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Article ; Online: Conditional Toxin Splicing Using a Split Intein System.

Alford, Spencer C / O'Sullivan, Connor / Howard, Perry L

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1495, Page(s) 197–216

Abstract: Protein toxin splicing mediated by split inteins can be used as a strategy for conditional cell ablation. The approach requires artificial fragmentation of a potent protein toxin and tethering each toxin fragment to a split intein fragment. The toxin- ... ...

Abstract	Protein toxin splicing mediated by split inteins can be used as a strategy for conditional cell ablation. The approach requires artificial fragmentation of a potent protein toxin and tethering each toxin fragment to a split intein fragment. The toxin-intein fragments are, in turn, fused to dimerization domains, such that addition of a dimerizing agent reconstitutes the split intein. These chimeric toxin-intein fusions remain nontoxic until the dimerizer is added, resulting in activation of intein splicing and ligation of toxin fragments to form an active toxin. Considerations for the engineering and implementation of conditional toxin splicing (CTS) systems include: choice of toxin split site, split site (extein) chemistry, and temperature sensitivity. The following method outlines design criteria and implementation notes for CTS using a previously engineered system for splicing a toxin called sarcin, as well as for developing alternative CTS systems.
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6451-2_13
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Article: Protecting Pax6 3' UTR from MicroRNA-7 Partially Restores PAX6 in Islets from an Aniridia Mouse Model.

Yongblah, Kevin / Alford, Spencer C / Ryan, Bridget C / Chow, Robert L / Howard, Perry L

Molecular therapy. Nucleic acids

2018 Volume 13, Page(s) 144–153

Abstract: Aniridia is a rare congenital syndrome that is associated with reduced visual acuity and progressive loss of vision. Aniridia patients may also develop systemic health issues associated with defects in the pancreas, digestive, and central nervous systems. ...

Abstract	Aniridia is a rare congenital syndrome that is associated with reduced visual acuity and progressive loss of vision. Aniridia patients may also develop systemic health issues associated with defects in the pancreas, digestive, and central nervous systems. The spectrum of symptoms associated with aniridia is due to haploinsufficiency of the paired box 6 gene (PAX6) and its role in the development and maintenance of the affected tissues. Here, we isolated pancreatic islets from mice heterozygous for Pax6 to test whether a Pax6-specific miRNA suppression (target protector) strategy can restore PAX6 protein levels. We show that miR-7 and miR-375 target specific sites within the Pax6 3' UTR in a mouse pancreatic β-insulinoma cell line. Tough decoys (Tuds) against miR-7 and miR-375 increase expression of a mouse Pax6 3' UTR luciferase reporter and increase PAX6 protein levels in these cells. Finally, we demonstrate that the shielding of the miR-7 binding site with a target protector restores PAX6 protein levels in the Pax6 heterozygous islets. The data presented here represent a proof of concept for RNA-based therapy for the progressive defects associated with aniridia and suggest the target protector approach may be a useful therapeutic strategy for other haploinsufficiency diseases.
Language	English
Publishing date	2018-09-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2018.08.018
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Article ; Online: Development of a Protease Biosensor Based on a Dimerization-Dependent Red Fluorescent Protein.

Mitchell, Aaron C / Alford, Spencer C / Hunter, Sean A / Kannan, Deepti / Parra Sperberg, R Andres / Chang, Cheryl H / Cochran, Jennifer R

ACS chemical biology

2017 Volume 13, Issue 1, Page(s) 66–72

Abstract: Dysregulated activity of the protease matriptase is a key contributor to aggressive tumor growth, cancer metastasis, and osteoarthritis. Methods for the detection and quantification of matriptase activity and inhibition would be useful tools. To address ... ...

Abstract	Dysregulated activity of the protease matriptase is a key contributor to aggressive tumor growth, cancer metastasis, and osteoarthritis. Methods for the detection and quantification of matriptase activity and inhibition would be useful tools. To address this need, we developed a matriptase-sensitive protein biosensor based on a dimerization-dependent red fluorescent protein (ddRFP) reporter system. In this platform, two adjoining protein domains, connected by a protease-labile linker, produce fluorescence when assembled and are nonfluorescent when the linker is cleaved by matriptase. A panel of ddRFP-based matriptase biosensor designs was created that contained different linker lengths between the protein domains. These constructs were characterized for linker-specific cleavage, matriptase activity, and matriptase selectivity; a biosensor containing a RSKLRVGGH linker (termed B4) was expressed at high yields and displayed both high catalytic efficiency and matriptase specificity. This biosensor detects matriptase inhibition by soluble and yeast cell surface expressed inhibitor domains with up to a 5-fold dynamic range and also detects matriptase activity expressed by human cancer cell lines. In addition to matriptase, we highlight a strategy that can be used to create effective biosensors for quantifying activity and inhibition of other proteases of interest.
MeSH term(s)	Biosensing Techniques/methods ; Blotting, Western ; Cell Line, Tumor ; Drug Evaluation, Preclinical/instrumentation ; Drug Evaluation, Preclinical/methods ; Escherichia coli/genetics ; Humans ; Luminescent Proteins/chemistry ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Peptide Hydrolases/analysis ; Peptide Hydrolases/metabolism ; Protein Multimerization ; Serine Endopeptidases/analysis ; Serine Endopeptidases/metabolism ; Serine Proteinase Inhibitors/pharmacology ; Structure-Activity Relationship ; Red Fluorescent Protein
Chemical Substances	Luminescent Proteins ; Serine Proteinase Inhibitors ; Peptide Hydrolases (EC 3.4.-) ; Serine Endopeptidases (EC 3.4.21.-) ; matriptase (EC 3.4.21.-)
Language	English
Publishing date	2017-12-12
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.
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.7b00715
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Article ; Online: Dimerization-dependent green and yellow fluorescent proteins.

Alford, Spencer C / Ding, Yidan / Simmen, Thomas / Campbell, Robert E

ACS synthetic biology

2012 Volume 1, Issue 12, Page(s) 569–575

Abstract: Dimerization-dependent fluorescent proteins (ddFP) are a recently introduced class of genetically encoded reporters that can be used for the detection of protein interactions in live cells. The progenitor of this class of tools was a red fluorescent ddFP ...

Abstract	Dimerization-dependent fluorescent proteins (ddFP) are a recently introduced class of genetically encoded reporters that can be used for the detection of protein interactions in live cells. The progenitor of this class of tools was a red fluorescent ddFP (ddRFP) derived from a homodimeric variant of Discosoma red fluorescent protein. Here, we describe the engineering and application of an expanded palette of ddFPs, which includes green (ddGFP) and yellow (ddYFP) variants. These optimized variants offer several advantages relative to ddRFP including increased in vitro contrast and brightness for ddGFP and increased brightness and a lowered pK a for ddYFP. We demonstrate that both variants are useful as biosensors for protease activity in live cells. Using the ddGFP tool, we generated a highly effective indicator of endomembrane proximity that can be used to image the mitochondria-associated membrane (MAM) interface of endoplasmic reticulum (ER) and mitochondria.
MeSH term(s)	Bacterial Proteins/analysis ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Biosensing Techniques/methods ; Endoplasmic Reticulum/metabolism ; Fluorescent Antibody Technique/methods ; Green Fluorescent Proteins/analysis ; Green Fluorescent Proteins/chemistry ; Green Fluorescent Proteins/metabolism ; Humans ; Luminescent Proteins/analysis ; Luminescent Proteins/chemistry ; Luminescent Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Protein Multimerization
Chemical Substances	Bacterial Proteins ; Luminescent Proteins ; yellow fluorescent protein, Bacteria ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2012-08-14
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/sb300050j
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Article ; Online: A fluorogenic red fluorescent protein heterodimer.

Alford, Spencer C / Abdelfattah, Ahmed S / Ding, Yidan / Campbell, Robert E

Chemistry & biology

2012 Volume 19, Issue 3, Page(s) 353–360

Abstract: The expanding repertoire of genetically encoded biosensors constructed from variants of Aequorea victoria green fluorescent protein (GFP) enable the imaging of a variety of intracellular biochemical processes. To facilitate the imaging of multiple ... ...

Abstract	The expanding repertoire of genetically encoded biosensors constructed from variants of Aequorea victoria green fluorescent protein (GFP) enable the imaging of a variety of intracellular biochemical processes. To facilitate the imaging of multiple biosensors in a single cell, we undertook the development of a dimerization-dependent red fluorescent protein (ddRFP) that provides an alternative strategy for biosensor construction. An extensive process of rational engineering and directed protein evolution led to the discovery of a ddRFP with a K(d) of 33 μM and a 10-fold increase in fluorescence upon heterodimer formation. We demonstrate that the dimerization-dependent fluorescence of ddRFP can be used for detection of a protein-protein interaction in vitro, imaging of the reversible Ca²⁺-dependent association of calmodulin and M13 in live cells, and imaging of caspase-3 activity during apoptosis.
MeSH term(s)	Apoptosis ; Biosensing Techniques ; Calcium/metabolism ; Calmodulin/metabolism ; Caspase 3/metabolism ; Dimerization ; Fluorescence Resonance Energy Transfer ; HeLa Cells ; Humans ; Luminescent Proteins/chemistry ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Protein Binding ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Red Fluorescent Protein
Chemical Substances	Calmodulin ; Luminescent Proteins ; Recombinant Proteins ; Caspase 3 (EC 3.4.22.-) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2012-03-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	917827-2
ISSN	1879-1301 ; 1074-5521
ISSN (online)	1879-1301
ISSN	1074-5521
DOI	10.1016/j.chembiol.2012.01.006
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Article ; Online: Conditional protein splicing of α-sarcin in live cells.

Alford, Spencer C / O'Sullivan, Connor / Obst, Jon / Christie, Jennifer / Howard, Perry L

Molecular bioSystems

2014 Volume 10, Issue 4, Page(s) 831–837

Abstract: Protein splicing technology harnesses the ability of inteins to ligate protein fragments, forming a mature protein. This report describes our effort to engineer rapamycin-dependent protein splicing of a ribotoxin, called α-sarcin. Engineering this system ...

Abstract	Protein splicing technology harnesses the ability of inteins to ligate protein fragments, forming a mature protein. This report describes our effort to engineer rapamycin-dependent protein splicing of a ribotoxin, called α-sarcin. Engineering this system required the investigation of important splicing parameters, including extein context and splicing temperature. We show α-sarcin splicing is dependent on rapamycin, is inducible with rapid kinetics, and triggers apoptosis in HeLa cells. These findings establish a proof-of-concept for a conditional cell ablation strategy.
MeSH term(s)	Apoptosis/genetics ; Cell Line, Tumor ; Endoribonucleases/biosynthesis ; Endoribonucleases/genetics ; Fungal Proteins/biosynthesis ; Fungal Proteins/genetics ; Green Fluorescent Proteins/genetics ; HeLa Cells ; Humans ; Inteins/genetics ; Protein Engineering/methods ; Protein Folding ; Protein Splicing/genetics ; Sirolimus/pharmacology
Chemical Substances	Fungal Proteins ; alpha-sarcin (1407-48-3) ; Green Fluorescent Proteins (147336-22-9) ; Endoribonucleases (EC 3.1.-) ; Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2014-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2188635-0
ISSN	1742-2051 ; 1742-206X
ISSN (online)	1742-2051
ISSN	1742-206X
DOI	10.1039/c3mb70387h
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Article ; Online: Optogenetic reporters.

Alford, Spencer C / Wu, Jiahui / Zhao, Yongxin / Campbell, Robert E / Knöpfel, Thomas

Biology of the cell

2013 Volume 105, Issue 1, Page(s) 14–29

Abstract: The discovery of naturally evolved fluorescent proteins and their subsequent tuning by protein engineering provided the basis for a large family of genetically encoded biosensors that report a variety of physicochemical processes occurring in living ... ...

Abstract	The discovery of naturally evolved fluorescent proteins and their subsequent tuning by protein engineering provided the basis for a large family of genetically encoded biosensors that report a variety of physicochemical processes occurring in living tissue. These optogenetic reporters are powerful tools for live-cell microscopy and quantitative analysis at the subcellular level. In this review, we present an overview of the transduction mechanisms that have been exploited for engineering these genetically encoded reporters. Finally, we discuss current and future efforts towards the combined use of various optogenetic actuators and reporters for simultaneously controlling and imaging the physiology of cells and tissues.
MeSH term(s)	Biosensing Techniques ; Genes, Reporter ; Humans ; Microscopy, Fluorescence ; Optogenetics/methods ; Protein Engineering/methods ; Proteins/chemistry
Chemical Substances	Proteins
Language	English
Publishing date	2013-01
Publishing country	England
Document type	Journal Article
ZDB-ID	245745-3
ISSN	1768-322X ; 0399-0311 ; 0248-4900
ISSN (online)	1768-322X
ISSN	0399-0311 ; 0248-4900
DOI	10.1111/boc.201200054
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Zs.A 758: Show issues

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Article ; Online: High-throughput analysis and protein engineering using microcapillary arrays.

Chen, Bob / Lim, Sungwon / Kannan, Arvind / Alford, Spencer C / Sunden, Fanny / Herschlag, Daniel / Dimov, Ivan K / Baer, Thomas M / Cochran, Jennifer R

Nature chemical biology

2015 Volume 12, Issue 2, Page(s) 76–81

Abstract: We describe a multipurpose technology platform, termed μSCALE (microcapillary single-cell analysis and laser extraction), that enables massively parallel, quantitative biochemical and biophysical measurements on millions of protein variants expressed ... ...

Abstract	We describe a multipurpose technology platform, termed μSCALE (microcapillary single-cell analysis and laser extraction), that enables massively parallel, quantitative biochemical and biophysical measurements on millions of protein variants expressed from yeast or bacteria. μSCALE spatially segregates single cells within a microcapillary array, enabling repeated imaging, cell growth and protein expression. We performed high-throughput analysis of cells and their protein products using a range of fluorescent assays, including binding-affinity measurements and dynamic enzymatic assays. A precise laser-based extraction method allows rapid recovery of live clones and their genetic material from microcapillaries for further study. With μSCALE, we discovered a new antibody against a clinical cancer target, evolved a fluorescent protein biosensor and engineered an enzyme to reduce its sensitivity to its inhibitor. These protein analysis and engineering applications each have unique assay requirements and different host organisms, highlighting the flexibility and technical capabilities of the μSCALE platform.
MeSH term(s)	Bacterial Proteins/analysis ; Biosensing Techniques/instrumentation ; Chemistry Techniques, Analytical/instrumentation ; Flow Cytometry ; Fluorescent Dyes/chemistry ; Fungal Proteins/analysis ; Gene Library ; Protein Array Analysis/instrumentation ; Protein Binding ; Protein Engineering/instrumentation ; Single-Cell Analysis/instrumentation
Chemical Substances	Bacterial Proteins ; Fluorescent Dyes ; Fungal Proteins
Language	English
Publishing date	2015-12-07
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	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/nchembio.1978
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Zs.A 6251: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Mutagenesis of ARS2 Domains To Assess Possible Roles in Cell Cycle Progression and MicroRNA and Replication-Dependent Histone mRNA Biogenesis.

O'Sullivan, Connor / Christie, Jennifer / Pienaar, Marcus / Gambling, Jake / Nickerson, Philip E B / Alford, Spencer C / Chow, Robert L / Howard, Perry L

Molecular and cellular biology

2015 Volume 35, Issue 21, Page(s) 3753–3767

Abstract: ARS2 is a regulator of RNA polymerase II transcript processing through its role in the maturation of distinct nuclear cap-binding complex (CBC)-controlled RNA families. In this study, we examined ARS2 domain function in transcript processing. Structural ... ...

Abstract	ARS2 is a regulator of RNA polymerase II transcript processing through its role in the maturation of distinct nuclear cap-binding complex (CBC)-controlled RNA families. In this study, we examined ARS2 domain function in transcript processing. Structural modeling based on the plant ARS2 orthologue, SERRATE, revealed 2 previously uncharacterized domains in mammalian ARS2: an N-terminal domain of unknown function (DUF3546), which is also present in SERRATE, and an RNA recognition motif (RRM) that is present in metazoan ARS2 but not in plants. Both the DUF3546 and zinc finger domain (ZnF) were required for association with microRNA and replication-dependent histone mRNA. Mutations in the ZnF disrupted interaction with FLASH, a key component in histone pre-mRNA processing. Mutations targeting the Mid domain implicated it in DROSHA interaction and microRNA biogenesis. The unstructured C terminus was required for interaction with the CBC protein CBP20, while the RRM was required for cell cycle progression and for binding to FLASH. Together, our results support a bridging model in which ARS2 plays a central role in RNA recognition and processing through multiple protein and RNA interactions.
MeSH term(s)	Amino Acid Sequence ; Animals ; Calcium-Binding Proteins/metabolism ; Cell Cycle ; Cells, Cultured ; Histones/genetics ; Histones/metabolism ; Mice, Inbred C57BL ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nuclear Cap-Binding Protein Complex ; Nuclear Proteins/chemistry ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Protein Structure, Tertiary ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; S Phase ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic ; Up-Regulation
Chemical Substances	Ars2 protein, mouse ; Calcium-Binding Proteins ; Casp8ap2 protein, mouse ; Histones ; MicroRNAs ; Nuclear Cap-Binding Protein Complex ; Nuclear Proteins ; RNA, Messenger ; Transcription Factors
Language	English
Publishing date	2015-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.00272-15
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Article ; Online: Mutagenesis of ARS2 Domains To Assess Possible Roles in Cell Cycle Progression and MicroRNA and Replication-Dependent Histone mRNA Biogenesis

O'Sullivan, Connor / Christie, Jennifer / Pienaar, Marcus / Gambling, Jake / Nickerson, Philip E. B. / Alford, Spencer C. / Chow, Robert L. / Howard, Perry L.

Molecular and Cellular Biology. 2015 Nov. 1, v. 35, no. 21 p.3753-3767

2015

Abstract	ARS2 is a regulator of RNA polymerase II transcript processing through its role in the maturation of distinct nuclear cap-binding complex (CBC)-controlled RNA families. In this study, we examined ARS2 domain function in transcript processing. Structural modeling based on the plant ARS2 orthologue, SERRATE, revealed 2 previously uncharacterized domains in mammalian ARS2: an N-terminal domain of unknown function (DUF3546), which is also present in SERRATE, and an RNA recognition motif (RRM) that is present in metazoan ARS2 but not in plants. Both the DUF3546 and zinc finger domain (ZnF) were required for association with microRNA and replication-dependent histone mRNA. Mutations in the ZnF disrupted interaction with FLASH, a key component in histone pre-mRNA processing. Mutations targeting the Mid domain implicated it in DROSHA interaction and microRNA biogenesis. The unstructured C terminus was required for interaction with the CBC protein CBP20, while the RRM was required for cell cycle progression and for binding to FLASH. Together, our results support a bridging model in which ARS2 plays a central role in RNA recognition and processing through multiple protein and RNA interactions.
Keywords	Animalia ; DNA-directed RNA polymerase ; biogenesis ; cell cycle ; histones ; mammals ; microRNA ; models ; mutagenesis ; zinc finger motif
Language	English
Dates of publication	2015-1101
Size	p. 3753-3767.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.00272-15
Database	NAL-Catalogue (AGRICOLA)

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