Analysis of QTL for high grain protein content in Canadian durum wheat

Non-Peer ReviewedDurum wheat (Triticum turgidum L. var. durum) varieties with high grain protein concentration (GPC) produce pasta products with greater cooking firmness and increased tolerance to overcooking. However, the large environmental effect on expression of GPC and the negative correlation between GPC and grain yield slow breeding progress of durum wheat varieties with elevated GPC. Identification of molecular markers associated with high GPC would aid durum wheat breeders to select for this important trait earlier. The objectives of this study were to identify molecular markers associated with quantitative trait loci (QTL) for elevated GPC in durum wheat. A preliminary genetic map was constructed by screening polymorphic microsatellite markers on a set of 95 double haploid lines derived from the cross Strongfield (high GPC) X DT695 (low GPC). QTL analysis using single marker regression was performed on GPC data collected at Swift Current and Regina in 2002 and Swift Current, Regina and Saskatoon in 2003. To date, we have identified two QTL for GPC flanked by Xgwm448 and Xgwm558 on chromosome 2AS, and on chromosome 2BL at wmc332. No QTL for high GPC could be detected on chromosome 6BS, the location of a high GPC gene isolated previously from durum, wheat suggesting that Strongfield contains novel QTL for high GPC not previously reported in the literature. The molecular markers flanking the QTL identified in this study can be used by durum wheat breeders to enhance selection of high GPC in durum wheat

An almost sure limit theorem for super-Brownian motion

We establish an almost sure scaling limit theorem for super-Brownian motion on $\mathbb{R}^d$ associated with the semi-linear equation $u_t = {1/2}\Delta u +\beta u-\alpha u^2$, where $\alpha$ and $\beta$ are positive constants. In this case, the spectral theoretical assumptions that required in Chen et al (2008) are not satisfied. An example is given to show that the main results also hold for some sub-domains in $\mathbb{R}^d$.Comment: 14 page

Special section on advances in reachability analysis and decision procedures: contributions to abstraction-based system verification

Reachability analysis asks whether a system can evolve from legitimate initial states to unsafe states. It is thus a fundamental tool in the validation of computational systems - be they software, hardware, or a combination thereof. We recall a standard approach for reachability analysis, which captures the system in a transition system, forms another transition system as an over-approximation, and performs an incremental fixed-point computation on that over-approximation to determine whether unsafe states can be reached. We show this method to be sound for proving the absence of errors, and discuss its limitations for proving the presence of errors, as well as some means of addressing this limitation. We then sketch how program annotations for data integrity constraints and interface specifications - as in Bertrand Meyers paradigm of Design by Contract - can facilitate the validation of modular programs, e.g., by obtaining more precise verification conditions for software verification supported by automated theorem proving. Then we recap how the decision problem of satisfiability for formulae of logics with theories - e.g., bit-vector arithmetic - can be used to construct an over-approximating transition system for a program. Programs with data types comprised of bit-vectors of finite width require bespoke decision procedures for satisfiability. Finite-width data types challenge the reduction of that decision problem to one that off-the-shelf tools can solve effectively, e.g., SAT solvers for propositional logic. In that context, we recall the Tseitin encoding which converts formulae from that logic into conjunctive normal form - the standard format for most SAT solvers - with only linear blow-up in the size of the formula, but linear increase in the number of variables. Finally, we discuss the contributions that the three papers in this special section make in the areas that we sketched above. © Springer-Verlag 2009

Compile-Time Analysis and Specialization of Clocks in Concurrent Programs

Clocks are a mechanism for providing synchronization barriers in concurrent programming languages. They are usually implemented using primitive communication mechanisms and thus spare the programmer from reasoning about low-level implementation details such as remote procedure calls and error conditions. Clocks provide flexibility, but programs often use them in specific ways that do not require their full implementation. In this paper, we describe a tool that mitigates the overhead of general-purpose clocks by statically analyzing how programs use them and choosing optimized implementations when available. We tackle the clock implementation in the standard library of the X10 programming language—a parallel, distributed object-oriented language. We report our findings for a small set of analyses and benchmarks. Our tool only adds a few seconds to analysis time, making it practical to use as part of a compilation chain

Does the Red Queen reign in the kingdom of digital organisms?

In competition experiments between two RNA viruses of equal or almost equal fitness, often both strains gain in fitness before one eventually excludes the other. This observation has been linked to the Red Queen effect, which describes a situation in which organisms have to constantly adapt just to keep their status quo. I carried out experiments with digital organisms (self-replicating computer programs) in order to clarify how the competing strains' location in fitness space influences the Red-Queen effect. I found that gains in fitness during competition were prevalent for organisms that were taken from the base of a fitness peak, but absent or rare for organisms that were taken from the top of a peak or from a considerable distance away from the nearest peak. In the latter two cases, either neutral drift and loss of the fittest mutants or the waiting time to the first beneficial mutation were more important factors. Moreover, I found that the Red-Queen dynamic in general led to faster exclusion than the other two mechanisms.Comment: 10 pages, 5 eps figure

AUTSEG: Automatic Test Set Generator for Embedded Reactive Systems

Part 2: Tools and FrameworksInternational audienceOne of the biggest challenges in hardware and software design is to ensure that a system is error-free. Small errors in reactive embedded systems can have disastrous and costly consequences for a project. Preventing such errors by identifying the most probable cases of erratic system behavior is quite challenging. In this paper, we introduce an automatic test set generator called AUTSEG. Its input is a generic model of the target system, generated using the synchronous approach. Our tool finds the optimal preconditions for restricting the state space of the model. It only works locally on significant subspaces. Our approach exhibits a simpler and efficient quasi-flattening algorithm than existing techniques and a useful compiled form to check security properties and reduce the combinatorial explosion problem of state space. To illustrate our approach, AUTSEG was applied to the case of a transportation contactless card

Discrete cilia modelling with singularity distributions

We discuss in detail techniques for modelling flows due to finite and infinite arrays of beating cilia. An efficient technique, based on concepts from previous ‘singularity models’ is described, that is accurate in both near and far-fields. Cilia are modelled as curved slender ellipsoidal bodies by distributing Stokeslet and potential source dipole singularities along their centrelines, leading to an integral equation that can be solved using a simple and efficient discretisation. The computed velocity on the cilium surface is found to compare favourably with the boundary condition. We then present results for two topics of current interest in biology. 1) We present the first theoretical results showing the mechanism by which rotating embryonic nodal cilia produce a leftward flow by a ‘posterior tilt,’ and track particle motion in an array of three simulated nodal cilia. We find that, contrary to recent suggestions, there is no continuous layer of negative fluid transport close to the ciliated boundary. The mean leftward particle transport is found to be just over 1 μm/s, within experimentally measured ranges. We also discuss the accuracy of models that represent the action of cilia by steady rotlet arrays, in particular, confirming the importance of image systems in the boundary in establishing the far-field fluid transport. Future modelling may lead to understanding of the mechanisms by which morphogen gradients or mechanosensing cilia convert a directional flow to asymmetric gene expression. 2) We develop a more complex and detailed model of flow patterns in the periciliary layer of the airway surface liquid. Our results confirm that shear flow of the mucous layer drives a significant volume of periciliary liquid in the direction of mucus transport even during the recovery stroke of the cilia. Finally, we discuss the advantages and disadvantages of the singularity technique and outline future theoretical and experimental developments required to apply this technique to various other biological problems, particularly in the reproductive system