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  • 1
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    The identification and characterization of novel transcripts from RNA-seq data (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-16
    Description: Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques ‘RNA sequencing (RNA-seq)’ is rapidly replacing microarray-based techniques in laboratories around the world. As more and more of such techniques are standardized, allowing technicians to perform these experiments with minimal hands-on time and reduced experimental/operator-dependent biases, the bottleneck of such techniques is clearly visible; that is, data analysis. Further complicating the matter, increasing evidence suggests most of the genome is transcribed into RNA; however, the majority of these RNAs are not translated into proteins. These RNAs that do not become proteins are called ‘noncoding RNAs (ncRNAs)’. Although some time has passed since the discovery of ncRNAs, their annotations remain poor, making analysis of RNA-seq data challenging. Here, we examine the current limitations of RNA-seq analysis using case studies focused on the detection of novel transcripts and examination of their characteristics. Finally, we validate the presence of novel transcripts using biological experiments, showing novel transcripts can be accurately identified when a series of filters is applied. In conclusion, novel transcripts that are identified from RNA-seq must be examined carefully before proceeding to biological experiments.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 2
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    C-It-Loci: a knowledge database for tissue-enriched loci (2015)
    Oxford University Press
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    Publication Date: 2015-10-21
    Description: Motivation: Increasing evidences suggest that most of the genome is transcribed into RNAs, but many of them are not translated into proteins. All those RNAs that do not become proteins are called ‘non-coding RNAs (ncRNAs)’, which outnumbers protein-coding genes. Interestingly, these ncRNAs are shown to be more tissue specifically expressed than protein-coding genes. Given that tissue-specific expressions of transcripts suggest their importance in the expressed tissue, researchers are conducting biological experiments to elucidate the function of such ncRNAs. Owing greatly to the advancement of next-generation techniques, especially RNA-seq, the amount of high-throughput data are increasing rapidly. However, due to the complexity of the data as well as its high volume, it is not easy to re-analyze such data to extract tissue-specific expressions of ncRNAs from published datasets. Results: Here, we introduce a new knowledge database called ‘C-It-Loci’, which allows a user to screen for tissue-specific transcripts across three organisms: human, mouse and zebrafish. C-It-Loci is intuitive and easy to use to identify not only protein-coding genes but also ncRNAs from various tissues. C-It-Loci defines homology through sequence and positional conservation to allow for the extraction of species-conserved loci. C-It-Loci can be used as a starting point for further biological experiments. Availability and implementation: C-It-Loci is freely available online without registration at http://c-it-loci.uni-frankfurt.de . Contact: uchida@med.uni-frankfurt.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    White polymer light-emitting electrochemical cells using emission from exciplexes with long intermolecular distances formed between polyfluorene and π-conjugated amine molecules (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-12-10
    Description: The authors present white polymer light-emitting electrochemical cells (PLECs) fabricated with polymer blend films of poly(9,9-di- n -dodecylfluorenyl-2,7-diyl) (PFD) and π-conjugated triphenylamine molecules. The PLECs have bulk heterojunction structures composed of van der Waals interfaces between the PFD segments and the amine molecules. White-light electroluminescence (EL) can be achieved via light-mixing of the blue exciton emission from PFD and long-wavelength exciplex emission from excited complexes consisting of PFD segments (acceptors (As)) and the amine molecules (donors (Ds)). Precise control of the distances between the PFD and the amine molecules, affected through proper choice of the concentrations of PFD, amine molecules, and polymeric solid electrolytes, is critical to realizing white emission. White PLECs can be fabricated with PFD and amine molecules whose highest occupied molecular orbital (HOMO) levels range from −5.3 eV to −5.0 eV. Meanwhile, PLECs fabricated with amine molecules whose HOMO levels are lower than −5.6 eV cannot produce exciplex emission. The distances between the PFD and amine molecules of the exciplexes appear to be larger than 0.4 nm. These experimental data are explained by perturbation theory using the charge-transfer state ( A − D + ), the locally excited state ( A * D ), which is assumed to be the locally excited acceptor state in which there is no interaction with the donor molecule; and the energy gap between the HOMO levels of the PFD and the amine molecules. Color-stable white PLECs were fabricated using 4,4′,4″-tris[ N -(2-naphthyl)- N -phenylamino]-triphenylamine, which has a HOMO level of −5.2 eV, as the amine molecule, and the color stability of the device is a function of the fact that PFD forms exciplexes with these molecules.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Impaired degradation of WNK1 and WNK4 kinases causes PHAII in mutant KLHL3 knock-in mice (2014)
    Oxford University Press
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    Publication Date: 2014-09-10
    Description: Pseudohypoaldosteronism type II (PHAII) is a hereditary disease characterized by salt-sensitive hypertension, hyperkalemia and metabolic acidosis, and genes encoding with-no-lysine kinase 1 (WNK1) and WNK4 kinases are known to be responsible. Recently, Kelch-like 3 (KLHL3) and Cullin3, components of KLHL3-Cullin3 E3 ligase, were newly identified as responsible for PHAII. We have reported that WNK4 is the substrate of KLHL3-Cullin3 E3 ligase-mediated ubiquitination. However, WNK1 and Na–Cl cotransporter (NCC) were also reported to be a substrate of KLHL3-Cullin3 E3 ligase by other groups. Therefore, it remains unclear which molecule is the target(s) of KLHL3. To investigate the pathogenesis of PHAII caused by KLHL3 mutation, we generated and analyzed KLHL3 R528H/+ knock-in mice. KLHL3 R528H/+ knock-in mice exhibited salt-sensitive hypertension, hyperkalemia and metabolic acidosis. Moreover, the phosphorylation of NCC was increased in the KLHL3 R528H/+ mouse kidney, indicating that the KLHL3 R528H/+ knock-in mouse is an ideal mouse model of PHAII. Interestingly, the protein expression of both WNK1 and WNK4 was significantly increased in the KLHL3 R528H/+ mouse kidney, confirming that increases in these WNK kinases activated the WNK-OSR1/SPAK-NCC phosphorylation cascade in KLHL3 R528H/+ knock-in mice. To examine whether mutant KLHL3 R528H can interact with WNK kinases, we measured the binding of TAMRA-labeled WNK1 and WNK4 peptides to full-length KLHL3 using fluorescence correlation spectroscopy, and found that neither WNK1 nor WNK4 bound to mutant KLHL3 R528H. Thus, we found that increased protein expression levels of WNK1 and WNK4 kinases cause PHAII by KLHL3 R528H mutation due to impaired KLHL3-Cullin3-mediated ubiquitination.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Temperature evolution of correlation strength in the superconducting state of high-T_{c} cuprates (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-11-19
    Description: Author(s): S. Kudo, T. Yoshida, S. Ideta, K. Takashima, H. Anzai, T. Fujita, Y. Nakashima, A. Ino, M. Arita, H. Namatame, M. Taniguchi, K. M. Kojima, S. Uchida, and A. Fujimori Using angle-resolved photoemission spectroscopy (ARPES), a collaboration of authors from Tokyo and Hiroshima, Japan study the evolution of the nodal d-wave quasiparticles in the trilayer Bi2223 cuprate superconductor across the phase transition into the normal state. [Phys. Rev. B 92, 195135] Published Wed Nov 18, 2015
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Reversed anisotropy of the in-plane resistivity in the antiferromagnetic phase of iron tellurides (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-04-09
    Description: Author(s): L. Liu, T. Mikami, M. Takahashi, S. Ishida, T. Kakeshita, K. Okazaki, A. Fujimori, and S. Uchida We systematically investigated the anisotropic in-plane resistivity of iron tellurides including three kinds of impurity atoms: excess Fe, Se substituted for Te, and Cu substituted for Fe. Sizable resistivity anisotropy was found in the magnetostructurally ordered phase, whereas the sign is opposite... [Phys. Rev. B 91, 134502] Published Wed Apr 08, 2015
    Keywords: Superfluidity and superconductivity
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 7
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    Dependence of electron correlation strength in Fe_{1+y} Te_{1−x} Se_{x} on Se content (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-07-05
    Description: Author(s): L. C. C. Ambolode, II, K. Okazaki, M. Horio, H. Suzuki, L. Liu, S. Ideta, T. Yoshida, T. Mikami, T. Kakeshita, S. Uchida, K. Ono, H. Kumigashira, M. Hashimoto, D.-H. Lu, Z.-X. Shen, and A. Fujimori The iron chalcogenide F e 1 + y T e 1 − x S e x on the Te-rich side is known to exhibit the strongest electron correlations among the Fe-based superconductors and is nonsuperconducting for x 〈 0.1 . In order to understand the origin of such behaviors, we have performed angle-resolved photoemission spectroscopy … [Phys. Rev. B 92, 035104] Published Thu Jul 02, 2015
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    Stability of the Zhang-Rice Singlet with Doping in Lanthanum Strontium Copper Oxide Across the Superconducting Dome and Above (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-07-08
    Description: Author(s): N. B. Brookes, G. Ghiringhelli, A.-M. Charvet, A. Fujimori, T. Kakeshita, H. Eisaki, S. Uchida, and T. Mizokawa The spin character of the states at the top of the valence band in doped La 2 − x Sr x CuO 4 ( x = 0.03 , 0.07, 0.15, 0.22, and 0.30) has been investigated using spin-polarized resonant photoemission. A clear Zhang-Rice singlet (ZRS) is observed at all doping levels. Its stability and polarization are preserve… [Phys. Rev. Lett. 115, 027002] Published Tue Jul 07, 2015
    Keywords: Condensed Matter: Electronic Properties, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Critical state soil constitutive model for methane hydrate soil (2012)
    Wiley
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    Publication Date: 2012-03-16
    Description: This paper presents a new constitutive model that simulates the mechanical behavior of methane hydrate-bearing soil based on the concept of critical state soil mechanics, referred to as the “Methane Hydrate Critical State (MHCS) model”. Methane hydrate-bearing soil is, under certain geological conditions, known to exhibit greater stiffness, strength and dilatancy, which are often observed in dense soils and also in bonded soils such as cemented soil and unsaturated soil. Those soils tend to show greater resistance to compressive deformation but the tendency disappears when the soil is excessively compressed or the bonds are destroyed due to shearing. The proposed model represents these features by introducing five extra model parameters to the conventional critical state model. It is found that, for an accurate prediction of ground settlement, volumetric yielding plays an important role when hydrate soil undergoes a significant change in effective stresses and hydrate saturation, which are expected during depressurization for methane gas recovery.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
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    Abrupt change in the energy gap of superconducting Ba_{1-x}K_{x}Fe_{2}As_{2} single crystals with hole doping (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-10-11
    Description: Author(s): W. Malaeb, T. Shimojima, Y. Ishida, K. Okazaki, Y. Ota, K. Ohgushi, K. Kihou, T. Saito, C. H. Lee, S. Ishida, M. Nakajima, S. Uchida, H. Fukazawa, Y. Kohori, A. Iyo, H. Eisaki, C.-T. Chen, S. Watanabe, H. Ikeda, and S. Shin We performed a laser angle-resolved photoemission spectroscopy (ARPES) study on a wide doping range of Ba 1- x K x Fe 2 As 2 (BaK) and precisely determined the doping evolution of the superconducting gaps in this compound. The gap size of the outer hole Fermi-surface (FS) sheet around the Brillouin zone (BZ... [Phys. Rev. B 86, 165117] Published Wed Oct 10, 2012
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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