Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach

The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations

Revised Lithostratigraphy of the Sonsela Member (Chinle Formation, Upper Triassic) in the Southern Part of Petrified Forest National Park, Arizona

BACKGROUND: Recent revisions to the Sonsela Member of the Chinle Formation in Petrified Forest National Park have presented a three-part lithostratigraphic model based on unconventional correlations of sandstone beds. As a vertebrate faunal transition is recorded within this stratigraphic interval, these correlations, and the purported existence of a depositional hiatus (the Tr-4 unconformity) at about the same level, must be carefully re-examined. METHODOLOGY/PRINCIPAL FINDINGS: Our investigations demonstrate the neglected necessity of walking out contacts and mapping when constructing lithostratigraphic models, and providing UTM coordinates and labeled photographs for all measured sections. We correct correlation errors within the Sonsela Member, demonstrate that there are multiple Flattops One sandstones, all of which are higher than the traditional Sonsela sandstone bed, that the Sonsela sandstone bed and Rainbow Forest Bed are equivalent, that the Rainbow Forest Bed is higher than the sandstones at the base of Blue Mesa and Agate Mesa, that strata formerly assigned to the Jim Camp Wash beds occur at two stratigraphic levels, and that there are multiple persistent silcrete horizons within the Sonsela Member. CONCLUSIONS/SIGNIFICANCE: We present a revised five-part model for the Sonsela Member. The units from lowest to highest are: the Camp Butte beds, Lot's Wife beds, Jasper Forest bed (the Sonsela sandstone)/Rainbow Forest Bed, Jim Camp Wash beds, and Martha's Butte beds (including the Flattops One sandstones). Although there are numerous degradational/aggradational cycles within the Chinle Formation, a single unconformable horizon within or at the base of the Sonsela Member that can be traced across the entire western United States (the "Tr-4 unconformity") probably does not exist. The shift from relatively humid and poorly-drained to arid and well-drained climatic conditions began during deposition of the Sonsela Member (low in the Jim Camp Wash beds), well after the Carnian-Norian transition

Impact of grassland burning on soil organic matter as revealed by a synchrotron- and pyrolysis-mass spectrometry-based multi-methodological approach.

Although the continuum of pyrolysed OM is an important part of soil OM (SOM) and therefore involved in global cycles, its formation and structural composition are not sufficiently known. Gaps in knowledge originate from methodological difficulties in detecting compounds formed via heating during vegetation burning. We therefore investigated soil samples (0-4 cm depth) from 33 yr treatments of periodic vegetation burning, mulching and natural succession at two grassland sites in Germany. Samples were investigated by way of X-ray absorption near edge structure (XANES) spectroscopy at the carbon (C) and nitrogen (N) K-edges, pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS), Py-single photon ionisation-MS (Py-SPI-MS) and Py-field ionisation MS (Py-FIMS). The XANES spectra differentiated the sites and indicated a relative enrichment in unsaturated C for the burned treatment at one site and substituted aromatic C and non-peptide N (nitriles and/or N in aromatic systems) at both sites. All three Py-MS methods distinguished the sampling sites via variation in content of polysaccharides, N-containing compounds and lignin derived substances. Vegetation burning depleted low molecular weight compounds (Py-SPI-MS and Py-FIMS) and formed high molecular substances (Py-SPI-MS and Py-FIMS) and some N-heterocyclic aromatic products (Py-GC-MS), which were only found in the burned samples. Furthermore, Py-FIMS revealed reaction products from m/z 614 to m/z 619 for both burned treatments. In general, all methods indicated the formation of N-heterocyclics and/or more recalcitrant SOM at almost equal total organic C and N content from periodic vegetation burning