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Article ; Online: Yapping at the autophagy door? The answer is flowing in the kidney proximal tubule.

Claude-Taupin, Aurore / Terzi, Fabiola / Codogno, Patrice / Dupont, Nicolas

2024 , Page(s) 1–2

Abstract: Shear stress induced by urinary flow stimulates macroautophagy (hereafter referred to as autophagy) in kidney proximal tubule epithelial cells. Autophagy and selective degradation of lipid droplets by lipophagy contribute to tubule homeostasis by the ... ...

Abstract	Shear stress induced by urinary flow stimulates macroautophagy (hereafter referred to as autophagy) in kidney proximal tubule epithelial cells. Autophagy and selective degradation of lipid droplets by lipophagy contribute to tubule homeostasis by the production of ATP and control of epithelial cell size. Autophagy/lipophagy is controlled by a signaling cascade emanating from the primary cilium, localized at the apical side of epithelial cells. Downstream of the primary cilium, AMPK controls mitochondrial biogenesis on the one hand and autophagy/lipophagy on the other hand, which together increase fatty acid production that fuels oxidative phosphorylation to increase energy production. Recently, we reported that the co-transcriptional factors YAP1 and WWTR1/TAZ act downstream of AMPK to control autophagy. In fact, YAP1 and the transcription factor TEAD control the expression of RUBCN/rubicon. Under shear stress, YAP1 is excluded from the nucleus in a SIRT1-dependent manner to favor autophagic flux by downregulating the expression of RUBCN. When simulating
Language	English
Publishing date	2024-02-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2024.2319023
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Article: Common origin and evolution of glycosyltransferases using Dol-P-monosaccharides as donor substrate.

Oriol, Rafael / Martinez-Duncker, Ivan / Chantret, Isabelle / Mollicone, Rosella / Codogno, Patrice

Molecular biology and evolution

2002 Volume 19, Issue 9, Page(s) 1451–1463

Abstract: ... for ALG and PIG enzymes using dolichyl-phospho-monosaccharide (Dol-P-monosaccharide) donors ... glycosyltransferases using Dol-P-monosaccharides as donor substrate have a multispan transmembrane topology ...

Abstract	On the basis of the analysis of 64 glycosyltransferases from 14 species we propose that several successive duplications of a common ancestral gene, followed by divergent evolution, have generated the mannosyltransferases and the glucosyltransferases involved in asparagine-linked glycosylation (ALG) and phosphatidyl-inositol glycan anchor (PIG or GPI), which use lipid-related donor and acceptor substrates. Long and short conserved peptide motifs were found in all enzymes. Conserved and identical amino acid positions were found for the alpha 2/6- and the alpha 3/4-mannosyltransferases and for the alpha 2/3-glucosyltransferases, suggesting unique ancestors for these three superfamilies. The three members of the alpha 2-mannosyltransferase family (ALG9, PIG-B, and SMP3) and the two members of the alpha 3-glucosyltransferase family (ALG6 and ALG8) shared 11 and 30 identical amino acid positions, respectively, suggesting that these enzymes have also originated by duplication and divergent evolution. This model predicts a common genetic origin for ALG and PIG enzymes using dolichyl-phospho-monosaccharide (Dol-P-monosaccharide) donors, which might be related to similar spatial orientation of the hydroxyl acceptors. On the basis of the multiple sequence analysis and the prediction of transmembrane topology we propose that the endoplasmic reticulum glycosyltransferases using Dol-P-monosaccharides as donor substrate have a multispan transmembrane topology with a first large luminal conserved loop containing the long motif and a small cytosolic conserved loop containing the short motif, different from the classical type II glycosyltransferases, which are anchored in the Golgi by a single transmembrane domain.
MeSH term(s)	Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Conserved Sequence ; Dolichol Monophosphate Mannose/chemistry ; Dolichol Monophosphate Mannose/metabolism ; Evolution, Molecular ; Glycosyltransferases/chemistry ; Glycosyltransferases/genetics ; Glycosyltransferases/metabolism ; Humans ; Molecular Sequence Data ; Phylogeny ; Polyisoprenyl Phosphate Monosaccharides/chemistry ; Polyisoprenyl Phosphate Monosaccharides/metabolism ; Protein Conformation ; Sequence Homology, Amino Acid ; Substrate Specificity
Chemical Substances	Polyisoprenyl Phosphate Monosaccharides ; Dolichol Monophosphate Mannose (55598-56-6) ; dolichol-D-glucosylmonophosphate (55607-88-0) ; Glycosyltransferases (EC 2.4.-)
Language	English
Publishing date	2002-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
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Article ; Online: A historical perspective of macroautophagy regulation by biochemical and biomechanical stimuli.

Dupont, Nicolas / Claude-Taupin, Aurore / Codogno, Patrice

FEBS letters

2023 Volume 598, Issue 1, Page(s) 17–31

Abstract: Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates, and organelles. The formation of the autophagosome, a double membrane-bound structure that sequesters cargoes before their delivery to the lysosome, ... ...

Abstract	Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates, and organelles. The formation of the autophagosome, a double membrane-bound structure that sequesters cargoes before their delivery to the lysosome, is regulated by several stimuli in multicellular organisms. Pioneering studies in rat liver showed the importance of amino acids, insulin, and glucagon in controlling macroautophagy. Thereafter, many studies have deciphered the signaling pathways downstream of these biochemical stimuli to control autophagosome formation. Two signaling hubs have emerged: the kinase mTOR, in a complex at the surface of lysosomes which is sensitive to nutrients and hormones; and AMPK, which is sensitive to the cellular energetic status. Besides nutritional, hormonal, and energetic fluctuations, many organs have to respond to mechanical forces (compression, stretching, and shear stress). Recent studies have shown the importance of mechanotransduction in controlling macroautophagy. This regulation engages cell surface sensors, such as the primary cilium, in order to translate mechanical stimuli into biological responses.
MeSH term(s)	Autophagy/physiology ; Macroautophagy ; Mechanotransduction, Cellular ; Autophagosomes/metabolism ; Phagocytosis ; Lysosomes/metabolism
Language	English
Publishing date	2023-10-15
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14744
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Article: Congenital disorders of glycosylation type Ig is defined by a deficiency in dolichyl-P-mannose:Man7GlcNAc2-PP-dolichyl mannosyltransferase.

Chantret, Isabelle / Dupré, Thierry / Delenda, Christophe / Bucher, Stéphanie / Dancourt, Julia / Barnier, Anne / Charollais, Aude / Heron, Delphine / Bader-Meunier, Brigitte / Danos, Olivier / Seta, Nathalie / Durand, Geneviève / Oriol, Rafael / Codogno, Patrice / Moore, Stuart E H

The Journal of biological chemistry

2002 Volume 277, Issue 28, Page(s) 25815–25822

Abstract: ... to the human ortholog of the yeast gene ALG12 that encodes the dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl ...

Abstract	Type I congenital disorders of glycosylation (CDG I) are diseases presenting multisystemic lesions including central and peripheral nervous system deficits. The disease is characterized by under-glycosylated serum glycoproteins and is caused by mutations in genes encoding proteins involved in the stepwise assembly of dolichol-oligosaccharide used for protein N-glycosylation. We report that fibroblasts from a type I CDG patient, born of consanguineous parents, are deficient in their capacity to add the eighth mannose residue onto the lipid-linked oligosaccharide precursor. We have characterized cDNA corresponding to the human ortholog of the yeast gene ALG12 that encodes the dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is thought to accomplish this reaction, and we show that the patient is homozygous for a point mutation (T571G) that causes an amino acid substitution (F142V) in a conserved region of the protein. As the pathological phenotype of the fibroblasts of the patient was largely normalized upon transduction with the wild type gene, we demonstrate that the F142V substitution is the underlying cause of this new CDG, which we suggest be called CDG Ig. Finally, we show that the fibroblasts of the patient are capable of the direct transfer of Man(7)GlcNAc(2) from dolichol onto protein and that this N-linked structure can be glucosylated by UDP-glucose:glycoprotein glucosyltransferase in the endoplasmic reticulum.
MeSH term(s)	Amino Acid Sequence ; Base Sequence ; Carbohydrate Metabolism, Inborn Errors/diagnosis ; Carbohydrate Metabolism, Inborn Errors/enzymology ; Carbohydrate Metabolism, Inborn Errors/genetics ; Cells, Cultured ; DNA Primers ; Expressed Sequence Tags ; Female ; Glycosylation ; Humans ; Infant, Newborn ; Mannosyltransferases/chemistry ; Mannosyltransferases/genetics ; Molecular Sequence Data ; Open Reading Frames ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid
Chemical Substances	DNA Primers ; Mannosyltransferases (EC 2.4.1.-) ; dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichol alpha-1,3-mannosyltransferase (EC 2.4.1.258)
Language	English
Publishing date	2002-04-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M203285200
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Article: A deficiency in dolichyl-P-glucose:Glc1Man9GlcNAc2-PP-dolichyl alpha3-glucosyltransferase defines a new subtype of congenital disorders of glycosylation.

Chantret, Isabelle / Dancourt, Julia / Dupré, Thierry / Delenda, Christophe / Bucher, Stéphanie / Vuillaumier-Barrot, Sandrine / Ogier de Baulny, Hélène / Peletan, Celine / Danos, Olivier / Seta, Nathalie / Durand, Geneviève / Oriol, Rafael / Codogno, Patrice / Moore, Stuart E H

The Journal of biological chemistry

2002 Volume 278, Issue 11, Page(s) 9962–9971

Abstract: ... the cells from the patient to possess only 10-20% normal amounts of mRNA encoding the enzyme, dolichyl-P ...

Abstract	The underlying causes of type I congenital disorders of glycosylation (CDG I) have been shown to be mutations in genes encoding proteins involved in the biosynthesis of the dolichyl-linked oligosaccharide (Glc(3)Man(9)GlcNAc(2)-PP-dolichyl) that is required for protein glycosylation. Here we describe a CDG I patient displaying gastrointestinal problems but no central nervous system deficits. Fibroblasts from this patient accumulate mainly Man(9)GlcNAc(2)-PP-dolichyl, but in the presence of castanospermine, an endoplasmic reticulum glucosidase inhibitor Glc(1)Man(9)GlcNAc(2)-PP-dolichyl predominates, suggesting inefficient addition of the second glucose residue onto lipid-linked oligosaccharide. Northern blot analysis revealed the cells from the patient to possess only 10-20% normal amounts of mRNA encoding the enzyme, dolichyl-P-glucose:Glc(1)Man(9)GlcNAc(2)-PP-dolichyl alpha3-glucosyltransferase (hALG8p), which catalyzes this reaction. Sequencing of hALG8 genomic DNA revealed exon 4 to contain a base deletion in one allele and a base insertion in the other. Both mutations give rise to premature stop codons predicted to generate severely truncated proteins, but because the translation inhibitor emetine was shown to stabilize the hALG8 mRNA from the patient to normal levels, it is likely that both transcripts undergo nonsense-mediated mRNA decay. As the cells from the patient were successfully complemented with wild type hALG8 cDNA, we conclude that these mutations are the underlying cause of this new CDG I subtype that we propose be called CDG Ih.
MeSH term(s)	Alleles ; Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; Blotting, Western ; Carbohydrate Metabolism, Inborn Errors/diagnosis ; Carbohydrate Metabolism, Inborn Errors/enzymology ; Carbohydrate Metabolism, Inborn Errors/genetics ; Cells, Cultured ; Chloroform/pharmacology ; Chromatography, Thin Layer ; Codon, Terminator ; DNA Mutational Analysis ; DNA, Complementary/metabolism ; Fibroblasts/metabolism ; Glucosyltransferases/chemistry ; Glucosyltransferases/metabolism ; Glycosylation ; Humans ; Lipids/chemistry ; Lymphocytes/metabolism ; Molecular Sequence Data ; Mutation ; Oligosaccharides/chemistry ; RNA, Messenger/metabolism ; Signal Transduction ; Time Factors
Chemical Substances	Codon, Terminator ; DNA, Complementary ; Lipids ; Oligosaccharides ; RNA, Messenger ; Chloroform (7V31YC746X) ; ALG8 protein, human (EC 2.4.1.-) ; Glucosyltransferases (EC 2.4.1.-) ; dolichol phosphate glucose-dolichol diphosphate oligosaccharide glucosyltransferase (EC 2.4.1.-)
Language	English
Publishing date	2002-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.M211950200
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Article ; Online: L’auto-digestion est invitée à la table de l’Institut Karolinska - Prix Nobel de Médecine 2016 : Yoshinori Ohsumi.

Codogno, Patrice

Medecine sciences : M/S

2016 Volume 32, Issue 12, Page(s) 1127–1129

Title translation	Self-eating is invited at the Karolinska Institute table.
MeSH term(s)	Autophagy/physiology ; Biomedical Research/history ; History, 21st Century ; Humans ; Japan ; Laboratory Personnel ; Nobel Prize ; Sweden
Language	French
Publishing date	2016-12
Publishing country	France
Document type	Biography ; Historical Article ; Journal Article
ZDB-ID	632733-3
ISSN	1958-5381 ; 0767-0974
ISSN (online)	1958-5381
ISSN	0767-0974
DOI	10.1051/medsci/20163212017
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Article: Autophagy and the primary cilium in cell metabolism: What's upstream?

Claude-Taupin, Aurore / Dupont, Nicolas / Codogno, Patrice

Frontiers in cell and developmental biology

2022 Volume 10, Page(s) 1046248

Abstract: The maintenance of cellular homeostasis in response to extracellular stimuli, i.e., nutrient and hormone signaling, hypoxia, or mechanical forces by autophagy, is vital for the health of various tissues. The primary cilium (PC) is a microtubule-based ... ...

Abstract	The maintenance of cellular homeostasis in response to extracellular stimuli, i.e., nutrient and hormone signaling, hypoxia, or mechanical forces by autophagy, is vital for the health of various tissues. The primary cilium (PC) is a microtubule-based sensory organelle that regulates the integration of several extracellular stimuli. Over the past decade, an interconnection between autophagy and PC has begun to be revealed. Indeed, the PC regulates autophagy and in turn, a selective form of autophagy called ciliophagy contributes to the regulation of ciliogenesis. Moreover, the PC regulates both mitochondrial biogenesis and lipophagy to produce free fatty acids. These two pathways converge to activate oxidative phosphorylation and produce ATP, which is mandatory for cell metabolism and membrane transport. The autophagy-dependent production of energy is fully efficient when the PC senses shear stress induced by fluid flow. In this review, we discuss the cross-talk between autophagy, the PC and physical forces in the regulation of cell biology and physiology.
Language	English
Publishing date	2022-11-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2022.1046248
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Article ; Online: A historical perspective of macroautophagy regulation by biochemical and biomechanical stimuli

Dupont, Nicolas / Claude‐Taupin, Aurore / Codogno, Patrice

FEBS Letters. 2024 Jan., v. 598, no. 1 p.17-31

2024

Abstract: Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates, and organelles. The formation of the autophagosome, a double membrane‐bound structure that sequesters cargoes before their delivery to the lysosome, ... ...

Abstract	Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates, and organelles. The formation of the autophagosome, a double membrane‐bound structure that sequesters cargoes before their delivery to the lysosome, is regulated by several stimuli in multicellular organisms. Pioneering studies in rat liver showed the importance of amino acids, insulin, and glucagon in controlling macroautophagy. Thereafter, many studies have deciphered the signaling pathways downstream of these biochemical stimuli to control autophagosome formation. Two signaling hubs have emerged: the kinase mTOR, in a complex at the surface of lysosomes which is sensitive to nutrients and hormones; and AMPK, which is sensitive to the cellular energetic status. Besides nutritional, hormonal, and energetic fluctuations, many organs have to respond to mechanical forces (compression, stretching, and shear stress). Recent studies have shown the importance of mechanotransduction in controlling macroautophagy. This regulation engages cell surface sensors, such as the primary cilium, in order to translate mechanical stimuli into biological responses.
Keywords	autophagosomes ; biomechanics ; glucagon ; insulin ; liver ; lysosomes ; macroautophagy ; mechanotransduction ; rats ; shear stress
Language	English
Dates of publication	2024-01
Size	p. 17-31.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	REVIEW
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14744
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Article ; Online: Shining light on autophagy.

Codogno, Patrice

Nature reviews. Molecular cell biology

2014 Volume 15, Issue 3, Page(s) 153

MeSH term(s)	Autophagy/physiology ; Autophagy-Related Protein-1 Homolog ; Disease ; Humans ; Intracellular Signaling Peptides and Proteins/physiology ; Protein-Serine-Threonine Kinases/physiology
Chemical Substances	Intracellular Signaling Peptides and Proteins ; Autophagy-Related Protein-1 Homolog (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; ULK1 protein, human (EC 2.7.11.1)
Language	English
Publishing date	2014-02-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2031313-5
ISSN	1471-0080 ; 1471-0072
ISSN (online)	1471-0080
ISSN	1471-0072
DOI	10.1038/nrm3751
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Zs.A 5446: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Links between autophagy and tissue mechanics.

Claude-Taupin, Aurore / Codogno, Patrice / Dupont, Nicolas

Journal of cell science

2021 Volume 134, Issue 17

Abstract: Physical constraints, such as compression, shear stress, stretching and tension, play major roles during development, tissue homeostasis, immune responses and pathologies. Cells and organelles also face mechanical forces during migration and ... ...

Abstract	Physical constraints, such as compression, shear stress, stretching and tension, play major roles during development, tissue homeostasis, immune responses and pathologies. Cells and organelles also face mechanical forces during migration and extravasation, and investigations into how mechanical forces are translated into a wide panel of biological responses, including changes in cell morphology, membrane transport, metabolism, energy production and gene expression, is a flourishing field. Recent studies demonstrate the role of macroautophagy in the integration of physical constraints. The aim of this Review is to summarize and discuss our knowledge of the role of macroautophagy in controlling a large panel of cell responses, from morphological and metabolic changes, to inflammation and senescence, for the integration of mechanical forces. Moreover, wherever possible, we also discuss the cell surface molecules and structures that sense mechanical forces upstream of macroautophagy.
MeSH term(s)	Autophagy ; Cell Membrane ; Homeostasis ; Immunity ; Stress, Mechanical
Language	English
Publishing date	2021-09-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.258589
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