Proteome driven re-evaluation and functional annotation of the Streptococcus pyogenes SF370 genome

<p>Abstract</p> <p>Background</p> <p>The genome data of <it>Streptococcus pyogenes </it>SF370 has been widely used by many researchers and provides a vast array of interesting findings. Nevertheless, approximately 40% of genes remain classified as hypothetical proteins, and several coding sequences (CDSs) have been unrecognized. In this study, we attempted a shotgun proteomic analysis with a six-frame database that was independent of genome annotation.</p> <p>Results</p> <p>Nine proteins encoded by novel ORFs were found by shotgun proteomic analysis, and their specific mRNAs were verified by reverse transcriptional PCR (RT-PCR). We also provided functional annotations for hypothetical genes using proteomic analysis from three different culture conditions that were separated into three fractions: supernatant, soluble, and insoluble. Consequently, we identified 567 proteins on re-evaluation of the proteomic data using an in-house database comprising 1,697 annotated and nine non-annotated CDSs. We provided functional annotations for 126 hypothetical proteins (18.9% out of the 668 hypothetical proteins) based on their cellular fractions and expression profiles under different culture conditions.</p> <p>Conclusions</p> <p>The list of amino acid sequences that were annotated by genome analysis contains outdated information and unrecognized protein-coding sequences. We suggest that the six-frame database derived from actual DNA sequences be used for reliable proteomic analysis. In addition, the experimental evidence from functional proteomic analysis is useful for the re-evaluation of previously sequenced genomes.</p

Spatial and Temporal Variability of Chlorophyll a Concentration and Primary Production in the Japan Sea Observed by Satellite Remote Sensing

長崎大学学位論文 学位記番号:博(生)甲第50号 学位授与年月日:平成17年3月18日Chapter2:Keiko Yamada, Joji Ishizaka, Sinjae Yoo, Hyun-cheol Kim and Sanae Chiba. Seasonal and interannual variability of sea surface chlorophyll a concentration in the Japan/East Sea (JES). Progress In Oceanography. 2004, 61(2-4), p.193-211.Chapter3:Yamada, K., J. Ishizaka, H. Nagata. Spatial and temporal variability of satellite estimated primary production in the Japan Sea from 1998 to 2002. Journal of Oceanography. 2005, 61(5), p.857-869

Record of Phototactic Tenebrionidae (Coleoptera) from Lambir Hills, Borneo, with description of a new genus and twelve new species

Fifty-two species of phototactic Tenebrionidae are recorded from Lambir Hills National Park and the secondary forests surrounding the park. One new genus and twelve new species are described under the following names: Anognathena gen. nov., Anognathena neraida sp. nov., Amarygmus hansbremeri sp. nov., Cleomis purpuricollis sp. nov., Cryphaeus irregularis sp. nov., Euhemicera hutanicola sp. nov., Hemicera (Hemicera) vittigera sp. nov., Hemicera (Hemicera) parca sp. nov., Pseudonautes viridinitidus sp. nov., Psydus virgulatus sp. nov., Uloma (Uloma) nyctelia sp. nov., Uloma (Uloma) sarawakensis sp. nov. and Uloma (Uloma) serripunctata sp. nov

Mechanisms in the development of limbic status epilepticus and hippocampal neuron loss: an experimental study in a model of status epilepticus induced by kindling-like electrical stimulation of the deep prepyriform cortex in rats.

A new model of status epilepticus (SE), which was induced by intermittent electrical stimulation (20 Hz for 20 sec every min for 180 min) of the deep prepyriform cortex, has been developed in the conscious rat. SE was induced in 9 of 16 rats in the drug-free group. The number of stimulation trains required to induce SE in this status subgroup was 125.6 +/- 12.7 (mean +/- SEM) and the mean duration of self-sustained seizure activity (SSSA) occurring after cessation of the stimulation session was 295.4 +/- 111.4 min. Some animals showed secondary generalized seizures. Significant cell loss was observed in the hippocampal CA3 pyramidal cell layer ipsilateral to the stimulation site and bilateral CA1 areas in the status subgroup compared with the group subjected to sham operation. In addition, there was a significant negative correlation between the duration of SSSA subsequent to the stimulation session and the total number of intact pyramidal neurons observed in the bilateral CA1 and ipsilateral CA3 subfields of the status subgroup. There were significant differences between the status and non-status subgroups with respect to the number of afterdischarges (ADs) and the total AD duration during the stimulation session. Pretreatment with phenobarbital (30 mg/kg) prevented the development of SE and hippocampal cell loss completely. Pretreatment with MK-801, a non-competitive N-methyl-D-aspartate (NMDA) receptor antagonist (0.25 or 1 mg/kg), also prevented hippocampal cell loss, although it did not block SE generation completely, which suggests dissociation of the mechanisms underlying the development of SE and hippocampal damage. These results indicate that prolonged SSSA actually causes hippocampal damage and it is critically dependent upon NMDA receptor participation.</p

ΩΩ\Omega\Omega interaction from 2+1 flavor lattice QCD

We investigate the interaction between $\Omega$ baryons in the $^1S_0$ channel from 2+1 flavor lattice QCD simulations. On the basis of the HAL QCD method, the $\Omega\Omega$ potential is extracted from the Nambu-Bethe-Salpeter wave function calculated on the lattice by using the PACS-CS gauge configurations with the lattice spacing $a\simeq 0.09$ fm, the lattice volume $L\simeq 2.9$ fm and the quark masses corresponding to $m_\pi \simeq 700$ MeV and $m_\Omega \simeq 1970$ MeV. The $\Omega\Omega$ potential has a repulsive core at short distance and an attractive well at intermediate distance. Accordingly, the phase shift obtained from the potential shows moderate attraction at low energies. Our data indicate that the $\Omega\Omega$ system with the present quark masses may appear close to the unitary limit where the scattering length diverges.Comment: 9 pages, 4 figures, 1 tabl

Plasma lipid profiling of different types of hepatic fibrosis induced by carbon tetrachloride and lomustine in rats

Supplementary tables. Table S1. Class, m/z, retention time, ion of detected and identified lipid molecules, and determined their fatty side chains. Table S2. Normalized levels of lipid molecules in individual samples. Table S3. Fold change and p-value of the levels of lipid molecules. (XLSX 317 kb