleted allogeneic stem cell graft followed by postponed donor lymphocyte infusion (DLI) can experience graft-versus-leukemia (GVL) reactivity, with a lower risk of graft-versus-host disease (GVHD). Here, we have investigated the magnitude, diversity, and specificity of alloreactive CD8 T cells in patients who developed GVL reactivity after DLI in the absence or presence of GVHD. We observed a lower magnitude and diversity of CD8 T cells for minor histocompatibility antigens (MiHAs) in patients with selective GVL reactivity without GVHD. Furthermore, we demonstrated that MiHA-specific T cell clones from patients with selective GVL reactivity showed lower reactivity against nonhematopoietic cells, even when pretreated with inflammatory cytokines. Expression analysis of MiHA-encoding genes showed that similar types of antigens were recognized in both patient groups, but in patients who developed GVHD, T cell reactivity was skewed to target broadly expressed MiHAs. As an inflammatory environment can render nonhematopoietic cells susceptible to T cell recognition, prevention of such circumstances favors induction of selective GVL reactivity without development of GVHD.

On-tissue digestion matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can be used to record spatially correlated molecular information from formalin-fixed, paraffin-embedded (FFPE) tissue sections. In this work, we present the in situ multimodal analysis of N-linked glycans and proteins from the same FFPE tissue section. The robustness and applicability of the method are demonstrated for several tumors, including epithelial and mesenchymal tumor types. Major analytical aspects, such as lateral diffusion of the analyte molecules and differences in measurement sensitivity due to the additional sample preparation methods, have been investigated for both N-glycans and proteolytic peptides. By combining the MSI approach with extract analysis, we were also able to assess which mass spectral peaks generated by MALDI-MSI could be assigned to unique N-glycan and peptide identities.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging is a rapidly evolving field in which mass spectrometry techniques are applied directly on tissues to characterize the spatial distribution of various molecules such as lipids, protein/peptides, and recently also N-glycans. Glycans are involved in many biological processes and several glycan changes have been associated with different kinds of cancer, making them an interesting target group to study. An important analytical challenge for the study of glycans by MALDI mass spectrometry is the labile character of sialic acid groups which are prone to in-source/postsource decay, thereby biasing the recorded glycan profile. We therefore developed a linkage-specific sialic acid derivatization by dimethylamidation and subsequent amidation and transferred this onto formalin-fixed paraffin-embedded (FFPE) tissues for MALDI imaging of N-glycans. Our results show (i) the successful stabilization of sialic acids in a linkage specific manner, thereby not only increasing the detection range, but also adding biological meaning, (ii) that no noticeable lateral diffusion is induced during to sample preparation, (iii) the potential of mass spectrometry imaging to spatially characterize the N-glycan expression within heterogeneous tissues.

We model the pump-probe spectrum of linear molecular aggregates measured by using ultrafast laser pulses. We analyze in particular the effects of coherences between exciton states created by the pump pulse and show that these give rise to a small induced-absorption peak that is red-shifted relative to the main one-exciton bleaching peak. The new coherent peak survives common values of the static disorder. With increasing pump-probe delay time, its amplitude oscillates and decays with a rate that is inversely proportional to the width of the absorption band. We also consider coupling to vibrations and show that with increasing temperature the frequency separation between the main bleaching and induced-absorption peaks increases and provides a measure for the exciton coherence size imposed by scattering on the vibrations. (C) 2007 Elsevier B.V. All rights reserved.

In the Eastern Mediterranean Sea, deep hypersaline anoxic basins (DHABs) and deep-sea sediment contain anoxic environments where sulfate reduction is an important microbial metabolic process. The objective of this study was to characterize the sulfate-reducing community in the brine and interface of the DHABs L'Atalante and Urania based on a phylogenetic analysis of the dissimilatory sulfite reductase gene (dsrA). Results demonstrated that the sulfate-reducing community was diverse, except for the sulfidogenic brine of the Urania basin. The similarity of the dsrA sequences between different environments was very low demonstrating that each environment had a unique sulfate-reducing community. Sequences had 67.6-93.3% similarity to dsrA sequences from GenBank database and were mostly related to the delta-proteobacteria. Each environment was dominated by a different family within the delta-proteobacteria except for the Urania interface, which was dominated by sequences related to the Gram-positive Peptococcaceae. We conclude that sulfate-reducing communities inhabiting the L'Atalante and Urania basins are highly diverse with low similarities to each other and contain a sulfate-reducing species composition that is very different from sulfate-reducing species compositions in previously studied ecosystems.

In mass spectrometry imaging (MSI), on-tissue proteolytic digestion is performed to access larger protein species and to assign protein identities through matching the detected peaks with those obtained by LC-MS/MS analyses of tissue extracts. The on-tissue proteolytic digestion also allows the analysis of proteins from formalin-fixed, paraffin-embedded tissues. For these reasons, on-tissue digestion-based MSI is frequently used in clinical investigations, for example, to determine changes in protein content and distribution associated with a disease. In this work, we sought to investigate the completeness and uniformity of the digestion in on-tissue digestion MSI. On the basis of an extensive experiment investigating three groups with varying incubation times: (i) 1.5 h, (ii) 3 h, and (iii) 18 h, we have found that longer incubation times improve the repeatability of the analyses. Furthermore, we discovered morphology-associated differences in the completeness of the proteolysis for short incubation times. These results support the notion that a more complete proteolysis allows better quantitation.

Mass spectrometry imaging (MSI) is widely used for clinical research because when combined with histopathological analysis the molecular signatures of specific cells/regions can be extracted from the often-complex histologies of pathological tissues. The ability of MSI to stratify patients according to disease, prognosis, and response is directly attributable to this cellular specificity. MSI developments are increasingly focused on further improving specificity, through higher spatial resolution to better localize the signals or higher mass resolution to better resolve molecular ions. Higher spatial/mass resolution leads to increased data size and longer data acquisition times. For clinical applications, which analyze large series of patient tissues, this poses a challenge to keep data load and acquisition time manageable. Here we report a new tool to perform histology guided MSI; instead of analyzing large parts of each tissue section the histology from adjacent tissue sections is used to focus the analysis on the areas of interest, e.g., comparable cell types in different patient tissues, thereby minimizing data acquisition time and data load. The histology tissue section is annotated and then automatically registered to the MSI-prepared tissue section; the registration transformation is then applied to the annotations, enabling them to be used to define the MSI measurement regions. Using a series of formalin-fixed, paraffin-embedded human myxoid liposarcoma tissues, we demonstrate an 80% reduction of data load and acquisition time, thereby enabling high resolution (mass or spatial) to be more readily applied to clinical research. The software is freely available for download.

Using a model of Frenkel excitons coupled to a bath of acoustic phonons in the host medium, we study the temperature dependence of the dephasing rates and homogeneous line width in linear molecular aggregates. The model includes localization by disorder and predicts a power-law thermal scaling of the effective homogeneous line width. The theory gives excellent agreement with temperature dependent absorption and hole-burning experiments on aggregates of the dye pseudoisocyanine., 11 pages, 3 PostScript figures

We study the incoherent transport of optical excitations created at the rim of a dendritic molecule to a trap occurring at the core. The corresponding discrete random walk is treated in a continuum approximation, resulting in a diffusion-like process which admits semi-analytical solutions. The thus obtained arrival time distribution for the excitation at the trap is compared with the one for the original, discrete problem. In the case of an inward bias or even a weak outward one, the agreement is very good and the continuum approximation provides a good alternative description of the energy transfer process, even for small dendrimers. In the case of a strong outward bias, the mean trapping time, which sets the time scale for the entire distribution, depends exponentially on the number of generations in both approaches, but with a different base. The failure of the continuum approximation for this case is explained from the peaked behavior of the excitation density near the rim. (c) 2004 Elsevier B.V. All rights reserved.

Recent field observations have identified the widespread occurrence of fluid seepage through the eastern Mediterranean Sea floor in association with mud volcanism or along deep faults. Gas hydrates and methane seeps are frequently found in cold seep areas and were anticipated targets of the MEDINAUT/MEDINETH initiatives. The study presented herein has utilized a multi-disciplinary approach incorporating observations and sampling of visually selected sites by the manned submersible Nautile and by ship-based sediment coring and geophysical surveys. The study focuses on the biogeochemical and ecological processes and conditions related to methane seepage, especially the anaerobic oxidation of methane (AOM), associated with ascending fluids on Kazan mud volcano in the eastern Mediterranean. Sampling of adjacent box cores for studies on the microbiology, biomarkers, pore water and solid phase geochemistry allowed us to integrate different biogeochemical data within a spatially highly heterogeneous system. Geophysical results clearly indicate the spatial heterogeneity of mud volcano environments. Results from pore water geochemistry and modeling efforts indicate that the rate of AOM is similar to 6 mol m(-2) year(-1), which is lower than at active seep sites associated with conditions of focused flow, but greater than diffusion-dominated sites. Furthermore, under the non-focused flow conditions at Kazan mud volcano advective flow velocities are of the order of a few centimeters per year and gas hydrate formation is predicted to occur at a sediment depth of about 2 m and below. The methane flux through these sediments supports a large and diverse community of micro- and macrobiota, as demonstrated by carbon isotopic measurements on bulk organic matter, authigenic carbonates, specific biomarker compounds, and macrofaunal tissues. Because the AOM community appears to be able to completely oxidize methane at the rate it is seeping through the sediments, ultimate sinks for methane in this environment are authigenic carbonates and biomass. Significant differences in organic geochemical data between this site and those of other cold seep environments, even within the eastern Mediterranean mud volcanoes, indicate that the microbiological communities carrying out AOM varies depending on specific conditions such as methane flux and salinity. (C) 2004 Elsevier B.V. All rights reserved.

On-tissue enzymatic digestion is performed in mass spectrometry imaging (MSI) experiments to access larger proteins and to assign protein identities. Most on-tissue digestion MSI studies have focused on method development rather than identifying the molecular features observed. Herein, we report a comprehensive study of the mouse brain proteome sampled by MSI. Using complementary proteases, we were able to identify 5337 peptides in the matrix-assisted laser desorption/ionization (MALDI) matrix, corresponding to 1198 proteins. 630 of these peptides, corresponding to 280 proteins, could be assigned to peaks in MSI data sets. Gene ontology and pathway analyses revealed that many of the proteins are involved in neurodegenerative disorders, such as Alzheimer's, Parkinson's, and Huntington's disease.

To understand the role played by microorganisms in the formation of cold seep carbonates, we conducted an integrated microbial, mineralogical and organic geochemical study of methane-related authigenic carbonate crusts formed on eastern Mediterranean mud volcanoes. We show that supersaturation with respect to carbonate minerals is induced by microbial anaerobic oxidation of methane. Combined lipid biomarker analysis and 16S rRNA gene surveys identified a highly diversified methane-consuming archaeal community possibly comprising novel species, implying that the anaerobic oxidation of methane is phylogenetically widespread and directly implicating these organisms in the process of crust precipitation. Moreover, pore-water sulphate gradients produced by co-occurring methane-based sulphate reduction exert the main control on aragonite versus magnesian calcite precipitation. We propose that this may be the dominant mode of carbonate crust formation at cold seeps world-wide, in agreement with aquatic chemistry predictions and explaining carbonate mineralogy. (C) 2002 Elsevier Science B.V. All rights reserved.

The relationship between the calcium concentration and the isometric tension obtained with different techniques of skinning provides information on the biochemical events of contraction in vascular smooth muscle. Muscle preparations of the rabbit femoral artery were skinned with triton X-100, saponin, β-escin and α-toxin and the relationship between the calcium concentration and isometric tension was determined at different preparation lengths. We determined the calcium sensitivity as a function of muscle length with different techniques of skinning. At a pCa of 6.0, triton X-100 skinned smooth muscle of the femoral artery generated 50% of the maximal tension. In α-toxin skinned preparations, this calcium sensitivity was shifted to a pCa of 5.6. The sensitivity of the saponin and β-escin skinned preparations were in between those of the triton X-100 and the α-toxin skinned preparations. The cooperativity of the regulation of contraction varied among the differently skinned preparations between 3 (α-toxin) and 6 (triton X-100). The relationships between the calcium concentration and the isometric tension of the differently skinned preparations up to the optimal length for tension generation did not exhibit any length dependency. The length tension relationship, obtained from the maximal response at the highest calcium concentration is in line with that from other studies. The presence of intracellular proteins and membranes affects the regulation of contraction in smooth muscle of the femoral artery.

Microbiological and environmental variables involved in the removal of free sulfide were studied along an eutrophication transect in the Bassin d'Arcachon (France). At four sites, analyses were carried out on reduced sulfur compounds, iron species and total numbers of viable sulfur bacteria (sulfide-producing bacteria, colorless sulfur bacteria and purple sulfur bacteria). In addition, the chemical buffering capacity towards free sulfide and the potential microbiological sulfide oxidation rates were determined. In the ecosystem, no free sulfide occurs in the top layers of the sediment at all four sites, despite a high nutrient load and hence favourable conditions for sulfide-producing bacteria. The explanation of this apparent discrepancy was shown to be the high biological sulfide oxidizing capacity in combination with a high chemical buffering capacity. The data presented illustrate that the buffering capacity of sediments towards free sulfide is the combined result of the chemical and biological processes. The ratio between these were found to depend on the degree of eutrophication. It was shown that the chemical buffering capacity towards sulfide is severely overestimated when based on the pool of chemically reactive iron, a more realistic value is obtained by estimating the total amount of sulfide that can be added before free sulfide can be detected. A clear difference was observed between the numbers of colorless sulfur bacteria and the activity of the entire population. For a proper quantification of the sulfide buffering capacity of sediments, it is essential to estimate the concentration of iron and sulfur compounds that actually can react with sulfide, as well as to analyze the activities of sulfide-oxidizing microbes.

Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eastern Mediterranean were characterized by sequencing 16S ribosomal RNA (rRNA) genes amplified from DNA directly retrieved from the samples. In combination with the mineralogical composition of the crusts and lipid analyses, sequence data were used to assess the possible role of prokaryotes in crust formation. Collectively, the obtained data showed the presence of highly diverse communities, which were distinct in each of the carbonate crusts studied. Bacterial 16S rRNA gene sequences were found in all crusts and the majority was classified as alpha-, gamma-, and delta- Proteobacteria. Interestingly, sequences of Proteobacteria related to Halomonas and Halovibrio sp., which can play an active role in carbonate mineral formation, were present in all crusts. Archaeal 16S rRNA gene sequences were retrieved from two of the crusts studied. Several of those were closely related to archaeal sequences of organisms that have previously been linked to the anaerobic oxidation of methane (AOM). However, the majority of archaeal sequences were not related to sequences of organisms known to be involved in AOM. In combination with the strongly negative delta C-13 values of archaeal lipids, these results open the possibility that organisms with a role in AOM may be more diverse within the Archaea than previously suggested. Different communities found in the crusts could carry out similar processes that might play a role in carbonate crust formation.

Energy transfer in a newly synthesized coumarin-tetraphenylporphyrin donor-acceptor system was studied by time- and frequency-resolved fluorescence spectroscopy. The energy transfer kinetics was shown to be fast (transfer time ca. 500 fs) and efficient (quantum yield ca. 97%). The influence of interactions between excitations on the energy transfer dynamics was studied by intensity-dependent experiments. Although annihilation of excitations occurs for high irradiation doses, this does not affect the observed fluorescence transients. A kinetic model was constructed to explain these findings. Both the difference between the rate constants of energy transfer to singly and doubly excited acceptor states and the rate of radiationless decay from such doubly excited states were shown to be key parameters in the explanation of the intensity-dependent effects.

Adoptive immunotherapy with donor T lymphocytes may be used as a treatment for relapsed leukemia after allogeneic hematopoietic stem cell transplantation (SCT). In vitro selected and expanded anti-leukemic T cells may be more effective in inducing a response in vivo. To identify the anti-leukemic reactivity of in vitro generated T cells, standard target cell read-out assays like the 51Cr-release assay are not always appropriate. We developed an assay in which the ability of T cells to antigen specifically inhibit the in vitro growth of leukemic progenitor cells in the presence of cytokines can be measured. This assay allows the evaluation of the cytolytic or suppressive potential of leukemia reactive T cells for prolonged periods of time. The assay is based on inhibition of [3H]thymidine incorporation by the leukemic progenitor cells induced by multiple hematopoietic growth factors. T cell clones with a known specificity were used to compare the analytic potential of the new assay with those of other cytotoxicity assays. Based on the results of the T cell clones, a modification of a limiting dilution assay was developed to identify anti-leukemic allogeneic T cells in HLA identical donor–recipient combinations selected on their ability to inhibit the in vitro growth of CML or AML progenitor cells, to be used for the generation of leukemia-reactive CTL lines for clinical use.

"Buffer capacities" has been defined in ecology as a holistic concept (e.g., Integration of Ecosystem Theories: A Pattern, second ed. Kluwer, Dordrecht, 1997, 388pp), but we show that it can also be worked out in mechanistic studies. Our mechanistic approach highlights that "buffering capacities" can be depleted progressively, and, therefore, we make a distinction between current and potential "buffering capacities". We have applied this concept to understand the limited "local stability" in seagrass ecosystems and their vulnerability towards structural changes into macro-algal dominated communities. We explored the following processes and studied how they confer buffering capacities to the seagrass ecosystem: (i) net autotrophy is persistent in Zostera noltli meadows where plant assimilation acts as a sink for nutrients, this contrasted with the Ulva system that shifted back and forth between net autotrophy and net heterotrophy; (ii) the Z. noltii ecosystem possesses a certain albeit rather limited capacity to modify the balance between nitrogen fixation and denitrification, i.e., it was found that in situ nitrogen fixation always exceeded denitrification; (iii) the nitrogen demand of organoheterotrophic bacteria in the sediment results in nitrogen retention of N in the sediment and hence a buffer against release of nitrogen compounds from sediments, (iv) habitat diversification in seagrass meadows provides shelter for meiofauna and hence buffering against adverse conditions, (v) sedimentary iron provides a buffer against noxious sulfide (note: bacterial sulfide production is enhanced in anoxic sediment niches by increased organic matter loading). On the other hand, in the coastal system we studied, sedimentary iron appears less important as a redox-coupled buffer system against phosphate loading. This is because most inorganic phosphate is bound to calcium rather than to iron. In addition, our studies have highlighted the importance of plant-microbe interactions in the seagrass meadows. [KEYWORDS: coastal lagoon; seagrass; macro-algae; sulfide; iron phosphate; community metabolism; rhizosphere; nitrogen fixation; 16-S RNA clone library introduction Sulfate-reduction rates; zostera-marina; nitrogen-fixation; bassin darcachon; rhizosphere; sediments; sulfide; noltii; carbon; france]

The production and consumption of sulfide and its influence on phosphorous cycling were studied in a hypertrophic coastal lagoon (Valle Smarlacca, Italy). Oxygen measurements revealed that the water phase was supersaturated except for the layer directly overlying the sediment. This layer was devoid of oxygen and contained sulfide at all times. Maximal rates of sulfide production, calculated from in situ profiles, were observed in the 0 to 2 cm sediment layer and the 1 cm water layer directly above. Sediment iron data suggested a moderate chemical buffering capacity towards free sulfide; however, the in situ buffering capacity was fully exploited. Stirring increased the chemical buffer, indicating that, in situ, part of the iron did not contribute to the chemical buffer. The potential rate of biological sulfide oxidation, estimated in sediment slurries amended with oxygen, was high; however, the actual rate was low due to a shortage of oxygen in the sediments and the overlying water. Evidence was obtained for enhanced release of phosphate caused by free sulfide. Under simulated natural conditions the release of phosphate exceeded the initial concentration of Fe-bound phosphate by an order of magnitude, indicating a significant contribution of non-iron- bound phosphate. The observations in Valle Smarlacca were used to shed Light on the virtually complete disappearance of Ruppia sp, from other lagoons of the Valli di Comacchio (Northern Italy). [KEYWORDS: eutrophication; phosphate mobilization; sulfide production; Ruppia; coastal lagoons Marine-sediments; bassin-darcachon; organic-matter; phosphorus; iron; ecosystems; fractionation; reduction; exchange; ferrara]

The Bassin d'Arcachon (south-west France) was chosen as a model ecosystem to study the chemical and microbiological buffering towards free sulphide. Data were collected on the vertical distribution of oxygen, sulphur and iron compounds and the vertical distribution of colourless sulphur bacteria and sulphide-producing bacteria. In addition, data on the chemical and biological buffering capacity towards free sulphide were collected in sediment slurries from defined depth layers using a biological sulphide and oxygen monitor (BOSM) equipped with electrodes for oxygen, sulphide, redox and pH. The data showed that a substantial population of aerobic sulphide-oxidizing bacteria was present, yet buffering towards free sulphide could mainly be attributed to chemical processes: in particular, reactions with iron were of importance. Interestingly, the potential microbiological rate of sulphide oxidation was orders of magnitude higher than the rate of sulphate reduction reported for this ecosystem. The ecological implications of these observations for the Bassin d'Arcachon are that the powerful biological buffering capacity towards the free sulphide present will become effective after the chemical buffering capacity has been depleted. Under such conditions the colourless sulphur bacteria will no longer face the competition with iron, and thus may be expected to proliferate. The crucial factor then becomes the availability of oxygen. [KEYWORDS: sulphide; iron; sulphur/sulphide oxidizing bacteria sulphate-reducing bacteria; buffering capacity; coastal lagoon; sediment; France coast Sulfate-reducing bacteria; marine microbial mat; sulfide oxidation; sulfur bacteria; oxygen limitation; salt-marsh; iron; pyrite; reduction; seawater]

This paper describes a new laboratory facility to study transport of radon through soil into a crawl space under controlled conditions. The facility consists of a 2 m high vessel with a diameter of 2 m to be filled with soil. The vessel is equipped with a movable lid, the space between the soil and the lid simulating a crawl space. At several heights multi-functional probes can be inserted radially into the vessel to measure near the axis of the vessel the values of pore water content, air permeability and the radon concentration in the soil gas. Results of some preparatory measurements concerning the choice of the soil to be used in the vessel are presented.