Epigenetic-scale comparison of human iPSCs generated by retrovirus, Sendai virus or episomal vectors

Human induced pluripotent stem cells (iPSCs) are established by introducing several reprogramming factors, such as OCT3/4, SOX2, KLF4, c-MYC. Because of their pluripotency and immortality, iPSCs are considered to be a powerful tool for regenerative medicine. To date, iPSCs have been established all over the world by various gene delivery methods. All methods induced high-quality iPSCs, but epigenetic analysis of abnormalities derived from differences in the gene delivery methods has not yet been performed. Here, we generated genetically matched human iPSCs from menstrual blood cells by using three kinds of vectors, i.e., retrovirus, Sendai virus, and episomal vectors, and compared genome-wide DNA methylation profiles among them. Although comparison of aberrant methylation revealed that iPSCs generated by Sendai virus vector have lowest number of aberrant methylation sites among the three vectors, the iPSCs generated by non-integrating methods did not show vector-specific aberrant methylation. However, the differences between the iPSC lines were determined to be the number of random aberrant hypermethylated regions compared with embryonic stem cells. These random aberrant hypermethylations might be a cause of the differences in the properties of each of the iPSC lines

Gene Organization in Rice Revealed by Full-Length cDNA Mapping and Gene Expression Analysis through Microarray

Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria

Calpain-1 C2L domain peptide protects mouse hippocampus-derived neuronal HT22 cells against glutamate-induced oxytosis

Calpains are Ca2+-dependent cysteine proteases; their aberrant activation is associated with several neurodegenerative diseases. The μ-calpain catalytic subunit, calpain-1, is located in the cytoplasm as well as in the mitochondria. Mitochondrial calpain-1 cleaves apoptosis-inducing factor (AIF), leading to apoptotic cell death. We have previously reported that short peptides of calpain-1 C2-like domain conjugated with cell penetrating peptide HIV-Tat (Tat-μCL) selectively inhibit mitochondrial calpain-1 and effectively prevent neurodegenerative diseases of the eye. In this study, we determined whether mitochondrial calpain-1 mediates oxytosis (oxidative glutamate toxicity) in hippocampal HT22 cells using Tat-μCL and newly generated polyhistidine-conjugated μCL peptide and compared their efficacies in preventing oxytosis. TUNEL assay and single strand DNA staining revealed that both μCL peptides inhibited glutamate-induced oxytosis. Additionally, both the peptides suppressed the mitochondrial AIF translocation into the nucleus. All polyhistidine-μCL peptides (containing 4–16 histidine residues) showed higher cell permeability than Tat-μCL. Notably, tetrahistidine (H4)-μCL exerted the highest cytoprotective activity. Thus, H4-μCL may be a potential peptide drug for calpain-1-mediated neurodegenerative diseases such as Alzheimer's disease

Transactions and Practical Uses for Education of Symbolic Living Things(woods,flowers,birds,fishes and insects) in Akita Prefecture

平成の大合併に伴い秋田県では69あった市町村が25になった。各市町村は平成の大合併以前から独自にシンボル生物(木、花、鳥、魚、昆虫など)を制定していることが多かった。本研究では、シンボル生物が平成の大合併に伴いどのように変遷されていったのか、またシンボル生物がどのように教育に利用されてきたのか(利用されているのか)を明らかにすることを目的とした。 秋田県に69あった市町村のうち、なんらかのシンボル生物を制定していたのは上小阿仁村と旧角館町を除く67市町村であった。そして合併の前後で変更がなかった秋田県内10市町村(上小阿仁村を含む)のシンボル生物にはもちろん変更がなかった。合併の形態には新設合併と編入合併がある。秋田県で新設された市町村のうち、シンボル生物をまだ制定していないのは3市1町(能代市、三種町、横手市、湯沢市)であった。また編入合併の場合では、廃止された自治体が制定していたシンボル生物は消滅し、編入先の自治体が制定していたシンボル生物がそのまま残っていた。 シンボル生物の教育現場への利用について秋田県の小中高の学校教員にアンケートを行ったところ、シンボル生物自体があまり意識されておらず、教育にシンボル生物を活用しているケースは少なかった。一方、教育現場ではないが、各地域のシンボル生物が自治体の章、デザインマンホール、カントリーサインなどに描写されていたり、地域の情報ブログなどでシンボル生物の名称が使用されていたりと地域にシンボル生物が密着しているケースもみられた。Cities,towns,and villages in Akita Prefecture were situated in the great Heisei merger.Each city independently established symbolic living things such as trees,flowers,birds,fishes,and insects before the great Heisei merger.In this paper,transitions and practical uses for education of symbolic living things in Akita Prefecture were reported.In Akita Prefecture,67 cities(among 69 cities)had some symbolic living things before merger.After merger,in Akita Prefecture,20 cities(among 25 cities) have symbolic living things.However,during merger,variety and number of symbolic living things were decreased.In education,a few practical uses of symbolic living things were found in Akita Prefecture,from the questionnaire survey