Orthogonal Translation Meets Electron Transfer: In Vivo Labeling of Cytochrome c for Probing Local Electric Fields

Cytochrome c (cyt c), a redox protein involved in diverse fundamental biological processes, is among the most traditional model proteins for analyzing biological electron transfer and protein dynamics both in solution and at membranes. Studying the role of electric fields in energy transduction mediated by cyt c relies upon appropriate reporter groups. Up to now these had to be introduced into cyt c by in vitro chemical modification. Here, we have overcome this restriction by incorporating the noncanonical amino acid p‐cyanophenylalanine (pCNF) into cyt c in vivo. UV and CD spectroscopy indicate preservation of the overall protein fold, stability, and heme coordination, whereas a small shift of the redox potential was observed by cyclic voltammetry. The C≡N stretching mode of the incorporated pCNF detected in the IR spectra reveals a surprising difference, which is related to the oxidation state of the heme iron, thus indicating high sensitivity to changes in the electrostatics of cyt c.     

A method for determination of length distributions of multiwalled carbon nanotubes before and after melt processing

A relatively simple method to determine the length distribution of carbon nanotubes (CNTs) before and after melt processing was developed. This involves the selection of a suitable solvent for dispersing pristine CNTs as well as to dissolve the matrix of melt mixed composites and the choice of an appropriate nanotube concentration. The length of suitably individualized CNTs was visualized using transmission electron microscopy and length distributions were measured using image analysis. Examples are shown for Baytubes® C150HP and Nanocyl™ NC7000 and their melt mixed composites with polycarbonate where the same procedure was applied to both, measuring the initial length distribution and the distribution after recovering from the composites. These results indicated a significant shortening after melt processing up to 30% of the initial length.     

The social bookmark and publication management system bibsonomy

Social resource sharing systems are central elements of the Web 2.0 and use the same kind of lightweight knowledge representation, called folksonomy. Their large user communities and ever-growing networks of user-generated content have made them an attractive object of investigation for researchers from different disciplines like Social Network Analysis, Data Mining, Information Retrieval or Knowledge Discovery. In this paper, we summarize and extend our work on different aspects of this branch of Web 2.0 research, demonstrated and evaluated within our own social bookmark and publication sharing system BibSonomy, which is currently among the three most popular systems of its kind. We structure this presentation along the different interaction phases of a user with our system, coupling the relevant research questions of each phase with the corresponding implementation issues. This approach reveals in a systematic fashion important aspects and results of the broad bandwidth of folksonomy research like capturing of emergent semantics, spam detection, ranking algorithms, analogies to search engine log data, personalized tag recommendations and information extraction techniques. We conclude that when integrating a real-life application like BibSonomy into research, certain constraints have to be considered; but in general, the tight interplay between our scientific work and the running system has made BibSonomy a valuable platform for demonstrating and evaluating Web 2.0 research.     

Capacities of membrane lipids to accumulate neutral organic chemicals

Lipids have been considered as the predominant components for bioaccumulation of organic chemicals. However, differences in accumulation properties between different types of lipid (e.g., storage and membrane lipids) have rarely been considered. Moreover, in view of toxic effects on organisms, chemical accumulation specifically in biological membranes is of particular importance. In this review article, partition coefficients of 240 neutral organic compounds between liposomes (phospholipid membrane vesicles) and water (K(lipw)), reported in the literature or measured additionally for this work, were evaluated. Values of log K(lipw) and log K(ow) (octanol-water partition coefficients) differ by 0.4 on average. Polyparameter linear free energy relationships (PP-LFERs) can describe the log K(lipw) data even better (standard deviations = 0.28-0.31) than the log K(ow) model. Recent experimental data for highly hydrophobic compounds fit well to the PP-LFERs and do not indicate the existence of a previously postulated "hydrophobicity cutoff". Predictive approaches based only on the molecular structure (KOWWIN, SPARC, COSMOthermX, COSMOmic) were also evaluated for K(lipw) prediction. The PP-LFERs revealed that partition coefficients into membrane lipids can be two log units higher than those into storage lipids for H-bond donor compounds, suggesting that distinguishing between the two lipids is necessary to account for the bioaccumulation of these compounds, and that tissues rich in membrane lipids (e.g., kidneys, liver) instead of fat tissue can be the primary phase for accumulation.     

Recent advances in environmental risk assessment of transformation products

When micropollutants degrade in the environment, they may form persistent and toxic transformation products, which should be accounted for in the environmental risk assessment of the parent compounds. Transformation products have become a topic of interest not only with regard to their formation in the environment, but also during advanced water treatment processes, where disinfection byproducts can form from benign precursors. In addition, environmental risk assessment of human and veterinary pharmaceuticals requires inclusion of human metabolites as most pharmaceuticals are not excreted into wastewater in their original form, but are extensively metabolized. All three areas have developed their independent approaches to assess the risk associated with transformation product formation including hazard identification, exposure assessment, hazard assessment including dose-response characterization, and risk characterization. This review provides an overview and defines a link among those areas, emphasizing commonalities and encouraging a common approach. We distinguish among approaches to assess transformation products of individual pollutants that are undergoing a particular transformation process, e.g., biotransformation or (photo)oxidation, and approaches with the goal of prioritizing transformation products in terms of their contribution to environmental risk. We classify existing approaches for transformation product assessment in degradation studies as exposure- or effect-driven. In the exposure-driven approach, transformation products are identified and quantified by chemical analysis followed by effect assessment. In the effect-driven approach, a reaction mixture undergoes toxicity testing. If the decrease in toxicity parallels the decrease of parent compound concentration, the transformation products are considered to be irrelevant, and only when toxicity increases or the decrease is not proportional to the parent compound concentration are the TPs identified. For prioritization of transformation products in terms of their contribution to overall environmental risk, we integrate existing research into a coherent model-based, risk-driven framework. In the proposed framework, read-across from data of the parent compound to the transformation products is emphasized, but limitations to this approach are also discussed. Most prominently, we demonstrate how effect data for parent compounds can be used in combination with analysis of toxicophore structures and bioconcentration potential to facilitate transformation product effect assessment.