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Article ; Online: Can phase separation buffer cellular noise?

Riback, Joshua A / Brangwynne, Clifford P

2020 Volume 367, Issue 6476, Page(s) 364–365

MeSH term(s)	Buffers ; Noise
Chemical Substances	Buffers
Language	English
Publishing date	2020-01-23
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aba0446
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: HDX-MS finds that partial unfolding with sequential domain activation controls condensation of a cellular stress marker.

Chen, Ruofan / Glauninger, Hendrik / Kahan, Darren N / Shangguan, Julia / Sachleben, Joseph R / Riback, Joshua A / Drummond, D Allan / Sosnick, Tobin R

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 13, Page(s) e2321606121

Abstract: Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen, ...

Abstract	Eukaryotic cells form condensates to sense and adapt to their environment [S. F. Banani, H. O. Lee, A. A. Hyman, M. K. Rosen,
MeSH term(s)	Poly(A)-Binding Proteins/genetics ; Temperature ; Heat-Shock Proteins/metabolism ; Thermodynamics ; Heat-Shock Response ; Deuterium Exchange Measurement/methods
Chemical Substances	Poly(A)-Binding Proteins ; Heat-Shock Proteins
Language	English
Publishing date	2024-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2321606121
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Article: Size distributions of intracellular condensates reflect competition between coalescence and nucleation.

Lee, Daniel S W / Choi, Chang-Hyun / Sanders, David W / Beckers, Lien / Riback, Joshua A / Brangwynne, Clifford P / Wingreen, Ned S

Nature physics

2023 Volume 19, Issue 4, Page(s) 586–596

Abstract: Phase separation of biomolecules into condensates has emerged as a mechanism for intracellular organization and affects many intracellular processes, including reaction pathways through the clustering of enzymes and pathway intermediates. Precise and ... ...

Abstract	Phase separation of biomolecules into condensates has emerged as a mechanism for intracellular organization and affects many intracellular processes, including reaction pathways through the clustering of enzymes and pathway intermediates. Precise and rapid spatiotemporal control of reactions by condensates requires tuning of their sizes. However, the physical processes that govern the distribution of condensate sizes remain unclear. Here we show that both native and synthetic condensates display an exponential size distribution, which is captured by Monte Carlo simulations of fast nucleation followed by coalescence. In contrast, pathological aggregates exhibit a power-law size distribution. These distinct behaviours reflect the relative importance of nucleation and coalescence kinetics. We demonstrate this by utilizing a combination of synthetic and native condensates to probe the underlying physical mechanisms determining condensate size. The appearance of exponential distributions for abrupt nucleation versus power-law distributions under continuous nucleation may reflect a general principle that determines condensate size distributions.
Language	English
Publishing date	2023-02-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2206346-8
ISSN	1745-2481 ; 1745-2473
ISSN (online)	1745-2481
ISSN	1745-2473
DOI	10.1038/s41567-022-01917-0
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Article ; Online: How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins.

Baxa, Michael C / Lin, Xiaoxuan / Mukinay, Cedrick D / Chakravarthy, Srinivas / Sachleben, Joseph R / Antilla, Sarah / Hartrampf, Nina / Riback, Joshua A / Gagnon, Isabelle A / Pentelute, Bradley L / Clark, Patricia L / Sosnick, Tobin R

Protein science : a publication of the Protein Society

2024 Volume 33, Issue 5, Page(s) e4986

Abstract: Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random ... ...

Abstract	Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.
MeSH term(s)	Protein Folding ; Intrinsically Disordered Proteins ; Water/chemistry ; Sodium Chloride ; Glycine/chemistry ; Hydrophobic and Hydrophilic Interactions
Chemical Substances	Intrinsically Disordered Proteins ; Water (059QF0KO0R) ; Sodium Chloride (451W47IQ8X) ; Glycine (TE7660XO1C)
Language	English
Publishing date	2024-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4986
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Zs.A 3407: 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: The nucleolus as a multiphase liquid condensate.

Lafontaine, Denis L J / Riback, Joshua A / Bascetin, Rümeyza / Brangwynne, Clifford P

Nature reviews. Molecular cell biology

2020 Volume 22, Issue 3, Page(s) 165–182

Abstract: The nucleolus is the most prominent nuclear body and serves a fundamentally important biological role as a site of ribonucleoprotein particle assembly, primarily dedicated to ribosome biogenesis. Despite being one of the first intracellular structures ... ...

Abstract	The nucleolus is the most prominent nuclear body and serves a fundamentally important biological role as a site of ribonucleoprotein particle assembly, primarily dedicated to ribosome biogenesis. Despite being one of the first intracellular structures visualized historically, the biophysical rules governing its assembly and function are only starting to become clear. Recent studies have provided increasing support for the concept that the nucleolus represents a multilayered biomolecular condensate, whose formation by liquid-liquid phase separation (LLPS) facilitates the initial steps of ribosome biogenesis and other functions. Here, we review these biophysical insights in the context of the molecular and cell biology of the nucleolus. We discuss how nucleolar function is linked to its organization as a multiphase condensate and how dysregulation of this organization could provide insights into still poorly understood aspects of nucleolus-associated diseases, including cancer, ribosomopathies and neurodegeneration as well as ageing. We suggest that the LLPS model provides the starting point for a unifying quantitative framework for the assembly, structural maintenance and function of the nucleolus, with implications for gene regulation and ribonucleoprotein particle assembly throughout the nucleus. The LLPS concept is also likely useful in designing new therapeutic strategies to target nucleolar dysfunction.
MeSH term(s)	Aging/genetics ; Aging/metabolism ; Aging/pathology ; Animals ; Cell Cycle/physiology ; Cell Nucleolus/chemistry ; Cell Nucleolus/genetics ; Cell Nucleolus/metabolism ; Chemical Fractionation ; Gene Expression ; Humans ; Liquid-Liquid Extraction ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Ribonucleoproteins/metabolism ; Ribosomes/physiology
Chemical Substances	Ribonucleoproteins
Language	English
Publishing date	2020-09-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2031313-5
ISSN	1471-0080 ; 1471-0072
ISSN (online)	1471-0080
ISSN	1471-0072
DOI	10.1038/s41580-020-0272-6
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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)
Zs.MG 26: Show issues

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Article ; Online: Viscoelasticity and advective flow of RNA underlies nucleolar form and function.

Riback, Joshua A / Eeftens, Jorine M / Lee, Daniel S W / Quinodoz, Sofia A / Donlic, Anita / Orlovsky, Natalia / Wiesner, Lennard / Beckers, Lien / Becker, Lindsay A / Strom, Amy R / Rana, Ushnish / Tolbert, Michele / Purse, Byron W / Kleiner, Ralph / Kriwacki, Richard / Brangwynne, Clifford P

Molecular cell

2023 Volume 83, Issue 17, Page(s) 3095–3107.e9

Abstract: The nucleolus is the largest biomolecular condensate and facilitates transcription, processing, and assembly of ribosomal RNA (rRNA). Although nucleolar function is thought to require multiphase liquid-like properties, nucleolar fluidity and its ... ...

Abstract	The nucleolus is the largest biomolecular condensate and facilitates transcription, processing, and assembly of ribosomal RNA (rRNA). Although nucleolar function is thought to require multiphase liquid-like properties, nucleolar fluidity and its connection to the highly coordinated transport and biogenesis of ribosomal subunits are poorly understood. Here, we use quantitative imaging, mathematical modeling, and pulse-chase nucleotide labeling to examine nucleolar material properties and rRNA dynamics. The mobility of rRNA is several orders of magnitude slower than that of nucleolar proteins, with rRNA steadily moving away from the transcriptional sites in a slow (∼1 Å/s), radially directed fashion. This constrained but directional mobility, together with polymer physics-based calculations, suggests that nascent rRNA forms an entangled gel, whose constant production drives outward flow. We propose a model in which progressive maturation of nascent rRNA reduces its initial entanglement, fluidizing the nucleolar periphery to facilitate the release of assembled pre-ribosomal particles.
MeSH term(s)	RNA/genetics ; RNA, Ribosomal/genetics ; Biomolecular Condensates ; Cell Nucleolus/genetics ; Nuclear Proteins/genetics
Chemical Substances	RNA (63231-63-0) ; RNA, Ribosomal ; Nuclear Proteins
Language	English
Publishing date	2023-09-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.08.006
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Article ; Online: Properties of protein unfolded states suggest broad selection for expanded conformational ensembles.

Bowman, Micayla A / Riback, Joshua A / Rodriguez, Anabel / Guo, Hongyu / Li, Jun / Sosnick, Tobin R / Clark, Patricia L

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 38, Page(s) 23356–23364

Abstract: Much attention is being paid to conformational biases in the ensembles of intrinsically disordered proteins. However, it is currently unknown whether or how conformational biases within the disordered ensembles of foldable proteins affect function in ... ...

Abstract	Much attention is being paid to conformational biases in the ensembles of intrinsically disordered proteins. However, it is currently unknown whether or how conformational biases within the disordered ensembles of foldable proteins affect function in vivo. Recently, we demonstrated that water can be a good solvent for unfolded polypeptide chains, even those with a hydrophobic and charged sequence composition typical of folded proteins. These results run counter to the generally accepted model that protein folding begins with hydrophobicity-driven chain collapse. Here we investigate what other features, beyond amino acid composition, govern chain collapse. We found that local clustering of hydrophobic and/or charged residues leads to significant collapse of the unfolded ensemble of pertactin, a secreted autotransporter virulence protein from
MeSH term(s)	Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Outer Membrane Proteins/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bordetella pertussis/chemistry ; Bordetella pertussis/genetics ; Bordetella pertussis/metabolism ; Protein Conformation ; Protein Folding ; Protein Unfolding ; Scattering, Small Angle ; Virulence Factors, Bordetella/chemistry ; Virulence Factors, Bordetella/genetics ; Virulence Factors, Bordetella/metabolism
Chemical Substances	Bacterial Outer Membrane Proteins ; Bacterial Proteins ; Virulence Factors, Bordetella ; pertactin (63GD90PP8X)
Language	English
Publishing date	2020-09-02
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	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2003773117
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Article ; Online: Structural basis for adhesion G protein-coupled receptor Gpr126 function.

Leon, Katherine / Cunningham, Rebecca L / Riback, Joshua A / Feldman, Ezra / Li, Jingxian / Sosnick, Tobin R / Zhao, Minglei / Monk, Kelly R / Araç, Demet

Nature communications

2020 Volume 11, Issue 1, Page(s) 194

Abstract: Many drugs target the extracellular regions (ECRs) of cell-surface receptors. The large and alternatively-spliced ECRs of adhesion G protein-coupled receptors (aGPCRs) have key functions in diverse biological processes including neurodevelopment, ... ...

Abstract	Many drugs target the extracellular regions (ECRs) of cell-surface receptors. The large and alternatively-spliced ECRs of adhesion G protein-coupled receptors (aGPCRs) have key functions in diverse biological processes including neurodevelopment, embryogenesis, and tumorigenesis. However, their structures and mechanisms of action remain unclear, hampering drug development. The aGPCR Gpr126/Adgrg6 regulates Schwann cell myelination, ear canal formation, and heart development; and GPR126 mutations cause myelination defects in human. Here, we determine the structure of the complete zebrafish Gpr126 ECR and reveal five domains including a previously unknown domain. Strikingly, the Gpr126 ECR adopts a closed conformation that is stabilized by an alternatively spliced linker and a conserved calcium-binding site. Alternative splicing regulates ECR conformation and receptor signaling, while mutagenesis of the calcium-binding site abolishes Gpr126 function in vivo. These results demonstrate that Gpr126 ECR utilizes a multi-faceted dynamic approach to regulate receptor function and provide relevant insights for ECR-targeted drug design.
MeSH term(s)	Alternative Splicing ; Animals ; Binding Sites ; Crystallography, X-Ray ; Drug Design ; Gene Expression Regulation, Developmental ; HEK293 Cells ; Humans ; Models, Molecular ; Protein Conformation ; Protein Domains ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Schwann Cells/metabolism ; Zebrafish/genetics ; Zebrafish/metabolism ; Zebrafish Proteins/chemistry ; Zebrafish Proteins/genetics ; Zebrafish Proteins/metabolism
Chemical Substances	ADGRG6 protein, human ; Receptors, G-Protein-Coupled ; Zebrafish Proteins ; stx7l protein, zebrafish
Language	English
Publishing date	2020-01-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-14040-1
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Article: Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response

Riback, Joshua A / Alexandra E. Rojek / Christopher D. Katanski / D. Allan Drummond / Evgeny V. Pilipenko / Jamie L. Kear-Scott / Tobin R. Sosnick

Cell. 2017 Mar. 09, v. 168

2017

Abstract: ... granules.Â InÂ vitro, stress-granule-associated proteins can demix to form liquids, hydrogels, and ...

Abstract	In eukaryotic cells, diverse stresses trigger coalescence of RNA-binding proteins into stress granules.Â InÂ vitro, stress-granule-associated proteins can demix to form liquids, hydrogels, and other assemblies lacking fixed stoichiometry. Observing these phenomena has generally required conditions far removed from physiological stresses. We show that poly(A)-binding protein (Pab1 in yeast), a defining marker of stress granules, phase separates and forms hydrogels inÂ vitro upon exposure to physiological stress conditions. Other RNA-binding proteins depend upon low-complexity regions (LCRs) or RNA for phase separation, whereas Pab1âs LCR is not required for demixing, and RNA inhibits it. Based on unique evolutionary patterns, we create LCR mutations, which systematically tune its biophysical properties and Pab1 phase separation inÂ vitro and inÂ vivo. Mutations that impede phase separation reduce organism fitness during prolonged stress. Poly(A)-binding protein thus acts as a physiological stress sensor, exploiting phase separation to precisely mark stress onset, a broadly generalizable mechanism.
Keywords	cytoplasmic granules ; eukaryotic cells ; hydrocolloids ; mutation ; RNA ; RNA-binding proteins ; stoichiometry ; yeasts
Language	English
Dates of publication	2017-0309
Size	p. 1028-1040.e19.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2017.02.027
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Article ; Online: Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.

Riback, Joshua A / Bowman, Micayla A / Zmyslowski, Adam M / Plaxco, Kevin W / Clark, Patricia L / Sosnick, Tobin R

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 18, Page(s) 8889–8894

Abstract: The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt in the absence of denaturant remain controversial. We developed an analysis procedure for small-angle X-ray scattering (SAXS) profiles and used it to ... ...

Abstract	The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt in the absence of denaturant remain controversial. We developed an analysis procedure for small-angle X-ray scattering (SAXS) profiles and used it to demonstrate that even relatively hydrophobic IDPs remain nearly as expanded in water as they are in high denaturant concentrations. In contrast, as demonstrated here, most fluorescence resonance energy transfer (FRET) measurements have indicated that relatively hydrophobic IDPs contract significantly in the absence of denaturant. We use two independent approaches to further explore this controversy. First, using SAXS we show that fluorophores employed in FRET can contribute to the observed discrepancy. Specifically, we find that addition of Alexa-488 to a normally expanded IDP causes contraction by an additional 15%, a value in reasonable accord with the contraction reported in FRET-based studies. Second, using our simulations and analysis procedure to accurately extract both the radius of gyration (R
MeSH term(s)	Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/chemistry ; Hydrazines/chemistry ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Proteins/chemistry ; X-Ray Diffraction
Chemical Substances	Alexa 488 hydrazide ; Fluorescent Dyes ; Hydrazines ; Proteins
Language	English
Publishing date	2019-04-16
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	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1813038116
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