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Article ; Online: Expression and characterization of SARS-CoV-2 spike proteins.

2021 Volume 16, Issue 11, Page(s) 5339–5356

Abstract: The severe acute respiratory syndrome coronavirus 2 spike protein is a critical component of coronavirus disease 2019 vaccines and diagnostics and is also a therapeutic target. However, the spike protein is difficult to produce recombinantly because it ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 spike protein is a critical component of coronavirus disease 2019 vaccines and diagnostics and is also a therapeutic target. However, the spike protein is difficult to produce recombinantly because it is a large trimeric class I fusion membrane protein that is metastable and heavily glycosylated. We recently developed a prefusion-stabilized spike variant, termed HexaPro for six stabilizing proline substitutions, that can be expressed with a yield of >30 mg/L in ExpiCHO cells. This protocol describes an optimized workflow for expressing and biophysically characterizing rationally engineered spike proteins in Freestyle 293 and ExpiCHO cell lines. Although we focus on HexaPro, this protocol has been used to purify over a hundred different spike variants in our laboratories. We also provide guidance on expression quality control, long-term storage, and uses in enzyme-linked immunosorbent assays. The entire protocol, from transfection to biophysical characterization, can be completed in 7 d by researchers with basic tissue cell culture and protein purification expertise.
MeSH term(s)	Animals ; CHO Cells ; Cricetinae ; Cricetulus ; Gene Expression Regulation, Viral/physiology ; HEK293 Cells ; Humans ; Models, Molecular ; Protein Conformation ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-10-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-021-00623-0
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Article ; Online: Molecular Modeling, de novo Design and Synthesis of a Novel, Extracellular Binding Fibroblast Growth Factor Receptor 2 Inhibitor Alofanib (RPT835).

Tsimafeyeu, Ilya / Daeyaert, Frits / Joos, Jean-Baptiste / Aken, Koen V / Ludes-Meyers, John / Byakhov, Mikhail / Tjulandin, Sergei

Medicinal chemistry (Shariqah (United Arab Emirates))

2015 Volume 12, Issue 4, Page(s) 303–317

Abstract: Background: Fibroblast growth factor (FGF) receptors (FGFRs) play a key role in tumor growth and angiogenesis. The present report describes our search for an extracellularly binding FGFR inhibitor using a combined molecular modeling and de novo design ... ...

Abstract	Background: Fibroblast growth factor (FGF) receptors (FGFRs) play a key role in tumor growth and angiogenesis. The present report describes our search for an extracellularly binding FGFR inhibitor using a combined molecular modeling and de novo design strategy. Methods: Based upon crystal structures of the receptor with its native ligand and knowledge of inhibiting peptides, we have developed a computational protocol that predicts the putative binding of a molecule to the extracellular domains of the receptor. This protocol, or scoring function, was used in combination with the de novo synthesis program 'SYNOPSIS' to generate high scoring and synthetically accessible compounds. Results: Eight compounds belonging to 3 separate chemical classes were synthesized. One of these compounds, alofanib (RPT835), was found to be an effective inhibitor of the FGF/FGFR2 pathway. The preclinical in vitro data support an allosteric inhibition mechanism of RPT835. RPT835 potently inhibited growth of KATO III gastric cancer cells expressing FGFR2, with GI50 value of 10 nmol/L. Conclusion: These results provide strong rationale for the evaluation of compound in advanced cancers.
MeSH term(s)	Allosteric Regulation ; Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Benzoates/chemical synthesis ; Benzoates/chemistry ; Benzoates/pharmacology ; Cell Line, Tumor ; Drug Screening Assays, Antitumor ; Humans ; Models, Chemical ; Molecular Docking Simulation ; Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors ; Structure-Activity Relationship ; Sulfonamides/chemical synthesis ; Sulfonamides/chemistry ; Sulfonamides/pharmacology
Chemical Substances	Antineoplastic Agents ; Benzoates ; Sulfonamides ; Receptor, Fibroblast Growth Factor, Type 2 (EC 2.7.10.1) ; alofanib (LQX7RFK8MZ)
Language	English
Publishing date	2015-12-16
Publishing country	Netherlands
Document type	Journal Article
ISSN	1875-6638
ISSN (online)	1875-6638
DOI	10.2174/1573406412666160106154726
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Article: WWOX protein expression in normal human tissues.

Nunez, Maria I / Ludes-Meyers, John / Aldaz, C Marcelo

Journal of molecular histology

2006 Volume 37, Issue 3-4, Page(s) 115–125

Abstract: WWOX is a putative tumor suppressor gene that spans approximately a 1 Mb genomic region and is the site for the second most common chromosomal fragile site, FRA16D at 16q23. Various studies have focused on the expression of WWOX in human cancer mostly at ...

Abstract	WWOX is a putative tumor suppressor gene that spans approximately a 1 Mb genomic region and is the site for the second most common chromosomal fragile site, FRA16D at 16q23. Various studies have focused on the expression of WWOX in human cancer mostly at the RNA level, but little is known about the normal pattern of WWOX protein expression in non-neoplastic tissues. In this study, a comprehensive analysis of WWOX protein expression in normal tissues was performed by means of immunohistochemistry utilizing a very specific anti-WWOX polyclonal antibody. We analyzed tissue cores of human samples representing more than 30 organs, using various tissue microarray (TMA) slides. Due to the potential role of WWOX in sex-steroid metabolism, whole sections from hormonally regulated organs like breast, ovaries, testes and prostate were also analyzed. The results from our study indicate that WWOX is preferentially highly expressed in secretory epithelial cells of reproductive, endocrine and exocrine organs, as well as in ductal epithelial cells from specific segments of the urinary system. Interestingly, we also observed significant WWOX protein expression in various cell types of neural origin including neurons, ependymal cells and astrocytes. No expression of WWOX was detected in adipose, connective, and lymphoid tissues, myelinized structures and blood vessels. By better defining the topographic distribution of WWOX in normal tissues this study provides some insight on the potential physiological role of this novel protein.
MeSH term(s)	Humans ; Immunohistochemistry ; Organ Specificity ; Oxidoreductases/analysis ; Tissue Array Analysis ; Tissue Distribution ; Tumor Suppressor Proteins/analysis ; WW Domain-Containing Oxidoreductase
Chemical Substances	Tumor Suppressor Proteins ; Oxidoreductases (EC 1.-) ; WW Domain-Containing Oxidoreductase (EC 1.1.1.-) ; WWOX protein, human (EC 1.1.1.-)
Language	English
Publishing date	2006-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2144021-9
ISSN	1567-2379
ISSN	1567-2379
DOI	10.1007/s10735-006-9046-5
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Article: Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes.

bioRxiv : the preprint server for biology

2020

Abstract: The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large ... ...

Abstract	The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ~10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-05-30
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.05.30.125484
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Article ; Online: Corrigendum to 'Targeting FGFR2 with alofanib (RPT835) shows potent activity in tumour models' [Eur J Cancer 61 (2016) 20-28].

Tsimafeyeu, Ilya / Ludes-Meyers, John / Stepanova, Evgenia / Daeyaert, Frits / Khochenkov, Dmitry / Joose, Jean-Baptiste / Solomko, Eliso / Van Akene, Koen / Peretolchina, Nina / Yin, Wei / Ryabaya, Oxana / Byakhov, Mikhail / Tjulandin, Sergei

European journal of cancer (Oxford, England : 1990)

2017 Volume 70, Page(s) 156

Language	English
Publishing date	2017-01
Publishing country	England
Document type	Published Erratum
ZDB-ID	82061-1
ISSN	1879-0852 ; 0277-5379 ; 0959-8049 ; 0964-1947
ISSN (online)	1879-0852
ISSN	0277-5379 ; 0959-8049 ; 0964-1947
DOI	10.1016/j.ejca.2016.11.001
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Article ; Online: Discovery of Sisunatovir (RV521), an Inhibitor of Respiratory Syncytial Virus Fusion.

Cockerill, G Stuart / Angell, Richard M / Bedernjak, Alexandre / Chuckowree, Irina / Fraser, Ian / Gascon-Simorte, Jose / Gilman, Morgan S A / Good, James A D / Harland, Rachel / Johnson, Sara M / Ludes-Meyers, John H / Littler, Edward / Lumley, James / Lunn, Graham / Mathews, Neil / McLellan, Jason S / Paradowski, Michael / Peeples, Mark E / Scott, Claire /

Tait, Dereck / Taylor, Geraldine / Thom, Michelle / Thomas, Elaine / Villalonga Barber, Carol / Ward, Simon E / Watterson, Daniel / Williams, Gareth / Young, Paul / Powell, Kenneth

Journal of medicinal chemistry

2021 Volume 64, Issue 7, Page(s) 3658–3676

Abstract: RV521 is an orally bioavailable inhibitor of respiratory syncytial virus (RSV) fusion that was identified after a lead optimization process based upon hits that originated from a physical property directed hit profiling exercise at Reviral. This exercise ...

Abstract	RV521 is an orally bioavailable inhibitor of respiratory syncytial virus (RSV) fusion that was identified after a lead optimization process based upon hits that originated from a physical property directed hit profiling exercise at Reviral. This exercise encompassed collaborations with a number of contract organizations with collaborative medicinal chemistry and virology during the optimization phase in addition to those utilized as the compound proceeded through preclinical and clinical evaluation. RV521 exhibited a mean IC
MeSH term(s)	Animals ; Antiviral Agents/chemical synthesis ; Antiviral Agents/pharmacokinetics ; Antiviral Agents/pharmacology ; Benzimidazoles/chemical synthesis ; Benzimidazoles/pharmacokinetics ; Benzimidazoles/pharmacology ; Biological Availability ; Cell Line, Tumor ; Clinical Trials as Topic ; Drug Discovery ; Humans ; Microbial Sensitivity Tests ; Protein Binding ; Respiratory Syncytial Virus, Human/drug effects ; Viral Fusion Proteins/metabolism ; Virus Internalization/drug effects
Chemical Substances	Antiviral Agents ; Benzimidazoles ; F protein, human respiratory syncytial virus ; Viral Fusion Proteins ; sisunatovir (KE63TTO7WK)
Language	English
Publishing date	2021-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.0c01882
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Article ; Online: Targeting FGFR2 with alofanib (RPT835) shows potent activity in tumour models.

European journal of cancer (Oxford, England : 1990)

2016 Volume 61, Page(s) 20–28

Abstract: Alofanib (RPT835) is a novel selective allosteric inhibitor of fibroblast growth factor receptor 2 (FGFR2). We showed previously that alofanib could bind to the extracellular domain of FGFR2 and has an inhibitory effect on FGF2-induced phoshphorylation ... ...

Abstract	Alofanib (RPT835) is a novel selective allosteric inhibitor of fibroblast growth factor receptor 2 (FGFR2). We showed previously that alofanib could bind to the extracellular domain of FGFR2 and has an inhibitory effect on FGF2-induced phoshphorylation of FRS2α. In the present study, we further showed that alofanib inhibited phosphorylation of FRS2α with the half maximal inhibitory concentration (IC50) values of 7 and 9 nmol/l in cancer cells expressing different FGFR2 isoforms. In a panel of four cell lines representing several tumour types (triple-negative breast cancer, melanoma, and ovarian cancer), alofanib inhibited FGF-mediated proliferation with 50% growth inhibition (GI50) values of 16-370 nmol/l. Alofanib dose dependently inhibited the proliferation and migration of human and mouse endothelial cells (GI50 11-58 nmol/l) compared with brivanib and bevacizumab. Treatment with alofanib ablated experimental FGF-induced angiogenesis in vivo. In a FGFR-driven human tumour xenograft model, oral administration of alofanib was well tolerated and resulted in potent antitumour activity. Importantly, alofanib was effective in FGFR2-expressing models. These results show that alofanib is a potent FGFR2 inhibitor and provide strong rationale for its evaluation in patients with FGFR2-driven cancers.
MeSH term(s)	Angiogenesis Inhibitors/pharmacology ; Animals ; Antineoplastic Agents/pharmacology ; Benzoates/pharmacology ; Cell Line, Tumor ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; Disease Models, Animal ; Endothelial Cells/drug effects ; Human Umbilical Vein Endothelial Cells/drug effects ; Humans ; Mice ; Molecular Targeted Therapy/methods ; Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors ; Sulfonamides/pharmacology ; Xenograft Model Antitumor Assays
Chemical Substances	Angiogenesis Inhibitors ; Antineoplastic Agents ; Benzoates ; Sulfonamides ; Receptor, Fibroblast Growth Factor, Type 2 (EC 2.7.10.1) ; alofanib (LQX7RFK8MZ)
Language	English
Publishing date	2016-04-29
Publishing country	England
Document type	Journal Article
ZDB-ID	82061-1
ISSN	1879-0852 ; 0277-5379 ; 0959-8049 ; 0964-1947
ISSN (online)	1879-0852
ISSN	0277-5379 ; 0959-8049 ; 0964-1947
DOI	10.1016/j.ejca.2016.03.068
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Article ; Online: Structure-based design of prefusion-stabilized SARS-CoV-2 spikes.

Hsieh, Ching-Lin / Goldsmith, Jory A / Schaub, Jeffrey M / DiVenere, Andrea M / Kuo, Hung-Che / Javanmardi, Kamyab / Le, Kevin C / Wrapp, Daniel / Lee, Alison G / Liu, Yutong / Chou, Chia-Wei / Byrne, Patrick O / Hjorth, Christy K / Johnson, Nicole V / Ludes-Meyers, John / Nguyen, Annalee W / Park, Juyeon / Wang, Nianshuang / Amengor, Dzifa /

Lavinder, Jason J / Ippolito, Gregory C / Maynard, Jennifer A / Finkelstein, Ilya J / McLellan, Jason S

Science (New York, N.Y.)

2020 Volume 369, Issue 6510, Page(s) 1501–1505

Abstract: The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
MeSH term(s)	Amino Acid Substitution ; Betacoronavirus/chemistry ; COVID-19 Vaccines ; Coronavirus Infections/prevention & control ; Cryoelectron Microscopy ; Humans ; Proline/chemistry ; Protein Domains ; Protein Stability ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Viral Vaccines/chemistry
Chemical Substances	COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus ; Viral Vaccines ; spike protein, SARS-CoV-2 ; Proline (9DLQ4CIU6V)
Keywords	covid19
Language	English
Publishing date	2020-07-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abd0826
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Article ; Online: Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes

bioRxiv

Abstract	The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ~10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-05-30
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.05.30.125484
Database	COVID19

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Article ; Online: Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes

bioRxiv

Abstract	The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ∼10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
Keywords	covid19
Publisher	BioRxiv
Document type	Article ; Online
DOI	10.1101/2020.05.30.125484
Database	COVID19

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