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Article ; Online: CUT & RUN to Profile Chromatin-Bound Proteins in Primary Mouse Neural Progenitor Cells.

Matsui, Yurika / Peng, Jamy C

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

2022 Volume 2599, Page(s) 99–111

Abstract: Cleavage under targets and release using nuclease (CUT & RUN) is an innovative method to profile histone modifications and chromatin-bound proteins genome-wide. CUT & RUN offers two distinct advantages of requiring much fewer cells and providing strong ... ...

Abstract	Cleavage under targets and release using nuclease (CUT & RUN) is an innovative method to profile histone modifications and chromatin-bound proteins genome-wide. CUT & RUN offers two distinct advantages of requiring much fewer cells and providing strong signal-to-noise ratios in deep-sequencing data. Here, we describe a workflow starting from dissociation and sorting of mouse embryonic brains, CUT & RUN, and DNA library preparation to deep sequencing. With our workflow, researchers can obtain high-quality sequencing data to profile histones and chromatin-associated proteins by using as few as 100,000 neural progenitor cells (NPCs).
MeSH term(s)	Mice ; Animals ; Chromatin/genetics ; Endonucleases/genetics ; Neural Stem Cells/metabolism ; Histones/metabolism ; Histone Code
Chemical Substances	Chromatin ; Endonucleases (EC 3.1.-) ; Histones
Language	English
Publishing date	2022-11-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2847-8_8
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Article ; Online: Bimolecular Fluorescence Complementation (BiFC) in Tissue Culture and in Developing Tissues of Drosophila to Study Protein-Protein Interactions.

Matsui, Yurika / Lai, Zhi-Chun

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

2018 Volume 1893, Page(s) 75–85

Abstract: Protein-protein interactions provide a common mechanism for regulating protein functions and also serve as the fundamental step of many biochemical reactions. To accurately determine the involvement and function of protein-protein interactions, it is ... ...

Abstract	Protein-protein interactions provide a common mechanism for regulating protein functions and also serve as the fundamental step of many biochemical reactions. To accurately determine the involvement and function of protein-protein interactions, it is crucial to detect the interactions with the minimum number of artifacts. In this chapter, we report the method of bimolecular fluorescence complementation (BiFC) in tissue culture and developing tissues of Drosophila, which allows the visualization of subcellular localization of protein-protein interactions in living cells.
MeSH term(s)	Animals ; Cell Line ; Drosophila/embryology ; Drosophila/genetics ; Drosophila/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Fluorescent Antibody Technique ; Gene Expression ; Humans ; Imaginal Discs ; Microscopy, Fluorescence/methods ; Molecular Imaging/methods ; Protein Interaction Mapping/methods ; Tissue Culture Techniques ; Wings, Animal
Chemical Substances	Drosophila Proteins
Language	English
Publishing date	2018-12-18
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8910-2_6
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Article ; Online: Author Correction: Ybx1 fine-tunes PRC2 activities to control embryonic brain development.

Evans, Myron K / Matsui, Yurika / Xu, Beisi / Willis, Catherine / Loome, Jennifer / Milburn, Luis / Fan, Yiping / Pagala, Vishwajeeth / Peng, Jamy C

Nature communications

2023 Volume 14, Issue 1, Page(s) 412

Language	English
Publishing date	2023-01-25
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36069-z
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Article ; Online: Correction: Efficient multiplexed genome engineering with a polycistronic tRNA and CRISPR guide-RNA reveals an important role of detonator in reproduction of Drosophila melanogaster.

Chon, Cristin / Chon, Grace / Matsui, Yurika / Zeng, Huiqing / Lai, Zhi-Chun / Liu, Aimin

PloS one

2021 Volume 16, Issue 4, Page(s) e0250188

Abstract: This corrects the article DOI: 10.1371/journal.pone.0245454.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pone.0245454.].
Language	English
Publishing date	2021-04-08
Publishing country	United States
Document type	Published Erratum
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0250188
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Article ; Online: Efficient multiplexed genome engineering with a polycistronic tRNA and CRISPR guide-RNA reveals an important role of detonator in reproduction of Drosophila melanogaster.

Chon, Cristin / Chon, Grace / Matsui, Yurika / Zeng, Huiqing / Lai, Zhi-Chun / Liu, Aimin

PloS one

2021 Volume 16, Issue 1, Page(s) e0245454

Abstract: Genome association studies in human and genetic studies in mouse implicated members of the transmembrane protein 132 (TMEM132) family in multiple conditions including panic disorder, hearing loss, limb and kidney malformation. However, the presence of ... ...

Abstract	Genome association studies in human and genetic studies in mouse implicated members of the transmembrane protein 132 (TMEM132) family in multiple conditions including panic disorder, hearing loss, limb and kidney malformation. However, the presence of five TMEM132 paralogs in mammalian genomes makes it extremely challenging to reveal the full requirement for these proteins in vivo. In contrast, there is only one TMEM132 homolog, detonator (dtn), in the genome of fruit fly Drosophila melanogaster, enabling straightforward research into its in vivo function. In the current study, we generate multiple loss-of-function dtn mutant fly strains through a polycistronic tRNA-gRNA approach, and show that most embryos lacking both maternal and paternal dtn fail to hatch into larvae, indicating an essential role of dtn in Drosophila reproduction.
MeSH term(s)	Animals ; Animals, Genetically Modified/genetics ; Animals, Genetically Modified/physiology ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Drosophila melanogaster/physiology ; Female ; Fertility ; Gene Editing/methods ; Loss of Function Mutation ; Male ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Transfer/genetics ; Reproduction
Chemical Substances	Drosophila Proteins ; RNA, Guide, CRISPR-Cas Systems ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2021-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0245454
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Article ; Online: Yap1 promotes proliferation of transiently amplifying stress erythroid progenitors during erythroid regeneration.

Hao, Siyang / Matsui, Yurika / Lai, Zhi-Chun / Paulson, Robert F

Experimental hematology

2019 Volume 80, Page(s) 42–54.e4

Abstract: In contrast to steady-state erythropoiesis, which generates new erythrocytes at a constant rate, stress erythropoiesis rapidly produces a large bolus of new erythrocytes in response to anemic stress. In this study, we illustrate that Yes-associated ... ...

Abstract	In contrast to steady-state erythropoiesis, which generates new erythrocytes at a constant rate, stress erythropoiesis rapidly produces a large bolus of new erythrocytes in response to anemic stress. In this study, we illustrate that Yes-associated protein (Yap1) promotes the rapid expansion of a transit-amplifying population of stress erythroid progenitors in vivo and in vitro. Yap1-mutated erythroid progenitors failed to proliferate in the spleen after transplantation into lethally irradiated recipient mice. Additionally, loss of Yap1 impaired the growth of actively proliferating erythroid progenitors in vitro. This role in proliferation is supported by gene expression profiles showing that transiently amplifying stress erythroid progenitors express high levels of genes associated with Yap1 activity and genes induced by Yap1. Furthermore, Yap1 promotes the proliferation of stress erythroid progenitors in part by regulating the expression of key glutamine-metabolizing enzymes. Thus, Yap1 acts as an erythroid regulator that coordinates the metabolic status with the proliferation of erythroid progenitors to promote stress erythropoiesis.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/physiology ; Alleles ; Animals ; Cell Cycle Proteins/physiology ; Cell Division ; Cells, Cultured ; Enzyme Induction ; Erythroid Precursor Cells/cytology ; Erythroid Precursor Cells/physiology ; Erythropoiesis/physiology ; Gene Deletion ; Gene Expression Profiling ; Gene Expression Regulation ; Mice ; Mice, Inbred C57BL ; RNA, Messenger/biosynthesis ; Radiation Chimera ; Radiation Tolerance ; Recombinant Proteins/metabolism ; Regeneration/physiology ; Spleen/cytology ; Stress, Physiological/genetics ; Transcription Factors/genetics
Chemical Substances	Adaptor Proteins, Signal Transducing ; Cell Cycle Proteins ; RNA, Messenger ; Recombinant Proteins ; Transcription Factors ; YAP1 protein, human ; Yap1 protein, mouse
Language	English
Publishing date	2019-11-19
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	185107-x
ISSN	1873-2399 ; 0531-5573 ; 0301-472X
ISSN (online)	1873-2399
ISSN	0531-5573 ; 0301-472X
DOI	10.1016/j.exphem.2019.11.002
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Article: Dynamics of Uncrystallized Water, Ice, and Hydrated Polymer in Partially Crystallized Poly(vinylpyrrolidone)–Water Mixtures

Fujii, Mitsuki / Sasaki, Kaito / Matsui, Yurika / Inoue, Shiori / Kita, Rio / Shinyashiki, Naoki / Yagihara, Shin

Journal of physical chemistry. 2020 Feb. 02, v. 124, no. 8

2020

Abstract: In this study, we investigated the cooperative molecular dynamics of poly(vinylpyrrolidone) (PVP), ice, and uncrystallized water (UCW) in partially crystallized PVP–water mixtures by means of broadband dielectric spectroscopy. Three relaxation processes, ...

Abstract	In this study, we investigated the cooperative molecular dynamics of poly(vinylpyrrolidone) (PVP), ice, and uncrystallized water (UCW) in partially crystallized PVP–water mixtures by means of broadband dielectric spectroscopy. Three relaxation processes, denoted I, II, and III, were observed at temperatures ranging from immediately below the crystallization temperature (Tc) to approximately 200 K. At temperatures of 173–193 K, processes I and II cannot be distinguished. Below 168 K, process II separates into two processes: process IV at higher frequencies and process V at lower frequencies. Process I contributes to process V. In partially crystallized mixtures, process I originates from UCW in an uncrystallized phase with PVP. Process II is attributed to ice in the mixture, with a relaxation time that is 2 orders of magnitude smaller than that of pure ice. The concentration dependence of the strength of process II and the relaxation time relative to that of ice in bovine serum albumin (BSA)–water and gelatin–water mixtures strongly support this conclusion. Observation of processes IV and V indicates the presence of multiple ice relaxation processes. Process III is attributed to the α process of PVP in the uncrystallized phase in 40 and 50 wt % PVP mixtures. For mixtures with 30 wt % PVP or less, process III is attributed not only to the α process of PVP but also to interfacial polarization.
Keywords	bovine serum albumin ; crystallization ; dielectric spectroscopy ; ice ; molecular dynamics ; polymers ; temperature
Language	English
Dates of publication	2020-0202
Size	p. 1521-1530.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.9b11552
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Article ; Online: Dynamics of Uncrystallized Water, Ice, and Hydrated Polymer in Partially Crystallized Poly(vinylpyrrolidone)-Water Mixtures.

Fujii, Mitsuki / Sasaki, Kaito / Matsui, Yurika / Inoue, Shiori / Kita, Rio / Shinyashiki, Naoki / Yagihara, Shin

The journal of physical chemistry. B

2020 Volume 124, Issue 8, Page(s) 1521–1530

Abstract: In this study, we investigated the cooperative molecular dynamics of poly(vinylpyrrolidone) (PVP), ice, and uncrystallized water (UCW) in partially crystallized PVP-water mixtures by means of broadband dielectric spectroscopy. Three relaxation processes, ...

Abstract	In this study, we investigated the cooperative molecular dynamics of poly(vinylpyrrolidone) (PVP), ice, and uncrystallized water (UCW) in partially crystallized PVP-water mixtures by means of broadband dielectric spectroscopy. Three relaxation processes, denoted I, II, and III, were observed at temperatures ranging from immediately below the crystallization temperature (
Language	English
Publishing date	2020-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.9b11552
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Article ; Online: SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development.

Matsui, Yurika / Djekidel, Mohamed Nadhir / Lindsay, Katherine / Samir, Parimal / Connolly, Nina / Wu, Gang / Yang, Xiaoyang / Fan, Yiping / Xu, Beisi / Peng, Jamy C

Nature communications

2023 Volume 14, Issue 1, Page(s) 4754

Abstract: Stem cell survival versus death is a developmentally programmed process essential for morphogenesis, sizing, and quality control of genome integrity and cell fates. Cell death is pervasive during development, but its programming is little known. Here, we ...

Abstract	Stem cell survival versus death is a developmentally programmed process essential for morphogenesis, sizing, and quality control of genome integrity and cell fates. Cell death is pervasive during development, but its programming is little known. Here, we report that Smad nuclear interacting protein 1 (SNIP1) promotes neural progenitor cell survival and neurogenesis and is, therefore, integral to brain development. The SNIP1-depleted brain exhibits dysplasia with robust induction of caspase 9-dependent apoptosis. Mechanistically, SNIP1 regulates target genes that promote cell survival and neurogenesis, and its activities are influenced by TGFβ and NFκB signaling pathways. Further, SNIP1 facilitates the genomic occupancy of Polycomb complex PRC2 and instructs H3K27me3 turnover at target genes. Depletion of PRC2 is sufficient to reduce apoptosis and brain dysplasia and to partially restore genetic programs in the SNIP1-depleted brain in vivo. These findings suggest a loci-specific regulation of PRC2 and H3K27 marks to toggle cell survival and death in the developing brain.
MeSH term(s)	Humans ; Intracellular Signaling Peptides and Proteins ; RNA-Binding Proteins ; Signal Transduction/physiology ; NF-kappa B ; Hyperplasia ; Brain
Chemical Substances	Intracellular Signaling Peptides and Proteins ; RNA-Binding Proteins ; NF-kappa B ; SNIP1 protein, human
Language	English
Publishing date	2023-08-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40487-4
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Article ; Online: Dual Role of a C-Terminally Truncated Isoform of Large Tumor Suppressor Kinase 1 in the Regulation of Hippo Signaling and Tissue Growth.

Matsui, Yurika / Zhang, Yifan / Paulson, Robert F / Lai, Zhi-Chun

DNA and cell biology

2018 Volume 38, Issue 1, Page(s) 91–106

Abstract: The considerable amount of experimental evidence has defined the Hippo pathway as a tumor suppressive pathway and increased expression and/or activity of its oncogenic effectors is frequently observed in cancer. However, clinical studies have failed to ... ...

Abstract	The considerable amount of experimental evidence has defined the Hippo pathway as a tumor suppressive pathway and increased expression and/or activity of its oncogenic effectors is frequently observed in cancer. However, clinical studies have failed to attribute cancer development and progression to mutations in the pathway. In explaining this conundrum, we investigated the expression and functions of a C-terminally truncated isoform of large tumor suppressor kinase 1 (LATS1) called short LATS1 (sLATS1) in human cell lines and Drosophila. Intriguingly, through overexpression of sLATS1, we demonstrated that sLATS1 either activates or suppresses the activity of Yes-associated protein (YAP), one of the effectors of the Hippo pathway, in a cell type-specific manner. The activation is mediated through inhibition of full-length LATS1, whereas suppression of YAP is accomplished through sLATS1-YAP interaction. In HEK293T cells, the former mechanism may affect the cellular response more dominantly, whereas in U2OS cells and developing tissues in Drosophila, the latter mechanism may be solely carried out. Finally, to find the clinical relevance of this molecule, we examined the expression of sLATS1 in breast cancer patients. The transcriptome analysis showed that the ratio of sLATS1 to LATS1 was increased in tumor tissues comparing to their adjacent normal tissues.
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Blotting, Western ; Breast Neoplasms/metabolism ; Carcinogenesis/metabolism ; Cell Culture Techniques ; Cell Fractionation ; Cell Proliferation/genetics ; Drosophila ; Drosophila Proteins/metabolism ; Female ; Flow Cytometry ; Fluorescent Antibody Technique ; HEK293 Cells ; Humans ; Immunoprecipitation ; Nuclear Proteins/metabolism ; Phosphoproteins/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Real-Time Polymerase Chain Reaction ; Signal Transduction ; Trans-Activators/metabolism ; Transcription Factors
Chemical Substances	Adaptor Proteins, Signal Transducing ; Drosophila Proteins ; Nuclear Proteins ; Phosphoproteins ; Trans-Activators ; Transcription Factors ; YAP1 protein, human ; Yki protein, Drosophila ; LATS1 protein, human (EC 2.7.1.-) ; Hippo protein, human (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2018-11-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1024454-2
ISSN	1557-7430 ; 0198-0238 ; 1044-5498
ISSN (online)	1557-7430
ISSN	0198-0238 ; 1044-5498
DOI	10.1089/dna.2018.4340
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Zs.A 2061: Show issues

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