Some considerations on aggregate sample supports for soil inventory and monitoring

Soil monitoring and inventory require a sampling strategy. One component of this strategy is the support of the basic soil observation: the size and shape of the volume of material that is collected and then analysed to return a single soil datum. Many, but not all, soil sampling schemes use aggregate supports in which material from a set of more than one soil cores, arranged in a given configuration, is aggregated and thoroughly mixed prior to analysis. In this paper, it is shown how the spatial statistics of soil information, collected on an aggregate support, can be computed from the covariance function of the soil variable on a core support (treated as point support). This is done via what is called here the discrete regularization of the core-support function. It is shown how discrete regularization can be used to compute the variance of soil sample means and to quantify the consistency of estimates made by sampling then re-sampling a monitoring network, given uncertainty in the precision with which sample sites are relocated. These methods are illustrated using data on soil organic carbon content from a transect in central England. Two aggregate supports, both based on a 20 m 20 m square, are compared with core support. It is shown that both the precision and the consistency of data collected on an aggregate support are better than data on a core support. This has implications for the design of sampling schemes for soil inventory and monitoring

PFKFB4 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4)

Review on PFKFB4 (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4), with data on DNA, on the protein encoded, and where the gene is implicated

Targeting atypical protein kinase C iota reduces viability in glioblastoma stem-like cells via a notch signaling mechanism

In a previous study, Protein Kinase C iota (PRKCI) emerged as an important candidate gene for glioblastoma (GBM) stem-like cell (GSC) survival. Here, we show that PKCι is overexpressed and activated in patient derived GSCs compared with normal neural stem cells and normal brain lysate, and that silencing of PRKCI in GSCs causes apoptosis, along with loss of clonogenicity and reduced proliferation. Notably, PRKCI silencing reduces tumor growth in vivo in a xenograft mouse model. PKCι has been intensively studied as a therapeutic target in non-small cell lung cancer, resulting in the identification of an inhibitor, aurothiomalate (ATM), which disrupts the PKCι/ERK signaling axis. However, we show that, although sensitive to pharmacological inhibition via a pseudosubstrate peptide inhibitor, GSCs are much less sensitive to ATM, suggesting that PKCι acts along a different signaling axis in GSCs. Gene expression profiling of PRKCI-silenced GSCs revealed a novel role of the Notch signaling pathway in PKCι mediated GSC survival. A proximity ligation assay showed that Notch1 and PKCι are in close proximity in GSCs. Targeting PKCι in the context of Notch signaling could be an effective way of attacking the GSC population in GBM

LGR5 regulates pro-survival MEK/ERK and proliferative Wnt/β-catenin signalling in neuroblastoma

LGR5 is a marker of normal and cancer stem cells in various tissues where it functions as a receptor for R-spondins and increases canonical Wnt signalling amplitude. Here we report that LGR5 is also highly expressed in a subset of high grade neuroblastomas. Neuroblastoma is a clinically heterogenous paediatric cancer comprising a high proportion of poor prognosis cases (~40%) which are frequently lethal. Unlike many cancers, Wnt pathway mutations are not apparent in neuroblastoma, although previous microarray analyses have implicated deregulated Wnt signalling in high-risk neuroblastoma. We demonstrate that LGR5 facilitates high Wnt signalling in neuroblastoma cell lines treated with Wnt3a and R-spondins, with SK-N-BE(2)-C, SK-N-NAS and SH-SY5Y cell-lines all displaying strong Wnt induction. These lines represent MYCN-amplified, NRAS and ALK mutant neuroblastoma subtypes respectively. Wnt3a/R-Spondin treatment also promoted nuclear translocation of β-catenin, increased proliferation and activation of Wnt target genes. Strikingly, short-interfering RNA mediated knockdown of LGR5 induces dramatic Wnt-independent apoptosis in all three cell-lines, accompanied by greatly diminished phosphorylation of mitogen/extracellular signal-regulated kinases (MEK1/2) and extracellular signal-regulated kinases (ERK1/2), and an increase of BimEL, an apoptosis facilitator downstream of ERK. Akt signalling is also decreased by a Rictor dependent, PDK1-independent mechanism. LGR5 expression is cell cycle regulated and LGR5 depletion triggers G1 cell-cycle arrest, increased p27 and decreased phosphorylated retinoblastoma protein. Our study therefore characterises new cancer-associated pathways regulated by LGR5, and suggest that targeting of LGR5 may be of therapeutic benefit for neuroblastomas with diverse etiologies, as well as other cancers expressing high LGR5

A Dereplication and Bioguided Discovery Approach to Reveal New Compounds from a Marine-Derived Fungus Stilbella fimetaria

A marine-derived Stilbella fimetaria fungal strain was screened for new bioactive compounds based on two different approaches: (i) bio-guided approach using cytotoxicity and antimicrobial bioassays; and (ii) dereplication based approach using liquid chromatography with both diode array detection and high resolution mass spectrometry. This led to the discovery of several bioactive compound families with different biosynthetic origins, including pimarane-type diterpenoids and hybrid polyketide-non ribosomal peptide derived compounds. Prefractionation before bioassay screening proved to be a great aid in the dereplication process, since separate fractions displaying different bioactivities allowed a quick tentative identification of known antimicrobial compounds and of potential new analogues. A new pimarane-type diterpene, myrocin F, was discovered in trace amounts and displayed cytotoxicity towards various cancer cell lines. Further media optimization led to increased production followed by the purification and bioactivity screening of several new and known pimarane-type diterpenoids. A known broad-spectrum antifungal compound, ilicicolin H, was purified along with two new analogues, hydroxyl-ilicicolin H and ilicicolin I, and their antifungal activity was evaluated

The Wnt secretion protein Evi/Gpr177 promotes glioma tumourigenesis

Malignant astrocytomas are highly aggressive brain tumours with poor prognosis. While a number of structural genomic changes and dysregulation of signalling pathways in gliomas have been described, the identification of biomarkers and druggable targets remains an important task for novel diagnostic and therapeutic approaches. Here, we show that the Wnt-specific secretory protein Evi (also known as GPR177/Wntless/Sprinter) is overexpressed in astrocytic gliomas. Evi/Wls is a core Wnt signalling component and a specific regulator of pan-Wnt protein secretion, affecting both canonical and non-canonical signalling. We demonstrate that its depletion in glioma and glioma-derived stem-like cells led to decreased cell proliferation and apoptosis. Furthermore, Evi/Wls silencing in glioma cells reduced cell migration and the capacity to form tumours in vivo. We further show that Evi/Wls overexpression is sufficient to promote downstream Wnt signalling. Taken together, our study identifies Evi/Wls as an essential regulator of glioma tumourigenesis, identifying a pathway-specific protein trafficking factor as an oncogene and offering novel therapeutic options to interfere with the aberrant regulation of growth factors at the site of production

dbDNV: a resource of duplicated gene nucleotide variants in human genome

Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotide polymorphism (SNP) from individuals. This imperfection is undistinguishable in current genotyping methods. As the next-generation sequencing technologies become more popular for sequence-based association studies, numerous ambiguous SNPs are rapidly accumulated. Thus, analyzing duplication variations in the reference genome to assist in preventing false positive SNPs is imperative. We have identified >10% of human genes associated with duplicated gene loci (DGL). Through meticulous sequence alignments of DGL, we systematically designated 1 236 956 variations as duplicated gene nucleotide variants (DNVs). The DNV database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) has been established to promote more accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304 110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. This is useful while ∼58% of exonic SNPs in DGL are DNV-coupled. Because of high accumulation of ambiguous SNPs, we suggest that annotating SNPs with DNVs possibilities should improve association studies of these variants with human diseases

Soil carbon determination by thermogravimetrics

Determination of soil constituents and structure has a vital role in agriculture generally. Methods for the determination of soil carbon have in particular gained greater currency in recent times because of the potential that soils offer in providing offsets for greenhouse gas (CO2-equivalent) emissions. Ideally, soil carbon which can also be quite diverse in its makeup and origin, should be measureable by readily accessible, affordable and reliable means. Loss-on-ignition is still a widely used method being suitably simple and available but may have limitations for soil C monitoring. How can these limitations be better defined and understood where such a method is required to detect relatively small changes during soil-C building? Thermogravimetric (TGA) instrumentation to measure carbonaceous components has become more interesting because of its potential to separate carbon and other components using very precise and variable heating programs. TGA related studies were undertaken to assist our understanding in the quantification of soil carbon when using methods such as loss-on-ignition. Combining instrumentation so that mass changes can be monitored by mass spectrometer ion currents has elucidated otherwise hidden features of thermal methods enabling the interpretation and evaluation of mass-loss patterns. Soil thermogravimetric work has indicated that loss-on-ignition methods are best constrained to temperatures from 200 to 430 °C for reliable determination for soil organic carbon especially where clay content is higher. In the absence of C-specific detection where mass only changes are relied upon, exceeding this temperature incurs increasing contributions from inorganic sources adding to mass losses with diminishing contributions related to organic matter. The smaller amounts of probably more recalcitrant organic matter released at the higher temperatures may represent mineral associated material and/or simply more refractory forms

Which sampling design to monitor saturated hydraulic conductivity?

Soil in a changing world is subject to both anthropogenic and environmental stresses. Soil monitoring is essential to assess the magnitude of changes in soil variables and how they affect ecosystem processes and human livelihoods. However, we cannot always be sure which sampling design is best for a given monitoring task. We employed a rotational stratified simple random sampling (rotStRS) for the estimation of temporal changes in the spatial mean of saturated hydraulic conductivity (Ks) at three sites in central Panama in 2009, 2010 and 2011. To assess this design's efficiency we compared the resulting estimates of the spatial mean and variance for 2009 with those gained from stratified simple random sampling (StRS), which was effectively the data obtained on the first sampling time, and with an equivalent unexecuted simple random sampling (SRS). The poor performance of geometrical stratification and the weak predictive relationship between measurements of successive years yielded no advantage of sampling designs more complex than SRS. The failure of stratification may be attributed to the small large-scale variability of Ks. Revisiting previously sampled locations was not beneficial because of the large small-scale variability in combination with destructive sampling, resulting in poor consistency between revisited samples. We conclude that for our Ks monitoring scheme, repeated SRS is equally effective as rotStRS. Some problems of small-scale variability might be overcome by collecting several samples at close range to reduce the effect of small-scale variation. Finally, we give recommendations on the key factors to consider when deciding whether to use stratification and rotation in a soil monitoring scheme