Automated monitoring of recovered water quality

Laboratory prototype water quality monitoring system provides automatic system for online monitoring of chemical, physical, and bacteriological properties of recovered water and for signaling malfunction in water recovery system. Monitor incorporates whenever possible commercially available sensors suitably modified

What comparative genomics tells us about the evolution of the eukaryotic recombination machinery

The growing number of completely deciphered genomic sequences provides an enormous reservoir of data, which can be used for addressing questions related to functional and evolutionary biology. The wealth of this approach is documented by the fast growing numbers of recent publications in the field of evolutionary biology based on comparative genomics. Many proteins of the recombination machinery are conserved between plants, fungi and animals but some of them also show remarkable differences regarding their presence, copy number or molecular structure. For example, the protein responsible for double strand break (DSB) induction during meiosis, SPO11, which is related to the subunit A of the archaebacterial topoisomerase VI, is coded by a single gene in animals and fungi. In contrast, plants harbour three distantly related homologues, which seem to have non-redundant functions either in meiosis or in somatic cells and are indispensable for viability. Moreover, plants possess a homologue of the subunit B of the archaebacterial topoisomerase VI, not present in other eukaryotes. We also summarise the recent progress in the usage of genomic data to analyse the evolution of other DNA recombination factors. Finally, several recent studies report on a strong conservation of a reasonable number of intron positions between plants, animals and fungi. This kind of study provides a basis for comparative genomic analyses across kingdoms and demonstrates the existence of ancient introns, a topic of intensive debate

The RecQ gene family in plants

structure and function. They are 30–50 DNA helicases resolving different recombinogenic DNA structures. The RecQ helicases are key factors in a number of DNA repair and recombination pathways involved in the maintenance of genome integrity. In eukaryotes the number of RecQ genes and the structure of RecQ proteins vary strongly between organisms. Therefore, they have been named RecQ-like genes. Knockouts of several RecQ-like genes cause severe diseases in animals or harmful cellular phenotypes in yeast. Until now the largest number of RecQ-like genes per organism has been found in plants. Arabidopsis and rice possess seven different RecQ-like genes each. In the almost completely sequenced genome of the moss Physcomitrella patens at least five RecQ-like genes are present. One of the major present and future research aims is to define putative plant-specific functions and to assign their roles in DNA repair and recombination pathways in relation to RecQ genes from other eukaryotes. Regarding their intron positions, the structures of six RecQ-like genes of dicots and monocots are virtually identical indicating a conservation over a time scale of 150 million years. In contrast to other eukaryotes one gene (RecQsim) exists exclusively in plants. It possesses an interrupted helicase domain but nevertheless seems to have maintained the RecQ function. Owing to a recent gene duplication besides the AtRecQl4A gene an additional RecQ-like gene (AtRecQl4B) exists in the Brassicaceae only. Genetic studies indicate that a AtRecQl4A knockout results in sensitivity to mutagens as well as an hyperrecombination phenotype. Since AtRecQl4B was still present, both genes must have non-redundant roles. Analysis of plant RecQ-like genes will not only increase the knowledge on DNA repair and recombination, but also on the evolution and radiation of protein families

On the efficient numerical solution of lattice systems with low-order couplings

We apply the Quasi Monte Carlo (QMC) and recursive numerical integration methods to evaluate the Euclidean, discretized time path-integral for the quantum mechanical anharmonic oscillator and a topological quantum mechanical rotor model. For the anharmonic oscillator both methods outperform standard Markov Chain Monte Carlo methods and show a significantly improved error scaling. For the quantum mechanical rotor we could, however, not find a successful way employing QMC. On the other hand, the recursive numerical integration method works extremely well for this model and shows an at least exponentially fast error scaling

Biochemical Characterization of an Exonuclease from Arabidopsis thaliana Reveals Similarities to the DNA Exonuclease of the Human Werner Syndrome Protein

The human Werner syndrome protein (hWRN-p) possessing DNA helicase and exonuclease activities is essential for genome stability. Plants have no homologue of this bifunctional protein, but surprisingly the Arabidopsis genome contains a small open reading frame (ORF) (AtWRNexo) with homology to the exonuclease domain of hWRN-p. Expression of this ORF in Escherichia coli revealed an exonuclease activity for AtWRNexo-p with similarities but also some significant differences to hWRN-p. The protein digests recessed strands of DNA duplexes in the 3\u27 -> 5\u27 direction but hardly single-stranded DNA or blunt-ended duplexes. In contrast to the Werner exonuclease, AtWRNexo-p is also able to digest 3\u27-protruding strands. DNA with recessed 3\u27-PO4 and 3\u27-OH termini is degraded to a similar extent. AtWRNexo-p hydrolyzes the 3\u27-recessed strand termini of duplexes containing mismatched bases. AtWRNexo-p needs the divalent cation Mg$^{2+}$ for activity, which can be replaced by Mn$^{2+}$. Apurinic sites, cholesterol adducts, and oxidative DNA damage (such as 8-oxoadenine and 8-oxoguanine) inhibit or block the enzyme. Other DNA modifications, including uracil, hypoxanthine and ethenoadenine, did not inhibit AtWRNexo-p. A mutation of a conserved residue within the exonuclease domain (E135A) completely abolished the exonucleolytic activity. Our results indicate that a type of WRN-like exonuclease activity seems to be a common feature of the DNA metabolism of animals and plants

Simple t-distribution Based Tests for Meta-Analysis

The variance function of the optimal estimator of the overall mean in a heteroscedastic one-way ANOVA model is dominated by positive semi-definite quadratic functions. This makes it possible to develop closely related tests on the nullity of the overall mean parameter, in one-way fifixed and random effects ANOVA models, which make use of the quantiles of the t-distribution. These tests are founded on the convexity arguments similar to Hartung (1976). Simulation results indicate that the proposed tests attain type I error rates which are far more acceptable than those of the commonly used tests

Alternative Test Procedures and Confidence Intervals on the Common Mean in the Fixed Effects Model for Meta-Analysis

The best linear unbiased estimator of the common mean in heteroscedastic one-way fixed effects model exists only if the values of the variance components are known. In practice this does not hold and so far there exists no consensus on the most suitable test for the common mean parameter. With respect to the attained significance levels, the

Positive estimation of the between-group variance component in one-way anova and meta-analysis

Positive estimators of the between-group (between-study) variance are proposed. Explicit variance formulae for the estimators are given and approximate confidence intervals for the between-group variance are constructed, as our proposal to a long outstanding problem. By Monte Carlo simulation, the bias and standard deviation of the proposed estimators are compared with the truncated versions of the maximum likelihood (ML) estimator, restricted maximum likelihood (REML) estimator and a (lately) standard estimator in meta-analysis. Attained confidence coefficients of the constructed confidence intervals are also presented