Relation of smoking and alcohol and coffee consumption to active Helicobacter pylori infection: cross sectional study.

OBJECTIVE: To assess the relation of smoking and alcohol and coffee consumption to active Helicobacter pylori infection. DESIGN: Cross sectional study of patients attending a general practitioner. Active H pylori infection was measured by the 15C-urea breath test and detailed quantitative information on smoking and on alcohol and coffee consumption was obtained by a standardised self administered questionnaire. SETTING: One general practice in Germany. SUBJECTS: 447 patients aged 15-79 who had not had peptic ulcer disease or treatment for H pylori infection. MAIN OUTCOME MEASURES: Prevalence of H pylori infection according to smoking and alcohol and coffee consumption. RESULTS: Overall prevalence of infection was 21% (94/447). There was no significant relation between smoking and active H pylori infection. Alcohol consumption showed a negative dose-response relation and coffee consumption a positive dose-response relation with active infection. After adjustment for potential confounders, the odds ratios for patients who drank < or = 75 g and > 75 g of ethanol a week compared with non-drinkers were 0.90 (95% confidence interval 0.55 to 1.59) and 0.33 (0.16 to 0.68), respectively (P value for trend 0.005, assuming that 1 litre of beer and 0.51 of wine contain on average 50 g of ethanol in south Germany). Adjusted odds ratios for patients who drank < 3 cups and > or = 3 cups of coffee per day compared with those who did not drink coffee were 1.49 (0.71 to 3.12) and 2.49 (1.23 to 5.03), respectively (P value for trend 0.007). CONCLUSION: These results suggest a protective effect of alcohol consumption against active infection with H pylori and an opposite effect of coffee consumption.     

Toll-like receptor 4 deficiency: Smaller infarcts,but nogain in function

Backgound  

It has been reported that Toll-like receptor 4 (TLR4) deficiency reduces infarct size after myocardial ischemia/reperfusion (MI/R). However, measurement of MI/R injury was limited and did not include cardiac function. In a chronic closed-chest model we assessed whether cardiac function is preserved in TLR4-deficient mice (C3H/HeJ) following MI/R, and whether myocardial and systemic cytokine expression differed compared to wild type (WT).     

State-of-the art data normalization methods improve NMR-based metabolomic analysis

Extracting biomedical information from large metabolomic datasets by multivariate data analysis is of considerable complexity. Common challenges include among others screening for differentially produced metabolites, estimation of fold changes, and sample classification. Prior to these analysis steps, it is important to minimize contributions from unwanted biases and experimental variance. This is the goal of data preprocessing. In this work, different data normalization methods were compared systematically employing two different datasets generated by means of nuclear magnetic resonance (NMR) spectroscopy. To this end, two different types of normalization methods were used, one aiming to remove unwanted sample-to-sample variation while the other adjusts the variance of the different metabolites by variable scaling and variance stabilization methods. The impact of all methods tested on sample classification was evaluated on urinary NMR fingerprints obtained from healthy volunteers and patients suffering from autosomal polycystic kidney disease (ADPKD). Performance in terms of screening for differentially produced metabolites was investigated on a dataset following a Latin-square design, where varied amounts of 8 different metabolites were spiked into a human urine matrix while keeping the total spike-in amount constant. In addition, specific tests were conducted to systematically investigate the influence of the different preprocessing methods on the structure of the analyzed data. In conclusion, preprocessing methods originally developed for DNA microarray analysis, in particular, Quantile and Cubic-Spline Normalization, performed best in reducing bias, accurately detecting fold changes, and classifying samples.

     

Effect of oleocellosis,desiccation, and fungal infection upon the terpenes of individual oil glands in Citrus latipes

Mono- and sesqui-terpenes of individual oil glands of Citrus latipes fruits were analyzed for their homogeneity. The effect of oleocellosis, desiccation, Penicillium and Phytophthora infection upon the individual terpene components was investigated and expressed in a discriminant analysis and in canonical variables. Each oil gland contained the entire spectrum of terpenes specific for each species, and the biggest difference in affected glands was due to Penicillium infection.     

Anions permeate and gate GCAC1, a voltage-dependent guard cell anion channel

GCAC1 is a strongly voltage-dependent anion channel in the guard-cell plasma membrane of Vicia faba . In patch–clamp experiments, we have investigated the permeation and gating properties of GCAC1 with respect to its anion dependence in the whole-cell and excised-patch configuration. The relative permeability followed the order SCN^– > NO₃^– > Br^– > Cl^–, while the single-channel conductances in symmetrical anionic solutions exhibited a nearly inverse sequence. The Cl^– dependence of inward currents (Cl^– release) is characterized by a maximum single-channel conductance of 89 pS half-saturating at 87 mM cytoplasmic chloride. In addition to this substrate saturation, anion release was also dependent on the external Cl^– activity ( K _m = 16 mM). In the presence of SCN^– and Cl^–, the single-channel conductance exhibited an anomalous mole-fraction dependence, identifying GCAC1 as a multi-ion single-file pore. Using anions with increasing ionic size, a minimum pore diameter of 0.5 nm was assumed from their relative permeabilities. In line with an anion-selective channel, a tenfold increase in the extracellular anion activity shifted the reversal potential by –59.8 mV. Simultaneously, the half-activation potential shifted negatively by about 23 mV. A further analysis of the anion dependence revealed that extracellular rather than cytosolic anions affect the gating process of GCAC1. From anion substitution experiments, we conclude that anion concentration and species determines both permeation and gating of the plant anion channel GCAC1.     

Combined UV and Liquid Scintillation Detection in HPLC. Formation and Depurination of Substitution Inert Pt(II) Complexes of Purine Nucleosides

Abstract

Combined UV- and liquid scintillation-HPLC has been applied to study the complexing of purine nucleosides with Pt(II)-diamine ions, and the effect of the complex formation on the acidic depurination.     

Crystal structure of a novel mid-gut procarboxypeptidase from the cotton pest Helicoverpa armigera.

The cotton bollworm Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) is one of the most serious insect pests in Australia, India and China. The larva causes substantial economical losses to legume, fibre, cereal oilseed and vegetable crops. This pest has proven to be difficult to control by conventional means, mainly due to the development of pesticide resistance. We present here the 2.5 A crystal structure from the novel procarboxypeptidase (PCPAHa) found in the gut extracts from H. armigera larvae, the first one reported for an insect. This metalloprotease is synthesized as a zymogen of 46.6 kDa which, upon in vitro activation with Lys-C endoproteinase, yields a pro-segment of 91 residues and an active carboxypeptidase moiety of 318 residues. Both regions show a three-dimensional structure quite similar to the corresponding structures in mammalian digestive carboxypeptidases, the most relevant structural differences being located in the loops between conserved secondary structure elements, including the primary activation site. This activation site contains the motif (Ala)(5)Lys at the C terminus of the helix connecting the pro- and the carboxypeptidase domains. A remarkable feature of PCPAHa is the occurrence of the same (Ala)(6)Lys near the C terminus of the active enzyme. The presence of Ser255 in PCPAHa instead of Ile and Asp found in the pancreatic A and B forms, respectively, enlarges the S1' specificity pocket and influences the substrate preferences of the enzyme. The C-terminal tail of the leech carboxypeptidase inhibitor has been modelled into the PCPAHa active site to explore the substrate preferences and the enzymatic mechanism of this enzyme.     

Identifying essential genes in bacterial metabolic networks with machine learning methods

Background  

Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell. However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective.