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Article ; Online: Uncovering targets of the Leader protease: Linking RNA-mediated pathways and antiviral defense.

Saiz, Margarita / Martinez-Salas, Encarnacion

2021 Volume 12, Issue 4, Page(s) e1645

Abstract: RNA viruses have developed specialized mechanisms to subvert host RNA-binding proteins (RBPs) favoring their own gene expression. The Leader (L) protein of foot-and-mouth disease virus, a member of the Picornaviridae family, is a papain-like cysteine ... ...

Abstract	RNA viruses have developed specialized mechanisms to subvert host RNA-binding proteins (RBPs) favoring their own gene expression. The Leader (L) protein of foot-and-mouth disease virus, a member of the Picornaviridae family, is a papain-like cysteine protease that self-cleaves from the polyprotein. Early in infection, the L protease cleaves the translation initiation factors eIF4GI and eIF4GII, inducing the shutdown of cap-dependent translation. However, the cleavage sites on the viral polyprotein, eIF4GI, and eIF4GII differ in sequence, challenging the definition of a consensus site for L targets. Identification of Gemin5 and Daxx proteolytic products in infected cells unveiled a motif centered on the RKAR sequence. The RBP Gemin5 is a member of the survival of motor neurons complex, a ribosome interacting protein, and a translation downregulator. Likewise, the Fas-ligand Daxx is a multifunctional adaptor that plays key roles in transcription control, apoptosis, and innate immune antiviral response. Remarkably, the cleavage site on the RNA helicases MDA5 and LGP2, two relevant immune sensors of the retinoic acid-inducible gene-I (RIG-I)-like receptors family, resembles the L target site of Gemin5 and Daxx, and similar cleavage sites have been reported in ISG15 and TBK1, two proteins involved in type I interferon response and signaling pathway, respectively. In this review we dissect the features of the L cleavage sites in essential RBPs, eventually helping in the discovery of novel L targets. This article is categorized under: RNA in Disease and Development > RNA in Disease Translation > Translation Regulation.
MeSH term(s)	Animals ; Antiviral Restriction Factors/immunology ; Foot-and-Mouth Disease Virus/enzymology ; Foot-and-Mouth Disease Virus/genetics ; Immunity, Innate ; RNA ; RNA Helicases
Chemical Substances	Antiviral Restriction Factors ; RNA (63231-63-0) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2021-02-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1645
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Article ; Online: MDA5 cleavage by the Leader protease of foot-and-mouth disease virus reveals its pleiotropic effect against the host antiviral response.

Pulido, Miguel Rodríguez / Martínez-Salas, Encarnación / Sobrino, Francisco / Sáiz, Margarita

Cell death & disease

2020 Volume 11, Issue 8, Page(s) 718

Abstract: The RIG-I-like receptor (RLR) melanoma differentiation-associated gene 5 (MDA5) plays a key role in triggering innate antiviral response during infection by RNA viruses. MDA5 activation leads to transcription induction of type-I interferon (IFN) and ... ...

Abstract	The RIG-I-like receptor (RLR) melanoma differentiation-associated gene 5 (MDA5) plays a key role in triggering innate antiviral response during infection by RNA viruses. MDA5 activation leads to transcription induction of type-I interferon (IFN) and proinflammatory cytokines. MDA5 has also been associated with autoimmune and autoinflammatory diseases by dysfunctional activation of innate immune response in the absence of infection. Here, we show how foot-and-mouth disease virus (FMDV) counteracts the specific antiviral effect exerted by MDA5 targeting the protein for cleavage by the viral Leader protease (Lpro). MDA5 overexpression had an inhibitory effect on FMDV infection in IFN-competent cells. Remarkably, immunostimulatory viral RNA co-immunoprecipitated with MDA5 in infected cells. Moreover, specific cleavage of MDA5 by Lpro was detected in co-transfected cells, as well as during the course of FMDV infection. A significant reduction in IFN induction associated with MDA5 cleavage was detected by comparison with a non-cleavable MDA5 mutant protein with preserved antiviral activity. The Lpro cleavage site in MDA5 was identified as the RGRAR sequence in the conserved helicase motif VI, coinciding with that recently reported for Lpro in LGP2, another member of the RLRs family involved in antiviral defenses. Interestingly, specific mutations within the MDA5 Lpro target sequence have been associated with immune disease in mice and humans. Our results reveal a pleiotropic strategy for immune evasion based on a viral protease targeting phylogenetically conserved domains of immune sensors. Identification of viral strategies aimed to disrupt MDA5 functionality may also contribute to develop new treatment tools for MDA5-related disorders.
MeSH term(s)	Animals ; Cell Line ; DEAD Box Protein 58/metabolism ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Foot-and-Mouth Disease Virus/genetics ; Foot-and-Mouth Disease Virus/metabolism ; Genetic Pleiotropy/genetics ; HEK293 Cells ; Humans ; Immunity, Innate ; Interferon Type I/metabolism ; Interferon-Induced Helicase, IFIH1/metabolism ; Interferon-Induced Helicase, IFIH1/physiology ; Proteolysis ; RNA, Viral/immunology ; Receptors, Immunologic/metabolism ; Signal Transduction ; Swine
Chemical Substances	Interferon Type I ; RNA, Viral ; Receptors, Immunologic ; Endopeptidases (EC 3.4.-) ; leader proteinase, foot-and-mouth disease virus (EC 3.4.99.-) ; RIGI protein, human (EC 3.6.1.-) ; IFIH1 protein, human (EC 3.6.1.-) ; DEAD Box Protein 58 (EC 3.6.4.13) ; Interferon-Induced Helicase, IFIH1 (EC 3.6.4.13)
Language	English
Publishing date	2020-09-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2541626-1
ISSN	2041-4889 ; 2041-4889
ISSN (online)	2041-4889
ISSN	2041-4889
DOI	10.1038/s41419-020-02931-x
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Article ; Online: Picornavirus translation strategies.

Francisco-Velilla, Rosario / Embarc-Buh, Azman / Abellan, Salvador / Martinez-Salas, Encarnacion

FEBS open bio

2022 Volume 12, Issue 6, Page(s) 1125–1141

Abstract: The genome of viruses classified as picornaviruses consists of a single monocistronic positive strand RNA. The coding capacity of these RNA viruses is rather limited, and thus, they rely on the cellular machinery for their viral replication cycle. Upon ... ...

Abstract	The genome of viruses classified as picornaviruses consists of a single monocistronic positive strand RNA. The coding capacity of these RNA viruses is rather limited, and thus, they rely on the cellular machinery for their viral replication cycle. Upon the entry of the virus into susceptible cells, the viral RNA initially competes with cellular mRNAs for access to the protein synthesis machinery. Not surprisingly, picornaviruses have evolved specialized strategies that successfully allow the expression of viral gene products, which we outline in this review. The main feature of all picornavirus genomes is the presence of a heavily structured RNA element on the 5´UTR, referred to as an internal ribosome entry site (IRES) element, which directs viral protein synthesis as well and, consequently, triggers the subsequent steps required for viral replication. Here, we will summarize recent studies showing that picornavirus IRES elements consist of a modular structure, providing sites of interaction for ribosome subunits, eIFs, and a selective group of RNA-binding proteins.
MeSH term(s)	Internal Ribosome Entry Sites/genetics ; Picornaviridae/genetics ; Picornaviridae/metabolism ; RNA, Messenger/genetics ; RNA, Viral/genetics ; Virus Replication
Chemical Substances	Internal Ribosome Entry Sites ; RNA, Messenger ; RNA, Viral
Language	English
Publishing date	2022-03-30
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13400
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Article ; Online: Structural insights of the pre-let-7 interaction with LIN28B.

Rangel-Guerrero, Sergio Israel / Franco-Urquijo, Pablo Alberto / Martínez-Salas, Encarnación / Alvarez-Salas, Luis Marat

Nucleosides, nucleotides & nucleic acids

2020 Volume 40, Issue 2, Page(s) 194–211

Abstract: The Let-7:LIN28 regulatory loop is a paradigm in miRNA regulation. LIN28 harbors two RNA binding domains, which interact with well-conserved sequences in pre-let-7 RNAs, the GNGAY and the GGAG motifs. Here, the differential binding between LIN28B and pre- ...

Abstract	The Let-7:LIN28 regulatory loop is a paradigm in miRNA regulation. LIN28 harbors two RNA binding domains, which interact with well-conserved sequences in pre-let-7 RNAs, the GNGAY and the GGAG motifs. Here, the differential binding between LIN28B and pre-let-7 members was associated with the structural characteristics of the pre-let-7 family mapped by SHAPE, uncovering diverse structural patterns within pre-let-7 members. Pre-let-7 mutants supported a relevant role of the GGAG motif location and the preE-stem stability for the interaction with LIN28B. Based on these results, we propose a core RNA structure for LIN28B interaction.
MeSH term(s)	Base Sequence ; Humans ; MicroRNAs/chemistry ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; RNA Precursors/chemistry ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA-Binding Proteins/metabolism
Chemical Substances	LIN28B protein, human ; MicroRNAs ; RNA Precursors ; RNA-Binding Proteins ; mirnlet7 microRNA, human
Language	English
Publishing date	2020-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2008956-9
ISSN	1532-2335 ; 1525-7770
ISSN (online)	1532-2335
ISSN	1525-7770
DOI	10.1080/15257770.2020.1859116
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Article ; Online: Structural insights into viral IRES-dependent translation mechanisms.

Lozano, Gloria / Martínez-Salas, Encarnación

Current opinion in virology

2015 Volume 12, Page(s) 113–120

Abstract: A diverse group of viruses subvert the host translational machinery to promote viral genome translation. This process often involves altering canonical translation initiation factors to repress cellular protein synthesis while viral proteins are ... ...

Abstract	A diverse group of viruses subvert the host translational machinery to promote viral genome translation. This process often involves altering canonical translation initiation factors to repress cellular protein synthesis while viral proteins are efficiently synthesized. The discovery of this strategy in picornaviruses, which is based on the use of internal ribosome entry site (IRES) elements, opened new avenues to study alternative translational control mechanisms evolved in different groups of RNA viruses. IRESs are cis-acting RNA sequences that adopt three-dimensional structures and recruit the translation machinery assisted by a subset of translation initiation factors and various RNA binding proteins. However, IRESs present in the genome of different RNA viruses perform the same function despite lacking conservation of primary sequence and secondary RNA structure, and differing in host factor requirement to recruit the translation machinery. Evolutionary conserved motifs tend to preserve sequences impacting on RNA structure and RNA-protein interactions important for IRES function. While some motifs are found in various picornavirus IRESs, others occur only in one type reflecting specialized factor requirements. This review is focused to describe recent advances on the principles and RNA structure features of picornavirus IRESs.
MeSH term(s)	Gene Expression Regulation ; Genome, Viral ; Humans ; Internal Ribosome Entry Sites ; Nucleic Acid Conformation ; Picornaviridae/genetics ; Picornaviridae/pathogenicity ; Picornaviridae/physiology ; Protein Biosynthesis ; RNA Viruses/genetics ; RNA Viruses/pathogenicity ; RNA Viruses/physiology ; RNA, Viral/chemistry ; RNA, Viral/metabolism ; Viral Proteins/metabolism
Chemical Substances	Internal Ribosome Entry Sites ; RNA, Viral ; Viral Proteins
Language	English
Publishing date	2015-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2611378-8
ISSN	1879-6265 ; 1879-6257
ISSN (online)	1879-6265
ISSN	1879-6257
DOI	10.1016/j.coviro.2015.04.008
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Article ; Online: RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements.

Embarc-Buh, Azman / Francisco-Velilla, Rosario / Martinez-Salas, Encarnacion

Viruses

2021 Volume 13, Issue 6

Abstract: Viral RNAs contain the information needed to synthesize their own proteins, to replicate, and to spread to susceptible cells. However, due to their reduced coding capacity RNA viruses rely on host cells to complete their multiplication cycle. This is ... ...

Abstract	Viral RNAs contain the information needed to synthesize their own proteins, to replicate, and to spread to susceptible cells. However, due to their reduced coding capacity RNA viruses rely on host cells to complete their multiplication cycle. This is largely achieved by the concerted action of regulatory structural elements on viral RNAs and a subset of host proteins, whose dedicated function across all stages of the infection steps is critical to complete the viral cycle. Importantly, not only the RNA sequence but also the RNA architecture imposed by the presence of specific structural domains mediates the interaction with host RNA-binding proteins (RBPs), ultimately affecting virus multiplication and spreading. In marked difference with other biological systems, the genome of positive strand RNA viruses is also the mRNA. Here we focus on distinct types of positive strand RNA viruses that differ in the regulatory elements used to promote translation of the viral RNA, as well as in the mechanisms used to evade the series of events connected to antiviral response, including translation shutoff induced in infected cells, assembly of stress granules, and trafficking stress.
MeSH term(s)	Biological Transport ; Cytoplasmic Granules/metabolism ; Gene Expression Regulation, Viral ; Host-Pathogen Interactions ; Humans ; Protein Biosynthesis ; RNA Virus Infections/metabolism ; RNA Virus Infections/virology ; RNA Viruses/physiology ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; RNA-Binding Proteins/metabolism ; Response Elements ; Stress, Physiological ; Transport Vesicles/metabolism ; Virus Replication
Chemical Substances	RNA, Viral ; RNA-Binding Proteins
Language	English
Publishing date	2021-05-21
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13060952
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Article ; Online: Picornavirus translation strategies

Rosario Francisco‐Velilla / Azman Embarc‐Buh / Salvador Abellan / Encarnacion Martinez‐Salas

FEBS Open Bio, Vol 12, Iss 6, Pp 1125-

2022 Volume 1141

Abstract	The genome of viruses classified as picornaviruses consists of a single monocistronic positive strand RNA. The coding capacity of these RNA viruses is rather limited, and thus, they rely on the cellular machinery for their viral replication cycle. Upon the entry of the virus into susceptible cells, the viral RNA initially competes with cellular mRNAs for access to the protein synthesis machinery. Not surprisingly, picornaviruses have evolved specialized strategies that successfully allow the expression of viral gene products, which we outline in this review. The main feature of all picornavirus genomes is the presence of a heavily structured RNA element on the 5´UTR, referred to as an internal ribosome entry site (IRES) element, which directs viral protein synthesis as well and, consequently, triggers the subsequent steps required for viral replication. Here, we will summarize recent studies showing that picornavirus IRES elements consist of a modular structure, providing sites of interaction for ribosome subunits, eIFs, and a selective group of RNA‐binding proteins.
Keywords	cap‐independent translation ; host translation shutdown ; IRES element ; RNA structure ; RNA virus ; RNA‐binding protein ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
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Article ; Online: The RBS1 domain of Gemin5 is intrinsically unstructured and interacts with RNA through conserved Arg and aromatic residues.

Embarc-Buh, Azman / Francisco-Velilla, Rosario / Camero, Sergio / Pérez-Cañadillas, José Manuel / Martínez-Salas, Encarnación

RNA biology

2021 Volume 18, Issue sup1, Page(s) 496–506

Abstract: Gemin5 is a multifaceted RNA-binding protein that comprises distinct structural domains, including a WD40 and TPR-like for which the X-ray structure is known. In addition, the protein contains a non-canonical RNA-binding domain (RBS1) towards the C- ... ...

Abstract	Gemin5 is a multifaceted RNA-binding protein that comprises distinct structural domains, including a WD40 and TPR-like for which the X-ray structure is known. In addition, the protein contains a non-canonical RNA-binding domain (RBS1) towards the C-terminus. To understand the RNA binding features of the RBS1 domain, we have characterized its structural characteristics by solution NMR linked to RNA-binding activity. Here we show that a short version of the RBS1 domain that retains the ability to interact with RNA is predominantly unfolded even in the presence of RNA. Furthermore, an exhaustive mutational analysis indicates the presence of an evolutionarily conserved motif enriched in R, S, W, and H residues, necessary to promote RNA-binding via π-π interactions. The combined results of NMR and RNA-binding on wild-type and mutant proteins highlight the importance of aromatic and arginine residues for RNA recognition by RBS1, revealing that the net charge and the π-amino acid density of this region of Gemin5 are key factors for RNA recognition.
MeSH term(s)	Amino Acid Sequence ; Arginine/chemistry ; Arginine/genetics ; Arginine/metabolism ; Binding Sites ; Humans ; Models, Molecular ; Protein Binding ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; RNA-Binding Motifs ; SMN Complex Proteins/chemistry ; SMN Complex Proteins/genetics ; SMN Complex Proteins/metabolism ; Sequence Homology ; Tryptophan/chemistry ; Tryptophan/genetics ; Tryptophan/metabolism
Chemical Substances	GEMIN5 protein, human ; SMN Complex Proteins ; RNA (63231-63-0) ; Tryptophan (8DUH1N11BX) ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2021-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.1080/15476286.2021.1962666
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Article ; Online: Emerging Roles of Gemin5: From snRNPs Assembly to Translation Control.

Martinez-Salas, Encarnacion / Embarc-Buh, Azman / Francisco-Velilla, Rosario

International journal of molecular sciences

2020 Volume 21, Issue 11

Abstract: RNA-binding proteins (RBPs) play a pivotal role in the lifespan of RNAs. The disfunction of RBPs is frequently the cause of cell disorders which are incompatible with life. Furthermore, the ordered assembly of RBPs and RNAs in ribonucleoprotein (RNP) ... ...

Abstract	RNA-binding proteins (RBPs) play a pivotal role in the lifespan of RNAs. The disfunction of RBPs is frequently the cause of cell disorders which are incompatible with life. Furthermore, the ordered assembly of RBPs and RNAs in ribonucleoprotein (RNP) particles determines the function of biological complexes, as illustrated by the survival of the motor neuron (SMN) complex. Defects in the SMN complex assembly causes spinal muscular atrophy (SMA), an infant invalidating disease. This multi-subunit chaperone controls the assembly of small nuclear ribonucleoproteins (snRNPs), which are the critical components of the splicing machinery. However, the functional and structural characterization of individual members of the SMN complex, such as SMN, Gemin3, and Gemin5, have accumulated evidence for the additional roles of these proteins, unveiling their participation in other RNA-mediated events. In particular, Gemin5 is a multidomain protein that comprises tryptophan-aspartic acid (WD) repeat motifs at the N-terminal region, a dimerization domain at the middle region, and a non-canonical RNA-binding domain at the C-terminal end of the protein. Beyond small nuclear RNA (snRNA) recognition, Gemin5 interacts with a selective group of mRNA targets in the cell environment and plays a key role in reprogramming translation depending on the RNA partner and the cellular conditions. Here, we review recent studies on the SMN complex, with emphasis on the individual components regarding their involvement in cellular processes critical for cell survival.
MeSH term(s)	Animals ; Humans ; Motor Neurons/metabolism ; Motor Neurons/pathology ; Protein Biosynthesis ; Protein Multimerization ; Ribonucleoproteins, Small Nuclear/chemistry ; Ribonucleoproteins, Small Nuclear/genetics ; Ribonucleoproteins, Small Nuclear/metabolism ; Ribosomes/metabolism ; SMN Complex Proteins/chemistry ; SMN Complex Proteins/genetics ; SMN Complex Proteins/metabolism
Chemical Substances	Ribonucleoproteins, Small Nuclear ; SMN Complex Proteins
Language	English
Publishing date	2020-05-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21113868
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Article ; Online: Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences.

Lozano, Gloria / Francisco-Velilla, Rosario / Martinez-Salas, Encarnacion

Open biology

2018 Volume 8, Issue 11

Abstract: Beyond the general cap-dependent translation initiation, eukaryotic organisms use alternative mechanisms to initiate protein synthesis. Internal ribosome entry site (IRES) elements ... ...

Abstract	Beyond the general cap-dependent translation initiation, eukaryotic organisms use alternative mechanisms to initiate protein synthesis. Internal ribosome entry site (IRES) elements are
MeSH term(s)	Animals ; Humans ; Internal Ribosome Entry Sites/physiology ; Nucleotide Motifs/physiology ; Peptide Chain Initiation, Translational/physiology ; RNA-Binding Proteins/metabolism
Chemical Substances	Internal Ribosome Entry Sites ; RNA-Binding Proteins
Language	English
Publishing date	2018-11-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2630944-0
ISSN	2046-2441 ; 2046-2441
ISSN (online)	2046-2441
ISSN	2046-2441
DOI	10.1098/rsob.180155
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