We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

/pdf/the-genome-of-the-mesopolyploid-crop-species-brassica-rapa-54ka2hnfpp.pdf

The genome of the mesopolyploid crop species Brassica rapa

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

http://science.sciencemag.org/content/sci/345/6199/950.full.pdf

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

ing WS1S Systems to Verify Parameterized Networks . . . . . . . . . . . . 188 Kai Baukus, Saddek Bensalem, Yassine Lakhnech and Karsten Stahl FMona: A Tool for Expressing Validation Techniques over Infinite State Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 J.-P. Bodeveix and M. Filali Transitive Closures of Regular Relations for Verifying Infinite-State Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220 Bengt Jonsson and Marcus Nilsson Diagnostic and Test Generation Using Static Analysis to Improve Automatic Test Generation . . . . . . . . . . . . . 235 Marius Bozga, Jean-Claude Fernandez and Lucian Ghirvu Efficient Diagnostic Generation for Boolean Equation Systems . . . . . . . . . . . . 251 Radu Mateescu Efficient Model-Checking Compositional State Space Generation with Partial Order Reductions for Asynchronous Communicating Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266 Jean-Pierre Krimm and Laurent Mounier Checking for CFFD-Preorder with Tester Processes . . . . . . . . . . . . . . . . . . . . . . . 283 Juhana Helovuo and Antti Valmari Fair Bisimulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299 Thomas A. Henzinger and Sriram K. Rajamani Integrating Low Level Symmetries into Reachability Analysis . . . . . . . . . . . . . 315 Karsten Schmidt Model-Checking Tools Model Checking Support for the ASM High-Level Language . . . . . . . . . . . . . . 331 Giuseppe Del Castillo and Kirsten Winter Table of

Tools and Algorithms for the Construction and Analysis of Systems. Proc. TACAS 2009

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

/pdf/sequencing-of-allotetraploid-cotton-gossypium-hirsutum-l-acc-3aex1man4n.pdf

Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

A 7-year-old, 1.76 kg Maltese dog presented with a 4-year history of a chronic pustular lesion and a wet cough. Erosive lesions were seen at the left thoracic wall. Radiology and computed tomography (CT) revealed a bronchocutaneous fistula connecting from the left cranial bronchus to the skin. On definitive surgery, a long wooden toothpick was observed within this tract, and clinical signs resolved after retrieval of the foreign body. Three-dimensional CT was useful to identify the characteristics of the bronchocutaneous fistula. However, the wooden foreign body was not apparent on CT. Here, we report the clinical, clinicopathological and diagnostic imaging findings of a chronic bronchocutaneous fistula caused by a foreign body in a dog.

Chronic Bronchocutaneous Fistula Caused by Toothpick Foreign Body in a Maltese Dog

A Preliminary Report on Static Analysis of C Code for Nuclear Reactor Protection System

Conventional solution-processing techniques such as the spin-coating method have been used successfully to reveal excellent properties of organic-inorganic halide perovskites (OHPs) for optoelectronic devices such as solar cell and light-emitting diode, but it is essential to explore other deposition techniques compatible with large-scale production. Single-source flash evaporation technique, in which a single source of materials of interest is rapidly heated to be deposited in a few seconds, is one of the candidate techniques for large-scale thin film deposition of OHPs. In this work, we investigated the reliability and controllability of the single-source flash evaporation technique for methylammonium lead iodide (MAPbI3) perovskite. In-depth statistical analysis was employed to demonstrate that the MAPbI3 films prepared via the flash evaporation have an ultrasmooth surface and uniform thickness throughout the 4-inch wafer scale. We also show that the thickness and grain size of the MAPbI3 film can be controlled by adjusting the amount of the source and number of deposition steps. Finally, the excellent large-area uniformity of the physical properties of the deposited thin films can be transferred to the uniformity in the device performance of MAPbI3 photodetectors prepared by flash evaporation which exhibited the responsivity of 0.2 A/W and detectivity of 3.82 × 1011 Jones.

/pdf/controllable-deposition-of-organic-metal-halide-perovskite-20gs1o7j47.pdf

Controllable deposition of organic metal halide perovskite films with wafer-scale uniformity by single source flash evaporation.

Resistive Switching by Percolative Conducting Filaments in Organometal Perovskite Unipolar Memory Devices Analyzed Using Current Noise Spectra

A memory device can include: a memory cell array including a memory cell and a word line that is connected to the memory cell; a clock generator configured to generate a first pumping clock signal from a system clock signal; a charge pump configured to provide a pumping voltage signal using a power supply voltage and the first pumping clock signal; a compensation circuit configured to compensate for variations in a first reference clock signal in accordance with variations in the power supply voltage, and provide a compensated first reference clock signal; and a pass/fail (P/F) determining circuit configured to determine whether the word line is defective by comparing the first pumping clock signal and the compensated first reference clock signal while the pumping voltage signal is provided to the word line.

Jonghoon Lee

Papers

Chronic Bronchocutaneous Fistula Caused by Toothpick Foreign Body in a Maltese Dog

A Preliminary Report on Static Analysis of C Code for Nuclear Reactor Protection System

Controllable deposition of organic metal halide perovskite films with wafer-scale uniformity by single source flash evaporation.

Resistive Switching by Percolative Conducting Filaments in Organometal Perovskite Unipolar Memory Devices Analyzed Using Current Noise Spectra

Memory devices including a word line defect detection circuit