Potentials and pitfalls of clinical peptidomics and metabolomics

Clinical peptidomics and metabolomics are two emerging "-omics" technologies with the potential not only to detect disease-specific markers, but also to give insight into the disease dependency of degradation processes and metabolic pathway alterations. However, despite their rapid evolution and major investments, a clinical breakthrough, such as the approval of a major cancer biomarker, is still out of sight. What are the reasons for this failure? In this review we focus on three important factors: sensitivity, specificity and the avoidance of bias. The way to clinical implementation of peptidomics and metabolomics is still hampered by many of the problems that had to be solved for genomics and proteomics in the past, as well as new ones that require the creation of new analytic, computational and interpretative techniques. The greatest challenge, however, will be the integration of information from different "-omics" subdisciplines into straightforward answers to clinical questions, for example, in the form of new, superior "meta-markers".

A systematized workflow for assessing land resources using readily available spatial datasets

Land degradation as well as land conservation maps at a (sub-) national scale are critical for pro-ject planning for sustainable land management. It has long been recognized that online accessible and low-cost raster data sets (e.g. Landsat imagery, SRTM-DEM’s) provide a readily available basis for land resource assessments for developing countries. However, choice of spatial, tempo-ral and spectral resolution of such data is often limited. Furthermore, while local expert knowl-edge on land degradation processes is abundant, difficulties are often encountered when linking existing knowledge with modern approaches including GIS and RS. The aim of this study was to develop an easily applicable, standardized workflow for preliminary spatial assessments of land degradation and conservation, which also allows the integration of existing expert knowledge. The core of the developed method consists of a workflow for rule-based land resource assess-ment. In a systematic way, this workflow leads from predefined land degradation and conserva-tion classes to field indicators, to suitable spatial proxy data, and finally to a set of rules for clas-sification of spatial datasets. Pre-conditions are used to narrow the area of interest. Decision tree models are used for integrating the different rules. It can be concluded that the workflow presented assists experts from different disciplines in col-laboration GIS/RS specialists in establishing a preliminary model for assessing land degradation and conservation in a spatially explicit manner. The workflow provides support when linking field indicators and spatial datasets, and when determining field indicators for groundtruthing.

Composition of bottom sediments and their exchange with seawater in the Amur and Zolotoy Rog bays, Sea of Japan

Transition of Zn, Cu, Cd, and Pb into solution is studied for experimental suspensions of coastal marine sediments with different degrees of pollution from the Amur Bay (Sea of Japan) over 30-70 days. Concentrations of dissolved metals were measured by a voltammetry method. Transition of Zn and Cd into solution was shown to be linearly dependent on initial pollution of sediments with these metals. Cadmium mobilization is due to gradual degradation of organic matter from sediments. Under degradation processes Zn quickly goes into solution during sedimentation and from silts, while in case of polluted sediments it is slowly mobilized during oxidation of sulfides. Behavior of Cu is complex because of binding of mobilized metal by dissolved organic compounds. Transition of lead into solution is negligible. Calculation of potential transition of metals from sediments into water on the basis of experimental data and its comparison with downward sedimentary flux showed that in the studied area secondary pollution of water by aerobic degradation of sediments is possible only for Cd.

Geochemistry and stable carbon isotope composition of kerogen of DSDP Site 124-767

Celebes Basin sediments from Ocean Drilling Program Site 767 (Leg 124) containing both marine and terrestrial organic matter have been investigated through palynofacies and geochemical analyses. The main degradation processes affecting or having affected organic matter are recorded in the sedimentary column as shown by ammonium, phosphate and sulfate pore-water profiles, and by petrographic and geochemical analyses of sediments. In the upper part of the sedimentary section (down to 200 mbsf), the decrease of the ratio of total organic carbon to sulfur (TOC/S) with depth, generally related to the sulfate reduction process, is accompanied by an increase of framboidal pyrite content in the marine organic matter, and by an increasing amount of amorphous marine organic matter relative to the total organic matter. However, as the terrestrial organic input also varies with depth, dilution effects are superimposed on diagenesis. This continental supply affects the TOC/S ratio by increasing total organic carbon and decreasing the ability of the bulk organic matter to be metabolized through sulfate reduction. A positive relationship between the TOC/P ratio and the amount of degraded organic matter of marine origin clearly displays the effect of an organic source on the composition of the sediment. Each lithostratigraphic unit possesses its own characteristics in terms of composition and preservation of organic matter. The effects of diagenesis can only be appreciated within a single lithostratigraphic unit and mainly affect the less-resistant marine organic matter.

Molecular dissolved organic matter composition in lakes across Sweden as relative intensities of FT-ICR-MS peaks and PARAFAC components and optical indices

Whether intrinsic molecular properties or extrinsic factors such as environmental conditions control the decomposition of natural organic matter across soil, marine and freshwater systems has been subject to debate. Comprehensive evaluations of the controls that molecular structure exerts on organic matter's persistence in the environment have been precluded by organic matter's extreme complexity. Here we examine dissolved organic matter from 109 Swedish lakes using ultrahigh-resolution mass spectrometry and optical spectroscopy to investigate the constraints on its persistence in the environment. We find that degradation processes preferentially remove oxidized, aromatic compounds, whereas reduced, aliphatic and N-containing compounds are either resistant to degradation or tightly cycled and thus persist in aquatic systems. The patterns we observe for individual molecules are consistent with our measurements of emergent bulk characteristics of organic matter at wide geographic and temporal scales, as reflected by optical properties. We conclude that intrinsic molecular properties are an important control of overall organic matter reactivity.

Organic geochemistry of Upper Albian sediments from the Kirchrode I borehole

In the framework of a multidisciplinary research program, an organic geochemical study was carried out on a drill core which comprises a 245 m thick sequence of light-colored, Upper Albian marlstones that were deposited in the central part of the Lower Saxony basin (northern Germany). For part of the Upper Albian sequence, high-resolution measurements of carbonate contents reveal cycles which can be related to earth orbital forcing. Based on these data, sediment accumulation rates were calculated to be in the order of 15 g/m**2/yr. These high accumulation rates contrast with very low organic carbon contents and an extremely poor preservation of the autochthonous organic matter. Most of the sedimentary organic matter is of terrigenous origin and mainly derived from the erosion of older sedimentary rocks. Organic petrography reveals only a very small fraction of marine organic particles. Carbon/sulphur ratios, pristane/phytane ratios as well as the predominance of resedimented organic particles over autochthonous organic particles suggest that aerobic degradation processes rather than anaerobic processes (sulphate reduction) were responsible for the degradation of the organic matter. Furthermore, the scarcity of terrigenous organic particles (vitrinite) indicates that there was little vegetation on nearby land areas. To explain these analytical results, a depositional model was developed which could explain the scarcity of organic matter in the Upper Albian sediments. This model is based on downwelling of oxygen-rich, saline waters of Tethyan origin, which reduces the nutrient content of surface waters and thus primary bioproductivity while degradation of primary organic matter in the water column is enhanced at the same time. These conditions contrast to those which existed in Barremian and early Aptian times in this basin, when limited water exchange with adjacent oceans caused oxygen deficiency and the deposition of numerous organic carbon-rich black shales. The thick, organic matter-poor Upper Albian sequence of northern Germany also contrasts with comparatively thin, time-equivalent, deep-sea black shales from Italy. This discrepancy indicates that local and regional oceanographic factors (at least in this case) have a greater influence on organic matter deposition than global events.