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Article ; Online: Cytological Approaches to Visualize Intracellular Dynamics of RNA-Binding Proteins at Active Genes in Drosophila.

Singh, Anand K / Lakhotia, Subhash C

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

2022 Volume 2609, Page(s) 271–293

Abstract: Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a family of RNA-binding proteins that modulate multiple aspects of gene activity and RNA processing, including transcription, splicing, localization, translation, and decay of RNA. Interaction of ... ...

Abstract	Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a family of RNA-binding proteins that modulate multiple aspects of gene activity and RNA processing, including transcription, splicing, localization, translation, and decay of RNA. Interaction of hnRNPs with RNA is a highly dynamic but regulated process. Poly(ADP-ribose) polymerase (PARP)-dependent PARylation of different hnRNPs is a well-known posttranslational modification that affects their interactions with RNA. Here, we described a protocol for in situ localization of RNA-binding proteins (RBPs) on giant polytene chromosomes in Drosophila larval salivary glands, which have been widely used to visualize the dynamic binding profiles of various RBPs and other transcription-related proteins at specific loci on chromosomes. This chapter also includes a stepwise description of RNA:RNA in situ hybridization, in conjunction with immunostaining, using polytene chromosome squashes or intact tissues. We also highlight advanced live cell imaging methods, including FRAP and FLIP, using transgenic lines that express fluorescent-tagged hnRNPs. These cytological approaches can be used to visualize the localization of RNA-binding proteins and their interacting RNAs under different cellular conditions.
MeSH term(s)	Animals ; Drosophila/genetics ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Heterogeneous-Nuclear Ribonucleoproteins/genetics ; Heterogeneous-Nuclear Ribonucleoproteins/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Poly(ADP-ribose) Polymerases/metabolism ; Polytene Chromosomes/genetics ; Polytene Chromosomes/metabolism ; RNA/metabolism
Chemical Substances	RNA-Binding Proteins ; Heterogeneous-Nuclear Ribonucleoproteins ; Drosophila Proteins ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; RNA (63231-63-0)
Language	English
Publishing date	2022-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2891-1_16
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Article ; Online: Evidence of slightly increased Pol II pausing in UPF1-depleted

Singh, Anand K / Zhang, Jie / Hebenstreit, Daniel / Brogna, Saverio

microPublication biology

2020 Volume 2020

Language	English
Publishing date	2020-10-16
Publishing country	United States
Document type	Journal Article
ISSN	2578-9430
ISSN (online)	2578-9430
DOI	10.17912/micropub.biology.000319
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Article ; Online: HDAC6 inhibition reverses long-term doxorubicin-induced cognitive dysfunction by restoring microglia homeostasis and synaptic integrity.

McAlpin, Blake R / Mahalingam, Rajasekaran / Singh, Anand K / Dharmaraj, Shruti / Chrisikos, Taylor T / Boukelmoune, Nabila / Kavelaars, Annemieke / Heijnen, Cobi J

Theranostics

2022 Volume 12, Issue 2, Page(s) 603–619

Abstract: Breast cancer is the most common female malignancy in both the developed and developing world. Doxorubicin is one of the most commonly used chemotherapies for breast cancer. Unfortunately, up to 60% of survivors report long-term chemotherapy-induced ... ...

Abstract	Breast cancer is the most common female malignancy in both the developed and developing world. Doxorubicin is one of the most commonly used chemotherapies for breast cancer. Unfortunately, up to 60% of survivors report long-term chemotherapy-induced cognitive dysfunction (CICD) characterized by deficits in working memory, processing speed and executive function. Currently, no therapeutic standard for treating CICD exists. Here, we hypothesized that treatment with a blood-brain barrier permeable histone deacetylase 6 (HDAC6) inhibitor can successfully reverse long-term doxorubicin-induced cognitive dysfunction.
MeSH term(s)	Animals ; Cognitive Dysfunction/chemically induced ; Cognitive Dysfunction/drug therapy ; Disks Large Homolog 4 Protein/metabolism ; Dose-Response Relationship, Drug ; Doxorubicin/antagonists & inhibitors ; Female ; Hippocampus/cytology ; Hippocampus/drug effects ; Histone Deacetylase 6/antagonists & inhibitors ; Homeostasis/drug effects ; Mice ; Mice, Inbred C57BL ; Microglia/drug effects ; Mitochondria/drug effects ; Pyridazines/pharmacology ; Synapses/drug effects ; Transcription, Genetic/drug effects
Chemical Substances	ACY1083 ; Disks Large Homolog 4 Protein ; Dlg4 protein, mouse ; Pyridazines ; Doxorubicin (80168379AG) ; Hdac6 protein, mouse (EC 3.5.1.98) ; Histone Deacetylase 6 (EC 3.5.1.98)
Language	English
Publishing date	2022-01-01
Publishing country	Australia
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2592097-2
ISSN	1838-7640 ; 1838-7640
ISSN (online)	1838-7640
ISSN	1838-7640
DOI	10.7150/thno.67410
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Article ; Online: The hnRNP A1 homolog Hrb87F/Hrp36 is important for telomere maintenance in Drosophila melanogaster.

Singh, Anand K / Lakhotia, Subhash C

Chromosoma

2015 Volume 125, Issue 3, Page(s) 373–388

Abstract: Unlike the telomerase-dependent mammalian telomeres, HeT-A, TART, and TAHRE (HTT) retroposon arrays regulate Drosophila telomere length. Cap prevents telomeric associations (TAs) and telomeric fusions (TFs). Our results suggest important roles of Hrb87F ... ...

Abstract	Unlike the telomerase-dependent mammalian telomeres, HeT-A, TART, and TAHRE (HTT) retroposon arrays regulate Drosophila telomere length. Cap prevents telomeric associations (TAs) and telomeric fusions (TFs). Our results suggest important roles of Hrb87F in telomeric HTT array and cap maintenance in Drosophila. All chromosome arms, except 2L, in Df(3R)Hrb87F homozygotes (Hrb87F-null) displayed significantly elongated telomeres with amplified HTT arrays and high TAs, all of which resolved without damage. Presence of FLAG-tagged Hrb87F (FLAG-Hrb87F) on cap and subtelomeric regions following hsFLAG-Hrb87F transgene expression in Df(3R)Hrb87F homozygotes suppressed TAs without affecting telomere length. A normal X-chromosome telomere expanded within five generations in Hrb87F-null background and displayed high TAs, but not when hsFLAG-Hrb87F was co-expressed. Tel (1) /Gaiano line or HP1 loss-of-function mutant-derived expanded telomeres carry Hrb87F on cap and HTT arrays while Hrb87F-null telomeres have HP1 and HOAP on caps and expanded HTT arrays. ISWI, seen only on cap on normal telomeres, was abundant on Hrb87F-null expanded HTT arrays. Extended telomeres derived from Tel (1) (Gaiano) or HP1-null mutation background interact with those from Hrb87F-null, since while the end association frequency was negligible in Df(3R)Hrb87F/+ nuclei, it increased significantly in co-presence of Tel (1) or HP1-null-based expanded telomere/s. Together, these suggest complex interactions between members of the proteome of telomere so that absence of any key member leads to telomere expansion and/or enhanced TAs/TFs. HTT expansion in Hrb87F-null condition is not developmental but a germline event presumably because absence of Hrb87F in germline may deregulate HTT retroposition/replication leading to telomere elongation.
MeSH term(s)	Animals ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster ; Heterogeneous-Nuclear Ribonucleoproteins/genetics ; Heterogeneous-Nuclear Ribonucleoproteins/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Telomere/genetics ; Telomere/metabolism ; Telomere Homeostasis/physiology ; X Chromosome/genetics ; X Chromosome/metabolism
Chemical Substances	Drosophila Proteins ; Heterogeneous-Nuclear Ribonucleoproteins ; Hrb87F protein, Drosophila ; Nuclear Proteins
Language	English
Publishing date	2015-09-16
Publishing country	Austria
Document type	Journal Article
ZDB-ID	203083-4
ISSN	1432-0886 ; 0009-5915
ISSN (online)	1432-0886
ISSN	0009-5915
DOI	10.1007/s00412-015-0540-y
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Article ; Online: Dynamics of hnRNPs and omega speckles in normal and heat shocked live cell nuclei of Drosophila melanogaster.

Singh, Anand K / Lakhotia, Subhash C

Chromosoma

2015 Volume 124, Issue 3, Page(s) 367–383

Abstract: The nucleus limited long-noncoding hsrω-n transcripts, hnRNPs, and some other RNA processing proteins organize nucleoplasmic omega speckles in Drosophila. Unlike other nuclear speckles, omega speckles rapidly disappear following cell stress, while hnRNPs ...

Abstract	The nucleus limited long-noncoding hsrω-n transcripts, hnRNPs, and some other RNA processing proteins organize nucleoplasmic omega speckles in Drosophila. Unlike other nuclear speckles, omega speckles rapidly disappear following cell stress, while hnRNPs and other associated proteins move away from chromosome sites, nucleoplasm, and the disappearing speckles to get uniquely sequestered at hsrω locus. Omega speckles reappear and hnRNPs get redistributed to normal locations during recovery from stress. With a view to understand the dynamics of omega speckles and their associated proteins, we used live imaging of GFP tagged hnRNPs (Hrb87F, Hrb98DE, or Squid) in unstressed and stressed Drosophila cells. Omega speckles display size-dependent mobility in nucleoplasmic domains with significant colocalization with nuclear matrix Tpr/Megator and SAFB proteins, which also accumulate at hsrω gene site after stress. Instead of moving towards the nuclear periphery located hsrω locus following heat shock or colchicine treatment, omega speckles rapidly disappear within nucleoplasm while chromosomal and nucleoplasmic hnRNPs move, stochastically or, more likely, by nuclear matrix-mediated transport to hsrω locus in non-particulate form. Continuing transcription of hsrω during cell stress is essential for sequestering incoming hnRNPs at the site. While recovering from stress, the sequestered hnRNPs are released as omega speckles in ISWI-dependent manner. Photobleaching studies reveal hnRNPs to freely move between nucleoplasm, omega speckles, chromosome regions, and hsrω gene site although their residence periods at chromosomes and hsrω locus are longer. A model for regulation of exchange of hnRNPs between nuclear compartments by hsrω-n transcripts is presented.
MeSH term(s)	Animals ; Cell Nucleus/genetics ; Cell Nucleus/physiology ; Drosophila melanogaster/genetics ; Heterogeneous-Nuclear Ribonucleoproteins/genetics ; Hot Temperature
Chemical Substances	Heterogeneous-Nuclear Ribonucleoproteins
Language	English
Publishing date	2015-09
Publishing country	Austria
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	203083-4
ISSN	1432-0886 ; 0009-5915
ISSN (online)	1432-0886
ISSN	0009-5915
DOI	10.1007/s00412-015-0506-0
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Article ; Online: Erratum to: Expression of hsrω-RNAi transgene prior to heat shock specifically compromises accumulation of heat shock-induced Hsp70 in Drosophila melanogaster.

Singh, Anand K / Lakhotia, Subhash C

Cell stress & chaperones

2015 Volume 21, Issue 1, Page(s) 121

Language	English
Publishing date	2015-10-29
Publishing country	Netherlands
Document type	Journal Article ; Published Erratum
ZDB-ID	1362749-1
ISSN	1466-1268 ; 1355-8145
ISSN (online)	1466-1268
ISSN	1355-8145
DOI	10.1007/s12192-015-0649-1
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Article ; Online: Expression of hsrω-RNAi transgene prior to heat shock specifically compromises accumulation of heat shock-induced Hsp70 in Drosophila melanogaster.

Singh, Anand K / Lakhotia, Subhash C

Cell stress & chaperones

2015 Volume 21, Issue 1, Page(s) 105–120

Abstract: A delayed organismic lethality was reported in Drosophila following heat shock when developmentally active and stress-inducible noncoding hsrω-n transcripts were down-regulated during heat shock through hs-GAL4-driven expression of the hsrω-RNAi ... ...

Abstract	A delayed organismic lethality was reported in Drosophila following heat shock when developmentally active and stress-inducible noncoding hsrω-n transcripts were down-regulated during heat shock through hs-GAL4-driven expression of the hsrω-RNAi transgene, despite the characteristic elevation of all heat shock proteins (Hsp), including Hsp70. Here, we show that hsrω-RNAi transgene expression prior to heat shock singularly prevents accumulation of Hsp70 in all larval tissues without affecting transcriptional induction of hsp70 genes and stability of their transcripts. Absence of the stress-induced Hsp70 accumulation was not due to higher levels of Hsc70 in hsrω-RNAi transgene-expressing tissues. Inhibition of proteasomal activity during heat shock restored high levels of the induced Hsp70, suggesting very rapid degradation of the Hsp70 even during the stress when hsrω-RNAi transgene was expressed ahead of heat shock. Unexpectedly, while complete absence of hsrω transcripts in hsrω (66) homozygotes (hsrω-null) did not prevent high accumulation of heat shock-induced Hsp70, hsrω-RNAi transgene expression in hsrω-null background blocked Hsp70 accumulation. Nonspecific RNAi transgene expression did not affect Hsp70 induction. These observations reveal that, under certain conditions, the stress-induced Hsp70 can be selectively and rapidly targeted for proteasomal degradation even during heat shock. In the present case, the selective degradation of Hsp70 does not appear to be due to down-regulation of the hsrω-n transcripts per se; rather, this may be an indirect effect of the expression of hsrω-RNAi transgene whose RNA products may titrate away some RNA-binding proteins which may also be essential for stability of the induced Hsp70.
MeSH term(s)	Animals ; Drosophila Proteins/biosynthesis ; Drosophila Proteins/genetics ; Drosophila melanogaster/embryology ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Gene Expression Regulation, Developmental/genetics ; HSP70 Heat-Shock Proteins/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Heat-Shock Response/genetics ; Larva/genetics ; Larva/metabolism ; RNA, Long Noncoding/genetics ; Transcription Factors/biosynthesis ; Transcription Factors/genetics ; Transcriptional Activation/genetics
Chemical Substances	Drosophila Proteins ; GAL4 protein, Drosophila ; HSP70 Heat-Shock Proteins ; RNA, Long Noncoding ; Transcription Factors
Language	English
Publishing date	2015-09-19
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1362749-1
ISSN	1466-1268 ; 1355-8145
ISSN (online)	1466-1268
ISSN	1355-8145
DOI	10.1007/s12192-015-0644-6
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Article: Visualisation of ribosomes in

Singh, Anand K / Abdullahi, Akilu / Soller, Matthias / David, Alexandre / Brogna, Saverio

Biology open

2020 Volume 8, Issue 12

Abstract: The distribution of assembled, and potentially translating, ribosomes within cells can be visualised ... ...

Abstract	The distribution of assembled, and potentially translating, ribosomes within cells can be visualised in
MeSH term(s)	Animals ; Axons/metabolism ; Drosophila/genetics ; Drosophila/metabolism ; Fluorescent Antibody Technique ; Humans ; Molecular Imaging/methods ; Molecular Structure ; Neurons/metabolism ; Photoreceptor Cells/metabolism ; Ribosomal Proteins/metabolism ; Ribosomes/chemistry ; Ribosomes/metabolism
Chemical Substances	Ribosomal Proteins
Language	English
Publishing date	2020-01-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2632264-X
ISSN	2046-6390
ISSN	2046-6390
DOI	10.1242/bio.047233
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Article: The hnRNP A1 homolog Hrb87F/Hrp36 is important for telomere maintenance in Drosophila melanogaster

Singh, Anand K / Subhash C. Lakhotia

Chromosoma. 2016 June, v. 125, no. 3

2016

Abstract	Unlike the telomerase-dependent mammalian telomeres, HeT-A, TART, and TAHRE (HTT) retroposon arrays regulate Drosophila telomere length. Cap prevents telomeric associations (TAs) and telomeric fusions (TFs). Our results suggest important roles of Hrb87F in telomeric HTT array and cap maintenance in Drosophila. All chromosome arms, except 2L, in Df(3R)Hrb87F homozygotes (Hrb87F-null) displayed significantly elongated telomeres with amplified HTT arrays and high TAs, all of which resolved without damage. Presence of FLAG-tagged Hrb87F (FLAG-Hrb87F) on cap and subtelomeric regions following hsFLAG-Hrb87F transgene expression in Df(3R)Hrb87F homozygotes suppressed TAs without affecting telomere length. A normal X-chromosome telomere expanded within five generations in Hrb87F-null background and displayed high TAs, but not when hsFLAG-Hrb87F was co-expressed. Tel Â¹ /Gaiano line or HP1 loss-of-function mutant-derived expanded telomeres carry Hrb87F on cap and HTT arrays while Hrb87F-null telomeres have HP1 and HOAP on caps and expanded HTT arrays. ISWI, seen only on cap on normal telomeres, was abundant on Hrb87F-null expanded HTT arrays. Extended telomeres derived from Tel Â¹ (Gaiano) or HP1-null mutation background interact with those from Hrb87F-null, since while the end association frequency was negligible in Df(3R)Hrb87F/+ nuclei, it increased significantly in co-presence of Tel Â¹ or HP1-null-based expanded telomere/s. Together, these suggest complex interactions between members of the proteome of telomere so that absence of any key member leads to telomere expansion and/or enhanced TAs/TFs. HTT expansion in Hrb87F-null condition is not developmental but a germline event presumably because absence of Hrb87F in germline may deregulate HTT retroposition/replication leading to telomere elongation.
Keywords	Drosophila melanogaster ; X chromosome ; gene expression ; germ cells ; homozygosity ; loss-of-function mutation ; mammals ; proteome ; telomeres
Language	English
Dates of publication	2016-06
Size	p. 373-388.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	203083-4
ISSN	1432-0886 ; 0009-5915
ISSN (online)	1432-0886
ISSN	0009-5915
DOI	10.1007/s00412-015-0540-y
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Tsyn-Seq: a T-cell Synapse-Based Antigen Identification Platform.

Cancer immunology research

2024 Volume 12, Issue 5, Page(s) 530–543

Abstract: Tools for genome-wide rapid identification of peptide-major histocompatibility complex targets of T-cell receptors (TCR) are not yet universally available. We present a new antigen screening method, the T-synapse (Tsyn) reporter system, which includes ... ...

Abstract	Tools for genome-wide rapid identification of peptide-major histocompatibility complex targets of T-cell receptors (TCR) are not yet universally available. We present a new antigen screening method, the T-synapse (Tsyn) reporter system, which includes antigen-presenting cells (APC) with a Fas-inducible NF-κB reporter and T cells with a nuclear factor of activated T cells (NFAT) reporter. To functionally screen for target antigens from a cDNA library, productively interacting T cell-APC aggregates were detected by dual-reporter activity and enriched by flow sorting followed by antigen identification quantified by deep sequencing (Tsyn-seq). When applied to a previously characterized TCR specific for the E7 antigen derived from human papillomavirus type 16 (HPV16), Tsyn-seq successfully enriched the correct cognate antigen from a cDNA library derived from an HPV16-positive cervical cancer cell line. Tsyn-seq provides a method for rapidly identifying antigens recognized by TCRs of interest from a tumor cDNA library. See related Spotlight by Makani and Joglekar, p. 515.
MeSH term(s)	Humans ; Receptors, Antigen, T-Cell/immunology ; Receptors, Antigen, T-Cell/genetics ; T-Lymphocytes/immunology ; High-Throughput Nucleotide Sequencing ; Papillomavirus E7 Proteins/immunology ; Papillomavirus E7 Proteins/genetics ; Gene Library ; Antigen-Presenting Cells/immunology ; NFATC Transcription Factors/metabolism ; NFATC Transcription Factors/immunology ; Cell Line, Tumor ; NF-kappa B/metabolism ; Immunological Synapses/immunology ; Human papillomavirus 16/immunology ; Human papillomavirus 16/genetics ; Female
Chemical Substances	Receptors, Antigen, T-Cell ; Papillomavirus E7 Proteins ; NFATC Transcription Factors ; oncogene protein E7, Human papillomavirus type 16 ; NF-kappa B
Language	English
Publishing date	2024-02-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2732489-8
ISSN	2326-6074 ; 2326-6066
ISSN (online)	2326-6074
ISSN	2326-6066
DOI	10.1158/2326-6066.CIR-23-0467
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