Purification and Characterization of a Gamma-Like DNA-Polymerase From \u3ci\u3eChenopodium album\u3c/i\u3e L.

A DNA polymerase activity from mitochondria of the dicotyledonous angiosperm Chenopodium album L. was purified almost 9000 fold by successive column chromatography steps on DEAE cellulose, heparin agarose and ssDNA cellulose. The enzyme was characterized as a gamma-class polymerase, based on its resistance to inhibitors of the nuclear DNA polymerase alpha and its preference for poly(rA).(dT)12-18 over activated DNA in vitro. The molecular weight was estimated to be 80,000 - 90,000. A 3\u27 to 5\u27 exonuclease activity was found to be tightly associated with the DNA polymerase activity through all purification steps. This is the first report of an association between a DNA polymerase and an exonuclease activity in plant mitochondria

Constraint Satisfaction with Counting Quantifiers

We initiate the study of constraint satisfaction problems (CSPs) in the presence of counting quantifiers, which may be seen as variants of CSPs in the mould of quantified CSPs (QCSPs). We show that a single counting quantifier strictly between exists^1:=exists and exists^n:=forall (the domain being of size n) already affords the maximal possible complexity of QCSPs (which have both exists and forall), being Pspace-complete for a suitably chosen template. Next, we focus on the complexity of subsets of counting quantifiers on clique and cycle templates. For cycles we give a full trichotomy -- all such problems are in L, NP-complete or Pspace-complete. For cliques we come close to a similar trichotomy, but one case remains outstanding. Afterwards, we consider the generalisation of CSPs in which we augment the extant quantifier exists^1:=exists with the quantifier exists^j (j not 1). Such a CSP is already NP-hard on non-bipartite graph templates. We explore the situation of this generalised CSP on bipartite templates, giving various conditions for both tractability and hardness -- culminating in a classification theorem for general graphs. Finally, we use counting quantifiers to solve the complexity of a concrete QCSP whose complexity was previously open

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. We also find that communication between different disciplines goes through specific "trading zones", ie sub-communities that create an interface around specific tools (a DNA microchip) or concepts (a network).Comment: Journal of the American Society for Information Science and Technology (2012) 10.1002/asi.2264

Quantifying structure in networks

We investigate exponential families of random graph distributions as a framework for systematic quantification of structure in networks. In this paper we restrict ourselves to undirected unlabeled graphs. For these graphs, the counts of subgraphs with no more than k links are a sufficient statistics for the exponential families of graphs with interactions between at most k links. In this framework we investigate the dependencies between several observables commonly used to quantify structure in networks, such as the degree distribution, cluster and assortativity coefficients.Comment: 17 pages, 3 figure

Chromosomal location and mapping of quantitative trait locus determining technological parameters of grain and flour in strong-flour bread wheat cultivar saratovskaya 29

Bread wheat is the primary bread crop in the majority of countries in the world. The most important product that is manufactured from its grain and flour is yeast bread. In order to obtain an excellent bread, grain with high physical properties is needed for flour and dough. The Russian spring wheat cultivar Saratovskaya 29 is characterized by its exclusively high physical properties of flour and dough. The purpose of this work was to identify the chromosomes carrying the main loci for these traits in Saratovskaya 29 and to map them using recombinant substitution lines genotyped with molecular markers. A set of inter-varietal substitution lines Saratovskaya 29 (Yanetzkis Probat) was used to identify the “critical” chromosomes. The donor of individual chromosomes is a spring cultivar with average dough strength and tenacity. Substitution of 1D and 4D*7A chromosomes in the genetic background of Saratovskaya 29 resulted in a significant decrease in the physical properties of the dough. Such a deterioration in the case of 1D chromosome might be related to the variability of gluten protein composition. With the help of recombinant substitution double haploid lines obtained from a Saratovskaya 29 (Yanetzkis Probat 4D*7A) substitution line the region on the 4D chromosome was revealed in the strong-flour cultivar Saratovskaya 29, with the microsatellite locus Xgwm0165 to be associated with the unique physical properties of flour and dough. The detected locus is not related to the composition gluten proteins. These locus may be recommended to breeders for the selection of strong-flour cultivars. Additionally, a QTL associated with vitreousness of grain was mapped in the short arm of chromosome 7A

Age of the Universe: Influence of the Inhomogeneities on the global Expansion-Factor

For the first time we calculate quantitatively the influence of inhomogeneities on the global expansion factor by averaging the Friedmann equation. In the framework of the relativistic second-order Zel'dovich-approximation scheme for irrotational dust we use observational results in form of the normalisation constant fixed by the COBE results and we check different power spectra, namely for adiabatic CDM, isocurvature CDM, HDM, WDM, Strings and Textures. We find that the influence of the inhomogeneities on the global expansion factor is very small. So the error in determining the age of the universe using the Hubble constant in the usual way is negligible. This does not imply that the effect is negligible for local astronomical measurements of the Hubble constant. Locally the determination of the redshift-distance relation can be strongly influenced by the peculiar velocity fields due to inhomogeneities. Our calculation does not consider such effects, but is contrained to comparing globally homogeneous and averaged inhomogeneous matter distributions. In addition we relate our work to previous treatments.Comment: 10 pages, version accepted by Phys. Rev.

Anharmonic double-phonon excitations in the interacting boson model

Double-$\gamma$ vibrations in deformed nuclei are analyzed in the context of the interacting boson model. A simple extension of the original version of the model towards higher-order interactions is required to explain the observed anharmonicities of nuclear vibrations. The influence of three- and four-body interactions on the moments of inertia of ground- and $\gamma$-bands, and on the relative position of single-$\gamma$ and double-$\gamma$ bands is studied in detail. As an example of a realistic calculation, spectra and transitions of the highly $\gamma$-anharmonic nuclei $^{164}$Dy, $^{166}$Er, and $^{168}$Er are interpreted in this approach.Comment: 38 pages, TeX (ReVTeX). 15 ps figures. Submitted to Phys. Rev.

Study of the neutron quantum states in the gravity field

We have studied neutron quantum states in the potential well formed by the earth's gravitational field and a horizontal mirror. The estimated characteristic sizes of the neutron wave functions in the two lowest quantum states correspond to expectations with an experimental accuracy. A position-sensitive neutron detector with an extra-high spatial resolution of ~2 microns was developed and tested for this particular experiment, to be used to measure the spatial density distribution in a standing neutron wave above a mirror for a set of some of the lowest quantum states. The present experiment can be used to set an upper limit for an additional short-range fundamental force. We studied methodological uncertainties as well as the feasibility of improving further the accuracy of this experiment

On globally static and stationary cosmologies with or without a cosmological constant and the Dark Energy problem

In the framework of spatially averaged inhomogeneous cosmologies in classical General Relativity, effective Einstein equations govern the regional and the global dynamics of averaged scalar variables of cosmological models. A particular solution may be characterized by a cosmic equation of state. In this paper it is pointed out that a globally static averaged dust model is conceivable without employing a compensating cosmological constant. Much in the spirit of Einstein's original model we discuss consequences for the global, but also for the regional properties of this cosmology. We then consider the wider class of globally stationary cosmologies that are conceivable in the presented framework. All these models are based on exact solutions of the averaged Einstein equations and provide examples of cosmologies in an out-of-equilibrium state, which we characterize by an information-theoretical measure. It is shown that such cosmologies preserve high-magnitude kinematical fluctuations and so tend to maintain their global properties. The same is true for a $\Lambda-$driven cosmos in such a state despite of exponential expansion. We outline relations to inflationary scenarios, and put the Dark Energy problem into perspective. Here, it is argued, on the grounds of the discussed cosmologies, that a classical explanation of Dark Energy through backreaction effects is theoretically conceivable, if the matter-dominated Universe emerged from a non-perturbative state in the vicinity of the stationary solution. We also discuss a number of caveats that furnish strong counter arguments in the framework of structure formation in a perturbed Friedmannian model.Comment: 33 pages, matches published version in Class. Quant. Gra

Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality

<p>Abstract</p> <p>Background</p> <p>The increasingly narrow genetic background characteristic of modern crop germplasm presents a challenge for the breeding of cultivars that require adaptation to the anticipated change in climate. Thus, high priority research aims at the identification of relevant allelic variation present both in the crop itself as well as in its progenitors. This study is based on the characterization of genetic variation in barley, with a view to enhancing its response to terminal drought stress.</p> <p>Results</p> <p>The expression patterns of drought regulated genes were monitored during plant ontogeny, mapped and the location of these genes was incorporated into a comprehensive barley SNP linkage map. Haplotypes within a set of 17 starch biosynthesis/degradation genes were defined, and a particularly high level of haplotype variation was uncovered in the genes encoding sucrose synthase (types I and II) and starch synthase. The ability of a panel of 50 barley accessions to maintain grain starch content under terminal drought conditions was explored.</p> <p>Conclusion</p> <p>The linkage/expression map is an informative resource in the context of characterizing the response of barley to drought stress. The high level of haplotype variation among starch biosynthesis/degradation genes in the progenitors of cultivated barley shows that domestication and breeding have greatly eroded their allelic diversity in current elite cultivars. Prospective association analysis based on core drought-regulated genes may simplify the process of identifying favourable alleles, and help to understand the genetic basis of the response to terminal drought.</p