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  • 1
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    DNA methylation analysis of human myoblasts during in vitro myogenic differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-24
    Description: Although DNA methylation is considered to play an important role during myogenic differentiation, chronological alterations in DNA methylation and gene expression patterns in this process have been poorly understood. Using the Infinium HumanMethylation450 BeadChip array, we obtained a chronological profile of the genome-wide DNA methylation status in a human myoblast differentiation model, where myoblasts were cultured in low-serum medium to stimulate myogenic differentiation. As the differentiation of the myoblasts proceeded, their global DNA methylation level increased and their methylation patterns became more distinct from those of mesenchymal stem cells. Gene ontology analysis revealed that genes whose promoter region was hypermethylated upon myoblast differentiation were highly significantly enriched with muscle-related terms such as ‘muscle contraction’ and ‘muscle system process’. Sequence motif analysis identified 8-bp motifs somewhat similar to the binding motifs of ID4 and ZNF238 to be most significantly enriched in hypermethylated promoter regions. ID4 and ZNF238 have been shown to be critical transcriptional regulators of muscle-related genes during myogenic differentiation. An integrated analysis of DNA methylation and gene expression profiles revealed that de novo DNA methylation of non-CpG island (CGI) promoters was more often associated with transcriptional down-regulation than that of CGI promoters. These results strongly suggest the existence of an epigenetic mechanism in which DNA methylation modulates the functions of key transcriptional factors to coordinately regulate muscle-related genes during myogenic differentiation.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    Direct injection of fully stripped carbon ions into a fast-cycling induction synchrotron and their capture by the barrier bucket (2017)
    American Physical Society (APS)
    Details
    Publication Date: 2017-08-12
    Description: Author(s): N. Munemoto, S. Takano, E. Kadokura, Taufik, T. Yoshimoto, X. Liu, T. Adachi, M. Ikeda, T. Kawakubo, K. Okamura, K. Takayama, and M. Wake Fully stripped carbon ions generated in a laser-ablation ion source are directly injected into a small-scale induction synchrotron. Carbon-ion beams of C 6 + , C 5 + , and C 4 + are trapped in the barrier bucket. Beam properties, such as the momentum spread and beam lifetime in the low-energy ring, are meas... [Phys. Rev. Accel. Beams 20, 080101] Published Wed Aug 09, 2017
    Keywords: Low- and Intermediate-Energy Accelerators
    Electronic ISSN: 1098-4402
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Induction acceleration of heavy ions in the KEK digital accelerator: Demonstration of a fast-cycling induction synchrotron (2014)
    American Physical Society (APS)
    Details
    Publication Date: 2014-01-30
    Description: Author(s): K. Takayama, T. Yoshimoto, M. Barata, Leo Kwee Wah, Liu Xingguang, T. Iwashita, S. Harada, T. Adachi, T. Arai, D. Arakawa, H. Asao, E. Kadokura, T. Kawakubo, H. Nakanishi, Y. Okada, K. Okamura, K. Okazaki, A. Takagi, S. Takano, and M. Wake A fast-cycling induction synchrotron was demonstrated. Ions with extremely low energies and mass-to-charge ratios (A/Q) in the range from 2 to 10 were injected, captured by barrier voltages, and accelerated to the end of the acceleration cycle of 50 ms by flat pulse voltages generated by pulse trans... [Phys. Rev. ST Accel. Beams 17, 010101] Published Wed Jan 29, 2014
    Keywords: Low- and Intermediate-Energy Accelerators
    Electronic ISSN: 1098-4402
    Topics: Physics
    Published by American Physical Society (APS)
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  • 4
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    KEK digital accelerator (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-07-21
    Description: Author(s): T. Iwashita, T. Adachi, K. Takayama, K. W. Leo, T. Arai, Y. Arakida, M. Hashimoto, E. Kadokura, M. Kawai, T. Kawakubo, Tomio Kubo, K. Koyama, H. Nakanishi, K. Okazaki, K. Okamura, H. Someya, A. Takagi, A. Tokuchi, and M. Wake The High Energy Accelerator Research Organization KEK digital accelerator (KEK-DA) is a renovation of the KEK 500 MeV booster proton synchrotron, which was shut down in 2006. The existing 40 MeV drift tube linac and rf cavities have been replaced by an electron cyclotron resonance (ECR) ion source e... [Phys. Rev. ST Accel. Beams 14, 071301] Published Wed Jul 20, 2011
    Keywords: New Acceleration Techniques
    Electronic ISSN: 1098-4402
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-09
    Description: In contrast to microRNAs and Piwi-associated RNAs, short interfering RNAs (siRNAs) are seemingly dispensable for host-directed gene regulation in Drosophila. This notion is based on the fact that mutants lacking the core siRNA-generating enzyme Dicer-2 or the predominant siRNA effector Argonaute 2 are viable, fertile and of relatively normal morphology. Moreover, endogenous Drosophila siRNAs have not yet been identified. Here we report that siRNAs derived from long hairpin RNA genes (hpRNAs) programme Slicer complexes that can repress endogenous target transcripts. The Drosophila hpRNA pathway is a hybrid mechanism that combines canonical RNA interference factors (Dicer-2, Hen1 (known as CG12367) and Argonaute 2) with a canonical microRNA factor (Loquacious) to generate approximately 21-nucleotide siRNAs. These novel regulatory RNAs reveal unexpected complexity in the sorting of small RNAs, and open a window onto the biological usage of endogenous RNA interference in Drosophila.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735555/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735555/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Okamura, Katsutomo -- Chung, Wei-Jen -- Ruby, J Graham -- Guo, Huili -- Bartel, David P -- Lai, Eric C -- GM067031/GM/NIGMS NIH HHS/ -- GM083300/GM/NIGMS NIH HHS/ -- R01 GM067031/GM/NIGMS NIH HHS/ -- R01 GM067031-01/GM/NIGMS NIH HHS/ -- R01 GM083300/GM/NIGMS NIH HHS/ -- R01 GM083300-01/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Jun 5;453(7196):803-6. doi: 10.1038/nature07015. Epub 2008 May 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sloan-Kettering Institute, Department of Developmental Biology, 521 Rockefeller Research Laboratories, 1275 York Avenue, Box 252, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18463630" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Argonaute Proteins ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/enzymology/*genetics/metabolism ; Methyltransferases/metabolism ; MicroRNAs/biosynthesis/genetics/metabolism ; *Nucleic Acid Conformation ; RNA Helicases/genetics/metabolism ; *RNA Interference ; RNA, Double-Stranded/chemistry/genetics/*metabolism ; RNA, Small Interfering/biosynthesis/genetics/*metabolism ; RNA-Binding Proteins/genetics/metabolism ; RNA-Induced Silencing Complex/genetics/metabolism ; Ribonuclease III
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Hybrid neurons in a microRNA mutant are putative evolutionary intermediates in insect CO2 sensory systems (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-03-01
    Description: Carbon dioxide (CO2) elicits different olfactory behaviors across species. In Drosophila, neurons that detect CO2 are located in the antenna, form connections in a ventral glomerulus in the antennal lobe, and mediate avoidance. By contrast, in the mosquito these neurons are in the maxillary palps (MPs), connect to medial sites, and promote attraction. We found in Drosophila that loss of a microRNA, miR-279, leads to formation of CO2 neurons in the MPs. miR-279 acts through down-regulation of the transcription factor Nerfin-1. The ectopic neurons are hybrid cells. They express CO2 receptors and form connections characteristic of CO2 neurons, while exhibiting wiring and receptor characteristics of MP olfactory receptor neurons (ORNs). We propose that this hybrid ORN reveals a cellular intermediate in the evolution of species-specific behaviors elicited by CO2.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714168/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714168/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cayirlioglu, Pelin -- Kadow, Ilona Grunwald -- Zhan, Xiaoli -- Okamura, Katsutomo -- Suh, Greg S B -- Gunning, Dorian -- Lai, Eric C -- Zipursky, S Lawrence -- DC006485/DC/NIDCD NIH HHS/ -- R01 GM083300/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Feb 29;319(5867):1256-60. doi: 10.1126/science.1149483.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18309086" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Animals, Genetically Modified ; Carbon Dioxide/*analysis/metabolism ; Drosophila/genetics/*physiology ; Drosophila Proteins/*genetics/metabolism ; Gene Expression Regulation ; Hybrid Cells/physiology ; MicroRNAs/genetics/*metabolism ; Mutation ; Olfactory Receptor Neurons/cytology/*physiology ; Receptors, Cell Surface/*metabolism ; Sense Organs/physiology ; Species Specificity ; Transcription Factors/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    The effect of magmatic activity on hydrothermal venting along the superfast-spreading East pacific rise (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1995-08-25
    Description: A survey of hydrothermal activity along the superfast-spreading (approximately 150 millimeters per year) East Pacific Rise shows that hydrothermal plumes overlay approximately 60 percent of the ridge crest between 13 degrees 50' and 18 degrees 40'S, a plume abundance nearly twice that known from any other rige portion of comparable length. Plumes were most abundant where the axial cross section is inflated and an axial magma chamber is present. Plumes with high ratios of volatile ((3)He, CH(4), and H(2)S) to nonvolatile (Mn and Fe) species marked where hydrothermal circulation has been perturbed by recent magmatic activity. The high proportion of volatile-rich plumes observed implies that such episodes are more frequent here than on slower spreading ridges.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Urabe, T -- Baker, E T -- Ishibashi, J -- Feely, R A -- Marumo, K -- Massoth, G J -- Maruyama, A -- Shitashima, K -- Okamura, K -- Lupton, J E -- Sonoda, A -- Yamazaki, T -- Aoki, M -- Gendron, J -- Greene, R -- Kaiho, Y -- Kisimoto, K -- Lebon, G -- Matsumoto, T -- Nakamura, K -- Nishizawa, A -- Okano, O -- Paradis, G -- Roe, K -- Shibata, T -- Tennant, D -- Vance, T -- Walker, S L -- Yabuki, T -- Ytow, N -- New York, N.Y. -- Science. 1995 Aug 25;269(5227):1092-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17755532" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Identification of functional elements and regulatory circuits by Drosophila modENCODE (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-24
    Description: To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉modENCODE Consortium -- Roy, Sushmita -- Ernst, Jason -- Kharchenko, Peter V -- Kheradpour, Pouya -- Negre, Nicolas -- Eaton, Matthew L -- Landolin, Jane M -- Bristow, Christopher A -- Ma, Lijia -- Lin, Michael F -- Washietl, Stefan -- Arshinoff, Bradley I -- Ay, Ferhat -- Meyer, Patrick E -- Robine, Nicolas -- Washington, Nicole L -- Di Stefano, Luisa -- Berezikov, Eugene -- Brown, Christopher D -- Candeias, Rogerio -- Carlson, Joseph W -- Carr, Adrian -- Jungreis, Irwin -- Marbach, Daniel -- Sealfon, Rachel -- Tolstorukov, Michael Y -- Will, Sebastian -- Alekseyenko, Artyom A -- Artieri, Carlo -- Booth, Benjamin W -- Brooks, Angela N -- Dai, Qi -- Davis, Carrie A -- Duff, Michael O -- Feng, Xin -- Gorchakov, Andrey A -- Gu, Tingting -- Henikoff, Jorja G -- Kapranov, Philipp -- Li, Renhua -- MacAlpine, Heather K -- Malone, John -- Minoda, Aki -- Nordman, Jared -- Okamura, Katsutomo -- Perry, Marc -- Powell, Sara K -- Riddle, Nicole C -- Sakai, Akiko -- Samsonova, Anastasia -- Sandler, Jeremy E -- Schwartz, Yuri B -- Sher, Noa -- Spokony, Rebecca -- Sturgill, David -- van Baren, Marijke -- Wan, Kenneth H -- Yang, Li -- Yu, Charles -- Feingold, Elise -- Good, Peter -- Guyer, Mark -- Lowdon, Rebecca -- Ahmad, Kami -- Andrews, Justen -- Berger, Bonnie -- Brenner, Steven E -- Brent, Michael R -- Cherbas, Lucy -- Elgin, Sarah C R -- Gingeras, Thomas R -- Grossman, Robert -- Hoskins, Roger A -- Kaufman, Thomas C -- Kent, William -- Kuroda, Mitzi I -- Orr-Weaver, Terry -- Perrimon, Norbert -- Pirrotta, Vincenzo -- Posakony, James W -- Ren, Bing -- Russell, Steven -- Cherbas, Peter -- Graveley, Brenton R -- Lewis, Suzanna -- Micklem, Gos -- Oliver, Brian -- Park, Peter J -- Celniker, Susan E -- Henikoff, Steven -- Karpen, Gary H -- Lai, Eric C -- MacAlpine, David M -- Stein, Lincoln D -- White, Kevin P -- Kellis, Manolis -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC2HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U01HG004261/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- U01HG004271/HG/NHGRI NIH HHS/ -- U01HG004274/HG/NHGRI NIH HHS/ -- U01HG004279/HG/NHGRI NIH HHS/ -- U41HG004269/HG/NHGRI NIH HHS/ -- ZIA DK015600-14/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177974" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Chromatin/genetics/metabolism ; Computational Biology/methods ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/growth & development/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genes, Insect ; *Genome, Insect ; Genomics/methods ; Histones/metabolism ; *Molecular Sequence Annotation ; Nucleosomes/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Small Untranslated/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Paternity and kin structure among neighbouring groups in wild bonobos at Wamba (2018)
    Royal Society
    Details
    Publication Date: 2018-02-01
    Description: Although both bonobos and chimpanzees are male-philopatric species, outcomes of male–male reproductive competition seem to be more closely associated with mating success in chimpanzees. This suggests that the extent of male reproductive skew is lower in bonobos. In addition, between-group male–male reproductive competition is more lethal in chimpanzees. This suggests that between-group differentiation in male kinship is lower in bonobos. We analysed the paternity of 17 offspring in two bonobo groups and estimated the relatedness of individuals among three neighbouring groups by using DNA extracted from non-invasive samples at Wamba, in the Democratic Republic of the Congo. The alpha males sired at least nine of 17 offspring. This supports a previous finding that the male reproductive skew is higher in bonobos than that in chimpanzees. Average relatedness among males within groups was significantly higher than that among males across groups, whereas there was no significant difference among females between within and across groups. These results are consistent with male philopatry, highly skewed reproductive success of males and female dispersal. Higher average relatedness among males within groups suggest that the differences in hostility towards males of different groups between bonobos and chimpanzees may be explained by factors other than kinship.
    Keywords: molecular biology, genetics, ecology
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 10
    Electronic Resource
    Electronic Resource
    A model system for tumor angiogenesis: Involvement of transforming growth factor-α in tube formation of human microvascular endothelial cells induced by esophageal cancer cells
    Amsterdam : Elsevier
    Biochemical and Biophysical Research Communications 186 (1992), S. 1471-1479 
    Details
    ISSN: 0006-291X
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0006-291X(05)81572-4
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