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Article ; Online: Xiaoyun, a model accession for functional genomics research in Brassica napus.

Wang, Pengfei / Song, Yixian / Xie, Zhaoqi / Wan, Ming / Xia, Rui / Jiao, Yushun / Zhang, Hui / Yang, Guangsheng / Fan, Zhixiong / Yang, Qing-Yong / Hong, Dengfeng

Plant communications

2023 Volume 5, Issue 1, Page(s) 100727

MeSH term(s)	Brassica napus/genetics ; Genomics ; Genome, Plant/genetics
Language	English
Publishing date	2023-09-30
Publishing country	China
Document type	Journal Article
ISSN	2590-3462
ISSN (online)	2590-3462
DOI	10.1016/j.xplc.2023.100727
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Article ; Online: A T cell-based SARS-CoV-2 spike protein vaccine provides protection without antibodies.

Shi, Juan / Zheng, Jian / Zhang, Xiujuan / Tai, Wanbo / Compas, Ryan / Deno, Jack / Jachym, Natalie / Verma, Abhishek K / Wang, Gang / Guan, Xiaoqing / Odle, Abby E / Wan, Yushun / Li, Fang / Perlman, Stanley / Qiao, Liang / Du, Lanying

JCI insight

2024 Volume 9, Issue 5

Abstract: SARS-CoV-2 spike-based vaccines are used to control the COVID-19 pandemic. However, emerging variants have become resistant to antibody neutralization and further mutations may lead to full resistance. We tested whether T cells alone could provide ... ...

Abstract	SARS-CoV-2 spike-based vaccines are used to control the COVID-19 pandemic. However, emerging variants have become resistant to antibody neutralization and further mutations may lead to full resistance. We tested whether T cells alone could provide protection without antibodies. We designed a T cell-based vaccine in which SARS-CoV-2 spike sequences were rearranged and attached to ubiquitin. Immunization of mice with the vaccine induced no specific antibodies, but strong specific T cell responses. We challenged mice with SARS-CoV-2 wild-type strain or an Omicron variant after the immunization and monitored survival or viral titers in the lungs. The mice were significantly protected against death and weight loss caused by the SARS-CoV-2 wild-type strain, and the viral titers in the lungs of mice challenged with the SARS-CoV-2 wild-type strain or the Omicron variant were significantly reduced. Importantly, depletion of CD4+ or CD8+ T cells led to significant loss of the protection. Our analyses of spike protein sequences of the variants indicated that fewer than one-third presented by dominant HLA alleles were mutated and that most of the mutated epitopes were in the subunit 1 region. As the subunit 2 region is conservative, the vaccines targeting spike protein are expected to protect against future variants due to the T cell responses.
MeSH term(s)	Animals ; Humans ; Mice ; Spike Glycoprotein, Coronavirus/genetics ; Pandemics ; COVID-19/prevention & control ; SARS-CoV-2 ; Antibodies ; Vaccines ; COVID-19 Vaccines
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Antibodies ; Vaccines ; COVID-19 Vaccines
Language	English
Publishing date	2024-03-08
Publishing country	United States
Document type	Journal Article
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.155789
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Article: Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein.

Wan, Yushun / Huang, Linfen / Zhang, Xiujuan / Shang, Jian / Perlman, Stanley / Du, Lanying / Li, Fang

Research square

2021

Abstract: SARS-CoV-2 spike protein plays a key role in viral entry and host immune responses. The conformation of the spike protein can be either open or closed, yet it is unclear how the conformations affect the protein's functions or what regulate the ... ...

Abstract	SARS-CoV-2 spike protein plays a key role in viral entry and host immune responses. The conformation of the spike protein can be either open or closed, yet it is unclear how the conformations affect the protein's functions or what regulate the conformational changes. Using SARS-CoV-1 and bat RaTG13-CoV as comparisons, we identified two molecular switches that regulate the conformations of SARS-CoV-2 spike protein: (i) a furin motif loop turns SARS-CoV-2 spike from a closed conformation to a mixture of open and closed conformations, and (ii) a K417V mutation turns SARS-CoV-2 spike from mixed conformations to an open conformation. We showed that the open conformation favors viral potency by exposing the RBD for receptor binding and viral entry, whereas the closed conformation supports viral immune evasion by hiding the RBD from neutralizing antibodies. Hence SARS-CoV-2 spike has evolved to reach a balance between potency and immune evasiveness, which may contribute to the pandemic spread of SARS-CoV-2. The dynamics between viral potency and invasiveness is likely to further evolve, providing insights into future evolution of SARS-CoV-2.
Language	English
Publishing date	2021-10-01
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-736159/v2
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Article ; Online: Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein.

Geng, Qibin / Wan, Yushun / Hsueh, Fu-Chun / Shang, Jian / Ye, Gang / Bu, Fan / Herbst, Morgan / Wilkens, Rowan / Liu, Bin / Li, Fang

eLife

2023 Volume 12

Abstract: SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these ... ...

Abstract	SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these conformational changes or how they influence the spike's functions. Here, we show that Lys417 in the RBD plays dual roles in the spike's structure: it stabilizes the closed conformation of the trimeric spike by mediating inter-spike-subunit interactions; it also directly interacts with ACE2 receptor. Hence, a K417V mutation has opposing effects on the spike's function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2. The net outcomes of this mutation are to allow the spike to bind ACE2 with higher probability and mediate viral entry more efficiently, but become more exposed to neutralizing antibodies. Given that residue 417 has been a viral mutational hotspot, SARS-CoV-2 may have been evolving to strike a balance between infection potency and immune evasion, contributing to its pandemic spread.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; COVID-19 ; Angiotensin-Converting Enzyme 2/metabolism ; Protein Binding
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.74060
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Article ; Online: Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein

Qibin Geng / Yushun Wan / Fu-Chun Hsueh / Jian Shang / Gang Ye / Fan Bu / Morgan Herbst / Rowan Wilkens / Bin Liu / Fang Li

eLife, Vol

2023 Volume 12

Abstract	SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these conformational changes or how they influence the spike’s functions. Here, we show that Lys417 in the RBD plays dual roles in the spike’s structure: it stabilizes the closed conformation of the trimeric spike by mediating inter-spike–subunit interactions; it also directly interacts with ACE2 receptor. Hence, a K417V mutation has opposing effects on the spike’s function: it opens up the spike for better ACE2 binding while weakening the RBD’s direct binding to ACE2. The net outcomes of this mutation are to allow the spike to bind ACE2 with higher probability and mediate viral entry more efficiently, but become more exposed to neutralizing antibodies. Given that residue 417 has been a viral mutational hotspot, SARS-CoV-2 may have been evolving to strike a balance between infection potency and immune evasion, contributing to its pandemic spread.
Keywords	SARS-CoV-2 ; spike protein ; viral entry ; immune evasiveness ; receptor-binding domain ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
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Article ; Online: Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus.

Wan, Yushun / Shang, Jian / Graham, Rachel / Baric, Ralph S / Li, Fang

Journal of virology

2020 Volume 94, Issue 7

Abstract: Recently, a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by severe acute respiratory syndrome coronavirus (SARS-CoV). Since the SARS-CoV outbreak in 2002, extensive structural analyses ... ...

Abstract	Recently, a novel coronavirus (2019-nCoV) has emerged from Wuhan, China, causing symptoms in humans similar to those caused by severe acute respiratory syndrome coronavirus (SARS-CoV). Since the SARS-CoV outbreak in 2002, extensive structural analyses have revealed key atomic-level interactions between the SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2), which regulate both the cross-species and human-to-human transmissions of SARS-CoV. Here, we analyzed the potential receptor usage by 2019-nCoV, based on the rich knowledge about SARS-CoV and the newly released sequence of 2019-nCoV. First, the sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor. Second, several critical residues in 2019-nCoV RBM (particularly Gln493) provide favorable interactions with human ACE2, consistent with 2019-nCoV's capacity for human cell infection. Third, several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission. Last, while phylogenetic analysis indicates a bat origin of 2019-nCoV, 2019-nCoV also potentially recognizes ACE2 from a diversity of animal species (except mice and rats), implicating these animal species as possible intermediate hosts or animal models for 2019-nCoV infections. These analyses provide insights into the receptor usage, cell entry, host cell infectivity and animal origin of 2019-nCoV and may help epidemic surveillance and preventive measures against 2019-nCoV.
MeSH term(s)	Amino Acid Sequence ; Angiotensin-Converting Enzyme 2 ; Animals ; Betacoronavirus/classification ; Betacoronavirus/physiology ; COVID-19 ; China ; Chiroptera/virology ; Coronavirus Infections/virology ; Host Specificity ; Humans ; Models, Molecular ; Peptidyl-Dipeptidase A/chemistry ; Phylogeny ; Pneumonia, Viral/virology ; Protein Domains ; Receptors, Virus/chemistry ; Severe acute respiratory syndrome-related coronavirus/physiology ; SARS-CoV-2 ; Sequence Alignment ; Spike Glycoprotein, Coronavirus/chemistry
Chemical Substances	Receptors, Virus ; Spike Glycoprotein, Coronavirus ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Ace2 protein, mouse (EC 3.4.17.23) ; Ace2 protein, rat (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00127-20
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Article ; Online: Cell entry mechanisms of SARS-CoV-2.

Shang, Jian / Wan, Yushun / Luo, Chuming / Ye, Gang / Geng, Qibin / Auerbach, Ashley / Li, Fang

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

2020 Volume 117, Issue 21, Page(s) 11727–11734

Abstract: A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) is causing the global coronavirus disease 2019 (COVID-19) pandemic. Understanding how SARS-CoV-2 enters human cells is a high priority for deciphering its mystery and curbing ... ...

Abstract	A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) is causing the global coronavirus disease 2019 (COVID-19) pandemic. Understanding how SARS-CoV-2 enters human cells is a high priority for deciphering its mystery and curbing its spread. A virus surface spike protein mediates SARS-CoV-2 entry into cells. To fulfill its function, SARS-CoV-2 spike binds to its receptor human ACE2 (hACE2) through its receptor-binding domain (RBD) and is proteolytically activated by human proteases. Here we investigated receptor binding and protease activation of SARS-CoV-2 spike using biochemical and pseudovirus entry assays. Our findings have identified key cell entry mechanisms of SARS-CoV-2. First, SARS-CoV-2 RBD has higher hACE2 binding affinity than SARS-CoV RBD, supporting efficient cell entry. Second, paradoxically, the hACE2 binding affinity of the entire SARS-CoV-2 spike is comparable to or lower than that of SARS-CoV spike, suggesting that SARS-CoV-2 RBD, albeit more potent, is less exposed than SARS-CoV RBD. Third, unlike SARS-CoV, cell entry of SARS-CoV-2 is preactivated by proprotein convertase furin, reducing its dependence on target cell proteases for entry. The high hACE2 binding affinity of the RBD, furin preactivation of the spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain efficient cell entry while evading immune surveillance. These features may contribute to the wide spread of the virus. Successful intervention strategies must target both the potency of SARS-CoV-2 and its evasiveness.
MeSH term(s)	Cell Line ; Humans ; Immune Evasion ; Peptidyl-Dipeptidase A/chemistry ; Peptidyl-Dipeptidase A/metabolism ; Protein Domains ; Receptors, Virus/chemistry ; Receptors, Virus/metabolism ; SARS Virus/chemistry ; SARS Virus/immunology ; SARS Virus/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/immunology ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Activation ; Virus Internalization
Chemical Substances	Receptors, Virus ; Spike Glycoprotein, Coronavirus ; coronavirus receptors ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; angiotensin converting enzyme 2 (EC 3.4.17.-)
Keywords	covid19
Language	English
Publishing date	2020-05-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2003138117
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Article ; Online: Structural basis of receptor recognition by SARS-CoV-2

Shang, Jian / Ye, Gang / Shi, Ke / Wan, Yushun / Luo, Chuming / Aihara, Hideki / Geng, Qibin / Auerbach, Ashley / Li, Fang

Nature

2020 Volume 581, Issue 7807, Page(s) 221–224

Keywords	Multidisciplinary ; covid19
Language	English
Publisher	Springer Science and Business Media LLC
Publishing country	us
Document type	Article ; Online
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2179-y
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Article ; Online: The development of

Ye, Gang / Gallant, Joseph / Zheng, Jian / Massey, Christopher / Shi, Ke / Tai, Wanbo / Odle, Abby / Vickers, Molly / Shang, Jian / Wan, Yushun / Du, Lanying / Aihara, Hideki / Perlman, Stanley / LeBeau, Aaron / Li, Fang

eLife

2021 Volume 10

Abstract: Combating the COVID-19 pandemic requires potent and low-cost therapeutics. We identified a series of single-domain antibodies (i.e., nanobody), ...

Abstract	Combating the COVID-19 pandemic requires potent and low-cost therapeutics. We identified a series of single-domain antibodies (i.e., nanobody),
MeSH term(s)	Angiotensin-Converting Enzyme 2/metabolism ; Animals ; Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; COVID-19/immunology ; COVID-19/metabolism ; HEK293 Cells ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Models, Molecular ; Pandemics ; Protein Binding ; Protein Conformation ; Receptors, Virus/immunology ; Receptors, Virus/metabolism ; SARS-CoV-2/drug effects ; Single-Domain Antibodies/chemistry ; Single-Domain Antibodies/pharmacology ; Spike Glycoprotein, Coronavirus/metabolism ; COVID-19 Drug Treatment
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Receptors, Virus ; Single-Domain Antibodies ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-08-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.64815
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Article ; Online: Structural basis of receptor recognition by SARS-CoV-2.

Shang, Jian / Ye, Gang / Shi, Ke / Wan, Yushun / Luo, Chuming / Aihara, Hideki / Geng, Qibin / Auerbach, Ashley / Li, Fang

Nature

2020 Volume 581, Issue 7807, Page(s) 221–224

Abstract: A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans, causing COVID- ... ...

Abstract	A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans, causing COVID-19
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Animals ; Betacoronavirus/chemistry ; Betacoronavirus/drug effects ; Betacoronavirus/metabolism ; Binding Sites ; COVID-19 ; China/epidemiology ; Chiroptera/virology ; Coronavirus/chemistry ; Coronavirus/isolation & purification ; Coronavirus Infections/drug therapy ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; Crystallization ; Crystallography, X-Ray ; Disease Reservoirs/virology ; Eutheria/virology ; Humans ; Models, Molecular ; Pandemics ; Peptidyl-Dipeptidase A/chemistry ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; Protein Binding ; Protein Domains ; Protein Stability ; Receptors, Virus/chemistry ; Receptors, Virus/metabolism ; Severe acute respiratory syndrome-related coronavirus/chemistry ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Zoonoses/epidemiology ; Zoonoses/transmission ; Zoonoses/virology
Chemical Substances	Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-03-30
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2179-y
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