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221.
222.
Kenji Sugimoto Takaaki Miyasaka Asao Fujiyama Yuji Kohara Tuneko Okazaki 《Molecular & general genetics : MGG》1988,211(3):400-406
Summary We have analyzed the transition sites between primer RNA and DNA in a 589 bp segment of the bacteriophage T7 genome. In the monomeric replication stage, RNA-DNA transition sites are predominantly on the light (L) strand (with, 53 polarity on the genetic map) but rarely on the heavy (H) strand, indicating that replication proceeds semidiscontinuously with the H and L strands corresponding to the leading and lagging strands, respectively. The direction of replication is that expected from the position of the primary origin and also indicates that secondary origins are seldom if ever used. In the concatemeric stage of replication, RNA-DNA transition sites are instead distributed on both strands of the segment with equally high frequency, showing that initiation occurs within the concatemeric molecule per se and by a different mechanism. 相似文献
223.
Rapid and precise mapping of the Escherichia coli release factor genes by two physical approaches. 总被引:11,自引:7,他引:4 下载免费PDF全文
C C Lee Y Kohara K Akiyama C L Smith W J Craigen C T Caskey 《Journal of bacteriology》1988,170(10):4537-4541
The termination of protein synthesis in Escherichia coli requires two codon-specific factors termed RF1 and RF2. RF1 mediates UAA- and UAG-directed termination, while RF2 mediates UAA- and UGA-directed termination. The genes encoding these factors have been isolated and sequenced, and RF2 was found to be encoded in two separate reading frames. The map position of RF1 has been reported as 27 min on the E. coli chromosome, while the RF2 map position has not yet been identified. In this study, two new and independent methods for gene mapping, using pulsed field gel electrophoresis and an ordered bacteriophage library spanning the entire chromosome, were used to localize the map position of the RF2 gene. In addition, the location of the RF1 gene was more precisely defined. The RF2 gene is located at 62.3 min on the chromosome, while the RF1 gene is located at 26.7 min. This approach to mapping cloned genes promises to be a rapid and simple means for determining the gene order of the genome. 相似文献
224.
Fumio Kasai Noriko Hirayama Midori Ozawa Motonobu Satoh Arihiro Kohara 《Human cell》2018,31(3):261-267
Human cell lines represent a valuable resource as in vitro experimental models. A hepatoma cell line, HuH-7 (JCRB0403), has been used extensively in various research fields and a number of studies using this line have been published continuously since it was established in 1982. However, an accurate genome profile, which can be served as a reliable reference, has not been available. In this study, we performed M-FISH, SNP microarray and amplicon sequencing to characterize the cell line. Single cell analysis of metaphases revealed a high level of heterogeneity with a mode of 60 chromosomes. Cytogenetic results demonstrated chromosome abnormalities involving every chromosome in addition to a massive loss of heterozygosity, which accounts for 55.3% of the genome, consistent with the homozygous variants seen in the sequence analysis. We provide empirical data that the HuH-7 cell line is composed of highly heterogeneous cell populations, suggesting that besides cell line authentication, the quality of cell lines needs to be taken into consideration in the future use of tumor cell lines. 相似文献
225.
Hatano Jiro Kusama Shoko Tanaka Kenya Kohara Ayaka Miyake Chikahiro Nakanishi Shuji Shimakawa Ginga 《Photosynthesis research》2022,153(1-2):113-120
Photosynthesis Research - Live cyanobacteria and algae integrated onto an extracellular electrode can generate a light-induced current (i.e., a photocurrent). Although the photocurrent is expected... 相似文献
226.
Mashiba T Udaka K Hirachi Y Hiasa Y Miyakawa T Satta Y Osoda T Kataoka S Kohara M Onji M 《Immunogenetics》2007,59(3):197-209
Developing a peptide-based vaccine for the highly variable hepatitis C virus (HCV) remains a challenging task. Variant viruses
not only escape antigen presentation but also persist in a patient as quasi-species. Such variants are often antagonistic
to the responding T cell repertoire. To overcome these problems, we herein propose a cocktail vaccine consisting of a few
epitope peptides, which make it possible to outpace the emergence of variant viruses. To design such a vaccine, we developed
a way to identify HLA-A*2402-binding peptides efficiently by means of the computational scanning of the whole genome of the
pathogen. Most of the predicted peptides exhibited strong binding to the HLA-A*2402 molecule, while also inducing CD8 T cell
responses from the patients’ peripheral blood mononuclear cells (PBMCs). Peptide-induced T cells were capable of lysing HCV-expressing
HepG2 cells which process antigens endogenously. The amount of HCV core antigen in the patients’ livers suggested that the
lytic activity of the peptide-induced T cells was clearly in a range suitable for therapeutic use. If T cells were activated
under optimal conditions by high density peptides, then they tended to be relatively tolerant of single amino acid variations
for cytolysis. Finally, an analysis of the viral population isolated in Japan suggested no obvious changes due to immune evasion
in the viral genome even in a host population highly biased toward HLA-A*2402.
Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. 相似文献
227.
Ono K Satoh M Yoshida T Ozawa Y Kohara A Takeuchi M Mizusawa H Sawada H 《In vitro cellular & developmental biology. Animal》2007,43(5-6):168-175
We developed a highly sensitive and convenient method of nested polymerase chain reaction (PCR) targeted to mitochondrial
deoxyribonucleic acid (DNA) to identify animal species quickly in cultured cells. Fourteen vertebrate species, including human,
cynomolgus monkey, African green monkey, mouse, rat, Syrian hamster, Chinese hamster, guinea pig, rabbit, dog, cat, cow, pig,
and chicken, could be distinguished from each other by nested PCR. The first PCR amplifies mitochondrial DNA fragments with
a universal primer pair complementary to the conserved regions of 14 species, and the second PCR amplifies the DNA fragments
with species-specific primer pairs from the first products. The species-specific primer pairs were designed to easily distinguish
14 species from each other under standard agarose gel electrophoresis. We further developed the multiplex PCR using a mixture
of seven species-specific primer pairs for two groups of animals. One was comprised of human, mouse, rat, cat, pig, cow, and
rabbit, and the other was comprised of African green monkey, cynomolgus monkey, Syrian hamster, Chinese hamster, guinea pig,
dog, and chicken. The sensitivity of the PCR assay was at least 100 pg DNA/reaction, which was sufficient for the detection
of each species of DNA. Furthermore, the nested PCR method was able to identify the species in the interspecies mixture of
DNA. Thus, the method developed in this study will provide a useful tool for the authentication of animal species. 相似文献
228.
Kenta Shirasawa Sachiko Isobe Hideki Hirakawa Erika Asamizu Hiroyuki Fukuoka Daniel Just Christophe Rothan Shigemi Sasamoto Tsunakazu Fujishiro Yoshie Kishida Mitsuyo Kohara Hisano Tsuruoka Tsuyuko Wada Yasukazu Nakamura Shusei Sato Satoshi Tabata 《DNA research》2010,17(6):381-391
Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/. 相似文献
229.
Akira Sakurai Katsuyoshi Takayama Namiko Nomura Tsubasa Munakata Naoki Yamamoto Tsuruki Tamura Jitsuho Yamada Masako Hashimoto Kazuhiko Kuwahara Yoshihiro Sakoda Yoshihiko Suda Yukuharu Kobayashi Nobuo Sakaguchi Hiroshi Kida Michinori Kohara Futoshi Shibasaki 《PloS one》2013,8(11)
Immunochromatography (IC) is an antigen-detection assay that plays an important role in the rapid diagnosis of influenza virus because the protocol is short time and easy to use. Despite the usability of IC, the sensitivity is approximately 103 pfu per reaction. In addition, antigen-antibody interaction-based method cannot be used for the detection of influenza viruses with major antigenic change. In this study, we established the use of fluorescent immunochromatography (FLIC) to detect a broad spectrum of H5 subtype influenza A viruses. This method has improved sensitivity 10–100 fold higher than traditional IC because of the use of fluorescent conjugated beads. Our Type-E FLIC kit detected all of the H5 subtype influenza viruses that were examined, as well as recombinant hemagglutinin (HA) proteins (rHAs) belonging to the Eurasian H5 subtype viruses and the Type-N diagnosed North American H5 subtype influenza A viruses. Thus, this kit has the improved potential to detect H5 subtype influenza viruses of different clades with both Type-E and Type-N FLIC kits. Compared with PCR-based diagnosis, FLIC has a strong advantage in usability, because the sample preparation required for FLIC is only mix-and-drop without any additional steps such as RNA extraction. Our results can provide new strategies against the spread and transmission of HPAI H5N1 viruses in birds and mammals including humans. 相似文献
230.
Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids. 总被引:5,自引:0,他引:5
Yasukazu Nakamura Takakazu Kaneko Shusei Sato Mamoru Mimuro Hideaki Miyashita Tohru Tsuchiya Shigemi Sasamoto Akiko Watanabe Kumiko Kawashima Yoshie Kishida Chiaki Kiyokawa Mitsuyo Kohara Midori Matsumoto Ai Matsuno Naomi Nakazaki Sayaka Shimpo Chie Takeuchi Manabu Yamada Satoshi Tabata 《DNA research》2003,10(4):137-145