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  1. Article ; Online: Coarse-graining of perplexity for the spatial distribution of molecules.

    Xu, Lili / Zhang, Chi / Oyama, Soho / Machida, Manabu / Kahyo, Tomoaki / Setou, Mitsutoshi

    Physical review. E

    2024  Volume 109, Issue 1-1, Page(s) 14402

    Abstract: Biological tissue consists of various molecules. Instead of focusing on a particular molecule, we consider the Shannon entropy which is calculated from the abundance of different molecules at each spot in the tissue. The spatial distribution of the ... ...

    Abstract Biological tissue consists of various molecules. Instead of focusing on a particular molecule, we consider the Shannon entropy which is calculated from the abundance of different molecules at each spot in the tissue. The spatial distribution of the Shannon entropy is of interest. In this paper, we first obtain the heat map of perplexity, whose logarithm is the entropy. To characterize the spatial variety of molecules, we propose a scalar k that is concerned with the coarse-graining of the perplexity heat map. To verify the usefulness of the number, experiments with mass spectrometry imaging were performed for mouse kidneys. We found that k has large values in the renal pelvis area, cortex area, veins, and arteries in the mouse kidney, whereas fractal dimensions fail to distinguish those regions.
    MeSH term(s) Animals ; Mice ; Entropy ; Fractals ; Cerebral Cortex
    Language English
    Publishing date 2024-02-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.109.014402
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A pair of primers facing at the double-strand break site enables to detect NHEJ-mediated indel mutations at a 1-bp resolution.

    Ijaz, Faryal / Nakazato, Ryota / Setou, Mitsutoshi / Ikegami, Koji

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 11681

    Abstract: The introduction of small insertion/deletion (indel) mutations in the coding region of genes by the site-specific nucleases such as Cas9 allows researchers to obtain frameshift null mutants. Technically simple and costly reasonable genotyping methods are ...

    Abstract The introduction of small insertion/deletion (indel) mutations in the coding region of genes by the site-specific nucleases such as Cas9 allows researchers to obtain frameshift null mutants. Technically simple and costly reasonable genotyping methods are awaited to efficiently screen the frameshift null mutant candidates. Here, we developed a simple genotyping method called DST-PCR (Double-strand break Site-Targeted PCR) using "face-to-face" primers where the 3' ends of forward and reverse primers face each other at the position between 3-bp and 4-bp upstream of the PAM sequence, which is generally the Cas9-mediated double-strand break site. Generated amplicons are directly subjected to TBE-High-Resolution PAGE, which contains a high concentration of bis-acrylamide, for mutant clones detection with 1-bp resolution. We present actual cases of screening of CRISPR/Cas9-engineered knockout (KO) cells for six genes, where we screen indels to obtain potential KO cell clones utilizing our approach. This method allowed us to detect 1-bp to 2-bp insertion and 1-bp to 4-bp deletion in one or both alleles of mutant cell clones. In addition, this technique also allowed the identification of heterozygous and homozygous biallelic functional KO candidates. Thus, DST-PCR is a simple and fast method to screen KO candidates generated by the CRISPR/Cas9 system before the final selection of clones with sequencing.
    MeSH term(s) CRISPR-Cas Systems ; DNA Primers ; Gene Editing/methods ; Genotyping Techniques ; INDEL Mutation ; Polymerase Chain Reaction/methods
    Chemical Substances DNA Primers
    Language English
    Publishing date 2022-07-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-15776-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book: Biomedical mass spectrometry

    Setou, Mitsutoshi

    (Analytical & bioanalytical chemistry ; 406.2014,5)

    2014  

    Author's details guest ed.: Mitsutoshi Setou
    Series title Analytical & bioanalytical chemistry ; 406.2014,5
    Language English
    Size S. 1273 - 1396
    Publisher Springer
    Publishing place Heidelberg
    Document type Book
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  4. Article: [Application of Quantum Science and Technology in the Living Body].

    Aramaki, Shuhei / Setou, Mitsutoshi

    No shinkei geka. Neurological surgery

    2019  Volume 47, Issue 7, Page(s) 719–731

    MeSH term(s) Humans ; Technology
    Language Japanese
    Publishing date 2019-07-29
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 197053-7
    ISSN 1882-1251 ; 0301-2603
    ISSN (online) 1882-1251
    ISSN 0301-2603
    DOI 10.11477/mf.1436204015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Associations between prefrontal PI (16:0/20:4) lipid,

    Sano, Fumito / Kikushima, Kenji / Benner, Seico / Xu, Lili / Kahyo, Tomoaki / Yamasue, Hidenori / Setou, Mitsutoshi

    Frontiers in psychiatry

    2023  Volume 14, Page(s) 1145437

    Abstract: Background: Though various mechanisms have been proposed for the pathophysiology of schizophrenia, the full extent of these mechanisms remains unclear, and little is known about the relationships among them. We carried out trans-omics analyses by ... ...

    Abstract Background: Though various mechanisms have been proposed for the pathophysiology of schizophrenia, the full extent of these mechanisms remains unclear, and little is known about the relationships among them. We carried out trans-omics analyses by comparing the results of the previously reported lipidomics, transcriptomics, and proteomics analyses; all of these studies used common post-mortem brain samples.
    Methods: We collected the data from three aforementioned omics studies on 6 common post-mortem samples (3 schizophrenia patients and 3 controls), and analyzed them as a whole group sample. Three correlation analyses were performed for each of the two of three omics studies in these samples. In order to discuss the strength of the correlations in a limited sample size, the
    Results: The following three factors were strongly correlated with each other: the lipid level of phosphatidylinositol (PI) (16:0/20:4), the amount of
    Conclusion: The current results suggest that these three factors may provide new clues to elucidate the relationships among the candidate mechanisms of schizophrenia, and support the potential of trans-omics analyses as a new analytical method.
    Language English
    Publishing date 2023-04-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564218-2
    ISSN 1664-0640
    ISSN 1664-0640
    DOI 10.3389/fpsyt.2023.1145437
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Visualization of Brain Gangliosides Using MALDI Imaging Mass Spectrometry.

    Sugiyama, Eiji / Setou, Mitsutoshi

    Methods in molecular biology (Clifton, N.J.)

    2018  Volume 1804, Page(s) 223–229

    Abstract: Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) is a histological method used for various molecules including gangliosides. The method is based on mass spectrometry, and thus target molecules with small structural ... ...

    Abstract Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) is a histological method used for various molecules including gangliosides. The method is based on mass spectrometry, and thus target molecules with small structural differences are directly and independently detected. Here we describe a general procedure and related key notes for analyzing major brain gangliosides by MALDI-IMS.
    MeSH term(s) Animals ; Brain/metabolism ; Cryoultramicrotomy ; Data Analysis ; Gangliosides/metabolism ; Mice, Inbred C57BL ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
    Chemical Substances Gangliosides
    Language English
    Publishing date 2018-06-20
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-8552-4_10
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Distribution of Antisense Oligonucleotides in Rat Eyeballs Using MALDI Imaging Mass Spectrometry.

    Nakashima, Yuko / Setou, Mitsutoshi

    Mass spectrometry (Tokyo, Japan)

    2018  Volume 7, Issue 1, Page(s) A0070

    Abstract: Oligonucleotide-based therapeutics such as antisense oligonucleotides, small interfering RNAs (siRNAs), decoy and aptamer have been extensively developed. To investigate the pharmacokinetics of oligonucleotide therapeutics, it is common to label a ... ...

    Abstract Oligonucleotide-based therapeutics such as antisense oligonucleotides, small interfering RNAs (siRNAs), decoy and aptamer have been extensively developed. To investigate the pharmacokinetics of oligonucleotide therapeutics, it is common to label a radioisotope in a nucleic acid and visualize it. However, if the labeled terminal nucleotide is decomposed by a nuclease
    Language English
    Publishing date 2018-09-11
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 2670439-0
    ISSN 2186-5116 ; 2187-137X
    ISSN (online) 2186-5116
    ISSN 2187-137X
    DOI 10.5702/massspectrometry.A0070
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Region-specific effects of Scrapper on the abundance of glutamate and gamma-aminobutyric acid in the mouse brain.

    Eto, Fumihiro / Sato, Shumpei / Setou, Mitsutoshi / Yao, Ikuko

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 7435

    Abstract: The brain consists of various areas with anatomical features. Neurons communicate with one another via excitatory or inhibitory synaptic transmission. Altered abundance of neurotransmitters, including glutamate and gamma-aminobutyric acid (GABA), in ... ...

    Abstract The brain consists of various areas with anatomical features. Neurons communicate with one another via excitatory or inhibitory synaptic transmission. Altered abundance of neurotransmitters, including glutamate and gamma-aminobutyric acid (GABA), in specific brain regions is closely involved in severe neurological diseases, such as schizophrenia and obsessive-compulsive disorder. SCRAPPER, a ubiquitin E3 ligase, regulates synaptic transmission. Scrapper gene deficiency results in defective neurotransmission due to excessive secretion of neurotransmitters. The present study employed matrix-assisted laser desorption/ionization imaging mass spectrometry to analyze the abundance of amino acid neurotransmitters in Scrapper knockout (SCR-KO) mice. SCR-KO mice exhibited significantly increased glutamate levels in the isocortex (CTX), corpus callosum (CC), thalamus (TH), midbrain (MB), cerebellar cortex (CBX), and caudoputamen (CP) and increased GABA levels in the CTX, CC, TH, MB, CBX and hypothalamus (HY) compared with wild-type mice. These findings indicate that Scrapper deficiency leads to upregulated glutamate and GABA levels in multiple regions. Our results show a differential, region-specific effect of Scrapper on the abundance of glutamate and GABA.
    MeSH term(s) Animals ; Brain/metabolism ; Chromatography, Liquid ; Excitatory Postsynaptic Potentials ; F-Box Proteins/genetics ; F-Box Proteins/metabolism ; Glutamic Acid/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Nerve Tissue Proteins/metabolism ; Neurons/metabolism ; Neurotransmitter Agents/metabolism ; Synapses/metabolism ; Synaptic Transmission ; Tandem Mass Spectrometry ; Tissue Distribution ; gamma-Aminobutyric Acid/metabolism
    Chemical Substances F-Box Proteins ; Fbxl20 protein, mouse ; Nerve Tissue Proteins ; Neurotransmitter Agents ; Glutamic Acid (3KX376GY7L) ; gamma-Aminobutyric Acid (56-12-2)
    Language English
    Publishing date 2020-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-64277-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: [Imaging mass spectrometry].

    Setou, Mitsutoshi

    Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan

    2011  Volume 132, Issue 4, Page(s) 499–506

    Abstract: Matrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry (IMS) enables the visualization of the distribution of a range of biomolecules that have varied structures in the cells and tissue sections. This emerging imaging technique was ...

    Abstract Matrix-assisted laser desorption/ionization (MALDI)-imaging mass spectrometry (IMS) enables the visualization of the distribution of a range of biomolecules that have varied structures in the cells and tissue sections. This emerging imaging technique was initially developed as a tool for protein imaging, but recently it is increasingly being used for the imaging of small organic molecules. IMS is an effective technique for the imaging of small metabolites, including endogenous metabolites such as lipids and exogenous drugs because of the following advantages: First, IMS does not require any specific labels or probes. Second, IMS is a non-targeted imaging method. Finally, the simultaneous imaging of many types of metabolite molecules is possible, and all these features are necessary for the assessment of metabolite localization. In this review, we discuss the capability of current IMS techniques for imaging small molecules, and introduce representative studies on imaging of endogenous and exogenous metabolites. In addition, the limitations and problems of the technique are also discussed, and reports of progress toward solving the problems with this technique are also introduced.
    MeSH term(s) Animals ; Brain/metabolism ; Mice ; Molecular Imaging/instrumentation ; Molecular Imaging/methods ; Peptides/analysis ; Pharmacokinetics ; Phospholipids/analysis ; Retina/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Tissue Distribution
    Chemical Substances Peptides ; Phospholipids
    Language Japanese
    Publishing date 2011-11-21
    Publishing country Japan
    Document type English Abstract ; Journal Article ; Review
    ZDB-ID 200514-1
    ISSN 1347-5231 ; 0031-6903 ; 0372-7750 ; 0919-2085 ; 0919-2131
    ISSN (online) 1347-5231
    ISSN 0031-6903 ; 0372-7750 ; 0919-2085 ; 0919-2131
    DOI 10.1248/yakushi.132.499
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 643: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

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  10. Book: Biomedical mass spectrometry

    Setou, Mitsutoshi

    (Analytical & bioanalytical chemistry ; 400.2011,7)

    2011  

    Author's details guest ed.: Mitsutoshi Setou
    Series title Analytical & bioanalytical chemistry ; 400.2011,7
    Language English
    Size S. 1813 - 2272, graph. Darst.
    Publisher Springer
    Publishing place Heidelberg
    Document type Book
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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