Computer Controlled Automated Assay for Comprehensive Studies of Enzyme Kinetic Parameters

Stability and biological activity of proteins is highly dependent on their physicochemical environment. The development of realistic models of biological systems necessitates quantitative information on the response to changes of external conditions like pH, salinity and concentrations of substrates and allosteric modulators. Changes in just a few variable parameters rapidly lead to large numbers of experimental conditions, which go beyond the experimental capacity of most research groups. We implemented a computer-aided experimenting framework (“robot lab assistant”) that allows us to parameterize abstract, human-readable descriptions of micro-plate based experiments with variable parameters and execute them on a conventional 8 channel liquid handling robot fitted with a sensitive plate reader. A set of newly developed R-packages translates the instructions into machine commands, executes them, collects the data and processes it without user-interaction. By combining script-driven experimental planning, execution and data-analysis, our system can react to experimental outcomes autonomously, allowing outcome-based iterative experimental strategies. The framework was applied in a response-surface model based iterative optimization of buffer conditions and investigation of substrate, allosteric effector, pH and salt dependent activity profiles of pyruvate kinase (PYK). A diprotic model of enzyme kinetics was used to model the combined effects of changing pH and substrate concentrations. The 8 parameters of the model could be estimated from a single two-hour experiment using nonlinear least-squares regression. The model with the estimated parameters successfully predicted pH and PEP dependence of initial reaction rates, while the PEP concentration dependent shift of optimal pH could only be reproduced with a set of manually tweaked parameters. Differences between model-predictions and experimental observations at low pH suggest additional protonation-sites at the enzyme or substrates critical for enzymatic activity. The developed framework is a powerful tool to investigate enzyme reaction specifics and explore biological system behaviour in a wide range of experimental conditions

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Planungs- und Kontrollprobleme in Unternehmungen und property rights- bzw. Transaktionskostentheorie

Available from Bibliothek des Instituts fuer Weltwirtschaft, ZBW, Duesternbrook Weg 120, D-24105 Kiel C 148733 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

Extranuclear inheritance: genetics and biogenesis of mitochondria

This chapter is a continuation of our previous articles in this series (Bauerfeind et al. 1997; Riemen et al. 1993). Research activities and progress in the field of mitochondrial genetics, mitochondrial biogenesis and nuclear-mitochondrial interactions refer to the complete sequence of new mitochondrial genomes, transcription of mitochondrial DNA, processing, editing, and stability of mitochondrial RNA, the import of proteins and RNA, and the characterization of many nuclear genes required for mitochondrial biogenesis. Three topics have been selected to be reviewed here. (1) The complete sequence of the mitochondrial genome of Arabidopsis thaliana will be discussed in the section on mitochondrial genomes. The mitochondrial DNA of the flagellate Reclinomonas americana may represent a very ancient type of mitochondrial genome and is much more eubacterial-like than any other mitochondrial DNA analyzed so far. (2) For several years, laboratories have been searching for genes encoding plant organelle RNA polymerases. Recently, the sequence of the first genes were published and are reviewed here. (3) The identification of a nuclear gene restoring cytoplasmic male sterility is another remarkable result that will be discussed

Extranuclear inheritance: genetics and biogenesis of mitochondria

In our previous review in Progress in Botany 54 (Riemen et al. 1993), complete sequences of the mitochondrial genomes from the chlorophyte Chlamydomonas reinhardtii and the liverwort Marchantia polymorpha were discussed. In the meantime, the complete sequences of the mitochondrial genomes from the colorless chlorophyte Prototheca wickerhamii and the red alga Chondrus crispus have been published, and will be discussed in this chapter

Optimal Marketing of Nursery Crops from Container-Based Production Systems

Optimal production and marketing decisions for a nursery producing ornamental plants from a container-based production system are determined. The stochastic dynamic programming model developed captures the existence of a value-added, serial-stage production process with multiple products and intra- and interyear dynamics. Results suggest price differentials play an important role in determining the optimal size of plant to market. Further, federal taxes are important for determining the optimal production and marketing decisions while discounting and state taxes play minor roles. Analysis of the transition probability matrices associated with the optimal decisions indicate that the long-run behavior of the system can be generalized. Copyright 1997, Oxford University Press.