A Cis-Regulatory Map of the Drosophila Genome

Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide1, 2 has successfully identified specific subtypes of regulatory elements3. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements4, chromatin states5, transcription factor binding sites6, 7, 8, 9, RNA polymerase II regulation8 and insulator elements10; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships

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

Solidification Modeling of a Spiral Casting to Determine Material Fluidity by DISTRIBUTION OF THIS DOCUMENT IS UNLIMITED Solidification Modeling of a Spiral Casting to Determine Material Fluidity

Abstract In casting, fluidity is the measure of the distance a metal can flow in a channel before being stopped by solidification. During mold filling, the metal loses heat to the surrounding mold, thereby cooling and becoming more viscous until the leading portion solidifies and no further flow is possible. A coupled heat-transfer and fluid-flow modeling of a spiral, involving the use of thermophysical properties to determine material fluidity, has been conducted. Fluidity experiments were performed by Caterpillar; several spiral test castings were poured. Simulations of these experiments utilized the Casting Process Simulator (CaPS) software developed at Argonne National Laboratory. Two types of spiral geometries with different assumptions were considered: (1) a two-dimensional laterally stretched spiral and (2) a three-dimensional lateral spiral. The computed extent of mold filling is in good agreement with the experimental results. Time required by the metal/gas interface to attain specific positions in the spiral arm also compares favorably with the experimental results. &apos;The influence of process variables, especially pour time, is discussed. The CaPS software has been used as a computational tool to investigate the validity of the dimensionality assumptions and to evaluate the ability of CaPS to model fluidity adequately. iii Content

Experiment data report IFA-226 postirradiation examination. [PWR, BWR]

IFA-226 contained twelve, mixed plutonium-uranium oxide fuel rods arranged in two, six-rod clusters. The assembly was designed to study fuel-cladding mechanical interaction, fuel thermal response, and fission gas release as a function of fuel density, initial fuel-to-cladding gap, rod power, and burnup. Data were obtained from fuel rod centerline thermocouples, fission gas pressure transducers, and cladding elongation sensors. Results of both nondestructive and destructive examinations are presented. The PIE indicated that one fuel rod failed during service as a result of internal hydriding of the end plug. Circumferential cladding ridges resulting from fuel-cladding interaction were present on all of the rods, with the largest ridges present on the rod with the smallest initial fuel-to-cladding gap. No incipient fuel rod failures were detected

Argonne National Laboratory Reports

In casting, fluidity is the measure of the distance a metal can flow in a channel before being stopped by solidification. During mold filling, the metal loses heat to the surrounding mold, thereby cooling and becoming more viscous until the leading portion solidifies and no further flow is possible. A coupled heat-transfer and fluid-flow modeling of a spiral, involving the use of thermophysical properties to determine material fluidity, has been conducted. Simulations of these experiments utilized the Casting Process Simulator (CaPS) software developed at Argonne National Laboratory. Two types of spiral geometries with different assumptions were considered: (1) a two-dimensional laterally stretched spiral and (2) a three-dimensional lateral spiral. The computer extent of mold filling is in good agreement with the experimental results. Time required by the metal/gas interface to attain specific positions in the spiral arm also compares favorably with the experimental results. The influence of process variables, especially pour time, is discussed. The CaPS software has been used as a computational tool to investigate the validity of the dimensionality assumptions and to evaluate the ability of CaPS to model fluidity adequately

Recent advances in the COMMIX and BODYFIT codes

Two general-purpose computer programs for thermal-hydraulic analysis have been developed. One is the COMMIX (COMponent MIXing code. The other one is the BODYFIT (BOunDary FITted Coordinate Transformation) code. Solution procedures based on both elliptical and parabolic systems of partial differential equations are provided in these two codes. The COMMIX code is designed to provide global analysis of thermal-hydraulic behavior of a component or multicomponent of engineering problems. The BODYFIT code is capable of treating irregular boundaries and gives more detailed local information on a subcomponent or component. These two codes are complementary to each other and represent the state-of-the-art of thermal-hydraulic analysis. Effort will continue to make further improvements and include additional capabilities in these codes

Application of volume-weighted skew-upwind differencing to thermal and fluid mixing in the cold leg and downcomer of a PWR

Upwind differencing has been the most common numerical scheme used in computational fluid flow and heat transfer in past years. However, the numerical diffusion induced by the use of upwind differencing can be significant in problems involving thermal mixing. Thermal and fluid mixing in a pressurized water reactor during high pressurized coolant injection is a typical example where numerical diffusion is significant. An improved volume-weighted skew-upwind differencing is used here to reduce numerical diffusion without overshooting or undershooting which is the major defect of original skew-upwind differencing proposed by Raithby. The basic concept of volume-weighted skew-upwind differencing is shown. Computations were performed using COMMIX-1B, an extended version of the COMMIX-1A. The experiment analyzed here is test No. 1 of the SAI experiment

In-vessel thermal-hydraulic analysis

This paper presents some recent results obtained from the COMMIX-1A code for the EBR-II reactor transient No. 10, Phase 2. Both the reactor vessel and the neutron shield assembly and assembly arrangement in the reactor core are shown. The computational grid system used in COMMIX-1A is presented. Reactor flow and power transients are shown. Velocity and temperature distributions at steady state and t (time) = 60 sec are included. Finally, a comparison between the calculated results from COMMIX-1A and experimental measurements are presented for outlet temperatures for driver subassembly of XX08, top-of-core temperature for driver subassembly of XX08, and low-pressure plenum mass flow respectively

Argonne National Laboratory Reports

COMMIX-SA-1 is a three-dimensional, transient, single-phase, compressible-flow, component computer program for thermohydrodynamic analysis. It was developed for solar applications in general, and for analysis of thermocline storage tanks in particular. The conservation equations (in cylindrical coordinates) for mass, momentum, and energy are solved as an initial-boundary-value problem. The detailed numerical-solution procedure based on a modified ICE (Implicit Continuous-Fluid Eulerian) technique is described. A method for treating the singularity problem arising at the origin of a cylindrical-coordinate system is presented. In addition, the thermal interactions between fluid and structures (tank walls, baffles, etc.) are explicitly accounted for. Finally, the COMMIX-SA-1 code structure is delineated, and an input description and sample problems are presented