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Cancer is a disease largely caused by genomic aberrations. Utilizing many rapidly emerging sequencing technologies, researchers have studied cancer genomes to understand the molecular statuses of cancer cells and to reveal their vulnerabilities, such as driver mutations or gene expression. Long-read technologies enable us to identify and characterize novel types of cancerous mutations, including complicated structural variants in haplotype resolution. In this review, we introduce three representative platforms for long-read sequencing and research trends of cancer genomics with long-read data. Further, we describe that aberrant transcriptome and epigenome statuses, namely, fusion transcripts, as well as aberrant transcript isoforms and the phase information of DNA methylation, are able to be elucidated by long-read sequencers. Long-read sequencing may shed light on novel types of aberrations in cancer genomics that are being missed by conventional short-read sequencing analyses.

Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. Here we show that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis leaf cells. We demonstrate that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts. Impaired histone acetylation predominantly affects transcription of auxin biosynthesis genes. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for cell cycle reactivation in protoplasts. These findings provide novel mechanistic model of how differentiated plant cells can revert their fate and reinitiate the cell cycle to become pluripotent.

Here, we report the application of a long-read sequencer, PromethION, for analyzing human cancer genomes. We first conducted whole-genome sequencing on lung cancer cell lines. We found that it is possible to genotype known cancerous mutations, such as point mutations. We also found that long-read sequencing is particularly useful for precisely identifying and characterizing structural aberrations, such as large deletions, gene fusions, and other chromosomal rearrangements. In addition, we identified several medium-sized structural aberrations consisting of complex combinations of local duplications, inversions, and microdeletions. These complex mutations occurred even in key cancer-related genes, such as STK11, NF1, SMARCA4, and PTEN. The biological relevance of those mutations was further revealed by epigenome, transcriptome, and protein analyses of the affected signaling pathways. Such structural aberrations were also found in clinical lung adenocarcinoma specimens. Those structural aberrations were unlikely to be reliably detected by conventional short-read sequencing. Therefore, long-read sequencing may contribute to understanding the molecular etiology of patients for whom causative cancerous mutations remain unknown and therapeutic strategies are elusive.

Here, we review single-cell sequencing techniques for individual and multiomics profiling in single cells. We mainly describe single-cell genomic, epigenomic, and transcriptomic methods, and examples of their applications. For the integration of multilayered data sets, such as the transcriptome data derived from single-cell RNA sequencing and chromatin accessibility data derived from single-cell ATAC-seq, there are several computational integration methods. We also describe single-cell experimental methods for the simultaneous measurement of two or more omics layers. We can achieve a detailed understanding of the basic molecular profiles and those associated with disease in each cell by utilizing a large number of single-cell sequencing techniques and the accumulated data sets., Single-cell sequencing: Greater insight through integrated data Combining data from different single-cell sequencing techniques could greatly improve understanding of the molecular profiles associated with disease. Sequencing studies provide valuable insights into diseased and healthy states at a single-cell level, for example the evolutionary paths of brain tumors and cancerous mutations. Ayako Suzuki at the University of Tokyo in Chiba, Japan, and co-workers examined the challenges of integrating data from various experimental and computational single-cell sequencing methods. These methods usually determine the genomic, epigenomic (DNA modifications) or transcriptomic (messenger RNAs) state of a cell, and can be combined to create a detailed picture. Other ‘multiomics’ techniques provide multilayered information from the same cell. The researchers recommend detailed analysis of individual data layers prior to integration, and highlight emerging techniques that analyze larger tissue sections, thus retaining the temporal and spatial information around a cell.

Here we report identification of a new class of local structural aberrations in lung cancers. The whole-genome sequencing of cell lines using a long read sequencer, PromethION, demonstrated that typical cancerous mutations, such as point mutations, large deletions and gene fusions can be detected also on this platform. Unexpectedly, we revealed unique structural aberrations consisting of complex combinations of local duplications, inversions and micro deletions. We further analyzed and found that these mutations also occurin vivo, even in key cancer-related genes. These mutations may elucidate the molecular etiology of patients for whom causative cancerous events and therapeutic strategies remain elusive.

Long-read whole-genome sequencing analysis of DNA methylation would provide useful information on the chromosomal context of gene expression regulation. Here we describe the development of a method that improves the read length generated by using the bisulfite-sequencing-based approach. In this method, we combined recently developed enzymatic base conversion, where an unmethylated cytosine (C) should be converted to thymine (T), with nanopore sequencing. After methylation-sensitive base conversion, the sequencing library was constructed using long-range polymerase chain reaction. This type of analysis is possible using a minimum of 1 ng genomic DNA, and an N50 read length of 3.4–7.6 kb is achieved. To analyze the produced data, which contained a substantial number of base mismatches due to sequence conversion and an inaccurate base read of the nanopore sequencing, a new analytical pipeline was constructed. To demonstrate the performance of long-read methylation sequencing, breast cancer cell lines and clinical specimens were subjected to analysis, which revealed the chromosomal methylation context of key cancer-related genes, allele-specific methylated genes, and repetitive or deletion regions. This method should convert the intractable specimens for which the amount of available genomic DNA is limited to the tractable targets.

The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure for full-length cDNA sequencing using the Nanopore sequencer MinION. We applied MinION RNA-Seq for various applications, which would not always be easy using the usual RNA-Seq by Illumina. First, we examined and found that even though the sequencing accuracy was still limited to 92.3%, practically useful RNA-Seq analysis is possible. Particularly, taking advantage of the long-read nature of MinION, we demonstrate the identification of splicing patterns and their combinations as a form of full-length cDNAs without losing precise information concerning their expression levels. Transcripts of fusion genes in cancer cells can also be identified and characterized. Furthermore, the full-length cDNA information can be used for phasing of the SNPs detected by WES on the transcripts, providing essential information to identify allele-specific transcriptional events. We constructed a catalogue of full-length cDNAs in seven major organs for two particular individuals and identified allele-specific transcription and splicing. Finally, we demonstrate that single-cell sequencing is also possible. RNA-Seq on the MinION platform should provide a novel approach that is complementary to the current RNA-Seq.

The functional relevancy of mutations occurring in the regulatory regions in cancers remains mostly elusive. Here, we identified and analyzed regulatory mutations having transcriptional consequences in lung adenocarcinoma-derived cell lines. We phased the mutations in the regulatory regions to the downstream heterozygous SNPs in the coding regions and examined whether the ChIP-Seq variant tags of the regulatory SNVs and the RNA-Seq variant tags of their target transcripts showed biased frequency between the mutant and reference alleles. We identified 137 potential regulatory mutations affecting the transcriptional regulation of 146 RefSeq transcripts with at least 84 SNVs that create and/or disrupt potential transcription factor binding sites. For example, in the regulatory region of NFATC1 gene, a novel and active binding site for the ETS transcription factor family was created. Further examination revealed that 31 of these disruptions were presented in clinical lung adenocarcinoma samples and were associated with prognosis of patients.

Objective: To investigate the diagnostic utility of endometrial (EM) cell block (CB) cytology for the detection of intrauterine malignancy in postmenopausal women. Methods: We reviewed the medical records of 104 postmenopausal women between January 2012 and November 2014. We reviewed symptoms upon admission, body mass index, parity, transvaginal ultrasonographic findings, and histopathological results based on CB and conventional cytology. Results: The mean age was 62.6 (range 48-95) years. The mean menopausal age was 50.8 years and the mean duration of menopause was 12.0 years. The sensitivity of CB and conventional cytology was 82.3% (29/35) and 85.7% (30/35) and the specificity was 98.6% (68/69) and 94.2% (65/69), respectively. The sensitivity and specificity of CB cytology combined with conventional cytology were 82.3% (29/35) and 94.2% (65/69), respectively. The predictive values for EM hyperplasia and type-II carcinoma were 100 and 85.7%, respectively. Conclusion: CB cytology provides specimens for examination in a single outpatient session. Additionally, immunohistochemical staining can provide useful information for histological diagnosis. A combination of CB and conventional cytology can improve the diagnostic accuracy of EM lesions and may be a valid method for screening in postmenopausal women.

症例は72歳,女性.下腹部痛と嘔気を主訴に来院.下腹部に圧痛を認めたが筋性防御はなかった.腹部単純X線で骨盤内にガス像と腹部CTで内部比較的均一な腫瘤を認めた.注腸造影では造影剤が腫瘤部に漏出した.腸間膜への穿孔を疑い来院より6時間後,緊急手術を行った.開腹所見では,腹水を認めたが便臭は伴っていなかった. S状結腸間膜が手拳大の腫瘤を形成し,この肛門側に大腸癌を認めた.手術は高位前方切除を施行した.切除標本では,亜全周性に2型の腫瘍を認め,その口側約2.5cmに穿孔部を認めた.病理組織診断では腫瘍と穿孔部の間は浮腫を伴った正常粘膜よりなり,閉塞性大腸炎による腸間膜への穿孔と診断した.術後13日目に軽快退院した.

鼻腔内腫瘍の犬3例に対して外科療法, 常電圧放射線療法, 化学療法による集学的治療を行った。症例1は軟骨肉腫 (T2N0M0) で, 症状空白期間と生存期間はそれぞれ8ヵ月間と21ヵ月間であった。症例2は腺癌 (T3N0M0) で, 症状空白期間は7ヵ月間であった。しかし, 腫瘍の再発とそれの脳内浸潤を認め, 診断後9ヵ月目に死亡した。症例3は未分化癌 (T2N0M0) で, 放射線療法後にバベシア症の重度貧血で死亡した。症状空白期間と生存期間はともに2ヵ月間であった。

Application of the modified Mosher method using high-field FT 1 H NMR to the 2-methoxy-2-phenyl-2-trifluoromethyl acetic acid (MTPA) derivatives of fluorinated secondary alcohols indicates that this method may be generally used to determine the absolute configurations of these materials.

(1) ロボットの寿命を摩耗現象の観点から解明し,これを予測する式を提案した.(2)これにより,ロボットの劣化モデルのデータベースを構築し,従来のオフラインプログラミングシステムと統合させた,ロボット寿命推定システムを完成した.(3)このシステムをロボットオーバホール業務に適用し,大きなコスト低減効果を得た.

To investigate cell cycle regulation at the S or G2 phase in Saccharomyces cerevisiae, we have isolated mutants displaying supersensitivity to hydroxyurea (HU), a chemical that inhibits DNA replication. Such mutants, which we have named hydroxyurea sensitive (hys), defined four linkage groups and we characterized the hys2 mutation in this study. The hys2-1 mutant displays temperature sensitive growth and a constellation of phenotypes indicating defective DNA metabolism. At the restrictive temperature, hys2-1 cells arrest as large budded cells with a single nucleus at the neck of the bud and a short spindle. The hys2-1 mutant exhibits increased rates of chromosome loss and recombination. Additionally, hys2-1 appears to accumulate incompletely replicated DNA that can be detected by a pulse field electrophoresis assay. Finally, deletion of RAD9 in a hys2-1 strain decreases the percentage of arrested cells, suggesting that an intact RAD9-checkpoint is required for the cell cycle arrest in hys2-1 cells. HYS2 encodes a 55 kDa protein that is essential for viability at all temperatures. Taken together, these data suggest that Hys2 plays a role in DNA replication.

Immunoelectron microscopic localization of endothelin (ET) using the mouse monoclonal anti-ET sera was performed on the pre-and postnatal rabbit umbilical vein during stages when Weibel-Palade (WP) bodies increase in number in the endothelial cells. The immunoreactions are localized in the rough endoplasmic reticulum, Golgi cisterns, and WP bodies that are actively segregated from the Golgi apparatus. After degranulation and extracellular release of WP bodies was induced by compound 48/80, heavy immunoreactions were seen in both vascular lumen and cytoplasm near the degranulated WP bodies. These results indicate that ET is stored in WP bodies after segregation from the Golgi apparatus and released from the endothelial cells concomitantly with other components of these granules by exocytosis. Because the immunoreactions are also seen in pinocytotic vesicles that are occasionally in contact with WP bodies, it seems likely that WP bodies are also involved in the uptake and storage of ET from blood plasma. © 1993 Wiley-Liss, Inc.

Enantioselective hydrolyses of 2-chloroacetates derived from racemic 1,1,1-trifluoro-2-alkanols were found to proceed very smoothly in the presence of a catalytic amount of lipase MY to yield the corresponding (R)-alcohols with high optical purity. In this procedure, Purification was easily carried out only by a simple distillation of the reaction mixture, enabling us to extend this reaction in a larger scale.

Application of the modified Mosher method using high-field FT 1 H NMR to the 2-methoxy-2-phenyl-2-trifluoromethyl acetic acid (MTPA) derivatives of fluorinated secondary alcohols indicates that this method may be generally used to determine the absolute configurations of these materials.

Simultaneous immunoelectron microscopic localization of histamine and factor VII-related antigen was examined on the same ultrathin section of the endothelium of the human umbilical vein from full-term deliveries by means of the double-immunolabeling technique. Small gold particles demonstrating antibody reaction with histamine are preferentially located in the cytoplasmic matrix and organelles, especially in mitochondria and on the luminal membrane surface of the endothelial cells. The gold particles representing histamine immunoreactivity also located on some of Weibel Palade (WP) bodies. In contrast, large gold particles demonstrating factor VII-related antigen are concentrated preferentially on most WP bodies. Single labeling of either histamine or factor VIII-related antigen shows similar results to those of the double labeling. The present study indicates that some WP bodies are involved in storage of both factor VIII-related antigen and histamine, but others store factor VIII-related antigen only. This difference in contents of WP bodies may be induced during the development and maturation process of this inclusion. At any rate, it is reasonable to consider that WP bodies have important roles in both vascular tonus and hemostasis during the vascular obliteration.

Subjects were 239 patients with colorectal cancer who underwent curative resection surgery from December 1994 to March 1997(Stage I-III b). The patients were given 5'-DFUR for postoperative 10 months as scheduled. They had been allocated into either a 1-year group or a 3-year group by dynamic randomization. 5'-DFUR was administered by an intermittent regimen such as 1,200 mg/body/day for five days followed by two days rest. All patients were followed for five years at least.239 patients were enrolled in the study. Favorable prognoses in both groups were observed. Although no statistically significant differences in overall survival curves of full analysis set based on the drug administration durations, were detected(log-rank test, p=0.734), a better prognosis was found in the 3-year group(5-year OS: 92.0%; 1- year group, 91.4%; 3-year group). Adverse drug reactions resulted in low rates such as 14.8% in the 1-year group and 19.5% in the 3-year group. Grade 3 was found in either group.Due to a result in the present study that 5-year survival rates in both groups were far higher than anticipated, we could not finally clarify the optimal administration duration of 5'-DFUR. However, the results of the present study indicate that 5'-DFUR results in a good prognosis for colorectal cancer patients and is safe over a long / administration period.

Gene delivery is an essential research tool for elucidating gene structure, regulation, and function in biomedical research and is the technological basis for gene therapy. However, the application of nonviral vectors in mammalian cell transfection and gene therapy is limited in that current methods require large amounts of exogenous DNA and/or exhibit high cytotoxicity and low transfection efficiency in primary cells. Here we describe the development of a novel, noninvasive gene delivery protocol using plasmid DNA vectors, based on the principle of electric field-induced molecular vibration. This method enables foreign DNA molecules to penetrate the plasma membrane and enter the cytoplasm of both primary mesenchymal progenitor cells and established cell lines of various species, at high efficiency and with low cell mortality. This procedure requires no special reagents, allows stable expression of transduced DNA, and does not interfere with the normal cellular differentiation activities of human and chick mesenchymal progenitors.

The burden of robot maintenance in the car industry (e.g. overhaul) is increasing drastically year after year. Although inspection and maintenance are indispensable in view of preventive maintenance, it is most important to accurately know the life expectancy of mechanical parts constituting a robot in order to execute the inspection and maintenance operations at the minimum investment. We therefore discuss the fact that the wear of gears is a dominant life expectancy factor of mechanical parts and we make observations on wear phenomenon in view of tribology. Based on the observations, we propose wear estimation models with improved lubrication and the improvement is applied to actual robots. In addition, we integrated the models with the robot off-line programming system and developed a CAE system capable of estimating the robot life expectancy at the time of preparation of robot teaching data.

We deposited Ta2O5 thin films on the (001) surfaces of 80K-phase Bi-Sr-Ca-Cu-O(BSCCO) single crystals, and investigated the growth modes by reflection high energy electron diffraction (RHEED) and the interfaces between the BSCCO single crystal and the Ta2O5 film by X-ray photoelectron spectroscopy (XPS). When the 200A Ta2O5 thin films were deposited on the BSCCO single crystal surfaces at the substrate temperatures of room temperature and 300°C, the growth modes were amorphous form. From the XPS results, we found that Ta2O5 of the Ta2O5/BSCCO specimen diffused into the BSCCO substrate, and that the deteriorated layer was formed at the interface.

The toxic effects of cadmium on the thyroid gland of pregnant rats were studied with an electron microscope and an X-ray microanalyzer. Serum levels of thyroid hormones (T3 and T4) were also analyzed. Deterioration of the rough-surfaced endoplasmic reticulum occurred in the thyroid follicular epithelium on the fifth day of cadmium treatment. Large intracellular vacuoles, which arose from dilated cisternae of the rough-surfaced endoplasmic reticulum, were fused together, and marked swelling of the mitochondria was also noted. Thyroglobulin-secreting granules at the apical cytoplasm were decreased in number. By energy dispersive X-ray microanalysis, cadmium peaks were preferentially obtained from swollen mitochondria in the follicular epithelial cells. Serum levels of T3 and T4 were significantly decreased in cadmium-treated rats dams when compared to those of controls. In the present experiment, cycloheximide also caused degenerative changes in the rough-surfaced endoplasmic reticulum and the disappearance of thyroglobulin-secreting granules. Cycloheximide is a known inhibitor of protein synthesis on cytosolic ribosomes. These results indicated that accumulated cadmium in the mitochondria of thyroid follicular epithelial cells might disturb the oxidative phosphorylation of this organelle and the loss of energy supply possibly caused the inhibition of the synthesis and release of thyroid hormones.