Lifetime of Singlet Oxygen and Quenching by NaN3 in Mixed Solvents

Singlet oxygen was generated by the photosensitization of erythrosine. The lifetime of singlet oxygen and the quenching rate constant for singlet oxygen by NaN3 were measured by a thermal lensing method in MeOH-H2O mixed solvents. The reciprocal of the lifetime increased linearly with the increase of the H2O mole fraction. Semi-log plot of the quenching constant against the reciprocal of the solvent polarity exhibited a linear relation. The quenching of the singlet oxygen by NaN3 may proceed through a partial charge-transfer intermediate. The activation energy for the quenching reaction of N3 - + 1O2 →[N3·1O2 -] increased with the increase of the solvent polarity. The lifetime was also measured in MeOH-ethyleneglycol mixed solvents, and its relation with viscosity was obtained

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)

BACKGROUND

Next generation sequencing based technologies are being extensively used to study transcriptomes. Among these, cap analysis of gene expression (CAGE) is specialized in detecting the most 5' ends of RNA molecules. After mapping the sequenced reads back to a reference genome CAGE data highlights the transcriptional start sites (TSSs) and their usage at a single nucleotide resolution.

RESULTS

We propose a pipeline to group the single nucleotide TSS into larger reproducible peaks and compare their usage across biological states. Importantly, our pipeline discovers broad peaks as well as the fine structure of individual transcriptional start sites embedded within them. We assess the performance of our approach on a large CAGE datasets including 156 primary cell types and two cell lines with biological replicas. We demonstrate that genes have complicated structures of transcription initiation events. In particular, we discover that narrow peaks embedded in broader regions of transcriptional activity can be differentially used even if the larger region is not.

CONCLUSIONS

By examining the reproducible fine scaled organization of TSS we can detect many differentially regulated peaks undetected by previous approaches.

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well as structures. They measure expression by sequencing from either the 5' end of capped molecules (CAGE) or tags randomly distributed along the length of a transcript (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation sequencing platforms typically employ PCR preamplification prior to clonal amplification, while third-generation, single-molecule sequencers can sequence unamplified libraries. Although these transcriptome profiling platforms have been demonstrated to be individually reproducible, no systematic comparison has been carried out between them. Here we compare CAGE, using both second- and third-generation sequencers, and RNA-seq, using a second-generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies that can be used to improve incomplete gene models. We also found systematic bias in the second- and third-generation platforms, which is likely due to steps such as linker ligation, cleavage by restriction enzymes, and PCR amplification. This study provides a perspective on the performance of these platforms, which will be a baseline in the design of further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells

Obesity confers an increased risk of developing specific cancer forms. Although the mechanisms are unclear, increased fat cell secretion of specific proteins (adipokines) may promote/facilitate development of malignant tumors in obesity via cross-talk between adipose tissue(s) and the tissues prone to develop cancer among obese. We searched for novel adipokines that were overexpressed in adipose tissue of obese subjects as well as in tumor cells derived from cancers commonly associated with obesity. For this purpose expression data from human adipose tissue of obese and non-obese as well as from a large panel of human cancer cell lines and corresponding primary cells and tissues were explored. We found expression of ceruloplasmin to be the most enriched in obesity-associated cancer cells. This gene was also significantly up-regulated in adipose tissue of obese subjects. Ceruloplasmin is the body's main copper carrier and is involved in angiogenesis. We demonstrate that ceruloplasmin is a novel adipokine, which is produced and secreted at increased rates in obesity. In the obese state, adipose tissue contributed markedly (up to 22%) to the total circulating protein level. In summary, we have through bioinformatic screening identified ceruloplasmin as a novel adipokine with increased expression in adipose tissue of obese subjects as well as in cells from obesity-associated cancers. Whether there is a causal relationship between adipose overexpression of ceruloplasmin and cancer development in obesity cannot be answered by these cross-sectional comparisons.

An atlas of active enhancers across human cell types and tissues

Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.

Compact 100Gb/s DP-QPSK integrated receiver module employing three-dimensional assembly technology

We demonstrate a compact 100 Gbit/s DP-QPSK receiver module that is only 18 mm (W) x 16 mm (D) x 2.8 mm (H). The module size is reduced by using a ball grid array (BGA) package with three-dimensional assembly technology and by applying a heterogeneous integrated PLC. Error-free DP-QPSK signal demodulation is successfully demonstrated.

Radioactive ion beam transportation for the fundamental symmetry study with laser-trapped atoms

The search for the violation of the fundamental symmetry in a radioactive atom is the promising candidate for precision tests of the standard model and its possible extensions. The subtle signal arising from the symmetry violation is enhanced in heavy atoms, such as a francium (Fr). To realize high precision measurements, a large amount of radioactive isotopes is required. The Fr is produced via a nuclear fusion reaction using a melted gold target with a (18)O primary beam at Cyclotron and Radioisotope Center, Tohoku University. The maximum extraction efficiency of the Fr ion was achieved at approximately 35%. The beam line consists of an electrostatic deflector, three electrostatic quadrupole triplets to the measurement area at 10 m away from the reaction point, and several beam diagnosis systems. We optimized parameters of the beam line.

Detecting expressed genes using CAGE

Cap analysis of gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. By the large-scale analysis of 5' end of transcripts using CAGE method, it enables not only determination of the transcription start site but also prediction of promoter region. Here we provide a protocol for the construction of no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE). We have excluded the commonly used PCR amplification and cleavage of restriction enzyme to eliminate any potential biases. As a result, we achieved less biased simple preparation process.

The ELISA-based detection of anti-Opisthorchis viverriniIgG and IgG4in samples of human urine and serum from an endemic area of north–eastern Thailand

The levels of correlation between the number of Opisthorchis viverrini eggs excreted in the faeces and levels of anti-Opisthorchis IgG and IgG(4) in the serum and urine (as indicated by absorbances in ELISA) have recently been evaluated in north-eastern Thailand. The 225 subjects investigated in detail, all of whom came from an endemic village in Chaiyaphum province, were selected on the basis of the numbers of O. viverrini eggs that they were excreting. ELISA based on a crude antigen extract of the trematode were then used to determine the levels of specific IgG and IgG(4) in serum and urine samples. Compared with the egg-negative, the villagers who were found to be egg-positive for O. viverrini had significantly higher levels of specific IgG in their urine and serum and significantly higher levels of specific IgG(4) in their serum. The serum levels of specific IgG and IgG(4) and the urine levels of specific IgG all correlated with the numbers of O. viverrini eggs/g faeces [with correlation coefficients (r) of 0.251, 0.121 and 0.142, respectively]. Although the serum levels of IgG were positively correlated with the urine levels of IgG (r=0.098), there was no significant relationship between the serum and urine levels of specific IgG(4) (r=0.051). When the 225 subjects investigated in the ELISA were divided according to whether they had no detectable Opisthorchis eggs in their faeces (N=57), or 1-100 (N=154), 101-1000 (N=5), 1001-1500 (N=5) or >1501 (N=4) eggs/g faeces, the serum and urine levels of specific IgG and the serum (but not urine) levels of specific IgG4 were also found to correlate significantly with the infection-intensity categories (with r-values of 0.550, 0.146 and 0.578, respectively). When the results of the faecal examinations were treated as the 'gold standard', the ELISA for the detection of (Opisthorchis-specific) serum IgG, serum IgG(4), urine IgG and urine IgG(4) had sensitivities of 99.2%, 23.1%, 43.0% and 45.9% and specificities of 93.0%, 29.6%, 45.9% and 67.2%, respectively. Although the study was limited by the small number of subjects with intense infections, it appears worth investigating urine samples for subclasses of specific IgG other than IgG(4).

Chronological changes of delayed-type hypersensitivity in mice immunised with testicular germ cells alone

Experimental autoimmune orchitis (EAO), comprising a breakdown of the testicular immune privilege, is one of the models of immunological male infertility. EAO is characterised by CD4 + T-cell-dependent lymphocytic inflammation and augmented delayed-type hypersensitivity (DTH) against testicular antigens. We previously established an EAO model in mice by immunisation with viable syngeneic testicular germ cells (TGC) alone. However, the sequential change of DTH during development of this EAO has not been analysed yet. In this study, the DTH response during TGC-induced EAO was investigated by the injection of syngeneic TGC protein into the ears of mice. The results showed that a significant DTH response was observed on injection of 20 μg TGC protein, but not on that of 0.2 or 2 μg TGC protein. Also, the level of the DTH response to 20 μg TGC protein was highly relevant to the pathology of EAO development. These results indicate that the DTH response on injection of 20 μg TGC protein into the ears of mice is effective for predicting the pathology of EAO development.

A case of severe progressive early-onset epileptic encephalopathy: unique GABAergic interneuron distribution and imaging

Early-onset epileptic encephalopathies include various diseases such as early-infantile epileptic encephalopathy with suppression burst. We experimentally investigated the unique clinicopathological features of a 28-month-old girl with early-onset epileptic encephalopathy. Her initial symptom was intractable epilepsy with a suppression-burst pattern of electroencephalography (EEG) from 7 days of age. The suppression-burst pattern was novel, appearing during sleep, but disappearing upon waking and after becoming 2 months old. The EEG showed multifocal spikes and altered with age. Her seizures demonstrated various clinical features and continued until death. She did not show any developmental features, including no social smiling or head control. Head MRI revealed progressive atrophy of the cerebral cortex and white matter after 1 month of age. (123)IMZ-SPECT demonstrated hypo-perfusion of the cerebral cortex, but normo-perfusion of the diencephalon and cerebellum. Such imaging information indicated GABA-A receptor dysfunction of the cerebral cortex. The genetic analyses of major neonatal epilepsies showed no mutation. The neuropathology revealed atrophy and severe edema of the cerebral cortex and white matter. GAD-immunohistochemistry exhibited imbalanced distribution of GABAergic interneurons between the striatum and cerebral cortex. The results were similar to those of focal cortical dysplasia with transmantle sign and X-linked lissencephaly with ARX mutation. We performed various metabolic examinations, detailed pathological investigations and genetic analyses, but could not identify the cause. To our knowledge, her clinical and pathological courses have never been described in the literature.

New pyrosequencing method to analyze the function of the Klenow fragment (EXO-) for unnatural nucleic acids: pyrophosphorolysis and incorporation efficiency

The incorporation of deoxynucleoside triphosphates (dNTPs) catalyzed by polymerases is conventionally examined using gel electrophoresis autoradiography. Here, we studied an alternative method, pyrosequencing, to verify the incorporation of dNTPs containing unnatural nucleotides by polymerases. We found that the pyrosequencing method more rapidly and easily confirmed the incorporation of dNTPs than the conventional method, especially in the presence of low-efficiency dNTP polymerases. Furthermore, the method can detect the pyrophosphorolysis reaction just before the position of the unnatural nucleic acid, and the efficiency of incorporation just after it.