Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa

DNA methylation is an epigenetic gene regulatory mechanism that plays an essential role in gene expression, transposon silencing, genome imprinting and plant development. We investigated the influence of DNA methylation on gene expression in Brassica rapa L., to understand whether epigenetic differences exist between inbred lines. Genome-wide DNA methylation was analysed by methylated DNA immunoprecipitation sequencing (MeDIP-seq) of 14-day-old first and second leaves from two inbred lines of Chinese cabbage, one susceptible and one resistant to fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans. MACS (model-based analysis for ChIP-seq) identified DNA methylation peaks in genic regions including 2 kb upstream, exon, intron and 2 kb downstream. More than 65% of genes showed similar patterns of DNA methylation in the genic regions in the two inbred lines. DNA methylation states of the two inbred lines were compared with their transcriptome. Genes having DNA methylation in the intron and in the 200 bp upstream and downstream regions were associated with a lower expression level in both lines. A small number of genes showed a negative correlation between differences in DNA methylation levels and differences in transcriptional levels in the two inbred lines, suggesting that DNA methylation in these genes results in transcriptional suppression

Long noncoding RNAs in Brassica rapa L. following vernalization

© 2019, The Author(s). Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species

The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L

© The Author(s) 2019. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene

ノウキョケツ ニ オケル TIMPs ノ BBB ホゴ コウカ

京都大学0048新制・課程博士博士(医学)甲第14499号医博第3344号新制||医||974(附属図書館)UT51-2009-D211京都大学大学院医学研究科脳統御医科学系専攻(主査)教授 野田 亮, 教授 福山 秀直, 教授 瀬原 淳子学位規則第4条第1項該当Doctor of Medical ScienceKyoto UniversityDA

Structural Analysis for Wingspan Stent in a Perforator Model

Perforator infarction represents a critical problem after intracranial Wingspan stent. To explore the mechanism of perforator infarction, we simulated the stent-artery interaction at an atheromatous plaque with perforator. Structural deformation and biomechanical stress distribution after stenting were analyzed. High radial stress values were located along the stent struts, which surrounded the area with high circumferential stress. Stretched perforator orifice in a circumferential direction after stenting was simulated. These results show that structural deformation could play a role in the mechanism of perforator occlusion after Wingspan stenting

Structural Analysis for Wingspan Stent in a Perforator Model

Perforator infarction represents a critical problem after intracranial Wingspan stent. To explore the mechanism of perforator infarction, we simulated the stent-artery interaction at an atheromatous plaque with perforator. Structural deformation and biomechanical stress distribution after stenting were analyzed. High radial stress values were located along the stent struts, which surrounded the area with high circumferential stress. Stretched perforator orifice in a circumferential direction after stenting was simulated. These results show that structural deformation could play a role in the mechanism of perforator occlusion after Wingspan stenting

Promotion of Neurite and Filopodium Formation by CD47: Roles of Integrins, Rac, and Cdc42

Axon extension during development is guided by many factors, but the signaling mechanisms responsible for its regulation remain largely unknown. We have now investigated the role of the transmembrane protein CD47 in this process in N1E-115 neuroblastoma cells. Forced expression of CD47 induced the formation of neurites and filopodia. Furthermore, an Fc fusion protein containing the extracellular region of the CD47 ligand SHPS-1 induced filopodium formation, and this effect was enhanced by CD47 overexpression. SHPS-1–Fc also promoted neurite and filopodium formation triggered by serum deprivation. Inhibition of Rac or Cdc42 preferentially blocked CD47-induced formation of neurites and filopodia, respectively. Overexpression of CD47 resulted in the activation of both Rac and Cdc42. The extracellular region of CD47 was sufficient for the induction of neurite formation by forced expression, but the entire structure of CD47 was required for enhancement of filopodium formation by SHPS-1–Fc. Neurite formation induced by CD47 was also inhibited by a mAb to the integrin β3 subunit. These results indicate that the interaction of SHPS-1 with CD47 promotes neurite and filopodium formation through the activation of Rac and Cdc42, and that integrins containing the β3 subunit participate in the effect of CD47 on neurite formation

Immunohistochemical analysis of a ruptured basilar top aneurysm autopsied 22 years after embolization with Guglielmi detachable coils

The authors report on the histologic and immunohistochemical analyses of a cerebral aneurysm embolized with platinum coils and with the longest observation period. A 58-year-old woman presenting with subarachnoid hemorrhage due to ruptured basilar top aneurysm was treated with Guglielmi detachable coils (GDC) 22 years ago. She was the 15th case since the GDC was introduced. After she died of unrelated causes, an autopsy and thorough histologic examination were performed. Gross examination revealed no adhesion between the aneurysm wall and the surrounding brain tissue. Histologic and immunohistochemical analyses demonstrated that the cavity of the aneurysm was filled with homogeneous collagenous fibrous tissue, while the neck was completely covered by a dense collagenous neointima and a smooth muscle cell layer. The unique histologic results of this case may contribute to a better understanding of the long-term evolution of the healing process in intracranial aneurysms successfully treated with the GDC