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Masahide Sasaki

Publications and source records attributed to Masahide Sasaki.

13 recordsLinked to original sources
PubMed2006

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.

Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates seven individual databases, Full-Parasites, consisting of numerous full-length cDNA clones that we have produced and sequenced: 12,484 cDNA sequences from Plasmodium falciparum, 11,262 from Plasmodium yoelii, 9633 from Plasmodium vivax, 1518 from Plasmodium berghei, 7400 from Toxoplasma gondii, 5921 from Cryptosporidium parvum and 10,966 from the tapeworm Echinococcus multilocularis. Putatively counterpart gene groups are clustered and comparative analysis of any combination of six apicomplexa species is implemented, such as interspecies comparisons regarding protein motifs (InterPro), predicted subcellular localization signals (PSORT), transmembrane regions (SOSUI) or upstream promoter elements. By specifying keywords and other search conditions, Comparasite retrieves putative counterpart gene groups containing a given feature in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism. Our full-length cDNA databases and Comparasite are accessible from http://fullmal.ims.u-tokyo.ac.jp.

Animals↗
PubMed2006

Binary projective measurement via linear optics and photon counting.

We investigate the implementation of binary projective measurements with linear optics. This problem can be viewed as a single-shot discrimination of two orthogonal pure quantum states. We show that any two orthogonal states can be perfectly discriminated using only linear optics, photon counting, coherent ancillary states, and feedforward. The statement holds in the asymptotic limit of a large number of these physical resources.

Journal Article↗
PubMed2006

Photon-number-resolving detection at a telecommunications wavelength with a charge-integration photon detector.

We demonstrate multiphoton discrimination at a telecommunications wavelength with the readout frequency of 40 Hz by a charge-integration photon detector (CIPD). The CIPD consists of an InGaAs pin photodiode and a GaAs junction field effect transistor as a preamplifier in a charge-integration circuit, which is cooled to 4.2 K to reduce thermal noise. The quantum efficiency of the CIPD (the detector itself) is 80% for 1530 nm light, and the readout noise is measured as 0.26 electrons at 40 Hz. We can construct Poisson distributions of photocarrier numbers with distinct peaks at each photocarrier number, corresponding to a signal-to-noise ratio of about 3.

Journal Article↗
PubMed2005

Photon number squeezing of ultrabroadband laser pulses generated by microstructure fibers.

To the best of our knowledge, we demonstrate for the first time the generation of photon number squeezing by spectral filtering for ultrabroadband light generated by microstructure fibers at 800 nm. A maximum squeezing of 4.6 dB is observed, corresponding to 10.3 dB after correcting for detection losses. We numerically analyzed the quantum dynamics of ultrashort laser pulse propagation through optical fibers by solving a nonlinear quantum Schrödinger equation that included Raman scattering, especially for the quantum correlation of photon number fluctuation among frequency modes in broadband pulses.

Journal Article↗
PubMed2005

Ultrahigh-sensitivity high-linearity photodetection system using a low-gain avalanche photodiode with an ultralow-noise readout circuit.

A highly sensitive photodetection system with a detection limit of 1 photon/s was developed. This system uses a commercially available 200-microm-diameter silicon avalanche photodiode (APD) and an in-house-developed ultralow-noise readout circuit, which are both cooled to 77 K. When the APD operates at a low gain of approximately 10, it has a high-linearity response to the number of incident photons and a low excess noise factor. The APD also has a high quantum efficiency and a dark current of less than 1 e/s at 77 K. This photodetection system will shorten measurement time and permit higher spatial and wavelength resolution for near-field scanning optical microscopes.

Journal Article↗
PubMed2004

Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species.

Full-malaria (http://fullmal.ims.u-tokyo.ac.jp), a database for full-length cDNAs from the human malaria parasite, Plasmodium falciparum has been updated in at least three points. (i) We added 8934 sequences generated from the addition of new libraries, so that our collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of our full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes.

Animals↗
PubMed2004

Prevalence of antibodies to hepatitis E virus among Japanese blood donors: identification of three blood donors infected with a genotype 3 hepatitis E virus.

Risk factors for acquiring hepatitis E among individuals in industrialized countries including Japan are not fully understood. We investigated whether Japanese blood donors with or without an elevated alanine aminotransferase (ALT) level are likely to have hepatitis E virus (HEV) infection. Serum samples were collected from 5,343 voluntary blood donors including 1,087 donors with elevated ALT of 61-966 IU/L and 4,256 donors with normal ALT (< or = 60 IU/L) at two Japanese Red Cross Blood Centers, and were tested for the presence of anti-HEV IgG by in-house enzyme-linked immunosorbent assay (ELISA). Overall, 200 donors (3.7%) were positive for anti-HEV IgG, including 32 (2.9%) with elevated ALT and 168 (3.9%) with normal ALT. Serum samples with anti-HEV IgG were further tested for the presence of anti-HEV IgM by in-house ELISA and for HEV RNA by reverse transcription (RT)-polymerase chain reaction (PCR). Three donors with ALT of 966, 62 or 61 IU/L were positive for anti-HEV IgM and HEV RNA. The HEV isolates obtained from the three viremic donors segregated into genotype 3, were 91.5-93.4% similar to each other in the 412 nucleotide sequence of open reading frame 2, and had the highest identity of 91.5-94.9% with the JRA1 isolate which was recovered from a Japanese patient with sporadic acute hepatitis E who had never been abroad, suggesting that these three HEV isolates are indigenous to Japan. This study suggests that a small but significant proportion of blood donors in Japan with or without elevated ALT are viremic and are potentially able to cause transfusion-associated hepatitis E.

Adult↗
PubMed2003

Experimental demonstration of quantum source coding.

We report an experimental demonstration of Schumacher's quantum noiseless coding theorem. Our experiment employs a sequence of single photons, each of which represents three qubits in terms of eight spatial and polarization modes. We initially prepare each photon in one of a set of eight nonorthogonal code word states corresponding to the value of a block of three binary letters. We use quantum coding to compress this quantum data into a two-qubit quantum channel and then uncompress the two-qubit channel to restore the original data with a fidelity approaching the theoretical limit.

Journal Article↗
PubMed2003

Fugu ESTs: new resources for transcription analysis and genome annotation.

The draft Fugu rubripes genome was released in 2002, at which time relatively few cDNAs were available to aid in the annotation of genes. The data presented here describe the sequencing and analysis of 24,398 expressed sequence tags (ESTs) generated from 15 different adult and juvenile Fugu tissues, 74% of which matched protein database entries. Analysis of the EST data compared with the Fugu genome data predicts that approximately 10,116 gene tags have been generated, covering almost one-third of Fugu predicted genes. This represents a remarkable economy of effort. Comparison with the Washington University zebrafish EST assemblies indicates strong conservation within fish species, but significant differences remain. This potentially represents divergence of sequence in the 5' terminal exons and UTRs between these two fish species, although clearly, complete EST data sets are not available for either species. This project provides new Fugu resources, and the analysis adds significant weight to the argument that EST programs remain an essential resource for genome exploitation and annotation. This is particularly timely with the increasing availability of draft genome sequence from different organisms and the mounting emphasis on gene function and regulation.

Animals↗
PubMed2003

Exceeding the classical capacity limit in a quantum optical channel.

The amount of information transmissible through a communications channel is determined by the noise characteristics of the channel and by the quantities of available transmission resources. In classical information theory, the amount of transmissible information can be increased twice at most when the transmission resource is doubled for fixed noise characteristics. In quantum information theory, however, the amount of information transmitted can increase even more than twice. We present a proof-of-principle demonstration of this superadditivity of classical capacity of a quantum channel by using the ternary symmetric states of a single photon, and by event selection from a weak coherent light source. We also show how the superadditive coding gain, even in a small code length, can boost the communication performance of the conventional coding technique.

Journal Article↗
PubMed2003

Generation of entanglement between frequency bands by nonlinear fiber propagation and spectral pulse shaping.

A novel fiber-based scheme for generating quadrature entanglement between a specific pair of frequency bands is proposed. The scheme is based on use of a nonlinear fiber, a spectral pulse shaper, and an adaptive feedback loop. It is numerically predicted that at least -5 dB of the quadrature entanglement will be created by preparation of an appropriate initial phase spectrum. Optimal control of the four-wave mixing terms of the Kerr Hamiltonian is crucial for improvement of the entanglement.

Journal Article↗
PubMed2002

Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel genes and diverse transcription start sites of messenger RNAs.

Now that the sequencing of the complete genome of the human malaria parasite Plasmodium falciparum is now underway, importance of analyses of complementary DNAs (cDNAs) is looming up. We constructed a full-length-enriched cDNA library from erythrocytic stage P. falciparum using the 'oligo-capping' method (Nucleic Acids Res. 29 (2001) 70). In this report we describe the novel genes identified using this library and detailed characterization of transcriptional start site of knob-associated histidine rich protein gene. Contrary to the previous report we conclude all the transcripts of plasmodium genes have diverse start sites. Sequence comparisons between the cDNAs and the complete sequences of chromosomes 2 identified three novel genes that had been missed by computational predictions. Moreover, analysis of transcriptional start sites revealed that the average length of the 5' untranslated region was 346 nt, which is much longer than that in humans. The transcriptional start sites of all the genes studied were far more diverse than those of human genes. These observations may reflect unique mechanism(s) of gene expression in this organism, which has an extremely AT-rich genome.

5' Untranslated Regions↗