DNA microarray experimental design and software based data normalization and analysis

[no abstract

The Impact of Photobleaching on Microarray Analysis

DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner's laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube's voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results

Translation initiation factor eIF3 promotes programmed stop codon readthrough.

Programmed stop codon readthrough is a post-transcription regulatory mechanism specifically increasing proteome diversity by creating a pool of C-terminally extended proteins. During this process, the stop codon is decoded as a sense codon by a near-cognate tRNA, which programs the ribosome to continue elongation. The efficiency of competition for the stop codon between release factors (eRFs) and near-cognate tRNAs is largely dependent on its nucleotide context; however, the molecular mechanism underlying this process is unknown. Here, we show that it is the translation initiation (not termination) factor, namely eIF3, which critically promotes programmed readthrough on all three stop codons. In order to do so, eIF3 must associate with pre-termination complexes where it interferes with the eRF1 decoding of the third/wobble position of the stop codon set in the unfavorable termination context, thus allowing incorporation of near-cognate tRNAs with a mismatch at the same position. We clearly demonstrate that efficient readthrough is enabled by near-cognate tRNAs with a mismatch only at the third/wobble position. Importantly, the eIF3 role in programmed readthrough is conserved between yeast and humans

Laserstrahllöten von umformfähigen hybriden Platinen aus Stahl-Aluminium-Mischverbindungen

[no abstract

Experimental and Numerical Based Defect Detection in a Model Combustion Chamber through Machine Learning

A disturbed combustion process in an aircraft engine has an impact on the internal flow and leads to specific irregularities in the species distribution in the exhaust jet. Measuring this distribution provides information about the combustion state and offers the possibility to reduce the engine down-time during inspection. The approach has the potential to improve the resource management as well as the availability and safety of the system. Aim of the research project is to evaluate the state of an aircraft engine by analyzing the emission field in the exhaust jet and using a support vector machine (SVM) algorithm for automatic defect detection and allocation

Concrete Support Structures for Offshore Wind Turbines: Current Status, Challenges, and Future Trends

Today’s offshore wind turbine support structures market is largely dominated by steel structures, since steel monopiles account for the vast majority of installations in the last decade and new types of multi-leg steel structures have been developed in recent years. However, as wind turbines become bigger, and potential sites for offshore wind farms are located in ever deeper waters and ever further from the shore, the conditions for the design, transport, and installation of support structures are changing. In light of these facts, this paper identifies and categorizes the challenges and future trends related to the use of concrete for support structures of future offshore wind projects. To do so, recent advances and technologies still under development for both bottom-fixed and floating concrete support structures have been reviewed. It was found that these new developments meet the challenges associated with the use of concrete support structures, as they will allow the production costs to be lowered and transport and installation to be facilitated. New technologies for concrete support structures used at medium and great water depths are also being developed and are expected to become more common in future offshore wind installations. Therefore, the new developments identified in this paper show the likelihood of an increase in the use of concrete support structures in future offshore wind farms. These developments also indicate that the complexity of future support structures will increase due to the development of hybrid structures combining steel and concrete. These evolutions call for new knowledge and technical know-how in order to allow reliable structures to be built and risk-free offshore installation to be executed

Ein mechanisch basiertes Dehnungsmodell für ermüdungsbeanspruchten Beton

[no abstract

Современные аспекты правовой защиты персональной информации в РФ

Motivation: Much is now known about the mechanistic details of gene translation. There are also rapid advances in high-throughput technologies to determine quantitative aspects of the system. As a consequence-realistic and system-wide simulation models of translation are now feasible. Such models are also needed as devices to integrate a large volume of highly fragmented data known about translation. Software: In this application note, we present a novel, highly efficient software tool to model translation. The tool represents the main aspects of translation. Features include a representation of exhaustible tRNA pools, ribosome–ribosome interactions and differential initiation rates for different mRNA species. The tool is written in Java, and is hence portable and can be parameterized for any organism. Availability: The model can be obtained from the authors or directly downloaded from the authors' home-page (http://goo.gl/JUWvI)

The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae

Protein synthesis translates information from messenger RNAs into functional proteomes. Because of the finite nature of the resources required by the translational machinery, both the overall protein synthesis activity of a cell and activity on individual mRNAs are controlled by the allocation of limiting resources. Upon introduction of heterologous sequences into an organism—for example for the purposes of bioprocessing or synthetic biology—limiting resources may also become overstretched, thus negatively affecting both endogenous and heterologous gene expression. In this study, we present a mean-field model of translation in Saccharomyces cerevisiae for the investigation of two particular translational resources, namely ribosomes and aminoacylated tRNAs. We firstly use comparisons of experiments with heterologous sequences and simulations of the same conditions to calibrate our model, and then analyse the behaviour of the translational system in yeast upon introduction of different types of heterologous sequences. Our main findings are that: competition for ribosomes, rather than tRNAs, limits global translation in this organism; that tRNA aminoacylation levels exert, at most, weak control over translational activity; and that decoding speeds and codon adaptation exert strong control over local (mRNA specific) translation rates

On translational control by ribosome speed in S. cerevisiae

Introduction: In addition to the widespread and well documented control of protein synthesis by translation initiation, recent evidence suggests that translation elongation can also control protein synthesis rates. One of the proposed mechanisms leading to elongation control is the interference of slow ribosome movement around the start codon with efficient translation initiation. Here we estimate the frequency with which this mode of control occurs in baker’s yeast growing in rich medium. Methods: We interrogate published genome-wide datasets for evidence of transcripts associated with queueing small ribosomal subunits, and confirm results from these surveys using additional experimental work. Results: Our analyses reveal that transcripts from around 20% of yeast genes show evidence of queueing ribosomes, which may be indicative of translation elongation control. Moreover, this subset of transcripts is sensitive to distinct regulatory signals compared to initiation-controlled mRNAs, and such distinct regulation occurs, for example, during the response to osmotic stress. Discussion: Our analyses provide a first quantitative estimate for the prevalence of translational control exerted via the elongation stage in a commonly used model organism, and suggest that transcript under elongation control form a separately addressable RNA regulon