Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization

•Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location. •We have employed a combination of classical genetics and three-point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization. •We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of sequence containing 82 S-linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair. •These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus

Binding and Normalization of Binary Sparse Distributed Representations by Context-Dependent Thinning

Distributed representations were often criticized as inappropriate for encoding of data with a complex structure. However Plate's Holographic Reduced Representations and Kanerva's Binary Spatter Codes are recent schemes that allow on-the-fly encoding of nested compositional structures by real-valued or dense binary vectors of fixed dimensionality. In this paper we consider procedures of the Context-Dependent Thinning which were developed for representation of complex hierarchical items in the architecture of Associative-Projective Neural Networks. These procedures provide binding of items represented by sparse binary codevectors (with low probability of 1s). Such an encoding is biologically plausible and allows a high storage capacity of distributed associative memory where the codevectors may be stored. In contrast to known binding procedures, Context-Dependent Thinning preserves the same low density (or sparseness) of the bound codevector for varied number of component codevectors. Besides, a bound codevector is not only similar to another one with similar component codevectors (as in other schemes), but it is also similar to the component codevectors themselves. This allows the similarity of structures to be estimated just by the overlap of their codevectors, without retrieval of the component codevectors. This also allows an easy retrieval of the component codevectors. Examples of algorithmic and neural-network implementations of the thinning procedures are considered. We also present representation examples for various types of nested structured data (propositions using role-filler and predicate-arguments representation schemes, trees, directed acyclic graphs) using sparse codevectors of fixed dimension. Such representations may provide a fruitful alternative to the symbolic representations of traditional AI, as well as to the localist and microfeature-based connectionist representations

The rich behavior of the Boltzmann equation for dissipative gases

Within the framework of the homogeneous non-linear Boltzmann equation, we present a new analytic method, without the intrinsic limitations of existing methods, for obtaining asymptotic solutions. This method permits extension of existing results for Maxwell molecules and hard spheres to large classes of particle interactions, from very hard spheres to softer than Maxwell molecules, as well as to more general forcing mechanisms, beyond free cooling and white noise driving. By combining this method with numerical solutions, obtained from the Direct Simulation Monte Carlo (DSMC) method, we study a broad class of models relevant for the dynamics of dissipative fluids, including granular gases. We establish a criterion connecting the stability of the non-equilibrium steady state to an exponentially bound form for the velocity distribution $F$, which varies depending on the forcing mechanism. Power laws arise in marginal stability cases, of which several new cases are reported. Our results provide a minimal framework for interpreting large classes of experiments on driven granular gases

Boltzmann equation for dissipative gases in homogeneous states with nonlinear friction

Combining analytical and numerical methods, we study within the framework of the homogeneous non-linear Boltzmann equation, a broad class of models relevant for the dynamics of dissipative fluids, including granular gases. We use the new method presented in a previous paper [J. Stat. Phys. 124, 549 (2006)] and extend our results to a different heating mechanism, namely a deterministic non-linear friction force. We derive analytically the high energy tail of the velocity distribution and compare the theoretical predictions with high precision numerical simulations. Stretched exponential forms are obtained when the non-equilibrium steady state is stable. We derive sub-leading corrections and emphasize their relevance. In marginal stability cases, power-law behaviors arise, with exponents obtained as the roots of transcendental equations. We also consider some simple BGK (Bhatnagar, Gross, Krook) models, driven by similar heating devices, to test the robustness of our predictions

Velocity Tails for Inelastic Maxwell Models

We study the velocity distribution function for inelastic Maxwell models, characterized by a Boltzmann equation with constant collision rate, independent of the energy of the colliding particles. By means of a nonlinear analysis of the Boltzmann equation, we find that the velocity distribution function decays algebraically for large velocities, with exponents that are analytically calculated.Comment: 4 pages, 2 figure

Lipopolysaccharide is a frequent contaminant of plasmid DNA preparations and can be toxic to primary cells in the presence of adenovirus

Endotoxin (lipopolysaccharide, LPS) is commonly found as a contaminant in plasmid DNA preparations. We demonstrate here that the quantities of LPS typically contaminating DNA preparations can generate a toxicity to primary cells (primary human skin fibroblasts, primary human melanoma cells) in the presence of entry-competent adenovirus particles. Toxicity can be observed with as little as 100 ng/ml free LPS or 100 pg/ml LPS when the LPS is assembled into polylysine/adenovirus complexes. Simple and effective methods of removing the contaminating LPS using either a polymyxin B resin or Triton X-114 extraction are described. Treatment of DNA samples to remove LPS eliminates the toxicity to primary cells

Automotive Stirling Engine Development Program

Activities performed on Mod I engine testing and test results; the manufacture, assembly, and test of a Mod I engine in the United States; design initiation of the Mod I-A engine system; transient performance testing; Stirling reference engine manufacturing and reduced size studies; components and subsystems; and the study and test of low cost alloys are summarized

Increased C3 productivity in Midwestern lawns since 1982 revealed by carbon isotopes in Amanita thiersii

How climate and rising carbon dioxide concentrations (pCO2) have influenced competition between C3 and C4 plants over the last 50 years is a critical uncertainty in climate change research. Here we used carbon isotope (δ13C) values of the saprotrophic lawn fungus Amanita thiersii to integrate the signal of C3 and C4 carbon in samples collected between 1982 and 2009 from the Midwestern USA. We then calculated 13C fractionation (Δ) to assess the balance between C3 and C4 photosynthesis as influenced by mean annual temperature (MAT), mean annual precipitation over a 30 year period (MAP‐30), and pCO2. Sporocarp Δ correlated negatively with MAT (−1.74‰ °C−1, 79% of variance) and positively with MAP (9.52‰ m−1, 15% of variance), reflecting the relative productivity of C3 and C4 grasses in lawns. In addition, Δ values correlated positively with pCO2 (0.072‰ ppm−1, 5% of variance). Reduced photorespiration with rising pCO2 accounted for 20% of this increased Δ, but the remaining 80% is consistent with increased assimilation of C3‐derived carbon by Amanita thiersii resulting from increased productivity of C3 grasses with rising pCO2. Between 1982 and 2009, pCO2 rose by 46 ppm and the relative contribution of C3 photosynthesis to Amanita thiersii carbon increased 18.5%. The δ13C value of Amanita thiersii may integrate both lawn maintenance practices and the physiological responses of turf grasses to rising CO2 concentrations