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Article ; Online: The nuclear transport factor CSE1 drives macronuclear volume increase and macronuclear node coalescence in

McGillivary, Rebecca M / Sood, Pranidhi / Hammar, Katherine / Marshall, Wallace F

iScience

2023 Volume 26, Issue 8, Page(s) 107318

Abstract: ... Stentor ... ...

Abstract	Stentor coeruleus
Language	English
Publishing date	2023-07-10
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107318
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Article ; Online: Modular, cascade-like transcriptional program of regeneration in

Sood, Pranidhi / Lin, Athena / Yan, Connie / McGillivary, Rebecca / Diaz, Ulises / Makushok, Tatyana / Nadkarni, Ambika V / Tang, Sindy K Y / Marshall, Wallace F

eLife

2022 Volume 11

Abstract: The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and ... ...

Abstract	The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis in a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half regenerates an intact cell. We used RNA sequencing (RNAseq) to assay the dynamic changes in Stentor's transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA -binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes. By comparing transcriptional profiles of different regeneration events, we identified distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression after blocking translation, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the RNA-binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. RNAi-mediated knockdown experiments indicate that Pumilio is required for regenerating oral structures of the correct size. E2F is involved in the completion of regeneration but is dispensable for earlier steps. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.
MeSH term(s)	Base Sequence ; Ciliophora/genetics ; Humans ; RNA Interference ; Sequence Analysis, RNA ; Transcriptome
Language	English
Publishing date	2022-08-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.80778
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Article ; Online: Determining protein polarization proteome-wide using physical dissection of individual Stentor coeruleus cells.

Lin, Athena / Piehowski, Paul D / Tsai, Chia-Feng / Makushok, Tatyana / Yi, Lian / Diaz, Ulises / Yan, Connie / Summers, Diana / Sood, Pranidhi / Smith, Richard D / Liu, Tao / Marshall, Wallace F

Current biology : CB

2022 Volume 32, Issue 10, Page(s) 2300–2308.e4

Abstract: Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell. ...

Abstract	Cellular components are non-randomly arranged with respect to the shape and polarity of the whole cell.
MeSH term(s)	Cell Polarity/genetics ; Ciliophora/genetics ; Morphogenesis/genetics ; Proteome/metabolism ; Proteomics ; Saccharomyces cerevisiae
Chemical Substances	Proteome
Language	English
Publishing date	2022-04-20
Publishing country	England
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	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2022.03.078
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Article ; Online: Stochastic de-repression of Rhodopsins in single photoreceptors of the fly retina.

Sood, Pranidhi / Johnston, Robert J / Kussell, Edo

PLoS computational biology

2012 Volume 8, Issue 2, Page(s) e1002357

Abstract: The photoreceptors of the Drosophila compound eye are a classical model for studying cell fate specification. Photoreceptors (PRs) are organized in bundles of eight cells with two major types - inner PRs involved in color vision and outer PRs involved in ...

Abstract	The photoreceptors of the Drosophila compound eye are a classical model for studying cell fate specification. Photoreceptors (PRs) are organized in bundles of eight cells with two major types - inner PRs involved in color vision and outer PRs involved in motion detection. In wild type flies, most PRs express a single type of Rhodopsin (Rh): inner PRs express either Rh3, Rh4, Rh5 or Rh6 and outer PRs express Rh1. In outer PRs, the K(50) homeodomain protein Dve is a key repressor that acts to ensure exclusive Rh expression. Loss of Dve results in de-repression of Rhodopsins in outer PRs, and leads to a wide distribution of expression levels. To quantify these effects, we introduce an automated image analysis method to measure Rhodopsin levels at the single cell level in 3D confocal stacks. Our sensitive methodology reveals cell-specific differences in Rhodopsin distributions among the outer PRs, observed over a developmental time course. We show that Rhodopsin distributions are consistent with a two-state model of gene expression, in which cells can be in either high or basal states of Rhodopsin production. Our model identifies a significant role of post-transcriptional regulation in establishing the two distinct states. The timescale for interconversion between basal and high states is shown to be on the order of days. Our results indicate that even in the absence of Dve, the Rhodopsin regulatory network can maintain highly stable states. We propose that the role of Dve in outer PRs is to buffer against rare fluctuations in this network.
MeSH term(s)	Animals ; Drosophila/genetics ; Drosophila/growth & development ; Drosophila/metabolism ; Drosophila/physiology ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Image Processing, Computer-Assisted ; Microscopy, Confocal ; Models, Genetic ; Photoreceptor Cells, Invertebrate/metabolism ; Photoreceptor Cells, Invertebrate/physiology ; Reproducibility of Results ; Retina/cytology ; Sensory Rhodopsins/analysis ; Sensory Rhodopsins/genetics ; Sensory Rhodopsins/metabolism ; Sensory Rhodopsins/physiology ; Stochastic Processes
Chemical Substances	Drosophila Proteins ; Homeodomain Proteins ; Sensory Rhodopsins ; dve protein, Drosophila
Language	English
Publishing date	2012-02-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1002357
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Article ; Online: Microfluidic guillotine for single-cell wound repair studies.

Blauch, Lucas R / Gai, Ya / Khor, Jian Wei / Sood, Pranidhi / Marshall, Wallace F / Tang, Sindy K Y

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

2017 Volume 114, Issue 28, Page(s) 7283–7288

Abstract: Wound repair is a key feature distinguishing living from nonliving matter. Single cells are increasingly recognized to be capable of healing wounds. The lack of reproducible, high-throughput wounding methods has hindered single-cell wound repair studies. ...

Abstract	Wound repair is a key feature distinguishing living from nonliving matter. Single cells are increasingly recognized to be capable of healing wounds. The lack of reproducible, high-throughput wounding methods has hindered single-cell wound repair studies. This work describes a microfluidic guillotine for bisecting single
MeSH term(s)	Animals ; Cell Membrane/metabolism ; Ciliophora/physiology ; Dimethylpolysiloxanes/chemistry ; Microfluidic Analytical Techniques ; Microfluidics ; Oocytes/cytology ; Pressure ; Reproducibility of Results ; Time Factors ; Viscosity ; Wound Healing ; Xenopus
Chemical Substances	Dimethylpolysiloxanes ; baysilon (63148-62-9)
Language	English
Publishing date	2017-06-26
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.1705059114
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Article: Cell-type-specific signatures of microRNAs on target mRNA expression.

Sood, Pranidhi / Krek, Azra / Zavolan, Mihaela / Macino, Giuseppe / Rajewsky, Nikolaus

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

2006 Volume 103, Issue 8, Page(s) 2746–2751

Abstract: Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue profiles has not been systematically elucidated. Here, we ... ...

Abstract	Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue profiles has not been systematically elucidated. Here, we show that predicted human mRNA targets of several highly tissue-specific miRNAs are typically expressed in the same tissue as the miRNA but at significantly lower levels than in tissues where the miRNA is not present. Conversely, highly expressed genes are often enriched in mRNAs that do not have the recognition motifs for the miRNAs expressed in these tissues. Together, our data support the hypothesis that miRNA expression broadly contributes to tissue specificity of mRNA expression in many human tissues. Based on these insights, we apply a computational tool to directly correlate 3' UTR motifs with changes in mRNA levels upon miRNA overexpression or knockdown. We show that this tool can identify functionally important 3' UTR motifs without cross-species comparison.
MeSH term(s)	3' Untranslated Regions/genetics ; 3' Untranslated Regions/metabolism ; Animals ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; MicroRNAs/analysis ; MicroRNAs/genetics ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Tissue Distribution
Chemical Substances	3' Untranslated Regions ; MicroRNAs ; RNA, Messenger
Language	English
Publishing date	2006-02-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0511045103
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Article ; Online: Non-model model organisms.

Russell, James J / Theriot, Julie A / Sood, Pranidhi / Marshall, Wallace F / Landweber, Laura F / Fritz-Laylin, Lillian / Polka, Jessica K / Oliferenko, Snezhana / Gerbich, Therese / Gladfelter, Amy / Umen, James / Bezanilla, Magdalena / Lancaster, Madeline A / He, Shuonan / Gibson, Matthew C / Goldstein, Bob / Tanaka, Elly M / Hu, Chi-Kuo / Brunet, Anne

BMC biology

2017 Volume 15, Issue 1, Page(s) 55

Abstract: Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to ... ...

Abstract	Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
MeSH term(s)	Animals ; Biology ; Eukaryota ; Models, Animal ; Plants
Language	English
Publishing date	2017-06-29
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2133020-7
ISSN	1741-7007 ; 1741-7007
ISSN (online)	1741-7007
ISSN	1741-7007
DOI	10.1186/s12915-017-0391-5
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Article ; Online: The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.

Slabodnick, Mark M / Ruby, J Graham / Reiff, Sarah B / Swart, Estienne C / Gosai, Sager / Prabakaran, Sudhakaran / Witkowska, Ewa / Larue, Graham E / Fisher, Susan / Freeman, Robert M / Gunawardena, Jeremy / Chu, William / Stover, Naomi A / Gregory, Brian D / Nowacki, Mariusz / Derisi, Joseph / Roy, Scott W / Marshall, Wallace F / Sood, Pranidhi

Current biology : CB

2017 Volume 27, Issue 4, Page(s) 569–575

Abstract: The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as ... ...

Abstract	The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities-if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. These biologists were also drawn to Stentor because it exhibits a rich repertoire of behaviors, including light avoidance, mechanosensitive contraction, food selection, and even the ability to habituate to touch, a simple form of learning usually seen in higher organisms [4]. While early microsurgical approaches demonstrated a startling array of regenerative and morphogenetic processes in this single-celled organism, Stentor was never developed as a molecular model system. We report the sequencing of the Stentor coeruleus macronuclear genome and reveal key features of the genome. First, we find that Stentor uses the standard genetic code, suggesting that ciliate-specific genetic codes arose after Stentor branched from other ciliates. We also discover that ploidy correlates with Stentor's cell size. Finally, in the Stentor genome, we discover the smallest spliceosomal introns reported for any species. The sequenced genome opens the door to molecular analysis of single-cell regeneration in Stentor.
MeSH term(s)	Ciliophora/genetics ; Genome, Protozoan ; Introns/genetics ; Phylogeny ; Spliceosomes/metabolism ; Whole Genome Sequencing
Keywords	covid19
Language	English
Publishing date	2017-02-09
Publishing country	England
Document type	Journal Article
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2016.12.057
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Article ; Online: Interlocked feedforward loops control cell-type-specific Rhodopsin expression in the Drosophila eye.

Johnston, Robert J / Otake, Yoshiaki / Sood, Pranidhi / Vogt, Nina / Behnia, Rudy / Vasiliauskas, Daniel / McDonald, Elizabeth / Xie, Baotong / Koenig, Sebastian / Wolf, Reinhard / Cook, Tiffany / Gebelein, Brian / Kussell, Edo / Nakagoshi, Hideki / Desplan, Claude

Cell

2011 Volume 145, Issue 6, Page(s) 956–968

Abstract: How complex networks of activators and repressors lead to exquisitely specific cell-type determination during development is poorly understood. In the Drosophila eye, expression patterns of Rhodopsins define at least eight functionally distinct though ... ...

Abstract	How complex networks of activators and repressors lead to exquisitely specific cell-type determination during development is poorly understood. In the Drosophila eye, expression patterns of Rhodopsins define at least eight functionally distinct though related subtypes of photoreceptors. Here, we describe a role for the transcription factor gene defective proventriculus (dve) as a critical node in the network regulating Rhodopsin expression. dve is a shared component of two opposing, interlocked feedforward loops (FFLs). Orthodenticle and Dve interact in an incoherent FFL to repress Rhodopsin expression throughout the eye. In R7 and R8 photoreceptors, a coherent FFL relieves repression by Dve while activating Rhodopsin expression. Therefore, this network uses repression to restrict and combinatorial activation to induce cell-type-specific expression. Furthermore, Dve levels are finely tuned to yield cell-type- and region-specific repression or activation outcomes. This interlocked FFL motif may be a general mechanism to control terminal cell-fate specification.
MeSH term(s)	Animals ; Drosophila/cytology ; Drosophila/embryology ; Drosophila/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Eye/embryology ; Feedback, Physiological ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Homeodomain Proteins/metabolism ; Photoreceptor Cells, Invertebrate/metabolism ; Rhodopsin/genetics ; Transcription Factors/metabolism
Chemical Substances	Drosophila Proteins ; Homeodomain Proteins ; Transcription Factors ; dve protein, Drosophila ; oc protein, Drosophila ; salm protein, Drosophila ; Rhodopsin (9009-81-8)
Language	English
Publishing date	2011-05-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2011.05.003
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Article: A genome-wide map of conserved microRNA targets in C. elegans.

Lall, Sabbi / Grün, Dominic / Krek, Azra / Chen, Kevin / Wang, Yi-Lu / Dewey, Colin N / Sood, Pranidhi / Colombo, Teresa / Bray, Nicolas / Macmenamin, Philip / Kao, Huey-Ling / Gunsalus, Kristin C / Pachter, Lior / Piano, Fabio / Rajewsky, Nikolaus

Current biology : CB

2006 Volume 16, Issue 5, Page(s) 460–471

Abstract: Background: Metazoan miRNAs regulate protein-coding genes by binding the 3' UTR of cognate mRNAs. Identifying targets for the 115 known C. elegans miRNAs is essential for understanding their function.: Results: By using a new version of PicTar and ... ...

Abstract	Background: Metazoan miRNAs regulate protein-coding genes by binding the 3' UTR of cognate mRNAs. Identifying targets for the 115 known C. elegans miRNAs is essential for understanding their function. Results: By using a new version of PicTar and sequence alignments of three nematodes, we predict that miRNAs regulate at least 10% of C. elegans genes through conserved interactions. We have developed a new experimental pipeline to assay 3' UTR-mediated posttranscriptional gene regulation via an endogenous reporter expression system amenable to high-throughput cloning, demonstrating the utility of this system using one of the most intensely studied miRNAs, let-7. Our expression analyses uncover several new potential let-7 targets and suggest a new let-7 activity in head muscle and neurons. To explore genome-wide trends in miRNA function, we analyzed functional categories of predicted target genes, finding that one-third of C. elegans miRNAs target gene sets are enriched for specific functional annotations. We have also integrated miRNA target predictions with other functional genomic data from C. elegans. Conclusions: At least 10% of C. elegans genes are predicted miRNA targets, and a number of nematode miRNAs seem to regulate biological processes by targeting functionally related genes. We have also developed and successfully utilized an in vivo system for testing miRNA target predictions in likely endogenous expression domains. The thousands of genome-wide miRNA target predictions for nematodes, humans, and flies are available from the PicTar website and are linked to an accessible graphical network-browsing tool allowing exploration of miRNA target predictions in the context of various functional genomic data resources.
MeSH term(s)	Animals ; Base Sequence ; Caenorhabditis elegans/anatomy & histology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Chromosome Mapping/methods ; Computational Biology/methods ; Conserved Sequence ; Gene Expression Profiling/methods ; Gene Expression Regulation ; Genes, Reporter ; Genome, Helminth ; Genomics/methods ; MicroRNAs/physiology ; Molecular Sequence Data ; Sequence Alignment
Chemical Substances	MicroRNAs
Language	English
Publishing date	2006-03-07
Publishing country	England
Document type	Evaluation Studies ; 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	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2006.01.050
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