Area-Optimized Fully-Flexible BCH Decoder for Multiple GF Dimensions

Recently, there are increasing demands for fully flexible Bose Chaudhuri Hocquenghem (BCH) decoders, which can support different dimensions of Galois fields (GF) operations. As the previous BCH decoders are mainly targeting the fixed GF operations, the conventional techniques are no longer suitable for multiple GF dimensions. For the area-optimized flexible BCH decoders, in this paper, we present several optimization schemes for reducing hardware costs of multi-dimensional GF operations. In the proposed optimizations, we first reformulate the matrix operations in syndrome calculation and Chien search for sharing more common sub-expressions between GF operations having different dimensions. The cell based multi-m GF multiplier is newly introduced for the area-efficient flexible key-equation solver. As case studies, we design several prototype flexible BCH decoders for digital video broadcasting systems and NAND flash memory controllers managing different page sizes. The implementation results show that the proposed fully-flexible BCH decoder architecture remarkably enhances the area-efficiency compared with the conventional solutions.112Ysciescopu

Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

<p>Abstract</p> <p>Background</p> <p>Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD).</p> <p>Description</p> <p>A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository.</p> <p>Conclusions</p> <p>The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at <url>http://fsd.snu.ac.kr/</url>.</p

Identification and analysis of in planta expressed genes of Magnaporthe oryzae

<p>Abstract</p> <p>Background</p> <p>Infection of plants by pathogens and the subsequent disease development involves substantial changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during these interactions represents a powerful strategy to obtain insights into the molecular events underlying these changes. We have employed expressed sequence tag (EST) analysis to identify rice genes involved in defense responses against infection by the blast fungus <it>Magnaporthe oryzae </it>and fungal genes involved in infectious growth within the host during a compatible interaction.</p> <p>Results</p> <p>A cDNA library was constructed with RNA from rice leaves (<it>Oryza sativa </it>cv. Hwacheong) infected with <it>M. oryzae </it>strain KJ201. To enrich for fungal genes, subtraction library using PCR-based suppression subtractive hybridization was constructed with RNA from infected rice leaves as a tester and that from uninfected rice leaves as the driver. A total of 4,148 clones from two libraries were sequenced to generate 2,302 non-redundant ESTs. Of these, 712 and 1,562 ESTs could be identified to encode fungal and rice genes, respectively. To predict gene function, Gene Ontology (GO) analysis was applied, with 31% and 32% of rice and fungal ESTs being assigned to GO terms, respectively. One hundred uniESTs were found to be specific to fungal infection EST. More than 80 full-length fungal cDNA sequences were used to validate <it>ab initio</it> annotated gene model of <it>M. oryzae</it> genome sequence.</p> <p>Conclusion</p> <p>This study shows the power of ESTs to refine genome annotation and functional characterization. Results of this work have advanced our understanding of the molecular mechanisms underpinning fungal-plant interactions and formed the basis for new hypothesis.</p

Fungal cytochrome P450 database

<p>Abstract</p> <p>Background</p> <p>Cytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.</p> <p>Results</p> <p>The Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.</p> <p>Conclusion</p> <p>The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site <url>http://p450.riceblast.snu.ac.kr/</url>.</p

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

<p>Abstract</p> <p>Background</p> <p>Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data.</p> <p>Results</p> <p>The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs.</p> <p>Conclusion</p> <p>The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site <url>http://www.imgd.org/</url>.</p

Trans-Sacral Epiduroscopic-Assisted 1,414-nm Nd:YAG Laser Decompression for Lumbar Discal Cyst: A Report of 9 Cases

Prevalence of lumbar discal cyst is very low, it can cause low back pain and radiating leg pain when present. Currently, trans-sacral epiduroscopic-assisted, 1,414-nm Nd:YAG laser decompression (SELD) is commonly used for spinal pathologies. However, the use of the laser for spinal procedures can be limited due to the risk of thermal injury. We reviewed nine consecutive patients who underwent SELD ablation for discal cyst between 2014 and 2015. Each patient underwent diagnostic imaging, including simple radiographs, computed tomography with discography, and magnetic resonance imaging (MRI). Pain relief and clinical outcome assessment of patient satisfaction was the primary outcome measure. All patients presented with back pain and unilateral radiating pain. The discal cyst was located in the lumbar region in all patients. Preoperative MRI showed a connection between the cyst and the involved intervertebral disc. All patients obtained immediate relief of symptoms after the discal cyst was treated with a SELD-assisted, 1,414-nm Nd:YAG laser. The mean visual analogue scale (VAS) for back pain was 7.89±0.78 preoperatively, 1.67±1.50 at the 1-month follow up, and 0.38±0.5 at the final follow up (p<0.01). All patients obtained excellent or good outcomes according to the modified MacNab's criteria. There were no complications. These cases demonstrated that trans-sacral, epiduroscopic-assisted, 1,414-nm Nd:YAG laser decompression was a safe, viable, and efficacious option for treating lumbar discal cyst because it lowers the risk of muscle injury and can be performed under local anesthesia

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

<p>Abstract</p> <p>Background</p> <p>Since the full genome sequences of <it>Saccharomyces cerevisiae</it> were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP) was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed.</p> <p>Results</p> <p>The Seoul National University Genome Browser (SNUGB) integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets) and 34 plant and animal (38 datasets) species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion.</p> <p>Conclusion</p> <p>The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site <url>http://genomebrowser.snu.ac.kr/</url>.</p

Recognition of Transmembrane Protein 39A as a Tumor-Specific Marker in Brain Tumor

Transmembrane protein 39A (TMEM39A) belongs to the TMEM39 family. TMEM39A gene is a susceptibility locus for multiple sclerosis. In addition, TMEM39A seems to be implicated in systemic lupus erythematosus. However, any possible involvement of TMEM39A in cancer remains largely unknown. In the present report, we provide evidence that TMEM39A may play a role in brain tumors. Western blotting using an anti-TMEM39A antibody indicated that TMEM39A was overexpressed in glioblastoma cell lines, including U87-MG and U251-MG. Deep-sequencing transcriptomic profiling of U87-MG and U251-MG cells revealed that TMEM39A transcripts were upregulated in such cells compared with those of the cerebral cortex. Confocal microscopic analysis of U251-MG cells stained with anti-TMEM39A antibody showed that TMEM39A was located in dot-like structures lying close to the nucleus. TMEM39A probably located to mitochondria or to endosomes. Immunohistochemical analysis of glioma tissue specimens indicated that TMEM39A was markedly upregulated in such samples. Bioinformatic analysis of the Rembrandt knowledge base also supported upregulation of TMEM39A mRNA levels in glioma patients. Together, the results afford strong evidence that TMEM39A is upregulated in glioma cell lines and glioma tissue specimens. Therefore, TMEM39A may serve as a novel diagnostic marker of, and a therapeutic target for, gliomas and other cancers