Biomedical subjects

Mayu Yamamoto

Publications and source records attributed to Mayu Yamamoto.

6 recordsLinked to original sources

PubMed2005

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/.

Chromosomes, Plant↗

PubMed2004

Composition and structure of the centromeric region of rice chromosome 8.

Understanding the organization of eukaryotic centromeres has both fundamental and applied importance because of their roles in chromosome segregation, karyotypic stability, and artificial chromosome-based cloning and expression vectors. Using clone-by-clone sequencing methodology, we obtained the complete genomic sequence of the centromeric region of rice (Oryza sativa) chromosome 8. Analysis of 1.97 Mb of contiguous nucleotide sequence revealed three large clusters of CentO satellite repeats (68.5 kb of 155-bp repeats) and >220 transposable element (TE)-related sequences; together, these account for approximately 60% of this centromeric region. The 155-bp repeats were tandemly arrayed head to tail within the clusters, which had different orientations and were interrupted by TE-related sequences. The individual 155-bp CentO satellite repeats showed frequent transitions and transversions at eight nucleotide positions. The 40 TE elements with highly conserved sequences were mostly gypsy-type retrotransposons. Furthermore, 48 genes, showing high BLAST homology to known proteins or to rice full-length cDNAs, were predicted within the region; some were close to the CentO clusters. We then performed a genome-wide survey of the sequences and organization of CentO and RIRE7 families. Our study provides the complete sequence of a centromeric region from either plants or animals and likely will provide insight into the evolutionary and functional analysis of plant centromeres.

Base Composition↗

PubMed2002

High-level expression of viral interleukin-10 in cardiac allografts fails to prolong graft survival.

BACKGROUND: Viral interleukin (vIL)-10, encoded in the Epstein-Barr virus genome, shares many of the anti-inflammatory properties of cellular IL-10 but is supposed to lack IL-10's immunostimulatory properties. Thus, vIL-10 is expected to offer superior immunosuppression. METHODS: We established transgenic mice (vIL-10 Tg) that express vIL-10 systemically and transplanted their hearts as vascularized allografts into unmodified major histocompatibility complex (MHC) full-mismatch or MHC class II-disparate mice. RESULTS: The vIL-10 Tg mice revealed high-level expression of vIL-10 in major organs including the heart. However, the heart grafts from the vIL-10 Tg mice failed to exhibit prolonged survival in combination with either the MHC full-mismatch or the class II-disparate mice. In the MHC class II-disparate mice, the vIL-10 Tg heart grafts showed severe CD8 T-cell infiltration and increased interferon (IFN)-gamma mRNA expression compared with non-Tg grafts. CONCLUSION: High level expression of vIL-10 in grafts can exacerbate immunological rejection in an allogenic transplantation model.

Animals↗

PubMed2002

Cultivated tomato has defects in both S-RNase and HT genes required for stylar function of self-incompatibility.

Cultivated tomato (Lycopersicon esculentum), a self-compatible species, evolved from self-incompatible (SI) species in the genus Lycopersicon following a breakdown of the self-incompatibility system. In order to elucidate the molecular basis of this breakdown in L. esculentum, we first analysed the stylar proteins with an in-gel assay for ribonuclease activity and 2D-PAGE. No S-RNase protein or its activity was detected in the style of L. esculentum. We then introduced the S6-RNase gene from an SI relative, L. peruvianum, into L. esculentum. However, the styles of transgenic plants expressing S6-RNase at levels comparable to those found in the L. peruvianum style were unable to reject self-pollen and L. peruvianum pollen in an allele-specific manner. This indicated that defect in the S-RNase expression was not the sole reason for the loss of self-incompatibility in tomato. The asparagine-rich HT protein, originally identified from the style of Nicotiana alata, is the other stylar factor involved in self-incompatibility reaction. We cloned and sequenced two distinct genes encoding HT-A and HT-B proteins from L. peruvianum (LpHT-A and LpHT-B) and L. esculentum (LeHT-A and LeHT-B). A frame shift mutation in the coding sequence of LeHT-A and a stop codon in the ORF of LeHT-B were found, and no LeHT-B transcript was detected in the style of L. esculentum. The results suggest that the breakdown of self-incompatibility in cultivated tomato is associated with loss-of-function mutations in both S-RNase and HT genes.

Amino Acid Sequence↗

PubMed2002

Insights into the evolution of self-compatibility in Lycopersicon from a study of stylar factors.

To elucidate the molecular basis of loss of self-incompatibility in Lycopersicon, S-RNases and HT-proteins were analysed in seven self-compatible (SC) and three self-incompatible (SI) taxa. No or low stylar RNase activity was a common feature in most SC taxa examined, in contrast to the uniformly high levels of activity found in all SI species. The S-RNase gene is most likely deleted in the four red-fruited SC taxa (L. esculentum, L. esculentum var. cerasiforme, L. pimpinellifolium and L. cheesmanii) because S-RNase genes could not be amplified from genomic DNA. S-RNase genes could, however, be amplified from the genomes of the three green-fruited SC taxa examined. L. chmielewskii and L. hirsutum f. glabratum show a decreased accumulation of transcripts, possibly reflecting changes in the 5' flanking regions of the S-RNase genes. The remaining green-fruited SC species, L. parviflorum, has a functional S-RNase gene in its genome that is expressed at high levels in the style, suggesting a genetic factor responsible for the low S-RNase activity. Together these results argue for several independent mutations in the S-RNase gene over the course of Lycopersicon diversification, and that loss of S-RNase function is unlikely to the primary cause of the loss of self-incompatibility. We also examined the HT-B genes that play a role in self-incompatibility. HT-B transcripts were markedly reduced in the styles of all the SC taxa examined. A scenario is described where a mutation causing reduced transcription of HT-B in an ancestral SI species was central to the loss of self-incompatibility in Lycopersicon.

Biological Evolution↗

PubMed1997

Growth phase-dependent transcription of emrKY, a homolog of multidrug efflux emrAB genes of Escherichia coli, is induced by tetracycline.

The genes emrK and emrY were found between genes dsdA and evgA at 51 min on the Escherichia coli chromosome and form an operon. EmrK and EmrY are 50.4 and 63.3% identical in amino acid sequences to EmrA and EmrB, respectively, which together make up a multidrug resistant pump. To show that the emrKY operon can be expressed, we cloned the promoter with pMC1403 and constructed an emrK-lacZ' protein fusion plasmid, pMKD1. In E. coli MC4100 containing pMKD1, its expression was increased in the presence of a subinhibitory concentration of tetracycline, chloramphenicol or salicylate, but not by carbonylcyanide m-chlorophenylhydrazone, nalidixic acid or kanamycin. Furthermore, we have shown that emrKY transcription dependent on the growth phase is actually induced by tetracycline using a S1 nuclease protection assay.

Journal Article↗