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Article: Potency Assay Development: A Keystone for Clinical Use.

Torggler, Raffaela / Margreiter, Eva / Marksteiner, Rainer / Thurner, Marco

Advances in experimental medicine and biology

2023 Volume 1420, Page(s) 13–28

Abstract: Potency can be described as the quantitative measure of biological activity, that is, the ability of an Advanced Therapy Medicinal Product (ATMP) to elicit the intended effect necessary for clinical efficacy. Potency testing is part of the quality ... ...

Abstract	Potency can be described as the quantitative measure of biological activity, that is, the ability of an Advanced Therapy Medicinal Product (ATMP) to elicit the intended effect necessary for clinical efficacy. Potency testing is part of the quality control strategy necessary for batch release and is required for market approval application of an ATMP. Thus, it is crucial to develop a reliable and accurate potency assay. As a prerequisite for potency assay development, it is essential to define the mode of action of the product and thereby also the relevant biological activity that should be measured. The establishment of a potency assay should be initiated already during early product development followed by its progressive implementation into an ATMP's manufacturing, quality control and release process. Potency testing is indispensable for clinical use with a wide range of applications. A potency assay is a valuable tool to determine the product's stability, detect the impact of changes in the manufacturing process on the product, demonstrate quality and manufacturing consistency from batch to batch, estimate clinical efficacy and define the effective dose. This chapter describes the requirements and challenges to be considered for potency assay development and the importance of a well-established potency assay for clinical use.
MeSH term(s)	Quality Control ; Treatment Outcome
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Journal Article
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-031-30040-0_2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Decoding the function of Atg13 phosphorylation reveals a role of Atg11 in bulk autophagy initiation.

Bhattacharya, Anuradha / Torggler, Raffaela / Reiter, Wolfgang / Romanov, Natalie / Licheva, Mariya / Ciftci, Akif / Mari, Muriel / Kolb, Lena / Kaiser, Dominik / Reggiori, Fulvio / Ammerer, Gustav / Hollenstein, David M / Kraft, Claudine

EMBO reports

2024 Volume 25, Issue 2, Page(s) 813–831

Abstract: Autophagy is initiated by the assembly of multiple autophagy-related proteins that form the phagophore assembly site where autophagosomes are formed. Atg13 is essential early in this process, and a hub of extensive phosphorylation. How these multiple ... ...

Abstract	Autophagy is initiated by the assembly of multiple autophagy-related proteins that form the phagophore assembly site where autophagosomes are formed. Atg13 is essential early in this process, and a hub of extensive phosphorylation. How these multiple phosphorylations contribute to autophagy initiation, however, is not well understood. Here we comprehensively analyze the role of phosphorylation events on Atg13 during nutrient-rich conditions and nitrogen starvation. We identify and functionally characterize 48 in vivo phosphorylation sites on Atg13. By generating reciprocal mutants, which mimic the dephosphorylated active and phosphorylated inactive state of Atg13, we observe that disrupting the dynamic regulation of Atg13 leads to insufficient or excessive autophagy, which are both detrimental to cell survival. We furthermore demonstrate an involvement of Atg11 in bulk autophagy even during nitrogen starvation, where it contributes together with Atg1 to the multivalency that drives phase separation of the phagophore assembly site. These findings reveal the importance of post-translational regulation on Atg13 early during autophagy initiation, which provides additional layers of regulation to control bulk autophagy activity and integrate cellular signals.
MeSH term(s)	Phosphorylation ; Autophagy/physiology ; Autophagy-Related Proteins/genetics ; Autophagy-Related Proteins/metabolism ; Signal Transduction ; Nitrogen ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Autophagy-Related Proteins ; Nitrogen (N762921K75) ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.1038/s44319-023-00055-9
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Article: Assays to Monitor Autophagy in Saccharomyces cerevisiae.

Torggler, Raffaela / Papinski, Daniel / Kraft, Claudine

Cells

2017 Volume 6, Issue 3

Abstract: Autophagy is an intracellular process responsible for the degradation and recycling of cytoplasmic components. It selectively removes harmful cellular material and enables the cell to survive starvation by mobilizing nutrients via the bulk degradation of ...

Abstract	Autophagy is an intracellular process responsible for the degradation and recycling of cytoplasmic components. It selectively removes harmful cellular material and enables the cell to survive starvation by mobilizing nutrients via the bulk degradation of cytoplasmic components. While research over the last decades has led to the discovery of the key factors involved in autophagy, the pathway is not yet completely understood. The first studies of autophagy on a molecular level were conducted in the yeast
Language	English
Publishing date	2017-07-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661518-6
ISSN	2073-4409
ISSN	2073-4409
DOI	10.3390/cells6030023
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Article ; Online: Assays to Monitor Autophagy in Saccharomyces cerevisiae

Raffaela Torggler / Daniel Papinski / Claudine Kraft

Cells, Vol 6, Iss 3, p

2017 Volume 23

Abstract	Autophagy is an intracellular process responsible for the degradation and recycling of cytoplasmic components. It selectively removes harmful cellular material and enables the cell to survive starvation by mobilizing nutrients via the bulk degradation of cytoplasmic components. While research over the last decades has led to the discovery of the key factors involved in autophagy, the pathway is not yet completely understood. The first studies of autophagy on a molecular level were conducted in the yeast Saccharomyces cerevisiae. Building up on these studies, many homologs have been found in higher eukaryotes. Yeast remains a highly relevant model organism for studying autophagy, with a wide range of established methods to elucidate the molecular details of the autophagy pathway. In this review, we provide an overview of methods to study both selective and bulk autophagy, including intermediate steps in the yeast Saccharomyces cerevisiae. We compare different assays, discuss their advantages and limitations and list potential applications.
Keywords	yeast ; bulk autophagy ; Cvt pathway ; selective autophagy ; PAS ; autophagosome ; autophagic body ; iPass ; M-Track ; Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2017-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion.

Bas, Levent / Papinski, Daniel / Licheva, Mariya / Torggler, Raffaela / Rohringer, Sabrina / Schuschnig, Martina / Kraft, Claudine

The Journal of cell biology

2018 Volume 217, Issue 10, Page(s) 3656–3669

Abstract: Autophagy mediates the bulk degradation of cytoplasmic material, particularly during starvation. Upon the induction of autophagy, autophagosomes form a sealed membrane around cargo, fuse with a lytic compartment, and release the cargo for degradation. ... ...

Abstract	Autophagy mediates the bulk degradation of cytoplasmic material, particularly during starvation. Upon the induction of autophagy, autophagosomes form a sealed membrane around cargo, fuse with a lytic compartment, and release the cargo for degradation. The mechanism of autophagosome-vacuole fusion is poorly understood, although factors that mediate other cellular fusion events have been implicated. In this study, we developed an in vitro reconstitution assay that enables systematic discovery and dissection of the players involved in autophagosome-vacuole fusion. We found that this process requires the Atg14-Vps34 complex to generate PI3P and thus recruit the Ypt7 module to autophagosomes. The HOPS-tethering complex, recruited by Ypt7, is required to prepare SNARE proteins for fusion. Furthermore, we discovered that fusion requires the R-SNARE Ykt6 on the autophagosome, together with the Q-SNAREs Vam3, Vam7, and Vti1 on the vacuole. These findings shed new light on the mechanism of autophagosome-vacuole fusion and reveal that the R-SNARE Ykt6 is required for this process.
MeSH term(s)	Autophagosomes/metabolism ; Class III Phosphatidylinositol 3-Kinases/genetics ; Class III Phosphatidylinositol 3-Kinases/metabolism ; Membrane Fusion ; Qa-SNARE Proteins/genetics ; Qa-SNARE Proteins/metabolism ; Qb-SNARE Proteins/genetics ; Qb-SNARE Proteins/metabolism ; R-SNARE Proteins/genetics ; R-SNARE Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Synaptosomal-Associated Protein 25/genetics ; Synaptosomal-Associated Protein 25/metabolism ; Vacuoles/genetics ; Vacuoles/metabolism ; rab GTP-Binding Proteins/genetics ; rab GTP-Binding Proteins/metabolism
Chemical Substances	Qa-SNARE Proteins ; Qb-SNARE Proteins ; R-SNARE Proteins ; Saccharomyces cerevisiae Proteins ; Synaptosomal-Associated Protein 25 ; VAM3 protein, S cerevisiae ; VAM7 protein, S cerevisiae ; VTI1 protein, S cerevisiae ; YKT6 protein, S cerevisiae ; Class III Phosphatidylinositol 3-Kinases (EC 2.7.1.137) ; YPT7 protein, S cerevisiae (EC 3.6.1.-) ; rab GTP-Binding Proteins (EC 3.6.5.2)
Language	English
Publishing date	2018-08-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201804028
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Article ; Online: Vac8 spatially confines autophagosome formation at the vacuole in

Hollenstein, David M / Gómez-Sánchez, Rubén / Ciftci, Akif / Kriegenburg, Franziska / Mari, Muriel / Torggler, Raffaela / Licheva, Mariya / Reggiori, Fulvio / Kraft, Claudine

Journal of cell science

2019 Volume 132, Issue 22

Abstract: Autophagy is initiated by the formation of a phagophore assembly site (PAS), the precursor of autophagosomes. In mammals, autophagosome formation sites form throughout the cytosol in specialized subdomains of the endoplasmic reticulum (ER). In yeast, the ...

Abstract	Autophagy is initiated by the formation of a phagophore assembly site (PAS), the precursor of autophagosomes. In mammals, autophagosome formation sites form throughout the cytosol in specialized subdomains of the endoplasmic reticulum (ER). In yeast, the PAS is also generated close to the ER, but always in the vicinity of the vacuole. How the PAS is anchored to the vacuole and the functional significance of this localization are unknown. Here, we investigated the role of the PAS-vacuole connection for bulk autophagy in the yeast
MeSH term(s)	Autophagosomes/metabolism ; Autophagy ; Membrane Proteins/metabolism ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Vacuoles/metabolism ; Vesicular Transport Proteins/metabolism
Chemical Substances	Membrane Proteins ; Saccharomyces cerevisiae Proteins ; VAC8 protein, S cerevisiae ; Vesicular Transport Proteins
Language	English
Publishing date	2019-11-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.235002
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Article: Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole

Torggler, Raffaela / Andrea Brezovich / Claudine Kraft / Daniel Papinski / David Schweida / Levent Bas / Martina Schuschnig / Sabrina Rohringer / Tamara Matzhold / Thaddäus Pfaffenwimmer / Thorsten Brach

Molecular cell. 2016 Oct. 20, v. 64, no. 2

2016

Abstract: Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, ... ...

Abstract	Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation.
Keywords	autophagy ; dimerization ; receptors ; scaffolding proteins ; space and time ; vacuoles
Language	English
Dates of publication	2016-1020
Size	p. 221-235.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.09.008
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Article ; Online: The Arrhythmogenic Calmodulin Mutation D129G Dysregulates Cell Growth, Calmodulin-dependent Kinase II Activity, and Cardiac Function in Zebrafish.

Berchtold, Martin W / Zacharias, Triantafyllos / Kulej, Katarzyna / Wang, Kevin / Torggler, Raffaela / Jespersen, Thomas / Chen, Jau-Nian / Larsen, Martin R / la Cour, Jonas M

The Journal of biological chemistry

2016 Volume 291, Issue 52, Page(s) 26636–26646

Abstract: Calmodulin (CaM) is a ... ...

Abstract	Calmodulin (CaM) is a Ca
MeSH term(s)	Animals ; Arrhythmias, Cardiac/genetics ; Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism ; Calmodulin/chemistry ; Calmodulin/genetics ; Calmodulin/metabolism ; Cell Proliferation/genetics ; Cells, Cultured ; Humans ; Long QT Syndrome/etiology ; Long QT Syndrome/metabolism ; Long QT Syndrome/pathology ; Mutation/genetics ; Myocytes, Cardiac/metabolism ; Myocytes, Cardiac/pathology ; Phosphorylation ; Protein Conformation ; Tachycardia, Ventricular/etiology ; Tachycardia, Ventricular/metabolism ; Tachycardia, Ventricular/pathology ; Zebrafish/genetics ; Zebrafish/growth & development ; Zebrafish/metabolism
Chemical Substances	Calmodulin ; Calcium-Calmodulin-Dependent Protein Kinase Type 2 (EC 2.7.11.17) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2016-11-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M116.758680
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Article ; Online: Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole.

Torggler, Raffaela / Papinski, Daniel / Brach, Thorsten / Bas, Levent / Schuschnig, Martina / Pfaffenwimmer, Thaddäus / Rohringer, Sabrina / Matzhold, Tamara / Schweida, David / Brezovich, Andrea / Kraft, Claudine

Molecular cell

2016 Volume 64, Issue 2, Page(s) 221–235

Abstract	Autophagy is a potent cellular degradation pathway, and its activation needs to be tightly controlled. Cargo receptors mediate selectivity during autophagy by bringing cargo to the scaffold protein Atg11 and, in turn, to the autophagic machinery, including the central autophagy kinase Atg1. Here we show how selective autophagy is tightly regulated in space and time to prevent aberrant Atg1 kinase activation and autophagy induction. We established an induced bypass approach (iPass) that combines genetic deletion with chemically induced dimerization to evaluate the roles of Atg13 and cargo receptors in Atg1 kinase activation and selective autophagy progression. We show that Atg1 activation does not require cargo receptors, cargo-bound Atg11, or Atg13 per se. Rather, these proteins function in two independent pathways that converge to activate Atg1 at the vacuole. This pathway architecture underlies the spatiotemporal control of Atg1 kinase activity, thereby preventing inappropriate autophagosome formation.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Aminopeptidases/genetics ; Aminopeptidases/metabolism ; Autophagy/genetics ; Autophagy-Related Proteins/genetics ; Autophagy-Related Proteins/metabolism ; Gene Expression Regulation, Fungal ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Phagosomes/metabolism ; Protein Kinases/genetics ; Protein Kinases/metabolism ; Protein Multimerization ; Protein Transport ; Receptors, Cell Surface/genetics ; Receptors, Cell Surface/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction ; Vacuoles/metabolism ; Vesicular Transport Proteins/genetics ; Vesicular Transport Proteins/metabolism
Chemical Substances	ATG13 protein, S cerevisiae ; ATG19 protein, S cerevisiae ; Adaptor Proteins, Signal Transducing ; Atg11 protein, S cerevisiae ; Autophagy-Related Proteins ; Receptors, Cell Surface ; Recombinant Fusion Proteins ; Saccharomyces cerevisiae Proteins ; Vesicular Transport Proteins ; Green Fluorescent Proteins (147336-22-9) ; Protein Kinases (EC 2.7.-) ; ATG1 protein, S cerevisiae (EC 2.7.1.-) ; Aminopeptidases (EC 3.4.11.-) ; APE1 protein, S cerevisiae (EC 3.4.11.22)
Language	English
Publishing date	2016-11-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.09.008
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