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Jun Kawai

Publications and source records attributed to Jun Kawai.

At least 37 records · Page 2Linked to original sources
PubMed2006

LOCATE: a mouse protein subcellular localization database.

We present here LOCATE, a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing >1700 peer-reviewed publications. LOCATE represents the first effort to catalogue the experimentally verified subcellular location and membrane organization of mammalian proteins using a high-throughput approach and provides localization data for approximately 40% of the mouse proteome. It is available at http://locate.imb.uq.edu.au.

Animals↗
PubMed2006

Subcellular localization of mammalian type II membrane proteins.

Application of a computational membrane organization prediction pipeline, MemO, identified putative type II membrane proteins as proteins predicted to encode a single alpha-helical transmembrane domain (TMD) and no signal peptides. MemO was applied to RIKEN's mouse isoform protein set to identify 1436 non-overlapping genomic regions or transcriptional units (TUs), which encode exclusively type II membrane proteins. Proteins with overlapping predicted InterPro and TMDs were reviewed to discard false positive predictions resulting in a dataset comprised of 1831 transcripts in 1408 TUs. This dataset was used to develop a systematic protocol to document subcellular localization of type II membrane proteins. This approach combines mining of published literature to identify subcellular localization data and a high-throughput, polymerase chain reaction (PCR)-based approach to experimentally characterize subcellular localization. These approaches have provided localization data for 244 and 169 proteins. Type II membrane proteins are localized to all major organelle compartments; however, some biases were observed towards the early secretory pathway and punctate structures. Collectively, this study reports the subcellular localization of 26% of the defined dataset. All reported localization data are presented in the LOCATE database (http://www.locate.imb.uq.edu.au).

Animals↗
PubMed2006

Dynamic usage of transcription start sites within core promoters.

BACKGROUND: Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends. RESULTS: In the present study we begin to explore the internal dynamics of mammalian promoters, and demonstrate that start site selection within many mouse core promoters varies among tissues. We also show that this dynamic usage of start sites is associated with CpG islands, broad and multimodal promoter structures, and imprinting. CONCLUSION: Our results reveal a new level of biologic complexity within promoters--fine-scale regulation of transcription starting events at the base pair level. These events are likely to be related to epigenetic transcriptional regulation.

Animals↗
PubMed2006

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.

The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.

Animals↗
PubMed2005

Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.

BACKGROUND: Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate as parts of complexes to regulate biological processes, we systematically analyzed protein-protein interactions in Pyrococcus using the mammalian two-hybrid system to determine the function of the hypothetical proteins. RESULTS: We examined 960 soluble proteins from Pyrococcus and selected 107 interactions based on luciferase reporter activity, which was then evaluated using a computational approach to assess the reliability of the interactions. We also analyzed the expression of the assay samples by western blot, and a few interactions by in vitro pull-down assays. We identified 11 hetero-interactions that we considered to be located at the same operon, as observed in Helicobacter pylori. We annotated and classified proteins in the selected interactions according to their orthologous proteins. Many enzyme proteins showed self-interactions, similar to those seen in other organisms. CONCLUSION: We found 13 unannotated proteins that interacted with annotated proteins; this information is useful for predicting the functions of the hypothetical Pyrococcus proteins from the annotations of their interacting partners. Among the heterogeneous interactions, proteins were more likely to interact with proteins within the same ortholog class than with proteins of different classes. The analysis described here can provide global insights into the biological features of the protein-protein interactions in P. horikoshii.

Genes, Archaeal↗
PubMed2005

Identification and characterization of photomedins: novel olfactomedin-domain-containing proteins with chondroitin sulphate-E-binding activity.

We screened more than 60000 RIKEN mouse cDNAs for novel ECM (extracellular matrix) proteins by extensive computational screening followed by recombinant expression and immunohistochemical characterization. We identified two novel olfactomedin-family proteins characterized by the presence of tandem CXCXCX9C motifs in the N-terminal region, a coiled-coil domain and an olfactomedin domain in the C-terminal region. These proteins, named photomedin-1 and photomedin-2, were secreted as disulphide-bonded dimers (photomedin-1) or oligomers/multimers (photomedin-2) with O-linked carbohydrate chains, although photomedin-1 was proteolytically processed in the middle of the molecule after secretion. In the retina, photomedin-1 was selectively expressed in the outer segment of photoreceptor cells and photomedin-2 was expressed in all retinal neurons. Among a panel of ECM components, including glycosaminoglycans, photomedins preferentially bound to chondroitin sulphate-E and heparin. These results, together, indicate that photomedins are novel olfactomedin-domain-containing extracellular proteins capable of binding to proteoglycans containing these glycosaminoglycan chains.

Amino Acid Motifs↗
PubMed2005

Analysis of wrapped or cased object by a hand-held X-ray fluorescence spectrometer.

Metals, alloys, and poisoned food were analyzed with a hand-held X-ray fluorescence (XRF) spectrometer, with a shield (wrapping or casing material) inserted between these objects and the spectrometer, in order to examine the possibility of analyzing the contents of packages. Elements such as Fe, Cr, Ni, Cu, Zn, Pb, Mo, and As were detected in the objects. The fluorescent intensity of each element in the object decreased exponentially as the thickness of the shield increased, and the degree of decrease depended on both the material of the shield and the energy of fluorescent X-rays. The thickness of the shield can be calculated by using the intensity ratio Fe Kbeta/Kalpha or Pb Lbeta/Lalpha when the object is iron or lead, or by using the intensity of the Compton scattering of incident X-rays. The original peak intensity, i.e. intensity without a shield, of an element in an object can be estimated with the thickness of the shield obtained. Because the original peak intensity is calculated using an exponential function of the thickness of the shield, calculation of the intensity ratio, e.g. Zn Kalpha/Cu Kalpha for brass, is effective for cancelling the estimation error for the thickness of the shield. The composition of brass and steel can be estimated with an error of less than 30% by using the intensity of the Compton scattering.

Journal Article↗
PubMed2005

Development of a spot reliability evaluation score for DNA microarrays.

We developed a reliability index named SRED (Spot Reliability Evaluation Score for DNA microarrays) that represents the probability that the calibrated gene expression level from a DNA microarray would be less than a factor of 2 different from that of quantitative real-time polymerase chain reaction assays whose dynamic quantification range is treated statistically to be similar to that of the DNA microarray. To define the SRED score, two parameters, the reproducibility of measurement value and the relative expression value were selected from nine candidate parameters. The SRED score supplies the probability that the expression level in each spot of a microarray is less than a certain-fold different compared to other expression profiling data, such as QRT-PCR. This score was applied to approximately 1,500,000 points of the expression profile in the RIKEN Expression Array Database.

Algorithms↗
PubMed2005

Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).

MOTIVATION: Transcription start site selection and alternative splicing greatly contribute to diversifying gene expression. Recent studies have revealed the existence of alternative first exons, but most have involved mammalian genes, and as yet the regulation of usage of alternative first exons has not been clarified, especially in plants. RESULTS: We systematically identified putative alternative first exon transcripts in rice, verified the candidates using RT-PCR, and searched for the promoter elements that might regulate the alternative first exons. As a result, we detected a number of unreported alternative first exons, some of which are regulated in a tissue-specific manner. SUPPLEMENTARY INFORMATION: http://www.bioinfo.sfc.keio.ac.jp/research/intron.

Alternative Splicing↗
PubMed2005

Skin irritation due to repetitive application of adhesive tape: the influence of adhesive strength and seasonal variability.

BACKGROUND/PURPOSE: Influence of the repetitive application of pressure-sensitive adhesive tapes on skin was evaluated. METHODS: Two kinds of tapes with different adhesive strengths were repetitively applied to the inside of the forearm of six volunteers in winter and summer, in order to examine the dermal peeling force, the amount of stripped corneocytes, transepidermal water loss (TEWL), hydration and deepened skin furrows (changes in skin surface topography) in the epidermal stratum corneum. RESULTS AND CONCLUSION: As adhesive tapes were applied repetitively, dermal peeling force gradually increased while the amount of stripped corneocytes decreased. As the cumulative amount of stripped corneocytes increased with repetitive applications, the skin irritation worsened as measured by increased destruction of the skin surface topography and TEWL. These phenomena were more marked with the stronger adhesive tape, and there was seasonal variability.

Adhesiveness↗
PubMed2005

Radiative auger effect and extended X-ray emission fine structure (EXEFS).

Radiative Auger spectra are weak X-ray emission spectra near the characteristic X-ray lines. Radiative Auger process is an intrinsic energy-loss process in an atom when a characteristic X-ray photon is emitted, due to an atomic many-body effect. The energy loss spectra correspond to the unoccupied conduction band structure of materials. Therefore the radiative Auger effect is an alternative tool to the X-ray absorption spectroscopy such as EXAFS (Extended X-ray Absorption Fine Structure) and XANES (X-ray Absorption Near Edge Structure), and thus it is named EXEFS (Extended X-ray Emission Fine Structure). By the use of a commercially available X-ray fluorescence spectrometer or an electron probe microanalyzer (EPMA), which are frequently used in materials industries, we can obtain an EXEFS spectrum within 20 min. The radiative Auger effect, as an example, demonstrates that the study on atomic many-body effects has become a powerful tool for crystal and electronic structure characterizations. The EXEFS method has already been used in many industries in Japan. Reviews about the applications and basic study results on the radiative Auger effect are reported in this paper.

Journal Article↗
PubMed2005

X-ray absorption spectral analysis with a 9 V battery X-ray generator.

X-ray absorption spectral (XAS) analysis is performed with a combination of a 9 V dry electric battery X-ray generator and a portable Si PIN X-ray detector. The calcium K edge (4.0 keV) in paper is measured with a grazing incidence geometry, which suppressed the artifact due to the Kalpha X-ray fluorescence peak at 3.5 keV. The 9 V dry battery X-ray emitter is useful for portable XAS measurements.

Journal Article↗
PubMed2005

Numerical simulation of C/C/C planar X-ray waveguides.

A numerical simulation was done to check the possibility of using planar C/C/C multilayers with density contrast 0.2 and 0.7 g/cm3 as an X-ray waveguide. After an optimization procedure, suitable waveguide layer thicknesses were found which provide a high degree of resonant standing wave field intensity enhancement in the core layer at incident beam energy of 13 keV. The obtained results were compared with those of the Mo/Be/Mo waveguide, whose high waveguiding capability at the same energy value was reported in the 1990s. The comparison shows that standing wave field intensity resonant enhancement provided by C/C/C planar multilayers is very high and, consequently, a guided beam can be well detected.

Journal Article↗
PubMed2005

Investigation of individual micrometer-size Kosa particle with on-site combination of electron microscope and synchrotron X-ray microscope.

The Kosa (yellow sand) aerosol affects the global environment as well as human health because it migrates from the interior of China to other areas, absorbing various atmospheric elements. Investigation into individual Kosa aerosol particles, which are submicroscopic to several tens of micrometers in diameter, is required to resolving the issue. We installed a scanning electron microscope (SEM) equipped with an energy dispersive X-ray spectrometer (EDX) on a synchrotron radiation (SR) beam line and introduced the SR beam into the SEM chamber for combinatorial application of SEM-EDX and SR X-ray fluorescence (SR-XRF) spectrometry to individual particles. It should be noted that detailed topographic observation by SEM and sensitive elemental analysis by SR-XRF, both crucial for individual particle measurement but which previously had to be carried out separately, were jointly performed inside the SEM chamber in this setup. Here, we show that SR-XRF results, in conjunction with SEM images, contributed toward resolving individual particle dispositions. Atmospheric sulfur primarily adheres to calcium in the aerosol particles and the particle surface roughens as a consequence of the chemical reaction between the two elements.

Journal Article↗
PubMed2005

Chemical effects in high-resolution nickel Kalpha X-ray fluorescence spectra.

The nickel Kalpha spectra of oxides, halides (NiF2, K2NiF6, NiCl2, NiBr2), complex compounds, and metal are measured with two different double-crystal X-ray fluorescence spectrometers. The peak shifts and line width changes due to the changes in the chemical states are reported. High reproducibility has been shown for the chemical shift and line width measurements. The DV-Xalpha molecular orbital calculation at the ground and the 1s(-1) hole states was performed to prove that the chemical effect originats from the charge-transfer mechanism.

Journal Article↗
PubMed2005

Strong X-ray emission from electrified insulators.

Terasawa reported strong X-ray emission from charged-up insulators, and proposed an X-ray production device only using the electrification. We constructed a similar device and studied the conditions of X-ray emission. It was shown that X-rays could be produced without supplying electrons from a filament.

Journal Article↗
PubMed2005

A simple X-ray emitter.

A compact X-ray emission instrument is made, and the X-ray spectra are measured by changing the applied electric potential. Strong soft X-rays are observed when evacuating roughly and applying a high voltage to an insulator settled in this device. The X-ray intensity is higher as the applied voltage is increased. A light-emitting phenomenon is observed when this device emits X-rays. The present X-ray emitter is made of a small cylinder with a radius of 20 mm and a height of 50 mm. This X-ray generator has a potential to be used as an X-ray source in an X-ray fluorescence spectrometer.

Journal Article↗