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

Physiological and Molecular Processes Associated with Long Duration of ABA Treatment

Plants need to respond to various environmental stresses such as abiotic stress for proper development and growth. The responses to abiotic stress can be biochemically demanding, resulting in a trade-off that negatively affects plant growth and development. Thus, plant stress responses must be fine-tuned depending on the stress severity and duration. Abscisic acid, a phytohormone, plays a key role in responses to abiotic stress. Here, we investigated time-dependent physiological and molecular responses to long-term ABA treatment in Arabidopsis as an approach to gain insight into the plant responses to long-term abiotic stress. Upon ABA treatment, the amount of cellular ABA increased to higher levels, reaching to a peak at 24 h after treatment (HAT), and then gradually decreased with time whereas ABA-GE was maintained at lower levels until 24 HAT and then abruptly increased to higher levels at 48 HAT followed by a gradual decline at later time points. Many genes involved in dehydration stress responses, ABA metabolism, chloroplast biogenesis, and chlorophyll degradation were strongly expressed at early time points with a peak at 24 or 48 HAT followed by gradual decreases in induction fold or even suppression at later time points. At the physiological level, long-term ABA treatment caused leaf yellowing, reduced chlorophyll levels, and inhibited chloroplast division in addition to the growth suppression whereas short-term ABA treatment did not affect chlorophyll levels. Our results indicate that the duration of ABA treatment is a crucial factor in determining the mode of ABA-mediated signaling and plant responses: active mobilization of cellular resources at early time points and suppressive responses at later time points.11Ysciescopu

Patterns of Striped order in the Classical Lattice Coulomb Gas

We obtain via Monte Carlo simulations the low temperature charge configurations in the lattice Coulomb gas on square lattices for charge filling ratio $f$ in the range $1/3 < f < 1/2$. We find a simple regularity in the low temperature charge configurations which consist of a suitable periodic combination of a few basic striped patterns characterized by the existence of partially filled diagonal channels. In general there exist two separate transitions where the lower temperature transition ($T_p$) corresponds to the freezing of charges within the partially filled channels. $T_p$ is found to be sensitively dependent on $f$ through the charge number density $\nu = p_{1}/q_{1}$ within the channels.Comment: 4 pages, 8 figure

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

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

Background: Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variableThis research has been supported by the USDA Agriculture and Food Research Initiative Competitive Grants Program (Grant no. 2010-65110-20488). The work in Lees lab has been supported by the National Research Foundation of Korea (2012–0001149 and 2012–0000141) and the NextGeneration Bio-Green 21 Program of Rural Development Administration in Korea (PJ00821201).OAIID:oai:osos.snu.ac.kr:snu2012-01/102/0000003441/6SEQ:6PERF_CD:SNU2012-01EVAL_ITEM_CD:102USER_ID:0000003441ADJUST_YN:YEMP_ID:A003535DEPT_CD:5321CITE_RATE:4.073FILENAME:첨부된 내역이 없습니다.DEPT_NM:농생명공학부EMAIL:[email protected]_YN:YCONFIRM:

Structural Relaxation, Self Diffusion and Kinetic Heterogeneity in the Two Dimensional Lattice Coulomb Gas

We present Monte Carlo simulation results on the equilibrium relaxation dynamics in the two dimensional lattice Coulomb gas, where finite fraction $f$ of the lattice sites are occupied by positive charges. In the case of high order rational values of $f$ close to the irrational number $1-g$ ($g\equiv(\sqrt{5} -1)/2$ is the golden mean), we find that the system exhibits, for wide range of temperatures above the first-order transition, a glassy behavior resembling the primary relaxation of supercooled liquids. Single particle diffusion and structural relaxation show that there exists a breakdown of proportionality between the time scale of diffusion and that of structural relaxation analogous to the violation of the Stokes-Einstein relation in supercooled liquids. Suitably defined dynamic cooperativity is calculated to exhibit the characteristic nature of dynamic heterogeneity present in the system.Comment: 12 pages, 20 figure

Experimental and theoretical studies on the structure of N-doped carbon nanotubes: Possibility of intercalated molecular N2

The concentration distribution and electronic structure of N atoms doped in multiwalled banboo-like carbon nanotubes (CNTs) are examined by photon energy-dependent x-ray photoelectron spectroscopy and x-ray absorption near edge structure. The inner part of the nanotube wall has a higher N concentration and contains molecular N-2 presumably intercalated between the graphite layers. These results are supported by the self-consistent charge-density-functional-based tight-binding calculation of double-walled CNTs, showing that the intercalation of N-2 is energetically possible and the graphite-like N structure conformer becomes more stable when the inner wall is more heavily doped. (C) 2004 American Institute of Physicsclose656