Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker

The aim of this study was to characterize the proteome of normal and malignant colonic tissue. We previously studied the colon proteome using 2‐DE and MALDI‐MS and identified 734 proteins (Roeßler, M., Rollinger, W., Palme S., Hagmann, M.‐L., et al.., Clin. Cancer Res. 2005, 11, 6550–6557). Here we report the identification of additional colon proteins from the same set of tissue samples using a complementary nano‐flow 2‐D‐LC‐ESI‐MS. In total, 484 proteins were identified in colon. Of these, 252 had also been identified by the 2‐DE/MALDI‐MS approach, whereas 232 proteins were unique to the 2‐D‐LC‐ESI‐MS analysis. Comparing protein expression in neoplastic and normal colon tissue indicated elevated expression of several proteins in colorectal cancer, among them the well established tumor marker carcinoembryonic antigen, as well as calnexin, 40S ribosomal protein S15a, serpin H1, and S100A12. Overexpression of these proteins was confirmed by immunoblotting. Serum levels of S100A12 were determined by ELISA and were found to be strongly elevated in colorectal cancer patients compared to healthy individuals. We conclude, that 2‐D‐LC‐ESI‐MS is a powerful approach to identify and compare protein profiles of tissue samples, that it is complementary to 2‐DE/MALDI‐MS approaches and has the potential to identify novel biomarkers.     

BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

The development of novel enzymes for biocatalytic processes requires knowledge on substrate profile and selectivity; this can be derived from databases and from publications. Often, these sources lack time‐course data for the substrate or product, and an unambiguous link between experiment and enzyme sequence. The lack of integrated, original data hampers the comprehensive analysis of enzyme kinetics and the evaluation of sequence–function relationships. In order to accelerate enzyme engineering, BioCatNet integrates protein sequence, protein structure, and experimental data for a given enzyme family. BioCatNet explicitly assigns the enzyme sequence to the experimental data, which consists of information on reaction conditions and time‐course data. BioCatNet facilitates the consistent documentation of reaction conditions, the archiving of time‐course data, and the efficient exchange of experimental data among collaborators. Data integration is demonstrated for three case studies by using the TEED (Thiamine diphosphate‐dependent Enzymes Engineering Database).     

通信网络可视化的基本原理

The human brain is built to process complex visual impressions within milliseconds. In comparison with sequentially coded spoken language and written texts, we are capable of consuming graphical information at a high bandwidth in a parallel fashion, producing a picture worth more than a thousand words. Effective information visualization can be a powerful tool to capture people’s attention and quickly communicate large amounts of data and complex information. This is par-ticularly important in the context of commu-nication data, which often describes entities (people, organizations) and their connections through communication. Visual analytics ap-proaches can optimize the user-computer in-teraction to gain insights into communication networks and learn about their structures. Network visualization is a perfect instrument to better communicate the results of analysis. The precondition for effective information visualization and successful visual reasoning is the capability to draw “good” pictures. Even though communication networks are often large, including thousands or even millions of people, underlying visualization principles are identical to those used for visualizing smaller networks. In this article, you will learn about these principles, giving you the ability to as-sess the quality of network visualizations and to draw better network pictures by yourself.     

The Mitochondrial Amidoxime Reducing Component (mARC): Involvement in Metabolic Reduction of N‐Oxides,Oximes and N‐Hydroxyamidinohydrazones

The mitochondrial amidoxime reducing component (mARC) is a molybdenum‐containing enzyme and capable of reducing N‐hydroxylated structures such as amidoxime prodrugs. In this study, we tested the involvement of mARC in the reduction of N‐oxides (amitriptyline‐N‐oxide, nicotinamide‐N‐oxide), oximes ((E)‐/(Z)‐2,4,6‐trimethylacetophenonoxime) and a N‐hydroxyamidinohydrazone (guanoxabenz). All groups are reduced by mARC proteins, and the enzymes are therefore involved in the interconversion of N‐oxygenated metabolites originating from cytochrome P450s and flavin‐containing monooxygenases. In addition, these structures open up further options for serving as prodrugs. Thus, with respect to these reactions, testing of candidates with N‐oxygenated structures should not solely be carried out in microsomal enzyme sources but as well in mitochondria. However, differences in the reduction of oximes and N‐oxides between the two isoforms, namely mARC1 and mARC2, were detectable; N‐oxides are exclusively reduced by mARC1. We therefore assume differences between the so far unknown 3D structures of the two proteins.     

X-ray absorption spectroscopy characterization of Zn underpotential deposition on Au(1 1 1) from phosphate supporting electrolyte

Zn K-edge X-ray absorption spectroscopy (XAS) has been used to investigate the structure of Zn monolayers prepared on Au(1 1 1) electrodes via underpotential deposition (UPD) from phosphate supporting electrolyte. Theoretical modeling of the XAS data indicates that the Zn adatoms adopt a commensurate (√3 × √3)R30° (θ_sc = 0.33) adlayer structure and reside within the 3-fold hollow sites of the Au(1 1 1) surface. Meanwhile, phosphate counter-ions co-adsorb on the UPD adlayer and bridge between the Zn adatoms in a (√3 × √3)R30° (θ_sc = 0.33) configuration, with each phosphorous atom residing above a vacant 3-fold hollow site of the Au(1 1 1). Significantly, this surface structure is invariant between the electrochemical potential for UPD adlayer formation and the onset of bulk Zn electrodeposition. Analysis of the Zn K-edge absorption onset also presents the possibility that the Zn adatoms do not fully discharge during the process of UPD, which had been proposed in prior voltammetric studies of the phosphate/Zn(UPD)/Au(1 1 1) system.     

Sacubitril/Valsartan Improves Diastolic Function But Not Skeletal Muscle Function in a Rat Model of HFpEF

The angiotensin receptor/neprilysin inhibitor Sacubitril/Valsartan (Sac/Val) has been shown to be beneficial in patients suffering from heart failure with reduced ejection fraction (HFrEF). However, the impact of Sac/Val in patients presenting with heart failure with preserved ejection fraction (HFpEF) is not yet clearly resolved. The present study aimed to reveal the influence of the drug on the functionality of the myocardium, the skeletal muscle, and the vasculature in a rat model of HFpEF. Female obese ZSF-1 rats received Sac/Val as a daily oral gavage for 12 weeks. Left ventricle (LV) function was assessed every four weeks using echocardiography. Prior to organ removal, invasive hemodynamic measurements were performed in both ventricles. Vascular function of the carotid artery and skeletal muscle function were monitored. Sac/Val treatment reduced E/é ratios, left ventricular end diastolic pressure (LVEDP) and myocardial stiffness as well as myocardial fibrosis and heart weight compared to the obese control group. Sac/Val slightly improved endothelial function in the carotid artery but had no impact on skeletal muscle function. Our results demonstrate striking effects of Sac/Val on the myocardial structure and function in a rat model of HFpEF. While vasodilation was slightly improved, functionality of the skeletal muscle remained unaffected.     

Mapping the Binding Sites of UDP and Prostaglandin E2 Glyceryl Ester in the Nucleotide Receptor P2Y6

Cyclooxygenase-2 catalyzes the biosynthesis of prostaglandins from arachidonic acid and the biosynthesis of prostaglandin glycerol esters (PG-Gs) from 2-arachidonoylglycerol. PG-Gs are mediators of several biological actions such as macrophage activation, hyperalgesia, synaptic plasticity, and intraocular pressure. Recently, the human UDP receptor P2Y₆ was identified as a target for the prostaglandin E2 glycerol ester (PGE₂-G). Here, we show that UDP and PGE₂-G are evolutionary conserved endogenous agonists at vertebrate P2Y₆ orthologs. Using sequence comparison of P2Y₆ orthologs, homology modeling, and ligand docking studies, we proposed several receptor positions participating in agonist binding. Site-directed mutagenesis and functional analysis of these P2Y₆ mutants revealed that both UDP and PGE₂-G share in parts one ligand-binding site. Thus, the convergent signaling of these two chemically very different agonists has already been manifested in the evolutionary design of the ligand-binding pocket.