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1. Characterization of the QUartz Photon Intensifying Detector (QUPID) for Noble Liquid Detectors

Author

Teymourian, A., Aharoni, D., Baudis, L., Beltrame, P., Brown, E., Cline, D., Ferella, A. D., Fukasawa, A., Lam, C. W., Lim, T., Lung, K., Meng, Y., Muramatsu, S., Pantic, E., Suyama, M., Wang, H., and Arisaka, K.

Subjects
Physics - Instrumentation and Detectors, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment
Abstract

Dark Matter and Double Beta Decay experiments require extremely low radioactivity within the detector materials. For this purpose, the University of California, Los Angeles and Hamamatsu Photonics have developed the QUartz Photon Intensifying Detector (QUPID), an ultra-low background photodetector based on the Hybrid Avalanche Photo Diode (HAPD) and entirely made of ultraclean synthetic fused silica. In this work we present the basic concept of the QUPID and the testing measurements on QUPIDs from the first production line. Screening of radioactivity at the Gator facility in the Laboratori Nazionali del Gran Sasso has shown that the QUPIDs safely fulfill the low radioactive contamination requirements for the next generation zero background experiments set by Monte Carlo simulations. The quantum efficiency of the QUPID at room temperature is > 30% at the xenon scintillation wavelength. At low temperatures, the QUPID shows a leakage current less than 1 nA and a global gain of 10^5. In these conditions, the photocathode and the anode show > 95% linearity up to 1 uA for the cathode and 3 mA for the anode. The photocathode and collection efficiency are uniform to 80% over the entire surface. In parallel with single photon counting capabilities, the QUPIDs have a good timing response: 1.8 +/- 0.1 ns rise time, 2.5 +/- 0.2 ns fall time, 4.20 +/- 0.05 ns pulse width, and 160 +/- 30 ps transit time spread. The QUPIDs have also been tested in a liquid xenon environment, and scintillation light from 57Co and 210Po radioactive sources were observed., Comment: 15 pages, 22 figures

Published
2011
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2. Megabits secure key rate quantum key distribution

Author

Zhang, Q., Takesue, H., Honjo, T., Wen, K., Hirohata, T., Suyama, M., Takiguchi, Y., Kamada, H., Tokura, Y., Tadanaga, O., Nishida, Y., Asobe, M., and Yamamoto, Y.

Subjects
Quantum Physics
Abstract

Quantum cryptography (QC) can provide unconditional secure communication between two authorized parties based on the basic principles of quantum mechanics. However, imperfect practical conditions limit its transmission distance and communication speed. Here we implemented the differential phase shift (DPS) quantum key distribution (QKD) with up-conversion assisted hybrid photon detector (HPD) and achieved 1.3 M bits per second secure key rate over a 10-km fiber, which is tolerant against the photon number splitting (PNS) attack, general collective attacks on individual photons, and any other known sequential unambiguous state discrimination (USD) attacks., Comment: 14 pages, 4 figures

Published
2008
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3. Detectors and flux instrumentation for future neutrino facilities

Author

Abe, T., Aihara, H., Andreopoulos, C., Ankowski, A., Badertscher, A., Battistoni, G., Blondel, A., Bouchez, J., Bross, A., Bueno, A., Camilleri, L., Campagne, J. E., Cazes, A., Cervera-Villanueva, A., De Lellis, G., Di Capua, F., Ellis, M., Ereditato, A., Esposito, L. S., Fukushima, C., Gschwendtner, E., Gomez-Cadenas, J. J., Iwasaki, M., Kaneyuki, K., Karadzhov, Y., Kashikhin, V., Kawai, Y., Komatsu, M., Kozlovskaya, E., Kudenko, Y., Kusaka, A., Kyushima, H., Longhin, A., Marchionni, A., Marotta, A., McGrew, C., Menary, S., Meregaglia, A., Mezzeto, M., Migliozzi, P., Mondal, N. K., Montanari, C., Nakadaira, T., Nakamura, M., Nakumo, H., Nakayama, H., Nelson, J., Nowak, J., Ogawa, S., Peltoniemi, J., Pla-Dalmau, A., Ragazzi, S., Rubbia, A., Sanchez, F., Sarkamo, J., Sato, O., Selvi, M., Shibuya, H., Shozawa, M., Sobczyk, J., Soler, F. J. P., Strolin, P., Suyama, M., Tanak, M., Terranova, F., Tsenov, R., Uchida, Y., Weber, A., and Zlobin, A.

Subjects
Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract

This report summarises the conclusions from the detector group of the International Scoping Study of a future Neutrino Factory and Super-Beam neutrino facility. The baseline detector options for each possible neutrino beam are defined as follows: 1. A very massive (Megaton) water Cherenkov detector is the baseline option for a sub-GeV Beta Beam and Super Beam facility. 2. There are a number of possibilities for either a Beta Beam or Super Beam (SB) medium energy facility between 1-5 GeV. These include a totally active scintillating detector (TASD), a liquid argon TPC or a water Cherenkov detector. 3. A 100 kton magnetized iron neutrino detector (MIND) is the baseline to detect the wrong sign muon final states (golden channel) at a high energy (20-50 GeV) neutrino factory from muon decay. A 10 kton hybrid neutrino magnetic emulsion cloud chamber detector for wrong sign tau detection (silver channel) is a possible complement to MIND, if one needs to resolve degeneracies that appear in the $\delta$-$\theta_{13}$ parameter space., Comment: Detector report of the International Scoping Study of a future Neutrino Factory and Super-Beam facility, 86 pages, 49 figures

Published
2007
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4. Development of a multi-pixel hybrid photo-detector with high quantum efficiency and gain

Author

Suyama, M., Fukasawa, A., Haba, J., Iijima, T., Iwata, S., Sakuda, M., Sumiyoshi, T., Takasaki, F., Tanaka, M., Tsuboyama, T., and Yamada, Y.

Subjects
Physics - Instrumentation and Detectors
Abstract

A hybrid photo-detector (HPD) consisting of a photocathode and a multi-pixel avalanche diode (MP-AD) was developed a few years ago. Our previous studies showed that its inherent potential for high resolution photon counting could be further enhanced by reducing fluctuations in charge loss in the dead layer at the entrance of the MP-AD. In this paper, we report on the improvement with the newly developed HPD whose encapsulated MP-AD has a thinner dead layer than before. It is demonstrated that the new HPD has much better energy resolution, which enables clearer counting up to nine photoelectrons. Further enhancement of the photocathode sensitivity of the HPD is also discussed., Comment: 5 page, 9 figures

Published
2004
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6. A case of breast milk-acquired cytomegalovirus infection in an extremely low birth weight infant.

Author

Kasai, R., Toriyabe, K., Goto, T., Hatano, M., Kondo, Y., Ohta, T., Suyama, M., Koide, W., Maki, K., Ushijima, K., and Ban, K.

Subjects
VERY low birth weight, UTERINE rupture, CYTOMEGALOVIRUS diseases, WEIGHT in infancy, BREAST milk, PREMATURE infants
Abstract

INTRODUCTION: Although breast milk is considered the optimal nutrition for infants, it is also the primary cause of postnatal cytomegalovirus (CMV) infection. Preterm infants with postnatal CMV infections are susceptible to a variety of life-threatening conditions. CASE SUMMARY: Twin male infants were delivered via emergency caesarian section at 27 weeks' gestation secondary to maternal complete uterine rupture. The Apgar scores at 1 and 5 min were 1 and 1 for the older twin (Twin A) and 0 and 3 for the younger twin (Twin B). Their birth weights were 1203 g (+ 0.65SD) and 495 g (– 3.79SD) respectively. On day 41, laboratory blood test results for Twin B showed a moderate elevation in C-reactive protein (CRP), thrombocytopenia. CMV quantitative polymerase chain reaction (qPCR) tests in Twin B's urine and blood as well as in the mother's breast milk were positive, but stored, dried umbilical cord CMV qPCR tests were negative. Twin B was diagnosed with a postnatal CMV infection secondary to infected breast milk and ganciclovir was commenced on day 52. Treatment was switched to valganciclovir at 74 days of age, but a negative CMV-DNA level in the blood was not achieved. Postnatal CMV infection in this infant led to an exacerbation of pre-existing bronchopulmonary dysplasia (BPD) and he demised at 182 days of age. CONCLUSION: Postnatal cytomegalovirus infections may lead to exacerbations of BPD. Early use of raw breast milk in preterm infants should be done with careful consideration of this potential complication. [ABSTRACT FROM AUTHOR]

Published
2023
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11. High speed HPD for photon counting

Author

Fukasawa, A., Haba, J., Kageyama, A., Nakazawa, H., and Suyama, M.

Subjects
Photodetectors -- Design and construction, Photons -- Properties, Diodes -- Properties, Business, Electronics, Electronics and electrical industries
Abstract

We have succeeded in the development of a high-speed Hybrid Photodetector (HPD), by using a reduced electron lens and a newly developed avalanche diode (AD) with very low capacitance. The HPD shows fast time response of less than 500 ps in both rise and fall times, and good timing resolution of 26 ps (one sigma) for single photons at full illumination on a photocathode 8 mm in diameter. Limiting factors of the timing resolution were further investigated, and were found to be the transit time difference of electrons in vacuum along the photocathode and the jitter of the electronics. The timing resolution is 15 ps for illumination of less than 5 mm on the central part of the photocathode, which includes the jitter of 13 ps from the electronics. This resolution is the world's highest for HPDs, and matches the resolution of MCP-PMTs. Both a GaAsP photocathode having close to 50% quantum efficiency in the visible and a bialkali photocathode having 34% QE in the UV were fabricated in view of making this device available for various applications. In this paper, we report the results of our evaluation, including discussion about the limiting factors of the timing resolution for the new HPD. Index Terms--HPD, hybrid photodetector, photon sensor, single photon.

Published
2008

15. Development of a multipixel hybrid photodetector with high quantum efficiency and gain

Author

Suyama, M., Fukasawa, A., Haba, J., Iijima, T., Iwata, S., Sakuda, M., Sumiyoshi, T., Takasaki, F., Tanaka, M., Tsuboyama, T., and Yamada, Y.

Subjects
Nuclear physics -- Research, Business, Electronics, Electronics and electrical industries
Abstract

A hybrid photodetector (HPD) consisting of a photocathode and a multipixel avalanche diode (MP-AD) was developed a few years ago. Our previous studies showed that its inherent potential for high resolution photon counting could be further enhanced by reducing fluctuations in charge loss in the dead layer at the entrance of the MP-AD. In this paper, we report on the improvement with the newly developed HPD whose encapsulated MP-AD has a thinner dead layer than before. It is demonstrated that the new HPD has much better energy resolution, which enables clearer counting up to nine photoelectrons. Further enhancement of the photocathode sensitivity of the HPD is also discussed. Index Terms--Hybrid photodetctor, HPD, multipixel, photon sensor, single photon.

Published
2004

22. A hybrid photodetector (HPD) with a III-V Photocathode

Author

Suyama, M., Hirano, K., Kawai, Y., Nagai, T., Kibune, A., Saito, T., Negi, Y., Asakura, N., Muramatsu, S., and Morita, T.

Subjects
Photodetectors -- Design and construction, Photoelectric devices -- Design and construction, Electron tubes -- Usage, Business, Electronics, Electronics and electrical industries
Abstract

A hybrid photodetector (HPD) combined with a III-V photocathode is considered to be an ideal photodetector, because the quantum efficiency (QE) is high, the collection efficiency is 100%, and the excess noise factor is negligible. An HPD combined with a GaAs photocathode or a blue enhanced GaAs (BE-GaAs) photocathode has been developed. Presently, the QE is approximately 20% from 550nm to 850nm, which is much higher than that of a conventional multi-alkali (S-20) photocathode. The 100% collection efficiency calculated by the computer simulation is supported by the test result of the flat uniformity. Considering the application in high energy physics using a wavelength shifter, energy resolutions of both the BE-GaAs-HPD and the conventional S20-HPD were measured using a 650nm LED light pulse. The BE-GaAs-HPD shows a resolution of 17%, as against 34% for the S20-HPD. The experimental results are consistent with the theoretical estimation. The QE of the HPD is especially important, because the electron multiplication process is noiseless.

Published
1998

23. A compact hybrid photodetector (HPD)

Author

Suyama, M., Kawai, Y., Kimura, S., Asakura, N., Hirano, K., Hasegawa, Y., Saito, T., Morita, T., Muramatsu, M., and Yamamoto, Kenichi

Subjects
Photodetectors -- Design and construction, Business, Electronics, Electronics and electrical industries
Abstract

In order to be utilized in such application fields as high energy physics or medical imaging, where a huge number of photodetectors are assembled in designated small area, the world's smallest hybrid photodetector (HPD), the compact HPD, has been developed. The overall diameter and the length of the tube are 16mm and 15mm, respectively. The effective photocathode area is 8mm in diameter. At applied voltage of -8kV to the photocathode, the electron multiplication gain of a PD incorporated HPD (PD-HPD) is 1,600, and that of an APD (APD-HPD) is 65,000. In the pulse height distribution measurement, photoelectron peaks up to 6 photoelectrons are clearly distinguishable with the APD-HPD. Experiments established that there was no degradation of gain in magnetic fields up to 1.5T, an important performance characteristic of the compact HPD for application in high energy physics.

Published
1997

24. Abstracts of Selected Papers Presented at the 31st Annual Meeting of the Japanese Society of Gastroenterology

Author

Karasawa, Eii, Saisho, Hiromitsu, Maguchi, Hiroyuki, Obara, Tsuyoshi, Saeki, Keizo, Yamasuji, Tadashi, Nishihara, Kenji, Suzuki, Takasi, Tajiri, Hisato, Ozaki, Hideo, Fujii, D., Suyama, M., Mogaki, Masatoshi, Fujii, Hideki, Yamamoto, Toshio, Isaji, Shuji, Itoh, Tohru, Idezuki, Yasuo, Baba, Nobuo, Manabe, Tadao, Imaizumi, Toshihide, Hanyu, Fujio, Tanno, Naoaki, Ishizuka, Jin, Yamamoto, F., Igimi, H., Yamamoto, S., Shimura, H., Takayama, Tetsuo, Noda, Aiji, Hirata, Nobuto, Kadowaki, Ken, Yazaki, Yasuyuki, Namiki, Masayoshi, Yamada, Hideo, Kouzu, Teruo, Ichikawa, Kazuo, Ichikawa, Masafumi, Seki, Hideichi, Kimura, Ken, Matsushiro, Takashi, Yamaguchi, Hisashi, Yamagata, Rin, Fujio, Toshiyuki, Furukawa, Masato, Kawata, Sumio, Imai, Yasuharu, Amuro, Yoshiki, Kudo, Kei, Nishimura, H., Akiyama, K., Tsukahara, Koushou, Kitani, Kenichi, Katagiri, K., Nakai, T., Watanabe, Norihito, Oda, Masaya, Takikawa, Hajime, Yamanaka, Masami, Sakisaka, Shotaro, Tanikawa, Kyuichi, Igimi, H., Kakazu, T., Tanaka, Naomi, Shoda, Junichi, Tazuma, Susumu, Kajiyama, Goro, Chijiiwa, Kazuo, Nakayama, Fumio, Hikasa, Yutaka, Tanida, Noritoshi, Narisawa, Tomio, Takahashi, Masahiro, Tanaka, Masahiro, Kimura, Ken, Matsumoto, Haruki, Kojima, Koichi, Takeda, Isao, Nakano, Satoshi, Shiina, Yasubumi, Harasawa, Shigeru, Okuyama, Shuji, Hara, Hisato, Iwafuchi, Mitsuya, Watanabe, Hidenobu, Morizumi, H., Matsumura, M., Sato, Akira, Asaki, Shigeru, Hosokawa, Yoshio, and Hirao, Masanori

Published
1991
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25. Fundamental investigation of vacuum PD tube

Author

Suyama, M., Hirano, K., Asakura, N., Kamiya, A., Kawai, Y., Suzuki, S., Morita, T., Tanaka, H., Muramatsu, M., and Yamamoto, Kenichi

Subjects
Vacuum-tubes -- Research, Photoelectric devices -- Research, Business, Electronics, Electronics and electrical industries
Abstract

As a fundamental study of photodiodes (PDs) for electron bombardment, two types of PDs have been experimentally investigated to be applied in electron tubes. A PD bombarded from the front surface (FB-PD), where pn junction of planer structure existed, was evaluated to measure fast response characteristics such as 2.1ns in rise time, however, more than an order of magnitude increase of dark current was also confirmed after a long term stability test of 1000 hours. On the other hand, a PD bombarded by electrons from the rear surface (RB-PD) showed no increase of dark current after the stability test and fast rise time of 2.7ns. However, it was clarified that the rise time of RB-PD depended on applied voltage to the PD, and applied voltage of 200V was necessary to achieve such fast response. Since it was a much higher voltage than expected, some modifications may be necessary to achieve fast response with lower applied voltage, considering the yield of the PDs. Comparison of two types of PDs on some other characteristics are discussed. Preliminary test results of an electron bombardment APD are also discussed.

Published
1994

28. Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis

Author

Shimaji, K., Konishi, T., Tanaka, S., Yoshida, H., Kato, Y., Ohkawa, Y., Sato, T., Suyama, M., Kimura, Hiroshi, and Yamaguchi, M.

Subjects
Epigenomics, Cytoplasm, Drosophila Proteins/genetics/metabolism, Euchromatin, Molecular Sequence Data, Histones/metabolism, Embryonic Development, Methylation, Epigenesis, Genetic, Histones, Histone H3, Histone methylation, Genetics, Drosophila Proteins, Animals, Embryonic Development/genetics, Epigenetics, Histone-Lysine N-Methyltransferase/*genetics/*metabolism, Cell Nucleus, biology, Drosophila embryogenesis, Cell Biology, Histone-Lysine N-Methyltransferase, Cytoplasm/metabolism, Histone, Drosophila melanogaster, Histone methyltransferase, Cell Nucleus/metabolism, biology.protein, Histone Methyltransferases, Transcriptome, Protein Processing, Post-Translational
Abstract

Post-translational modification of the histone plays important roles in epigenetic regulation of various biological processes. Among the identified histone methyltransferases (HMTases), G9a is a histone H3 Lys 9 (H3K9)-specific example active in euchromatic regions. Drosophila G9a (dG9a) has been reported to feature H3K9 dimethylation activity in vivo. Here, we show that the time required for hatching of a homozygous dG9a null mutant and heteroallelic combination of dG9a null mutants is delayed, suggesting that dG9a is at least partially responsible for progression of embryogenesis. Immunocytochemical analyses of the wild-type and the dG9a null mutant flies indicated that dG9a localizes in cytoplasm up to nuclear division cycle 7 where it is likely responsible for di-methylation of nucleosome-free H3K9. From cycles 8-11, dG9a moves into the nucleus and is responsible for di-methylating H3K9 in nucleosomes. RNA-sequence analysis utilizing early wild-type and dG9a mutant embryos showed that dG9a down-regulates expression of genes responsible for embryogenesis. RNA fluorescent in situ hybridization analysis further showed temporal and spatial expression patterns of these mRNAs did not significantly change in the dG9a mutant. These results indicate that dG9a controls transcription levels of some zygotic genes without changing temporal and spatial expression patterns of the transcripts of these genes.

Published
2015

30. Transcriptome complexity in a genome-reduced bacterium

Author

G�ell, M., van Noort, V., Yus, E., Chen, W. H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, Takuji, Arumugam, M., Doerks, T., K�hner, S., Rode, M., Suyama, M., Schmidt, S., Gavin, A. C., Bork, P., and Serrano, L.

Subjects
Genetics, Messenger RNA, RNA, Untranslated, Multidisciplinary, Tiling array, Base Sequence, Transcription, Genetic, Operon, Gene Expression Profiling, Molecular Sequence Data, Gene Expression Regulation, Bacterial, Biology, Genome, Mycoplasma pneumoniae, Transcriptome, Gene expression profiling, RNA, Bacterial, Genes, Bacterial, RNA, Antisense, RNA, Messenger, Gene, Genome, Bacterial, Oligonucleotide Array Sequence Analysis, Genomic organization
Abstract

Simply Mycoplasma The bacterium Mycoplasma pneumoniae , a human pathogen, has a genome of reduced size and is one of the simplest organisms that can reproduce outside of host cells. As such, it represents an excellent model organism in which to attempt a systems-level understanding of its biological organization. Now three papers provide a comprehensive and quantitative analysis of the proteome, the metabolic network, and the transcriptome of M. pneumoniae (see the Perspective by Ochman and Raghavan ). Anticipating what might be possible in the future for more complex organisms, Kühner et al. (p. 1235 ) combine analysis of protein interactions by mass spectrometry with extensive structural information on M. pneumoniae proteins to reveal how proteins work together as molecular machines and map their organization within the cell by electron tomography. The manageable genome size of M. pneumoniae allowed Yus et al. (p. 1263 ) to map the metabolic network of the organism manually and validate it experimentally. Analysis of the network aided development of a minimal medium in which the bacterium could be cultured. Finally, G‡ell et al. (p. 1268 ) applied state-of-the-art sequencing techniques to reveal that this “simple” organism makes extensive use of noncoding RNAs and has exon- and intron-like structure within transcriptional operons that allows complex gene regulation resembling that of eukaryotes.

Published
2009

31. Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells

Author

Shishido, Y., Baba, T., Sato, T., Shima, Y., Miyabayashi, K., Inoue, M., Akiyama, H., Kimura, Hiroshi, Kanai, Y., Ishihara, Y., Haraguchi, S., Miyazaki, A., Rozman, D., Yamazaki, T., Choi, M. H., Ohkawa, Y., Suyama, M., and Morohashi, K. I.

Subjects
0301 basic medicine, Male, endocrine system, X Chromosome, Karyotype, Disorders of Sex Development, Article, 03 medical and health sciences, Mice, Y Chromosome, medicine, Animals, Epigenetics, Lactic Acid, Cells, Cultured, Histone Demethylases, Multidisciplinary, Sertoli Cells, biology, social sciences, Sertoli cell, Sex-Determining Region Y Protein, Cell biology, Histone Code, 030104 developmental biology, Histone, medicine.anatomical_structure, Testis determining factor, Cholesterol, biology.protein, H3K4me3, Demethylase, Female, Germ cell, geographic locations
Abstract

SRY, a sex-determining gene, induces testis development in chromosomally female (XX) individuals. However, mouse XX Sertoli cells carrying Sry (XX/Sry Sertoli cells) are incapable of fully supporting germ cell development, even when the karyotype of the germ cells is XY. While it has therefore been assumed that XX/Sry Sertoli cells are not functionally equivalent to XY Sertoli cells, it has remained unclear which specific functions are affected. To elucidate the functional difference, we compared the gene expression of XY and XX/Sry Sertoli cells. Lactate and cholesterol metabolisms, essential for nursing the developing germ cells, were down-regulated in XX/Sry cells, which appears to be caused at least in part by the differential expression of histone modification enzymes SMCX/SMCY (H3K4me3 demethylase) and UTX/UTY (H3K27me3 demethylase) encoded by the sex chromosomes. We suggest that down-regulation of lactate and cholesterol metabolism that may be due to altered epigenetic modification affects the nursing functions of XX/Sry Sertoli cells., This work was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Number 21249018 and 16H05142 (K. Mo.), Ministry of Education, Culture, Sports, Science, and Technology, Japan (MEXT) KAKENHI Grant Number 22132002 (K. Mo.), the Uehara Memorial Foundation, and Takeda Science Foundation (T.B.).

Published
2017

32. Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1

Author

Baba, T., Otake, H., Sato, T., Miyabayashi, K., Shishido, Y., Wang, C. Y., Shima, Y., Kimura, Hiroshi, Yagi, M., Ishihara, Y., Hino, S., Ogawa, H., Nakao, M., Yamazaki, T., Kang, D., Ohkawa, Y., Suyama, M., Chung, B. C., and Morohashi, K.

Subjects
Steroidogenic factor 1, Chromatin Immunoprecipitation, Small interfering RNA, Adenosine Triphosphate/metabolism, Glycolysis/genetics/physiology, Cell Proliferation/physiology, General Physics and Astronomy, Electrophoretic Mobility Shift Assay, Biology, Steroidogenic Factor 1, General Biochemistry, Genetics and Molecular Biology, Cell Line, Mice, chemistry.chemical_compound, Adenosine Triphosphate, Cell Line, Tumor, Glucose/metabolism, Animals, Humans, RNA, Small Interfering, Receptor, Gene, Transcription factor, Cell Proliferation, RNA, Small Interfering/genetics, Binding Sites, Multidisciplinary, Reverse Transcriptase Polymerase Chain Reaction, General Chemistry, NADP/metabolism, Pregnenolone/metabolism, Steroidogenic Factor 1/genetics/*metabolism, Cell biology, Glucose, chemistry, Biochemistry, Nuclear receptor, Pregnenolone, Glycolysis, Chromatin immunoprecipitation, NADP, Nicotinamide adenine dinucleotide phosphate
Abstract

Genetic deficiencies in transcription factors can lead to the loss of certain types of cells and tissue. The steroidogenic tissue-specific nuclear receptor Ad4BP/SF-1 (NR5A1) is one such gene, because mice in which this gene is disrupted fail to develop the adrenal gland and gonads. However, the specific role of Ad4BP/SF-1 in these biological events remains unclear. Here we use chromatin immunoprecipitation sequencing to show that nearly all genes in the glycolytic pathway are regulated by Ad4BP/SF-1. Suppression of Ad4BP/SF-1 by small interfering RNA reduces production of the energy carriers ATP and nicotinamide adenine dinucleotide phosphate, as well as lowers expression of genes involved in glucose metabolism. Together, these observations may explain tissue dysgenesis as a result of Ad4BP/SF-1 gene disruption in vivo. Considering the function of estrogen-related receptor α, the present study raises the possibility that certain types of nuclear receptors regulate sets of genes involved in metabolic pathways to generate energy carriers.

Published
2014

34. Selective maintenance of Drosophila tandemly-arranged duplicated genes during evolution

Author

Quijano, C., Tomancak, P., Lopez-Marti, J., Suyama, M., Bork, P., Milan, M., Torrents, D., and Manzanares, M.

Subjects
Cardiovascular and Metabolic Diseases
Abstract

BACKGROUND: The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along the genome by random shuffling of DNA segments. Higher order structuring of the genome occurs in eukaryotes, where groups of physically linked genes are co-expressed. However, the contribution of gene duplication to gene order has been not analyzed in detail, as it is believed that co-expression due to recent duplicates would obscure other domains of co-expression. RESULTS: We have catalogued ordered duplicated genes in Drosophila melanogaster, and found that one in five of all genes are organized as tandem arrays. Furthermore, among arrays that have been spatially conserved over longer periods than would be expected on the basis of random shuffling, a disproportionate number contain genes encoding developmental regulators. Using in-situ gene expression data for more than half of the Drosophila genome, we find that genes in these conserved clusters are co-expressed to a much higher extent than other duplicated genes. CONCLUSIONS: These results reveal the existence of functional constraints in insects that retain copies of genes encoding developmental and regulatory proteins as neighbours, allowing their co-expression. This co-expression may be the result of shared cis regulatory elements or a shared need for a specific chromatin structure. Our results highlight the association between genome architecture and the gene regulatory networks involved in the construction of the body plan.

Published
2008

35. International scoping study of a future Neutrino Factory and super-beam facility : summary of the Detector Working Group

Author

Abe, T, Aihara, H, Andreopoulos, C, Ankowski, A, Badertscher, A, Battistoni, C, Blondel, A, Bouchez, J, Bross, A, Bueno, A, Camilleri, L, Campagne, JE, Cazes, A, Cervera-Villanueva, A, De Lellis, G, Di Capua, F, Ellis, M, Ereditato, A, Esposito, LS, Fukushima, C, Gschwendtner, E, Gomez-Cadenas, JJ, Iwasaki, M, Kaneyuki, K, Karadzhov, Y, Kashikhin, V, Kawai, Y, Komatsu, M, Kozlovskaya, E, Kudeno, Y, Kusaka, A, Kyushima, H, Longhin, A, Marchionni, A, Marotta, A, McGrew, C, Menary, S, Meregaglia, A, Mezzeto, M, Migliozzi, P, Mondal, NK, Mmontanari, C, Nakadaira, T, Nakamura, M, Nakumo, H, Nakayama, H, Nelson, J, Nowak, J, Ogawa, S, Peltoniemi, J, Pla-Dalmau, A, Ragazzi, S, Rubbia, A, Sanchez, F, Sarkamo, J, Sato, O, Selvi, M, Shibuya, H, Shozawa, M, Sobczyk, J, Soler, FJP, Strolin, P, Suyama, M, Tanak, M, Terranova, F, Tsenov, R, Uchida, Y, Weber, A, and Zlobin, A

Published
2007
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39. Identification of attenuation and antitermination regulation in prokaryotes

Author

Lathe, W.C., Suyama, M., and Bork, P.

Subjects
Cardiovascular and Metabolic Diseases
Abstract

Many operons of biochemical pathways in bacterial genomes are regulated by processes called attenuation and antitermination. Though the specific mechanism can be quite different, attenuation and antitermination in these operons have in common the termination of transcription by a RNA 'terminator' fold upstream of the first gene in the operon. In the past, detecting regulation by attenuation or antitermination has often been a long process of experimental trial and error, on a case by case basis. We report here the prediction of over 290 upstream regions of genes with attenuation or antitermination regulation structures in the completed genomes of Bacillis subtilis and Escherichia coli for which extensive experimental studies have been done on attenuation and antitermination regulation. These predictions are based on a computational method devised from characteristics of known terminator fold candidates and benchmark regions of entire genomes. We extend this methodology to 24 additional complete genomes and are thus able to give a more complete picture of attenuation and antitermination regulation in bacteria.

Published
2002

40. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames

Author

Dandekar, T., Huynen, M.A., Regula, J., Ueberle, B., Zimmermann, C.U., Andrade, M.A., Doerks, T., Sanches-Pulido, L., Snel, B., Suyama, M., Yuan, Y.P., Herrmann, R., and Bork, P.

Subjects
Cardiovascular and Metabolic Diseases
Abstract

Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.

Published
2000

41. Extracorporeal dialysis: techniques and adequacy - A

Author

Steckiph, D., primary, Calabrese, G., additional, Bertucci, A., additional, Mazzotta, A., additional, Vagelli, G., additional, Gonella, M., additional, Stamopoulos, D., additional, Manios, E., additional, Papachristos, N., additional, Grapsa, E., additional, Papageorgiou, G., additional, Gogola, V., additional, So, B., additional, Dey, V., additional, Spalding, E. M., additional, Libetta, C., additional, Esposito, P., additional, Margiotta, E., additional, Maffioli, P., additional, Bonaventura, A., additional, Bianchi, L., additional, Romano, D., additional, Rampino, T., additional, De Rosa, G., additional, Mauric, A., additional, Haug, U., additional, Enzinger, G., additional, Kern-Derstvenscheg, E., additional, Sluga, A., additional, Ausserwinkler, C., additional, Beck, W., additional, Rosenkranz, A. R., additional, Maheshwari, V., additional, Haroon, S., additional, Loy, Y., additional, Samavedham, L., additional, Rangaiah, G. P., additional, Lau, T., additional, Mpakirtzi, N., additional, Panagiotou, M., additional, Barbarousi, D., additional, Matsouka, C., additional, Bunani, A. D., additional, Kowalczyk, M., additional, Bartnicki, P., additional, Banach, M., additional, Rysz, J., additional, Lentini, P., additional, Zanoli, L., additional, Granata, A., additional, Contestabile, A., additional, Basso, A., additional, Berlingo, G., additional, Pellanda, V., additional, de Cal, M., additional, Grazia, V., additional, Clementi, A., additional, Insalaco, M., additional, Dell'Aquila, R., additional, Karkar, A., additional, Abdelrahman, M., additional, Martins, A. R., additional, Parreira, L., additional, Duque, A. S., additional, Rodrigues, I., additional, Baffoun, A. B., additional, Youssfi, M. A., additional, Sayeh, A., additional, Beji, M., additional, Ben Khadra, R., additional, Hmida, J., additional, Akazawa, M., additional, Horiuchi, H., additional, Hori, Y., additional, Yamada, A., additional, Satou, H., additional, Odamaki, S., additional, Nakai, S., additional, Satou, K., additional, Aoki, K., additional, Saito, I., additional, Kamijo, Y., additional, Ogata, S., additional, Ishibashi, Y., additional, Basso, F., additional, Wojewodzka-Zelezniakowicz, M., additional, Cruz, D., additional, Giuliani, A., additional, Blanca Martos, L., additional, Piccinni, P., additional, Ronco, C., additional, Potier, J., additional, Queffeulou, G., additional, Bouet, J., additional, Nilsson, A., additional, Sternby, J., additional, Grundstrom, G., additional, Alquist, M., additional, Ferraresi, M., additional, Di Vico, M. C., additional, Vigotti, F. N., additional, Deagostini, M., additional, Scognamiglio, S., additional, Consiglio, V., additional, Clari, R., additional, Moro, I., additional, Mongilardi, E., additional, Piccoli, G. B., additional, Hancock, V., additional, Huang, S., additional, Nilsson Ekdahl, K., additional, Steckiph, D., additional, Baldin, C., additional, Petrarulo, M., additional, Mancuso, D., additional, Inguaggiato, P., additional, Canepari, G., additional, Gigliola, G., additional, Ferrando, C., additional, Meinero, S., additional, Sicuso, C., additional, Pacitti, A., additional, Afentakis, N., additional, Tomo, T., additional, Matsuyama, K., additional, Nakata, T., additional, Ishida, K., additional, Takeno, T., additional, Kadota, J.-i., additional, Minakuchi, J., additional, Kastl, J., additional, Merello, M., additional, Boccato, C., additional, Giordana, G., additional, Mazzone, S., additional, Moscardo, V., additional, Reinhardt, B., additional, Knaup, R., additional, Kruger, W., additional, Tovbin, D., additional, Kim, S., additional, Avnon, L., additional, Zlotnik, M., additional, Storch, S., additional, Umimoto, K., additional, Shimamoto, Y., additional, Suyama, M., additional, Miyata, M., additional, Bosch Benitez-Parodi, E., additional, Baamonde Laborda, E. E., additional, Perez, G., additional, Ramirez, J. I., additional, Ramirez Puga, A., additional, Guerra, R., additional, Garcia Canton, C., additional, Lago Alonso, M. M., additional, Toledo, A., additional, Checa Andres, M. D., additional, Latif, F. E., additional, Mochida, Y., additional, Matsumoto, K., additional, Morita, K., additional, Tsutsumi, D., additional, Ishioka, K., additional, Maesato, K., additional, Oka, M., additional, Moriya, H., additional, Hidaka, S., additional, Ohtake, T., additional, Kobayashi, S., additional, Ficheux, A., additional, Gayrard, N., additional, Duranton, F., additional, Guzman, C., additional, Szwarc, I., additional, Bismuth-Mondolfo, J., additional, Brunet, P., additional, Servel, M.-F., additional, Argiles, A., additional, Tsikliras, N., additional, Mademtzoglou, S., additional, Balaskas, E., additional, Zeid, M., additional, Mostafa, A., additional, Mowafy, M. N., additional, Abdo, E. I., additional, Al Amin, O. M., additional, Ksiazek, A., additional, Zaluska, W., additional, Waniewski, J., additional, Debowska, M., additional, Wojcik-Zaluska, A., additional, Elias, M., additional, Francois, H., additional, Obada, E., additional, Lorenzo, H. K., additional, Charpentier, B., additional, Durrbach, A., additional, Beaudreuil, S., additional, Imamovic, G., additional, Marcelli, D., additional, Bayh, I., additional, Hrvacevic, R., additional, Kapun, S., additional, Grassmann, A., additional, Scatizzi, L., additional, Maslovaric, J., additional, Daelemans, R., additional, Mesens, S., additional, Mohamed, E. A., additional, Wafae, A., additional, Kawtar, H., additional, Mohamed Amine, H., additional, Driss, K., additional, and Mohammed, B., additional

Published
2013
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42. Status of Qupid, a novel photosensor for noble liquid detectors

Author

Pantic, E., primary, Aharoni, D., additional, Arisaka, K., additional, Beltrame, P., additional, Brown, E., additional, Cline, D., additional, Fukasawa, A., additional, Ghag, C., additional, Lam, C.W., additional, Lim, T., additional, Lung, K., additional, Meng, Y., additional, Muramatsu, S., additional, Scovell, P., additional, Suyama, M., additional, Teymourian, A., additional, and Wang, H., additional

Published
2012
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44. Characterization of the QUartz Photon Intensifying Detector (QUPID) for noble liquid detectors

Author

Teymourian, A., primary, Aharoni, D., additional, Baudis, L., additional, Beltrame, P., additional, Brown, E., additional, Cline, D., additional, Ferella, A.D., additional, Fukasawa, A., additional, Lam, C.W., additional, Lim, T., additional, Lung, K., additional, Meng, Y., additional, Muramatsu, S., additional, Pantic, E., additional, Suyama, M., additional, Wang, H., additional, and Arisaka, K., additional

Published
2011
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46. A new traction device for facilitating endoscopic submucosal dissection (ESD) for early gastric cancer: the “medical ring”

Author

Matsumoto, K., primary, Nagahara, A., additional, Sakamoto, N., additional, Suyama, M., additional, Konuma, H., additional, Morimoto, T., additional, Sagawa, E., additional, Ueyama, H., additional, Takahashi, T., additional, Beppu, K., additional, Shibuya, T., additional, Osada, T., additional, Yoshizawa, T., additional, Ogihara, T., additional, and Watanabe, S., additional

Published
2011
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48. International Scoping Study (ISS) for a future neutrino factory and Super-Beam facility. Detectors and flux instrumentation for future neutrino facilities

Author

Group, The ISS Detector Working, primary, Abe, T, additional, Aihara, H, additional, oulos, C Andreop, additional, Ankowski, A, additional, Badertscher, A, additional, Battistoni, G, additional, Blondel, A, additional, Bouchez, J, additional, Bross, A, additional, Bueno, A, additional, Camilleri, L, additional, Campagne, J E, additional, Cazes, A, additional, Cervera-Villanueva, A, additional, Lellis, G De, additional, Capua, F Di, additional, Ellis, M, additional, Ereditato, A, additional, Esposito, L S, additional, Fukushima, C, additional, Gschwendtner, E, additional, Gomez-Cadenas, J J, additional, Iwasaki, M, additional, Kaneyuki, K, additional, Karadzhov, Y, additional, Kashikhin, V, additional, Kawai, Y, additional, Komatsu, M, additional, Kozlovskaya, E, additional, Kudenko, Y, additional, Kusaka, A, additional, Kyushima, H, additional, Laing, A, additional, Long, K, additional, Longhin, A, additional, Marchionni, A, additional, Marotta, A, additional, McGrew, C, additional, Menary, S, additional, Meregaglia, A, additional, Mezzeto, M, additional, Migliozzi, P, additional, Mondal, N K, additional, Montanari, C, additional, Nakadaira, T, additional, Nakamura, M, additional, Nakumo, H, additional, Nakayama, H, additional, Nelson, J, additional, Nowak, J, additional, Ogawa, S, additional, Peltoniemi, J, additional, Pla-Dalmau, A, additional, Ragazzi, S, additional, Rubbia, A, additional, Sanchez, F, additional, Sarkamo, J, additional, Sato, O, additional, Selvi, M, additional, Shibuya, H, additional, Shozawa, M, additional, Sobczyk, J, additional, Soler, F J P, additional, Strolin, P, additional, Suyama, M, additional, Tanaka, M, additional, Terranova, F, additional, Tsenov, R, additional, Uchida, Y, additional, Weber, A, additional, and Zlobin, A, additional

Published
2009
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49. Megabits secure key rate quantum key distribution

Author

Zhang, Q, primary, Takesue, H, additional, Honjo, T, additional, Wen, K, additional, Hirohata, T, additional, Suyama, M, additional, Takiguchi, Y, additional, Kamada, H, additional, Tokura, Y, additional, Tadanaga, O, additional, Nishida, Y, additional, Asobe, M, additional, and Yamamoto, Y, additional

Published
2009
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50. The production of copper phthalocyanine and/or its derivatives

Author

Segawa, T, Matsuzaki, K, Sawada, H, Ninomiya, R, and Suyama, M

Subjects
Inorganic And Physical Chemistry
Abstract

This document discusses the production of copper phthalocyanine and/or its derivatives, which are useful for dye pigments. The method described uses urea, a copper compound and/or a catalyst which have been suspended in an inert reaction medium. The copper compound, catalyst and urea fused and the reaction is performed by using the obtained fusion. The advantages of the invention are listed.

Published
1984

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