Tsutomu Suzuki

Bio: Tsutomu Suzuki is an academic researcher from University of Tokyo. The author has contributed to research in topics: Transfer RNA & RNA. The author has an hindex of 67, co-authored 256 publications receiving 17767 citations. Previous affiliations of Tsutomu Suzuki include Nippon Medical School & National Institute of Advanced Industrial Science and Technology.

An Unusual Supernova in the Error Box of the Gamma-Ray Burst of 25 April 1998

Abstract: The discovery of afterglows associated with gamma-ray bursts at X-ray, optical and radio wavelengths and the measurement of the redshifts of some of these events has established that gamma-ray bursts lie at extreme distances, making them the most powerful photon-emitters known in the Universe. Here we report the discovery of transient optical emission in the error box of the gamma-ray burst GRB980425, the light curve of which was very different from that of previous optical afterglows associated with gamma-ray bursts. The optical transient is located in a spiral arm of the galaxy ESO 184-GS2, which has a redshift velocity of only 2,550 km/ s. Its optical spectrum and location indicate that it is a very luminous supernova, which has been identified as SN1998bw. If this supernova and GRB980425 are indeed associated, the energy radiated in gamma-rays is at least four orders of magnitude less than in other gamma-ray bursts, although its appearance was otherwise unremarkable: this indicates that very different mechanisms can give rise to gamma-ray bursts. But independent of this association, the supernova is itself unusual, exhibiting an unusual light curve at radio wavelengths that requires that the gas emitting the radio photons be expanding relativistically.

Cell-free translation reconstituted with purified components

Abstract: We have developed a protein-synthesizing system reconstituted from recombinant tagged protein factors purified to homogeneity. The system was able to produce protein at a rate of about 160 μg/ml/h in a batch mode without the need for any supplementary apparatus. The protein products were easily purified within 1 h using affinity chromatography to remove the tagged protein factors. Moreover, omission of a release factor allowed efficient incorporation of an unnatural amino acid using suppressor transfer RNA (tRNA).

A hypernova model for the supernova associated with the gamma ray burst of 25 April 1998

Abstract: The discovery of the unusual supernova SN1998bw, and its possible association with the γ-ray burst GRB 9804251,2,3, provide new insights into the explosion mechanism of very massive stars and the origin of some classes of γ-ray bursts. Optical spectra indicate that SN1998bw is a type Ic supernova3,4, but its peak luminosity is unusually high compared with typical type Ic supernovae3. Here we report our findings that the optical spectra and the light curve of SN1998bw can be well reproduced by an extremely energetic explosion of a massive star composed mainly of carbon and oxygen (having lost its hydrogen and helium envelopes). The kinetic energy of the ejecta is as large as +(2–5)× 1052 erg, more than ten times that of previously observed supernovae. This type of supernova could therefore be termed ‘hypernova’. The extremely large energy suggests the existence of a new mechanism of massive star explosion that can also produce the relativistic shocks necessary to generate the observed γ-rays.

Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases.

Abstract: Mitochondria are eukaryotic organelles that generate most of the energy in the cell by oxidative phosphorylation (OXPHOS). Each mitochondrion contains multiple copies of a closed circular double-stranded DNA genome (mtDNA). Human (mammalian) mtDNA encodes 13 essential subunits of the inner membrane complex responsible for OXPHOS. These mRNAs are translated by the mitochondrial protein synthesis machinery, which uses the 22 species of mitochondrial tRNAs (mt tRNAs) encoded by mtDNA. The unique structural features of mt tRNAs distinguish them from cytoplasmic tRNAs bearing the canonical cloverleaf structure. The genes encoding mt tRNAs are highly susceptible to point mutations, which are a primary cause of mitochondrial dysfunction and are associated with a wide range of pathologies. A large number of nuclear factors involved in the biogenesis and function of mt tRNAs have been identified and characterized, including processing endonucleases, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases. These nuclear factors are also targets of pathogenic mutations linked to various diseases, indicating the functional importance of mt tRNAs for mitochondrial activity.

Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi- interacting RNAs at their 3′ ends

Abstract: Piwi-interacting RNAs (piRNAs) consist of a germline-specific group of small RNAs derived from distinct intergenic loci in the genome. piRNAs function in silencing selfish transposable elements through binding with the PIWI subfamily proteins of Argonautes. Here we show that piRNAs in Drosophila are 2'-O-methylated at their 3' ends. Loss of Pimet (piRNA methyltransferase), the Drosophila homolog of Arabidopsis HEN1 methyltransferase for microRNAs (miRNAs), results in loss of 2'-O-methylation of fly piRNAs. Recombinant Pimet shows single-stranded small RNA methylation activity in vitro and interacts with the PIWI proteins within Pimet mutant ovary. These results show that Pimet mediates piRNA 2'-O-methylation in Drosophila.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

Regulation of microRNA biogenesis

Abstract: MicroRNAs (miRNAs) are small non-coding RNAs that function as guide molecules in RNA silencing. Targeting most protein-coding transcripts, miRNAs are involved in nearly all developmental and pathological processes in animals. The biogenesis of miRNAs is under tight temporal and spatial control, and their dysregulation is associated with many human diseases, particularly cancer. In animals, miRNAs are ∼22 nucleotides in length, and they are produced by two RNase III proteins--Drosha and Dicer. miRNA biogenesis is regulated at multiple levels, including at the level of miRNA transcription; its processing by Drosha and Dicer in the nucleus and cytoplasm, respectively; its modification by RNA editing, RNA methylation, uridylation and adenylation; Argonaute loading; and RNA decay. Non-canonical pathways for miRNA biogenesis, including those that are independent of Drosha or Dicer, are also emerging.

The widespread regulation of microRNA biogenesis, function and decay.

Abstract: MicroRNAs (miRNAs) are a large family of post-transcriptional regulators of gene expression that are ~21 nucleotides in length and control many developmental and cellular processes in eukaryotic organisms. Research during the past decade has identified major factors participating in miRNA biogenesis and has established basic principles of miRNA function. More recently, it has become apparent that miRNA regulators themselves are subject to sophisticated control. Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein-protein and protein-RNA interactions. Such regulation has an important role in the context-specific functions of miRNAs.