Carbon redistribution by erosion processes in an intensively disturbed catchment

29 Pags.- 6 Tabls.- 6 Figs. This article belongs to a special issue of Catena titled "Geoecology in Mediterranean mountain areas. Tribute to Professor José María García Ruiz". The definitive version is available at: http://www.sciencedirect.com/science/journal/03418162Understanding how organic carbon (OC) moves with sediments along the fluvial system is crucial to determining catchment scale carbon budgets and helps the proper management of fragile ecosystems. Especially challenging is the analysis of OC dynamics during fluvial transport in heterogeneous, fragile, and disturbed environments with ephemeral and intense hydrological pulses, typical of Mediterranean conditions. This paper explores the catchment scale OC redistribution by lateral flows in extreme Mediterranean environmental conditions, from a geomorphological perspective. The study area is a catchment (Cárcavo) in SE Spain with a semiarid climate, erodible lithologies, and shallow soils, which is highly disturbed by agricultural terraces, land levelling, reforestation, and construction of check-dams. To increase our understanding of catchment scale OC redistribution induced by erosion, we studied in detail the subcatchments of eight check-dams distributed along the catchments main channel. We determined 137Cs, physicochemical characteristics, and the OC pools of the catchment soils and sediments deposited behind each check-dam, performed spatial analysis of catchment properties and buffer areas around the check-dams, and carried out geomorphological analysis of the slope-channel connections. The soils showed very low total organic carbon (TOC) values, oscillating between 15.2 and 4.4 g kg− 1 for forest and agricultural soils, respectively. Sediments mobilized by erosion were poor in TOC (6.6 ± 0.7 g kg– 1) compared to the eroded (forest) soils, and the redistribution of OC through the catchment, especially of the mineral associated organic carbon (MAC) pool, showed the same pattern as clay particles and 137Cs. The TOC erosion rates estimated for the Cárcavo watershed are relatively low (0.031 ± 0.03 Mg ha− 1 y− 1) but similar to those reported for subhumid Mediterranean catchments that are less fragile and more conducive to plant growth. The TOC erosion/total erosion ratio was lower (0.06%) than other estimates, although the average OC concentration of the sediments was higher than that of the agricultural soils of the catchment, underlining the problem of maintaining sustainable soil OC contents. The OC in deposited sediments came not only from surface erosion processes, but also from deeper soil or sediment layers mobilized by concentrated erosion processes. Sediment richer in OC came from the surface soil of vegetated (reforested) areas close and well connected to the channels. Subcatchments dominated by laminar erosion processes showed a TOC erosion/total erosion ratio that was two times higher than that of subcatchments dominated by concentrated flow erosion processes. The lithology, soils, and geomorphology exert a more important control on OC redistribution than land use and vegetation cover in this geomorphologically very active catchment.This work was financially supported by the projects ADAPT (CGL2013-42009-R) and DISECO (CGL2014-55-405-R) from the Spanish Government, National Plan of Science; the project CAMBIO (18933/JLI/13) of the Seneca Foundation, Regional Government of Murcia (Spain); and the project SOGLO (P7/24 IAP BELSPO) from the Belgian Government. Joris de Vente was supported by a ‘Ramón y Cajal’ grant (RYC-2012-10375).Peer reviewe

StreptomeDB:a resource for natural compounds isolated from <i>Streptomyces</i> species

Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties

Low-Dosage Inhibition of DII4 Signaling Promotes Wound Healing by Inducing Functional Neo-Angiogenesis

Recent findings regarding Dll4 function in physiological and pathological conditions indicate that this Notch ligand may constitute an important therapeutic target. Dll4 appears to be a major anti-angiogenic agent, occupying a central role in various angiogenic pathways. The first trials of anti-Dll4 therapy in mice demonstrated a paradoxical effect, as it reduced tumor perfusion and growth despite leading to an increase in vascular density. This is seen as the result of insufficient maturation of the newly formed vasculature causing a circulatory defect and increased tumor hypoxia. As Dll4 function is known to be closely dependent on expression levels, we envisioned that the therapeutic anti-Dll4 dosage could be modulated to result in the increase of adequately functional blood vessels. This would be useful in conditions where vascular function is a limiting factor for recovery, like wound healing and tissue hypoxia, especially in diabetic patients. Our experimental results in mice confirmed this possibility, revealing that low dosage inhibition of Dll4/Notch signaling causes improved vascular function and accelerated wound healing

Multiple Signals Converge on a Differentiation MAPK Pathway

An important emerging question in the area of signal transduction is how information from different pathways becomes integrated into a highly coordinated response. In budding yeast, multiple pathways regulate filamentous growth, a complex differentiation response that occurs under specific environmental conditions. To identify new aspects of filamentous growth regulation, we used a novel screening approach (called secretion profiling) that measures release of the extracellular domain of Msb2p, the signaling mucin which functions at the head of the filamentous growth (FG) MAPK pathway. Secretion profiling of complementary genomic collections showed that many of the pathways that regulate filamentous growth (RAS, RIM101, OPI1, and RTG) were also required for FG pathway activation. This regulation sensitized the FG pathway to multiple stimuli and synchronized it to the global signaling network. Several of the regulators were required for MSB2 expression, which identifies the MSB2 promoter as a target “hub” where multiple signals converge. Accessibility to the MSB2 promoter was further regulated by the histone deacetylase (HDAC) Rpd3p(L), which positively regulated FG pathway activity and filamentous growth. Our findings provide the first glimpse of a global regulatory hierarchy among the pathways that control filamentous growth. Systems-level integration of signaling circuitry is likely to coordinate other regulatory networks that control complex behaviors

Integration of Global Signaling Pathways, cAMP-PKA, MAPK and TOR in the Regulation of FLO11

The budding yeast, Saccharomyces cerevisiae, responds to various environmental cues by invoking specific adaptive mechanisms for their survival. Under nitrogen limitation, S. cerevisiae undergoes a dimorphic filamentous transition called pseudohyphae, which helps the cell to forage for nutrients and reach an environment conducive for growth. This transition is governed by a complex network of signaling pathways, namely cAMP-PKA, MAPK and TOR, which controls the transcriptional activation of FLO11, a flocculin gene that encodes a cell wall protein. However, little is known about how these pathways co-ordinate to govern the conversion of nutritional availability into gene expression. Here, we have analyzed an integrative network comprised of cAMP-PKA, MAPK and TOR pathways with respect to the availability of nitrogen source using experimental and steady state modeling approach. Our experiments demonstrate that the steady state expression of FLO11 was bistable over a range of inducing ammonium sulphate concentration based on the preculturing condition. We also show that yeast switched from FLO11 expression to accumulation of trehalose, a STRE response controlled by a transcriptional activator Msn2/4, with decrease in the inducing concentration to complete starvation. Steady state analysis of the integrative network revealed the relationship between the environment, signaling cascades and the expression of FLO11. We demonstrate that the double negative feedback loop in TOR pathway can elicit a bistable response, to differentiate between vegetative growth, filamentous growth and STRE response. Negative feedback on TOR pathway function to restrict the expression of FLO11 under nitrogen starved condition and also with re-addition of nitrogen to starved cells. In general, we show that these global signaling pathways respond with specific sensitivity to regulate the expression of FLO11 under nitrogen limitation. The holistic steady state modeling approach of the integrative network revealed how the global signaling pathways could differentiate between multiple phenotypes

HP1 Recruits Activity-Dependent Neuroprotective Protein to H3K9me3 Marked Pericentromeric Heterochromatin for Silencing of Major Satellite Repeats

H3 lysine 9 trimethylation (H3K9me3) is a histone posttranslational modification (PTM) that has emerged as hallmark of pericentromeric heterochromatin. This constitutive chromatin domain is composed of repetitive DNA elements, whose transcription is differentially regulated. Mammalian cells contain three HP1 proteins, HP1α, HP1β and HP1γ These have been shown to bind to H3K9me3 and are thought to mediate the effects of this histone PTM. However, the mechanisms of HP1 chromatin regulation and the exact functional role at pericentromeric heterochromatin are still unclear. Here, we identify activity-dependent neuroprotective protein (ADNP) as an H3K9me3 associated factor. We show that ADNP does not bind H3K9me3 directly, but that interaction is mediated by all three HP1 isoforms in vitro. However, in cells ADNP localization to areas of pericentromeric heterochromatin is only dependent on HP1α and HP1β. Besides a PGVLL sequence patch we uncovered an ARKS motif within the ADNP homeodomain involved in HP1 dependent H3K9me3 association and localization to pericentromeric heterochromatin. While knockdown of ADNP had no effect on HP1 distribution and heterochromatic histone and DNA modifications, we found ADNP silencing major satellite repeats. Our results identify a novel factor in the translation of H3K9me3 at pericentromeric heterochromatin that regulates transcription