Assessment of soil organic matter supply: Challenges and opportunities

Soil organic matter (SOM) is recognized as an important factor for sustainable land use. Several analyzing techniques were focused on fractionation of soil organic carbon (SOC), on carbon sequestration, soil functions, or other approaches. We combined SOC fractionation with studies on carbon sequestration. Thermogravimetry (TG, recording of mass losses during heating up of soil samples) was selected as a supplemental method to standard analyzing techniques for soils. TG provides recording of thermal mass losses in dependency on temperature what facilitate fractionation together with SOM content determination via mass losses on ignition (MLI). Autocorrelation analyses of TG data enable to assess the carbon sequestration processes. After a gentle sample preparation, more than 370 soil samples in eight sample sets were analyzed from different types of soils and regions of origin. The results extend literature data by revealing quantifiable interrelations between content of SOM, SOC and clay with a coefficient of determination around 0.98. Deviations from the relationship become lower during incubation experiments, with increasing sampling depth, and with decreasing organic fertilization in plots of long term agriculture field experiments etc. We explained these results with changing quantities of extraneous (mostly fresh) organic residues not affected by soil carbon content regulation. These organic residues seems to be quantifiable via difference between measured MLI and the MLI calculated from content of SOC and clay both determined by standard methods. The practical use of found interrelation implies an acceptance of traditional definition of soil and SOM as products of long term ecosystem succession with content regulation as a unifying over regions soil feature. In contrast, the more common and simplified understanding of soil as carbon containing mineral substrates supports public recognition of soils. However, it does not facilitate the comparison of results from different regions and studies about soils. We conclude from these considerations about obligatory distinction between following types of organic carbon as an essential precondition for assessment of SOM supply: 1. SOC (or humus) as a product of long term carbon regulation processes, 2. fresh organic residues, and carbon of 3. geologic (turf, coal, graphite, diamond, …) or 4. anthropogenic origin (black carbon in ashes, cinder, soot, asphalt)

Quaternary exhumation of the Carpathians: a record from the Orava-Nowy Targ intramontane basin, Western Carpathians, Polish Galicia and Slovakia

Quaternary exhumation of the Carpathians: a record from the Orava-Nowy Targ Intramontane Basin, Western Carpathians (Poland and Slovakia)The Neogene-Quaternary infill of the Orava-Nowy Targ Intramontane Basin comprises two tiers showing contrasting lithologies. The Neogene tier is largely composed of claystones and siltstones, whereas the Quaternary tier is dominated by gravels. The two sequences are separated by an erosional surface underlain by a regolith. Deposition of the Neogene sequence took place during subsidence of the basin. No prominent relief existed in the area of the present-day mountains actually surrounding the basin at that time. The regolith started to form at the onset of basin inversion. Still, no prominent relief existed in the present-day mountains. The onset of deposition of Quaternary gravels in the basin corresponds to acceleration of uplift of the surrounding mountains, which has been continuing until now. The Pieniny Klippen Belt has been subject to erosion, at least locally, from the deposition of the basal part of the Neogene sequence filling the Orava-Nowy Targ Basin until present times. In contrast, the Paleogene cover of the Tatra Mts was removed only during the Quaternary.</jats:p

Organic carbon content determination in soils: challenges and opportunities of elemental analysis versus thermogravimetry

Sustainable soil management needs reliable and accurate monitoring of soil organic carbon (SOC) content. However, despite of the development of analytical techniques during last decades, the detection opportunities for short term and rather small changes in SOC induced by organic fertilization, organic amendments or land use changes are still limited with the available methods. This study aims to quantify the theoretical detection opportunities for changes in SOC content with elemental analysis (EA) as the standard method in comparing with thermogravimetry (TG) as an enhanced traditional approach derived from soil organic matter determination via mass losses on ignition. The carried out experiments consist of mixing soil samples from non-fertilized plots of three long-term agricultural experiments in Bad Lauchstaedt, Großbeeren and Muencheberg (silty loam, loamy sand and silty sand) with straw, farmyard manure, sheep faeces and charcoal in four quantities (3 t×ha-1, 20 t×ha-1, 60 t×ha-1 and 180 t×ha‑1fresh matter) under laboratory conditions.The quantities were based on fresh matter application in agricultural practice accepting different amounts of added organic carbon. The results confirm EA as a method of higher reliability and accuracy for carbon content determination. TG allows to distinguish the different types of added amendments with high sensitivity. This was achieved by using newly developed evaluation algorithms for the thermal decay dynamics. We conclude from these results that TG cannot substitute EA to determine organic carbon on a routine base. However, TG could be a supplementary fingerprinting technique for the detection of added organic carbon to soils from organic fertilizers and to distinguish sources of geological or anthropogenic origin enabling a future assessment of soil organic carbon quality

Cenários para o manejo e a conservação da bacia hidrográfica do Alto Tocantins.

RESUMO - Esse estudo tem como objetivo integrar informações no sentido de auxiliar a gestão participativa da Bacia Hidrográfica do Alto Tocantins que possui uma área de aproximadamente 12.380.000 hectares inserida no Domínio do Cerrado, composta por 87 unidades administrativas (84 municípios em Goiás e Tocantins e 03 regiões administrativas do Distrito Federal). A precipitação média anual é de 1.557 mm. No período entre 1988 a 2002, o uso antrópico da bacia saltou de 18 para 27 %, com 45% representado pelo desmatamento de Cerrado-Floresta Estacional, e 41% pelo Cerrado stricto sensu. A população estimada da bacia é de 1,2 milhão de habitantes, 21% vivendo no meio rural. O Índice de Desenvolvimento Humano médio era de 0,70 (d.p.= ±0,1) em 2000, sendo que o percentual de renda apropriado pelos 10% mais ricos era de 47,3% (d.p.= ±8,5). Entre 1990 e 2005 houve um aumento da área plantada com a cultura da soja e cana-de-açúcar - em média 180%; a produção de amêndoas de pequi por extrativismo decresceu de 42% para 7% da produção nacional, enquanto que a produção de carvão pelo extrativismo aumentou de 6% para 7,3% da produção nacional. A vazão média acumulada de longo período de montante para jusante é da ordem de 1.580 m3 s-1, sendo a maior demanda para irrigação (61%), cuja relação entre demanda total e disponibilidade de água não alcança 5% – condição em que a água é considerada um bem livre. O aumento da produtividade agropecuária e as mudanças no uso do solo não refletiram em aumento na distribuição de renda da população residente na bacia

Novel insights into host-fungal pathogen interactions derived from live-cell imaging

Acknowledgments The authors acknowledge funding from the Wellcome Trust (080088, 086827, 075470 and 099215) including a Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377 and FP7-2007–2013 grant agreement HEALTH-F2-2010-260338–ALLFUN to NARG.Peer reviewedPublisher PD

Inhibiting ex-vivo Th17 responses in Ankylosing Spondylitis by targeting Janus kinases

Treatment options for Ankylosing Spondylitis (AS) are still limited. The T helper cell 17 (Th17) pathway has emerged as a major driver of disease pathogenesis and a good treatment target. Janus kinases (JAK) are key transducers of cytokine signals in Th17 cells and therefore promising targets for the treatment of AS. Here we investigate the therapeutic potential of four different JAK inhibitors on cells derived from AS patients and healthy controls, cultured in-vitro under Th17-promoting conditions. Levels of IL-17A, IL-17F, IL-22, GM-CSF and IFN gamma were assessed by ELISA and inhibitory effects were investigated with Phosphoflow. JAK1/2/3 and TYK2 were silenced in CD4+ T cells with siRNA and effects analyzed by ELISA (IL-17A, IL-17F and IL-22), Western Blot, qPCR and Phosphoflow. In-vitro inhibition of CD4+ T lymphocyte production of multiple Th17 cytokines (IL-17A, IL-17F and IL-22) was achieved with JAK inhibitors of differing specificity, as well as by silencing of JAK1-3 and Tyk2, without impacting on cell viability or proliferation. Our preclinical data suggest JAK inhibitors as promising candidates for therapeutic trials in AS, since they can inhibit multiple Th17 cytokines simultaneously. Improved targeting of TYK2 or other JAK isoforms may confer tailored effects on Th17 responses in AS

Crystal Structures of ABL-Related Gene (ABL2) in Complex with Imatinib, Tozasertib (VX-680), and a Type I Inhibitor of the Triazole Carbothioamide Class†

ABL2 (also known as ARG (ABL related gene)) is closely related to the well-studied Abelson kinase cABL. ABL2 is involved in human neoplastic diseases and is deregulated in solid tumors. Oncogenic gene translocations occur in acute leukemia. So far no structural information for ABL2 has been reported. To elucidate structural determinants for inhibitor interaction, we determined the cocrystal structure of ABL2 with the oncology drug imatinib. Interestingly, imatinib not only interacted with the ATP binding site of the inactive kinase but was also bound to the regulatory myristate binding site. This structure may therefore serve as a tool for the development of allosteric ABL inhibitors. In addition, we determined the structures of ABL2 in complex with VX-680 and with an ATP-mimetic type I inhibitor, which revealed an interesting position of the DFG motif intermediate between active and inactive conformations, that may also serve as a template for future inhibitor design

The state of the art in the analysis of two-dimensional gel electrophoresis images

Software-based image analysis is a crucial step in the biological interpretation of two-dimensional gel electrophoresis experiments. Recent significant advances in image processing methods combined with powerful computing hardware have enabled the routine analysis of large experiments. We cover the process starting with the imaging of 2-D gels, quantitation of spots, creation of expression profiles to statistical expression analysis followed by the presentation of results. Challenges for analysis software as well as good practices are highlighted. We emphasize image warping and related methods that are able to overcome the difficulties that are due to varying migration positions of spots between gels. Spot detection, quantitation, normalization, and the creation of expression profiles are described in detail. The recent development of consensus spot patterns and complete expression profiles enables one to take full advantage of statistical methods for expression analysis that are well established for the analysis of DNA microarray experiments. We close with an overview of visualization and presentation methods (proteome maps) and current challenges in the field

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems