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Biomedical subjects

Yukio Kurihara

Publications and source records attributed to Yukio Kurihara.

6 recordsLinked to original sources
PubMed2006

The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis.

It has been reported that some double-stranded RNA (dsRNA) binding proteins interact with small RNA biogenesis-related RNase III enzymes. However, their biological significance is poorly understood. Here we examine the relationship between the Arabidopsis microRNA- (miRNA) producing enzyme DCL1 and the dsRNA binding protein HYL1. In the hyl1-2 mutant, the processing steps of miR163 biogenesis were partially impaired; increased accumulation of pri-miR163 and reduced accumulation of short pre-miR163 and mature miR163 as well as misplaced cleavages in the stem structure of pri-miR163 were detected. These misplaced cleavages were similar to those previously observed in the dcl1-9 mutant, in which the second double-stranded RNA binding domain of the protein was disrupted. An immunoprecipitation assay using Agrobacterium-mediated transient expression in Nicotiana benthamiana showed that HYL1 was able to form a complex with wild-type DCL1 protein, but not with the dcl1-9 mutant protein. We also examined miR164b and miR166a biogenesis in hyl1-2 and dcl1-9. Increased accumulation of pri-miRNAs and reduced accumulation of pre-miRNAs and mature miRNAs were detected. Misplaced cleavage on pri-miR164b was observed only in dcl1-9 but not in hyl1-2, whereas not on pri-miR166a in either mutant. These results indicate that HYL1 has a function in assisting efficient and precise cleavage of pri-miRNA through interaction with DCL1.

Arabidopsis↗
PubMed2004

Multidimensional vector space representation for convergent evolution and molecular phylogeny.

With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models can support incorrect topologies significantly because of the high signal-to-noise ratio. We propose a procedure to locate sequences in a multidimensional vector space (MVS), in which the geometry of the space is uniquely determined in such a way that the vectors of sequence evolution are orthogonal among different branches. In this paper, the MVS approach is developed to detect and remove biases in models of molecular evolution caused by unrecognized convergent evolution among lineages or unexpected patterns of substitutions. Biases in the estimated pairwise distances are identified as deviations (outliers) of sequence spatial vectors from the expected orthogonality. Modifications to the estimated distances are made by minimizing an index to quantify the deviations. In this way, it becomes possible to reconstruct the phylogenetic tree, taking account of possible biases in the model of molecular evolution. The efficacy of the modification procedure was verified by simulating evolution on various topologies with rate heterogeneity and convergent change. The phylogeny of placental mammals in previous analyses of large data sets has varied according to the genes being analyzed. Systematic deviations caused by convergent evolution were detected by our procedure in all representative data sets and were found to strongly affect the tree structure. However, the bias correction yielded a consistent topology among data sets. The existence of strong biases was validated by examining the sites of convergent evolution between the hedgehog and other species in mitochondrial data set. This convergent evolution explains why it has been difficult to determine the phylogenetic placement of the hedgehog in previous studies.

Animals↗
PubMed2004

Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions.

Micro-RNAs (miRNAs) are small, noncoding RNAs of 18-25 nt in length that negatively regulate their complementary mRNAs at the posttranscriptional level. Previous work has shown that some RNase III-like enzymes such as Drosha and Dicer are known to be involved in miRNA biogenesis in animals. However, the mechanism of plant miRNA biogenesis still remains poorly understood. In this article, the process of Arabidopsis miR163 biogenesis was examined. The results revealed that two types of miR163 primary transcripts (pri-miR163s) are transcribed from a single gene by RNA polymerase II and that miR163 biogenesis requires at least three cleavage steps by RNase III-like enzymes at 21-nt-long intervals. The first step is from pri-miR163 to long miR163 precursor (premiR163), the second step is from long pre-miR163 to short premiR163, and the last step is from short pre-miR163 to mature miR163 and the remnant. It is interesting that, during the process, four small RNAs including miR163 are released. By using dcl1 mutants, it was demonstrated that Arabidopsis Dicer homologue Dicer-like 1 (DCL1) catalyzes at least the first and second cleavage steps and that double-stranded RNA-binding domains of DCL1 are involved in positioning of the cleavage sites. Our result is direct evidence that DCL1 is involved in processing of pri- and pre-miRNA.

Arabidopsis↗
PubMed2004

A TMV-Cg mutant with a truncated coat protein induces cell death resembling the hypersensitive response in Arabidopsis.

Tobacco mosaic virus (TMV)-Cg is able to propagate and multiply systemically to high levels in Arabidopsis thaliana ecotype Col-0. In this study, we obtained a Cg mutant, Cgk1, which expresses a coat protein with a truncated carboxyl terminus. Interestingly, Cgk1 induced necrosis that resembled the hypersensitive response and caused more pronounced disease symptoms than wild type Cg in Arabidopsis Col-0 plants. A reactive oxidative burst occurred prior to this necrosis. We found that expression of the pathogenesis-related gene PR-1 was induced by Cgk1 infection, and also by infection with wild type Cg, but only in npr1-2 mutant plants, not in NahG transgenic plants. These results suggested that PR-1 expression is dependent on the salicylic acid signaling pathway, but is independent of NPR1.

Amino Acid Sequence↗
PubMed2004

Academic performance and comparative effectiveness of computer- and textbook-based self-instruction.

We intended to clarify the influence of student academic ability on the effectiveness of CAI, using data of a study to assess the effectiveness of a new type of CAI software, cyberPatient (CP), at Kochi Medical School (KMS). A total of 59 third-year students were randomly assigned to four groups: Group-1 used a textbook for self-instruction, Group-2 used CP, Group-3 used both types of learning materials, and Group-4 did not learn. Learning performance was evaluated by multiple-choice examination and OSCE. In order to clarify the influence of students' academic ability on the effectiveness of CAI, statistical analyses were conducted, assigning students as either high or medium or low performance students. High performance students from Group-1, -2 and -3 did not differ significantly in test performance after self-instruction. However, low performance students in Group-1 scored significantly lower than those in Group-2 and -3. All students in Group-2 and -3 reported that CP stimulated willingness to learn and assisted understanding. The present analysis suggested that effectiveness of CAI might be associated with the academic ability of students.

Computer-Assisted Instruction↗