Formation of a new oxidative metabolite from kobophenol A by human intestinal bacterium Klebsiella pneumoniae

During our studies on the metabolism of kobophenol A (1) in rats, we had isolated, purified, and identified the main new oxidative metabolite of 1, koboquinone A (2) from rats' feces. To elucidate the metabolic pathway of 1 in rats, we conducted the in vitro metabolic experiments of 1 by human intestinal bacteria and found that Klebsiella pneumoniae produced appreciable amounts of 2. This was verified by means of high performance liquid chromatography mass/mass spectrometry (HPLC/MS/MS) analysis.     

Rapid and visual detection of berberine hydrochloride based on a water‐soluble pyrene derivative

In this study, a rapid method for the detection of berberine hydrochloride (BRH) was developed based on a water‐soluble pyrenyl probe, 8‐hydroxypyrene‐1,3,6‐trisulfonic acid (HPTS). This method features low cost, good selectivity, high sensitivity and a fast response. The sensing mechanism of this probe is attributed to the formation of a complex between HPTS and BRH induced by electrostatic interaction and π–π stacking. To the best of our knowledge, this is the first fluorescent sensor for BRH based on organic materials that has low cost and a visual response. The detection limit of this method was as low as 1.24 μM and the linear response range is 2–50 μM. This method also allowed rapid detection of BRH real samples.     

Impedance-Based Monitoring of Ongoing Cardiomyocyte Death Induced by Tumor Necrosis Factor-α

Deregulated cardiomyocyte death is a critical risk factor in a variety of cardiovascular diseases. Although various assays have been developed to detect cell responses during cell death, the capability of monitoring cell detachment will enhance the understanding of death processes by providing instant information at its early phase. In this work, we developed an impedance-sensing assay for real-time monitoring of cardiomyocyte death induced by tumor necrosis factor-α based on recording the change in cardiomyocyte adhesion to extracellular matrix. Electrochemical impedance spectroscopy was employed in impedance data processing, followed by calibration with the electrical cell-substrate impedance-sensing technique. The adhesion profile of cardiomyocytes undergoing cell death processes was recorded as the time course of equivalent cell-substrate distance. The cell detachment was detected with our assay and proved related to cell death in the following experiments, indicating its advantage against the conventional assays, such as Trypan blue exclusion. An optimal concentration of tumor necrosis factor-α (20 ng/mL) was determined to induce cardiomyocyte apoptosis rather than the combinative cell death of necrosis and apoptosis by comparing the concentration-related adhesion profiles. The cardiomyocytes undergoing apoptosis experienced an increase of cell-substrate distance from 59.1 to 89.2 nm within 24 h. The early change of cell adhesion was proved related to cardiomyocyte apoptosis in the following TUNEL test at t = 24 h, which suggested the possibility of early and noninvasive detection of cardiomyocyte apoptosis.     

The N-terminal hydrophobic segment of Streptomyces coelicolor FtsY forms a transmembrane structure to stabilize its membrane localization

FtsY is the receptor of the signal recognition particle that mediates the targeting of integral membrane proteins in bacteria. It was shown that in Escherichia coli, the N-terminal region of FtsY contributes to its interaction with the membrane, but it is not inserted into the membrane. However, this study presents evidence that in Streptomyces coelicolor, FtsY has a hydrophobic region at its N-terminus, which forms a membrane insertion structure and contributes significantly to the binding between FtsY and membrane. Through membrane protein extraction followed by immunoblotting, we demonstrated that deletion of the N-terminal residues 11-39 from the S. coelicolor FtsY (ScFtsY) drastically reduced its membrane-binding capability and that the N-terminus of ScFtsY alone was capable of targeting the soluble EGFP protein onto the membrane with high efficiency. Furthermore, in a labeling experiment with the membrane-impermeable probe Mal-PEG, the ScFtsY N-terminal region was protected by the membrane and was not labeled. This observation indicates that this region was inserted into the membrane.     

A Time-Series DDP for Functional Proteomics Profiles

Summary Using a new type of array technology, the reverse phase protein array (RPPA), we measure time-course protein expression for a set of selected markers that are known to coregulate biological functions in a pathway structure. To accommodate the complex dependent nature of the data, including temporal correlation and pathway dependence for the protein markers, we propose a mixed effects model with temporal and protein-specific components. We develop a sequence of random probability measures (RPM) to account for the dependence in time of the protein expression measurements. Marginally, for each RPM we assume a Dirichlet process model. The dependence is introduced by defining multivariate beta distributions for the unnormalized weights of the stick-breaking representation. We also acknowledge the pathway dependence among proteins via a conditionally autoregressive model. Applying our model to the RPPA data, we reveal a pathway-dependent functional profile for the set of proteins as well as marginal expression profiles over time for individual markers.     

Convergence of multiple signaling cascades at glycogen synthase kinase 3: Edg receptor-mediated phosphorylation and inactivation by lysophosphatidic acid through a protein kinase C-dependent intracellular pathway

Lysophosphatidic acid (LPA) is a natural phospholipid with multiple biological functions. We show here that LPA induces phosphorylation and inactivation of glycogen synthase kinase 3 (GSK-3), a multifunctional serine/threonine kinase. The effect of LPA can be reconstituted by expression of Edg-4 or Edg-7 in cells lacking LPA responses. Compared to insulin, LPA stimulates only modest phosphatidylinositol 3-kinase (PI3K)-dependent activation of protein kinase B (PKB/Akt) that does not correlate with the magnitude of GSK-3 phosphorylation induced by LPA. PI3K inhibitors block insulin- but not LPA-induced GSK-3 phosphorylation. In contrast, the effect of LPA, but not that of insulin or platelet-derived growth factor (PDGF), is sensitive to protein kinase C (PKC) inhibitors. Downregulation of endogenous PKC activity selectively reduces LPA-mediated GSK-3 phosphorylation. Furthermore, several PKC isotypes phosphorylate GSK-3 in vitro and in vivo. To confirm a specific role for PKC in regulation of GSK-3, we further studied signaling properties of PDGF receptor beta subunit (PDGFRbeta) in HEK293 cells lacking endogenous PDGF receptors. In clones expressing a PDGFRbeta mutant wherein the residues that couple to PI3K and other signaling functions are mutated with the link to phospholipase Cgamma (PLCgamma) left intact, PDGF is fully capable of stimulating GSK-3 phosphorylation. The process is sensitive to PKC inhibitors in contrast to the response through the wild-type PDGFRbeta. Therefore, growth factors, such as PDGF, which control GSK-3 mainly through the PI3K-PKB/Akt module, possess the ability to regulate GSK-3 through an alternative, redundant PLCgamma-PKC pathway. LPA and potentially other natural ligands primarily utilize a PKC-dependent pathway to modulate GSK-3.     

山西葛萝槭天然种群表型多样性研究

为揭示山西葛萝槭种群表型变异程度及变异规律,采用巢式方差分析、主成分分析、相关分析及聚类分析等方法,对天然分布的8个种群的叶片、果实、种子21个表型性状进行表型多样性分析。结果显示:（1)葛萝槭表型性状在种群间和种群内存在着极其丰富的变异。种群间平均表型分化系数(V_ST)为50.16%,与种群内变异(49.84%)相当;表型变异系数（CV）为19.16%,变化幅度7.89%~37.04%,种子性状较果实、叶片性状稳定;8个不同种群的Shannon-Wiener多样性指数为1.692 3,表明葛萝槭种群具有较高的表型多样性。(2)相关性分析表明,葛萝槭表型性状受地理生态因子的影响,种群内表型变异呈梯度性变化,随着经、纬度的增加,叶形逐渐由长卵形向宽卵形变异;随着海拔的升高,果实、种子逐渐减小。(3)利用种群间欧式距离进行系统聚类分析,可以将8个葛萝槭种群分为两大支,表型性状主要依地理距离而聚类。研究表明,葛萝槭种内存在丰富的变异,这与其生物学特性及分布生境密切相关。     

Erratum to: Modeling precision treatment of breast cancer

During the type-setting of the final version of the article [1] some of the additional files were swapped. The correct files are republished in this Erratum.The online version of the original article can be found under doi:10.1186/s13059-015-0658-5.