BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)

<p>Abstract</p> <p>Background</p> <p>In animals, signaling of Bone Morphogenetic Proteins (BMPs) is essential for dorsoventral (DV) patterning of the embryo, but how BMP signaling evolved with changes in embryonic DV differentiation is largely unclear. Based on the extensive knowledge of BMP signaling in <it>Drosophila melanogaster</it>, the morphological diversity of extraembryonic tissues in different fly species provides a comparative system to address this question. The closest relatives of <it>D. melanogaster </it>with clearly distinct DV differentiation are hover flies (Diptera: Syrphidae). The syrphid <it>Episyrphus balteatus </it>is a commercial bio-agent against aphids and has been established as a model organism for developmental studies and chemical ecology. The dorsal blastoderm of <it>E. balteatus </it>gives rise to two extraembryonic tissues (serosa and amnion), whereas in <it>D. melanogaster</it>, the dorsal blastoderm differentiates into a single extraembryonic epithelium (amnioserosa). Recent studies indicate that several BMP signaling components of <it>D. melanogaster</it>, including the BMP ligand Screw (Scw) and other extracellular regulators, evolved in the dipteran lineage through gene duplication and functional divergence. These findings raise the question of whether the complement of BMP signaling components changed with the origin of the amnioserosa.</p> <p>Results</p> <p>To search for BMP signaling components in <it>E. balteatus</it>, we generated and analyzed transcriptomes of freshly laid eggs (0-30 minutes) and late blastoderm to early germband extension stages (3-6 hours) using Roche/454 sequencing. We identified putative <it>E. balteatus </it>orthologues of 43% of all annotated <it>D. melanogaster </it>genes, including the genes of all BMP ligands and other BMP signaling components.</p> <p>Conclusion</p> <p>The diversification of several BMP signaling components in the dipteran linage of <it>D. melanogaster </it>preceded the origin of the amnioserosa.</p> <p>[Transcriptome sequence data from this study have been deposited at the NCBI Sequence Read Archive (SRP005289); individually assembled sequences have been deposited at GenBank (<ext-link ext-link-id="JN006969" ext-link-type="gen">JN006969</ext-link>-<ext-link ext-link-id="JN006986" ext-link-type="gen">JN006986</ext-link>).]</p

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

Interactive SIMD ray tracing for large deformable tetrahedral meshes

We introduce an interactive ray tracing method for large deformable tetrahedral meshes which has carefully been designed for supporting general single instruction multiple data (SIMD) operations. It uses memory aligned and SIMD-friendly hierarchical acceleration structures and tetrahedron acceleration data allowing SIMD ray traversal and a newly proposed SIMD barycentric tetrahedron-plane intersection test. The method is very general and allows volume-, opaque- and accelerated (semi) iso surface-rendering as well as visualizing multidimensional data. It scales for static data sets sublinear to data size, such that it is well suited for visualizing massive data sets. The method is also very portable and not restricted to specialized hardware, such that it natively supports near future hardware which will be many core architectures supporting up to 512-bit register operations, allowing for each core to trace up to 16 rays at once through the mesh

Formal verification of a grid resource allocation protocol

As the adoption of grid technology moves from science to industry, new requirements arise. In todays grid middlewares, the notion of paying for a job is a secondary requirement. In addition, the concept of selling computational power on a market is not established. On the other hand, the lack of billing capabilities hinders the commercial adoption. In this paper, we present our resource allocation protocol that suits the needs of commercial solution providers. We have developed an auction-based resource broker which uses a distributed agent infrastructure to communicate the user's requirements to resource providers and monetary prices back. The protocol has been formally verified and guarantees certain properties - for example, we can guarantee that the right stakeholder is billed for a job

Infiniband-verbs on GPU: A case study of controlling an infiniband network device from the GPU

Due to their massive parallelism and high performance per watt GPUs gain high popularity in high performance computing and are a strong candidate for future exacscale systems. But communication and data transfer in GPU accelerated systems remain a challenging problem. Since the GPU normally is not able to control a network device, today a hybrid-programming model is preferred, whereby the GPU is used for calculation and the CPU handles the communication. As a result, communication between distributed GPUs suffers from unnecessary overhead, introduced by switching control flow from GPUs to CPUs and vice versa. In this work, we modify user space libraries and device drivers of GPUs and the Infiniband network device in a way to enable the GPU to control an Infiniband network device to independently source and sink communication requests without any involvements of the CPU. Our performance analysis shows the differences to hybrid communication models in detail, in particular that the CPU's advantage in generating work requests outshines the overhead associated with context switching. In other terms, our results show that complex networking protocols like IBVERBS are better handled by CPUs in spite of time penalties due to context switching, since overhead of work request generation cannot be parallelized and is not suitable with the high parallel programming model of GPUs

on parallel

On the efficiency of simulation methods for the Boltzmann equatio

Adaptive Load Balance Techniques in Parallel Rarefied Gas Simulations

The paper presents some adaptive load balance techniques for the simulation of rarefied gas flows on parallel computers. It is shown that a static load balance is insufficient to obtain a scalable parallel efficiency. Hence, two adaptive techniques are investigated which are based on simple algorithms. Numerical results show that using heuristic techniques one can achieve a sufficiently high efficiency over a wide range of different hardware platforms. 1 Introduction Particle or Monte--Carlo methods are efficient numerical tools to predict rarefied gas flows around re--entry bodies. Besides the well--known DSMC approach developed by Bird [5], the Finite--Pointset Method as described in [8] has been widely used to investigate rarefied gas flows [3], [4], [10]. Moreover, is is known, that -- in general -- Monte--Carlo methods can be implemented more easy on parallel architecture then other methods, like, e.g., FEM--computations. The same holds for particle schemes for rarefied gas simul..

A method for the analysis and control of mica tape impregnation processes

The impregnation of mica tape insulations usually is monitored with dielectric capacitance measurements. In this work, a method is developed that translates measured capacitance and loss into an average drag coefficient that characterizes flow resistance, which is the critical parameter of the process. In a first step, the impregnation depth is determined based on an appropriate model of the dielectric measurement. The impregnation depth curve and its derivative are then used to compute the average drag coefficient, which is defined in the framework of a standard porous media flow model. The method has been developed and tested for cylindrical insulators. Appropriate extensions to rectangular insulators are indicated