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Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map
Nozomu Yachie,Rintaro Saito ,Naoyuki Sugiyama,Masaru Tomita,Yasushi Ishihama
PLOS Computational Biology , 2011, DOI: 10.1371/journal.pcbi.1001064
Abstract: Following recent advances in high-throughput mass spectrometry (MS)–based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylation is control of protein signaling, our understanding of the phosphoproteome remains limited. Here, we report unexpected, large-scale connections revealed between the phosphoproteome and protein interactome by integrative data-mining of yeast multi-omics data. First, new phosphoproteome data on yeast cells were obtained by MS-based proteomics and unified with publicly available yeast phosphoproteome data. This revealed that nearly 60% of ~6,000 yeast genes encode phosphoproteins. We mapped these unified phosphoproteome data on a yeast protein–protein interaction (PPI) network with other yeast multi-omics datasets containing information about proteome abundance, proteome disorders, literature-derived signaling reactomes, and in vitro substratomes of kinases. In the phospho-PPI, phosphoproteins had more interacting partners than nonphosphoproteins, implying that a large fraction of intracellular protein interaction patterns (including those of protein complex formation) is affected by reversible and alternative phosphorylation reactions. Although highly abundant or unstructured proteins have a high chance of both interacting with other proteins and being phosphorylated within cells, the difference between the number counts of interacting partners of phosphoproteins and nonphosphoproteins was significant independently of protein abundance and disorder level. Moreover, analysis of the phospho-PPI and yeast signaling reactome data suggested that co-phosphorylation of interacting proteins by single kinases is common within cells. These multi-omics analyses illuminate how wide-ranging intracellular phosphorylation events and the diversity of physical protein interactions are largely affected by each other.
Multi-parametric Solution-path Algorithm for Instance-weighted Support Vector Machines
Masayuki Karasuyama,Naoyuki Harada,Masashi Sugiyama,Ichiro Takeuchi
Computer Science , 2010,
Abstract: An instance-weighted variant of the support vector machine (SVM) has attracted considerable attention recently since they are useful in various machine learning tasks such as non-stationary data analysis, heteroscedastic data modeling, transfer learning, learning to rank, and transduction. An important challenge in these scenarios is to overcome the computational bottleneck---instance weights often change dynamically or adaptively, and thus the weighted SVM solutions must be repeatedly computed. In this paper, we develop an algorithm that can efficiently and exactly update the weighted SVM solutions for arbitrary change of instance weights. Technically, this contribution can be regarded as an extension of the conventional solution-path algorithm for a single regularization parameter to multiple instance-weight parameters. However, this extension gives rise to a significant problem that breakpoints (at which the solution path turns) have to be identified in high-dimensional space. To facilitate this, we introduce a parametric representation of instance weights. We also provide a geometric interpretation in weight space using a notion of critical region: a polyhedron in which the current affine solution remains to be optimal. Then we find breakpoints at intersections of the solution path and boundaries of polyhedrons. Through extensive experiments on various practical applications, we demonstrate the usefulness of the proposed algorithm.
HybGFS: a hybrid method for genome-fingerprint scanning
Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, Masaru Tomita
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-479
Abstract: Here, we present a hybrid method for genome-fingerprint scanning, known as HybGFS. This technique combines genome sequence-based peptide MS/MS ion searching with liquid-chromatography elution-time (LC-ET) prediction, to improve the reliability of identification. The hybrid method allows the simultaneous identification and mapping of proteins without a priori information about their coding sequences. The current study used standard LC-MS/MS data to query an in silico-generated six-reading-frame translation and the enzymatic digest of an entire genome. Used in conjunction with precursor/product ion-mass searching, the LC-ETs increased confidence in the peptide-identification process and reduced the number of false-positive matches. The power of this method was demonstrated using recombinant proteins from the Escherichia coli K12 strain.The novel hybrid method described in this study will be useful for the large-scale experimental confirmation of genome coding sequences, without the need for transcriptome-level expression analysis or costly MS database searching.Mass spectrometry (MS) is one of the major proteomics tools of the post-genomic era. Protein identification has traditionally been conducted by peptide mass fingerprinting (PMF) [1-3] or tandem MS (MS/MS) database searching and, while the former performs well with highly purified samples, the latter is the de facto standard for identifying proteins in complex samples. However, these approaches are only capable of detecting proteins already listed in databases. PMF implicitly assumes that all genes are annotated and that their complete protein sequences, including post-translational modifications, are known; however, in reality, most of these sequences are inadequately represented in existing databases. As alternative approaches, de novo peptide sequencing can be performed by the Edman degradation method [4], MS/MS [5,6], and controlled protein hydrolysis [7]. However, although amino-acid sequences can provide s
Iridium Orbital Crossover at the Structural Phase Transition in Ca10(Ir4As8)(Fe2-xIrxAs2)5
Kento Sugawara,Naoyuki Katayama,Yuki Sugiyama,Takafumi Higuchi,Kazutaka Kudo,Daisuke Mitsuoka,Minoru Nohara,Hiroshi Sawa
Physics , 2014,
Abstract: We report a structural transition found in Ca10(Ir4As8)(Fe2-xIrxAs2)5, which exhibits superconductivity at 16 K, with a layer of divalent iridium coordinated by arsenic in between Fe2As2 layers. The c-axis parameter is doubled below a structural transition temperature of approximately 100 K, while the tetragonal symmetry with space group P4/n (No.85) is unchanged at all temperatures measured. Our synchrotron x-ray diffraction study clearly shows displacements along the z-direction occur in half of the iridium sites, resulting in a complex orbital ordering pattern. Combining our theoretical calculation of the 5d orbital energies with structural data, we propose the iridium orbital crossover transition between the dxy and dz2 orbitals.
Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment
Minako Izutsu, Jun Zhou, Yuzo Sugiyama, Osamu Nishimura, Tomoyuki Aizu, Atsushi Toyoda, Asao Fujiyama, Kiyokazu Agata, Naoyuki Fuse
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033288
Abstract: Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.
Synchrotron X-ray Diffraction Study of Structural Phase Transition in Ca10(Ir4As8)(Fe2-xIrxAs2)
Naoyuki Katayama,Kento Sugawara,Yuki Sugiyama,Takafumi Higuchi,Kazutaka Kudo,Daisuke Mitsuoka,Takashi Mizokawa,Minoru Nohara,Hiroshi Sawa
Physics , 2014, DOI: 10.7566/JPSJ.83.113707
Abstract: We report a structural transition found in Ca10(Ir4As8)(Fe2-xIrxAs2)5, which exhibits superconductivity at 16 K. The c-axis parameter is doubled below a structural transition temperature of approximately 100 K, while the tetragonal symmetry with space group P4/n (No.85) is unchanged at all temperatures measured. Our synchrotron x-ray diffraction study clearly shows iridium ions at a non-coplanar position shift along the z-direction at the structural phase transition. We discuss that the iridium displacements affect superconductivity in Fe2As2 layers.
Magnetic Field and Pressure Phase Diagrams of Uranium Heavy-Fermion Compound U$_2$Zn$_{17}$
Naoyuki Tateiwa,Shugo Ikeda,Yoshinori Haga,Tatsuma D. Matsuda,Etsuji Yamamoto,Kiyohiro Sugiyama,Masayuki Hagiwara,Koichi Kindo,Yoshichika Onuki
Physics , 2011, DOI: 10.1143/JPSJ.80.014706
Abstract: We have performed magnetization measurements at high magnetic fields of up to 53 T on single crystals of a uranium heavy-fermion compound U$_2$Zn$_{17}$ grown by the Bridgman method. In the antiferromagnetic state below the N\'{e}el temperature $T_{\rm N}$ = 9.7 K, a metamagnetic transition is found at $H_c$ $\simeq$ 32 T for the field along the [11$\bar{2}$0] direction ($a$-axis). The magnetic phase diagram for the field along the [11$\bar{2}$0] direction is given. The magnetization curve shows a nonlinear increase at $H_m$ $\simeq$ 35 T in the paramagnetic state above $T_{\rm N}$ up to a characteristic temperature $T_{{\chi}{\rm max}}$ where the magnetic susceptibility or electrical resistivity shows a maximum value. This metamagnetic behavior of the magnetization at $H_m$ is discussed in comparison with the metamagnetic magnetism of the heavy-fermion superconductors UPt$_3$, URu$_2$Si$_2$, and UPd$_2$Al$_3$. We have also carried out high-pressure resistivity measurement on U$_2$Zn$_{17}$ using a diamond anvil cell up to 8.7 GPa. Noble gas argon was used as a pressure-transmitting medium to ensure a good hydrostatic environment. The N\'{e}el temperature $T_{\rm N}$ is almost pressure-independent up to 4.7 GPa and starts to increase in the higher-pressure region. The pressure dependences of the coefficient of the $T^2$ term in the electrical resistivity $A$, the antiferromagnetic gap $\Delta$, and the characteristic temperature $T_{{\rho}{\rm max}}$ are discussed. It is found that the effect of pressure on the electronic states in U$_2$Zn$_{17}$ is weak compared with those in the other heavy fermion compounds.
RETRACTED: Endotoxin Occurrence in Raw and Reclaimed Wastewater  [PDF]
Guizani Mokhtar, Funamizu Naoyuki
Journal of Water Resource and Protection (JWARP) , 2014, DOI: 10.4236/jwarp.2014.67066

Short Retraction Notice

The paper does not meet the standards of \"Journal of Water Resource and Protection\".

This article has been retracted to straighten the academic record. In making this decision the Editorial Board follows COPE's Retraction Guidelines. The aim is to promote the circulation of scientific research by offering an ideal research publication platform with due consideration of internationally accepted standards on publication ethics. The Editorial Board would like to extend its sincere apologies for any inconvenience this retraction may have caused.

Editor guiding this retraction: Prof. Dr. Jian Shen (EiC of JWARP).

The full retraction notice in PDF is preceding the original paper which is marked \"RETRACTED\".

Superconductivity in Ca1-xLaxFeAs2: A Novel 112-Type Iron Pnictide with Arsenic Zigzag Bonds
Naoyuki Katayama,Kazutaka Kudo,Seiichiro Onari,Tasuku Mizukami,Kento Sugawara,Yuki Sugiyama,Yutaka Kitahama,Keita Iba,Kazunori Fujimura,Naoki Nishimoto,Minoru Nohara,Hiroshi Sawa
Physics , 2013, DOI: 10.7566/JPSJ.82.123702
Abstract: We report superconductivity in the novel 112-type iron-based compound Ca1-xLaxFeAs2. Single-crystal X-ray diffraction analysis revealed that the compound crystallizes in a monoclinic structure (space group P21), in which Fe2As2 layers alternate with Ca2As2 spacer layers such that monovalent arsenic forms zigzag chains. Superconductivity with a transition temperature (Tc) of 34 K was observed for the x = 0.1 sample, while the x = 0.21 sample exhibited trace superconductivity at 45 K. First-principles band calculations demonstrated the presence of almost cylindrical Fermi surfaces, favorable for the high Tc in La-doped CaFeAs2.
Superconductivity in Ca10(Ir4As8)(Fe2As2)5 with Square-Planar Coordination of Iridium
Kazutaka Kudo,Daisuke Mitsuoka,Masaya Takasuga,Yuki Sugiyama,Kento Sugawara,Naoyuki Katayama,Hiroshi Sawa,Hiroaki S. Kubo,Kenta Takamori,Masanori Ichioka,Tatsuo Fujii,Takashi Mizokawa,Minoru Nohara
Physics , 2013, DOI: 10.1038/srep03101
Abstract: We report the unprecedented square-planar coordination of iridium in the iron iridium arsenide Ca10(Ir4As8)(Fe2As2)5. This material experiences superconductivity at 16 K. X-ray photoemission spectroscopy and first- principles band calculation suggest Ir(II) oxidation state, which yields electrically conductive Ir4As8 layers. Such metallic spacer layers are thought to enhance the interlayer coupling of Fe2As2, in which superconductivity emerges, thus offering a way to control the superconducting transition temperature.
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