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Article: Intracellular Lactate Dynamics Reveal the Metabolic Diversity of

Price, Matthew S / Moore, Travis I / Venkatachalam, Kartik

bioRxiv : the preprint server for biology

2024

Abstract: Lactate, an intermediary between glycolysis and mitochondrial oxidative phosphorylation, reflects the metabolic state of neurons. Here, we utilized a genetically-encoded lactate FRET biosensor to uncover subpopulations of distinct metabolic states ... ...

Abstract	Lactate, an intermediary between glycolysis and mitochondrial oxidative phosphorylation, reflects the metabolic state of neurons. Here, we utilized a genetically-encoded lactate FRET biosensor to uncover subpopulations of distinct metabolic states among
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.26.582095
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Article ; Online: Publisher Correction: NDUFS4 regulates cristae remodeling in diabetic kidney disease.

Mise, Koki / Long, Jianyin / Galvan, Daniel L / Ye, Zengchun / Fan, Guizhen / Sharma, Rajesh / Serysheva, Irina I / Moore, Travis I / Jeter, Collene R / Anna Zal, M / Araki, Motoo / Wada, Jun / Schumacker, Paul T / Chang, Benny H / Danesh, Farhad R

Nature communications

2024 Volume 15, Issue 1, Page(s) 3022

Language	English
Publishing date	2024-04-08
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/s41467-024-47414-1
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Article ; Online: NDUFS4 regulates cristae remodeling in diabetic kidney disease.

Nature communications

2024 Volume 15, Issue 1, Page(s) 1965

Abstract: The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney ... ...

Abstract	The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generate diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that conditional male mice with genetic overexpression of Ndufs4 exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping protein STOML2 in linking NDUFS4 with improved cristae morphology. Together, we provide the evidence on the central role of NDUFS4 as a regulator of cristae remodeling and mitochondrial function in kidney podocytes. We propose that targeting NDUFS4 represents a promising approach to slow the progression of DKD.
MeSH term(s)	Male ; Animals ; Mice ; Diabetic Nephropathies/genetics ; Diabetes Mellitus, Experimental/genetics ; Mitochondrial Membranes ; Kidney ; Mitochondria ; Electron Transport Complex I/genetics
Chemical Substances	Ndufs4 protein, mouse ; Electron Transport Complex I (EC 7.1.1.2)
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46366-w
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Article: Unveiling the Intercompartmental Signaling Axis: Mitochondrial to ER Stress Response (MERSR) and its Impact on Proteostasis.

Li, Jeson J / Xin, Nan / Yang, Chunxia / Tavizon, Larissa A / Hong, Ruth / Moore, Travis I / Tharyan, Rebecca George / Antebi, Adam / Kim, Hyun-Eui

bioRxiv : the preprint server for biology

2023

Abstract: Maintaining protein homeostasis is essential for cellular health. During times of proteotoxic stress, cells deploy unique defense mechanisms to achieve resolution. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress ... ...

Abstract	Maintaining protein homeostasis is essential for cellular health. During times of proteotoxic stress, cells deploy unique defense mechanisms to achieve resolution. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress Response (MCSR), a unique stress response activated by the perturbation of mitochondrial proteostasis, which ultimately results in the improvement of proteostasis in the cytosol. Here, we found that this signaling axis also influences the unfolded protein response of the endoplasmic reticulum (UPR
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.07.556674
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Article: NDUFS4 Regulates Cristae Remodeling in Diabetic Kidney Disease.

Mise, Koki / Long, Jianyin / Galvan, Daniel L / Ye, Zengchun / Fan, Guizhen / Serysheva, Irina I / Moore, Travis I / Wada, Jun / Schumacker, Paul T / Chang, Benny H / Danesh, Farhad R

Research square

2023

Abstract	The mitochondrial electron transport chain (ETC) is a highly adaptive process to meet metabolic demands of the cell, and its dysregulation has been associated with diverse clinical pathologies. However, the role and nature of impaired ETC in kidney diseases remains poorly understood. Here, we generated diabetic mice with podocyte-specific overexpression of Ndufs4, an accessory subunit of mitochondrial complex I, as a model to investigate the role of ETC integrity in diabetic kidney disease (DKD). We find that these conditional mice exhibit significant improvements in cristae morphology, mitochondrial dynamics, and albuminuria. By coupling proximity labeling with super-resolution imaging, we also identify the role of cristae shaping proteins in linking NDUFS4 with improved cristae morphology. Taken together, we discover the central role of NDUFS4 as a powerful regulator of cristae remodeling, respiratory supercomplexes assembly, and mitochondrial ultrastructure
Language	English
Publishing date	2023-06-30
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3070079/v1
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Article ; Online: Measuring Integrin Conformational Change on the Cell Surface with Super-Resolution Microscopy.

Moore, Travis I / Aaron, Jesse / Chew, Teng-Leong / Springer, Timothy A

Cell reports

2018 Volume 22, Issue 7, Page(s) 1903–1912

Abstract: We use super-resolution interferometric photoactivation and localization microscopy (iPALM) and a constrained photoactivatable fluorescent protein integrin fusion to measure the displacement of the head of integrin lymphocyte function-associated 1 (LFA-1) ...

Abstract	We use super-resolution interferometric photoactivation and localization microscopy (iPALM) and a constrained photoactivatable fluorescent protein integrin fusion to measure the displacement of the head of integrin lymphocyte function-associated 1 (LFA-1) resulting from integrin conformational change on the cell surface. We demonstrate that the distance of the LFA-1 head increases substantially between basal and ligand-engaged conformations, which can only be explained at the molecular level by integrin extension. We further demonstrate that one class of integrin antagonist maintains the bent conformation, while another antagonist class induces extension. Our molecular scale measurements on cell-surface LFA-1 are in excellent agreement with distances derived from crystallographic and electron microscopy structures of bent and extended integrins. Our distance measurements are also in excellent agreement with a previous model of LFA-1 bound to ICAM-1 derived from the orientation of LFA-1 on the cell surface measured using fluorescence polarization microscopy.
MeSH term(s)	Allosteric Regulation ; Cell Adhesion ; Cell Membrane/metabolism ; Cell Movement ; Fibronectins/metabolism ; Fluorescent Dyes/metabolism ; HEK293 Cells ; Humans ; Integrins/chemistry ; Integrins/metabolism ; Intercellular Adhesion Molecule-1/metabolism ; Jurkat Cells ; Lymphocyte Function-Associated Antigen-1/metabolism ; Microscopy/methods ; Models, Biological ; Protein Conformation ; Recombinant Fusion Proteins/metabolism
Chemical Substances	Fibronectins ; Fluorescent Dyes ; Integrins ; Lymphocyte Function-Associated Antigen-1 ; Recombinant Fusion Proteins ; Intercellular Adhesion Molecule-1 (126547-89-5)
Language	English
Publishing date	2018-03-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2018.01.062
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Article ; Online: Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization.

Zhu, Xiaoyu / Qi, Chuangye / Wang, Ruoyu / Lee, Joo-Hyung / Shao, Jiaofang / Bei, Lanxin / Xiong, Feng / Nguyen, Phuoc T / Li, Guojie / Krakowiak, Joanna / Koh, Su-Pin / Simon, Lukas M / Han, Leng / Moore, Travis I / Li, Wenbo

Cell reports

2022 Volume 41, Issue 5, Page(s) 111576

Abstract: The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct ... ...

Abstract	The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.
MeSH term(s)	Humans ; Nuclear Pore Complex Proteins/genetics ; Nuclear Proteins/genetics ; Transcription Factors/genetics ; Nuclear Pore ; Genome ; Chromatin ; Cell Cycle Proteins/genetics
Chemical Substances	Nuclear Pore Complex Proteins ; Nuclear Proteins ; Transcription Factors ; Chromatin ; BRD4 protein, human ; Cell Cycle Proteins
Language	English
Publishing date	2022-10-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111576
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Article: Alternative cell polarity behaviours arise from changes in G-protein spatial dynamics.

Chou, Ching-Shan / Moore, Travis I / Nie, Qing / Yi, Tau-Mu

IET systems biology

2015 Volume 9, Issue 2, Page(s) 52–63

Abstract: Yeast cells form a single mating projection when exposed to mating pheromone, a classic example of cell polarity. Prolonged treatment with pheromone or specific mutations results in alternative cell polarity behaviours. The authors performed mathematical ...

Abstract	Yeast cells form a single mating projection when exposed to mating pheromone, a classic example of cell polarity. Prolonged treatment with pheromone or specific mutations results in alternative cell polarity behaviours. The authors performed mathematical modelling to investigate these unusual cell morphologies from the perspective of balancing spatial amplification (i.e. positive feedback that localises components) with spatial tracking (i.e. negative feedback that allows sensing of gradient). First, they used generic models of cell polarity to explore different cell polarity behaviours that arose from changes in the model spatial dynamics. By exploring the positive and negative feedback loops in each stage of a two-stage model, they simulated a variety of cell morphologies including single bending projections, single straight projections, periodic multiple projections and simultaneous double projections. In the second half of the study, they used a two-stage mechanistic model of yeast cell polarity focusing on G-protein signalling to integrate the modelling results more closely with the authors' previously published experimental observations. In summary, the combination of modelling and experiments describes how yeast cells exhibit a diversity of cell morphologies arising from two-stage G-protein signalling dynamics modulated by positive and negative feedbacks.
MeSH term(s)	Adaptor Proteins, Signal Transducing/physiology ; Cell Polarity/physiology ; Computer Simulation ; Feedback, Physiological/physiology ; GTP-Binding Proteins/physiology ; Mechanotransduction, Cellular/physiology ; Models, Biological ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/physiology
Chemical Substances	Adaptor Proteins, Signal Transducing ; Saccharomyces cerevisiae Proteins ; BEM1 protein, S cerevisiae (146706-23-2) ; GTP-Binding Proteins (EC 3.6.1.-)
Language	English
Publishing date	2015-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1751-8849
ISSN	1751-8849
DOI	10.1049/iet-syb.2013.0018
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Article: Signaling regulated endocytosis and exocytosis lead to mating pheromone concentration dependent morphologies in yeast

Chou, Ching-Shan / Moore, Travis I / Chang, Steven D / Nie, Qing / Yi, Tau-Mu

FEBS letters. 2012 Nov. 30, v. 586, no. 23

2012

Abstract: Polarized cell morphogenesis requires actin cytoskeleton rearrangement for polarized transport of proteins, organelles and secretory vesicles, which fundamentally underlies cell differentiation and behavior. During yeast mating, Saccharomyces cerevisiae ... ...

Abstract	Polarized cell morphogenesis requires actin cytoskeleton rearrangement for polarized transport of proteins, organelles and secretory vesicles, which fundamentally underlies cell differentiation and behavior. During yeast mating, Saccharomyces cerevisiae responds to extracellular pheromone gradients by extending polarized projections, which are likely maintained through vesicle transport to (exocytosis) and from (endocytosis) the membrane. We experimentally demonstrate that the projection morphology is pheromone concentration-dependent, and propose the underlying mechanism through mathematical modeling. The inclusion of membrane flux and dynamically evolving cell boundary into our yeast mating signaling model shows good agreement with experimental measurements, and provides a plausible explanation for pheromone-induced cell morphology.
Keywords	Saccharomyces cerevisiae ; cell differentiation ; endocytosis ; exocytosis ; mathematical models ; microfilaments ; morphogenesis ; pheromones ; secretory granules ; yeasts
Language	English
Dates of publication	2012-1130
Size	p. 4208-4214.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2012.10.024
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Yeast G-proteins mediate directional sensing and polarization behaviors in response to changes in pheromone gradient direction.

Moore, Travis I / Tanaka, Hiromasa / Kim, Hyung Joon / Jeon, Noo Li / Yi, Tau-Mu

Molecular biology of the cell

2012 Volume 24, Issue 4, Page(s) 521–534

Abstract: Yeast cells polarize by projecting up mating pheromone gradients, a classic cell polarity behavior. However, these chemical gradients may shift direction. We examine how yeast cells sense and respond to a 180(o) switch in the direction of ... ...

Abstract	Yeast cells polarize by projecting up mating pheromone gradients, a classic cell polarity behavior. However, these chemical gradients may shift direction. We examine how yeast cells sense and respond to a 180(o) switch in the direction of microfluidically generated pheromone gradients. We identify two behaviors: at low concentrations of α-factor, the initial projection grows by bending, whereas at high concentrations, cells form a second projection toward the new source. Mutations that increase heterotrimeric G-protein activity expand the bending-growth morphology to high concentrations; mutations that increase Cdc42 activity result in second projections at low concentrations. Gradient-sensing projection bending requires interaction between Gβγ and Cdc24, whereas gradient-nonsensing projection extension is stimulated by Bem1 and hyperactivated Cdc42. Of interest, a mutation in Gα affects both bending and extension. Finally, we find a genetic perturbation that exhibits both behaviors. Overexpression of the formin Bni1, a component of the polarisome, makes both bending-growth projections and second projections at low and high α-factor concentrations, suggesting a role for Bni1 downstream of the heterotrimeric G-protein and Cdc42 during gradient sensing and response. Thus we demonstrate that G-proteins modulate in a ligand-dependent manner two fundamental cell-polarity behaviors in response to gradient directional change.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cell Polarity ; Chemotaxis/drug effects ; Gene Expression Regulation, Fungal/drug effects ; Guanine Nucleotide Exchange Factors/genetics ; Guanine Nucleotide Exchange Factors/metabolism ; Mating Factor ; Microfilament Proteins/genetics ; Microfilament Proteins/metabolism ; Microfluidics ; Mutation ; Peptides/metabolism ; Peptides/pharmacology ; Pheromones/metabolism ; Pheromones/pharmacology ; Protein Binding ; Saccharomyces cerevisiae/drug effects ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction/drug effects ; cdc42 GTP-Binding Protein, Saccharomyces cerevisiae/genetics ; cdc42 GTP-Binding Protein, Saccharomyces cerevisiae/metabolism
Chemical Substances	Adaptor Proteins, Signal Transducing ; Bni1 protein, S cerevisiae ; CDC24 protein, S cerevisiae ; Cell Cycle Proteins ; Guanine Nucleotide Exchange Factors ; Microfilament Proteins ; Peptides ; Pheromones ; Saccharomyces cerevisiae Proteins ; BEM1 protein, S cerevisiae (146706-23-2) ; Mating Factor (61194-02-3) ; cdc42 GTP-Binding Protein, Saccharomyces cerevisiae (EC 3.6.5.2)
Language	English
Publishing date	2012-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E12-10-0739
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