Spatial Input for Temporal Navigation in Scientific Visualizations

Scientific-visualization tools can make time-varying simulations easier to understand. The growing efficiency of today's high-performance computers enables simulation of physical phenomena with a high temporal resolution. Consequently, visualization systems require efficient navigation in the temporal dimension. This 3D user interface employs direct-manipulation metaphors for temporal navigation in scientific visualizations. By interacting with objects using their 3D trajectory, users can navigate in time by specifying spatial inputs. This article is part of a special issue on 3D user interfaces.     

Multi‐phosphorylation of the Intrinsically Disordered Unique Domain of c‐Src Studied by In‐Cell and Real‐Time NMR Spectroscopy

Intrinsically disordered regions (IDRs) are preferred sites for post‐translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase–phosphatase networks. Here we used real‐time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the “unique domain” of c‐Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin‐dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP‐dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK‐dependent sites, thus suggesting indirect effects of kinase–phosphatase networks. This study provides a proof‐of‐concept of the use of real‐time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains.     

Molecular analysis of yeasts from Indonesian cassava and glutinous rice tapé

Tapé is a popular delicacy in Indonesia that is prepared by fermenting starch-rich material. Yeast plays an important role in the making of tapé especially in the aroma and taste of the product. In this study, yeasts were isolated from tapé and subjected to diversity analysis using the restriction fragment length polymorphism (RFLP) technique on 5.8S rRNA encoding gene and the internal transcribed spacer (ITS). A total of 21 yeast isolates were obtained from 3 different types of Indonesian tapé (cassava tapé, white-, and black-glutinous rice tapé). The identified yeast species from cassava tapé were Pichia jadinii, Candida glabrata, and Clavispora lusitaniae. P. fabianii, Rhodotorula mucilaginosa, and Ogataea polymorpha were obtained from white glutinous rice tapé, while Saccharomycopsis fibuligera and Wickerhamomyces anomalus were obtained from black glutinous rice tapé.     

Solid‐phase extraction of phenolic compounds with poly[metalloprotoporphyrin IX]

A highly insoluble metalloporphyrin polymeric material was used as sorbent for the solid‐phase extraction of phenolic compounds. Substantial quantities of phenols (40 to 60 mg/g polymer) were absorbed from aqueous solution comparing satisfactorily with other extraction methods. The polymeric phase presented similar K_SPE values for the hydrophobic compounds tested such as p‐chlorophenol, BPA, p‐nitrophenol, and a significant lower value for the more hydrophilic p‐aminophenol and cresol. Several metallic complexes of protoporphyrin IX (Co²⁺, Cu²⁺, Ni²⁺, Zn²⁺, and Fe³⁺) have been tested. The analytes were extracted with high recoveries at acid and neutral pH values, whereas at pH 10 low recoveries were obtained. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 81: 3038–3043, 2001     

Quantification of the Alternaria mycotoxin tenuazonic acid in beer

Tenuazonic acid (TA) is a major water soluble Alternaria mycotoxin. In the present work, a method for the quantification of TA in beer by liquid chromatography–ion-trap multistage mass spectrometry after derivatization with 2,4-dinitrophenylhydrazine is described. The method is based on a rapid workup procedure and features a LOD of 2 μg/kg without preconcentration using 400 mg of sample. Validation was performed for a working range of 8–500 μg/kg.     

Antiviral activity of donkey milk protein fractions on echovirus type 5

Antiviral activity of Ragusano donkeys' milk proteins was investigated for the effect on echovirus type 5, known to infect the gastrointestinal tract of humans. Three protein fractions were tested; casein (CN), whey protein (WP) and a low molecular whey protein fraction (LWP; <30,000 Da). The antiviral activity of WP and LWP was tested on echovirus type 5 at three concentrations (1, 5 and 10 mg mL^?1); CN was assessed only at the lower concentration. All donkey milk protein fractions showed significant inhibition on virus replication at the concentration of 1 mg mL^?1, and both WP and LWP fractions showed significant inhibition on the virus replication at all concentrations tested. The strongest antiviral effect was observed for the WP fraction. These findings show that the different whey proteins in donkey milk, probably acting in synergy, exert antiviral activity on echovirus 5 and might contribute to prevent gastrointestinal virus infections in humans.     

The social norms of alcohol-related negative consequences.

Social norms for alcohol use are important influences on individual college student drinking. The present study extends social norms research by examining alcohol-related consequences and, in particular, whether similar misperceptions exist regarding the frequency and evaluation of these consequences over time. College student drinkers (N = 624) participating in a longitudinal study completed Web-based surveys assessing alcohol use and related consequences, as well as their beliefs about frequency and evaluation of consequences for the typical college student. Findings suggest that students overestimated how often typical college students experience negative consequences and underestimated how negatively other students evaluated those consequences. Finally, results support a bidirectional model for alcohol-related consequences, possibly indicating a reciprocal, mutually influential feed-forward loop of norms and consequences that promotes maintenance of college student drinking and consequences. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Protein aggregation induced during glass bead lysis of yeast

Yeast cell lysates produced by mechanical glass bead disruption are widely used in a variety of applications, including for the analysis of native function, e.g. protein–protein interaction, enzyme assays and membrane fractionations. Below, we report a striking case of protein denaturation and aggregation that is induced by this lysis protocol. Most of this analysis focuses on the type 1 casein kinase Yck2, which normally tethers to the plasma membrane through C‐terminal palmitoylation. Surprisingly, when cells are subjected to glass bead disruption, non‐palmitoylated, cytosolic forms of the kinase denature and aggregate, while membrane‐associated forms, whether attached through their native palmitoyl tethers or through a variety of artificial membrane‐tethering sequences, are wholly protected from denaturation and aggregation. A wider look at the yeast proteome finds that, while the majority of proteins resist glass bead‐induced aggregation, a significant subset does, in fact, succumb to such denaturation. Thus, yeast researchers should be aware of this potential artifact when embarking on biochemical analyses that employ glass bead lysates to look at native protein function. Finally, we demonstrate an experimental utility for glass bead‐induced aggregation, using its fine discrimination of membrane‐associated from non‐associated Yck2 forms to discern fractional palmitoylation states of Yck2 mutants that are partially defective for palmitoylation. Copyright © 2010 John Wiley & Sons, Ltd.     

Low molecular weight oligo-β-hydroxybutyric acids and 3-hydroxy-N-phenethyl-butyramide – new products from microorganisms

Summary A new group of low-molecular weight channel-forming oligo(hydroxybutyric acids) (cPHBs, 1 with n = 8–30; main component MW ≈ 1300 dalton) was isolated from microorganisms of different origin. Inclusion bodies were electron-microscopically visible in cells in the state of autolysis, not in cells in the exponential phase of growth. cPHB and high-molecular poly(l3-hydroxybutyric acid) (sPHB) is cleaved by phenylethylamine and forms the corresponding monomeric hydroxybutyramide and – under drastic conditions, the crotylamide. One of these compounds, the 3-hydroxy-N-phenethyl-butyramide (5), was isolated as a new natural product now. Received: 28 March 2002/Revised version: 26 July 2002/ Accepted: 26 July 2002 RID="*" ID="*"Marine Bakterien, XVII. XVI: R.P. Maskey, R.N. Asolkar, E. Helmke, and H. Laatsch, Chalcomycin B, a new antibiotic from a marine Streptomyces sp. B7064. J. Antibiot., submitted 2002 Correspondence to Hartmut Laatsch, e-mail: hlaatsc@gwdg.de, Fax: +49-551-399660