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Article: How neurons maintain their axons long-term: an integrated view of axon biology and pathology.

Smith, Gaynor / Sweeney, Sean T / O'Kane, Cahir J / Prokop, Andreas

2023 Volume 17, Page(s) 1236815

Abstract: Axons are processes of neurons, up to a metre long, that form the essential biological cables wiring nervous systems. They must survive, often far away from their cell bodies and up to a century in humans. This requires self-sufficient cell biology ... ...

Abstract	Axons are processes of neurons, up to a metre long, that form the essential biological cables wiring nervous systems. They must survive, often far away from their cell bodies and up to a century in humans. This requires self-sufficient cell biology including structural proteins, organelles, and membrane trafficking, metabolic, signalling, translational, chaperone, and degradation machinery-all maintaining the homeostasis of energy, lipids, proteins, and signalling networks including reactive oxygen species and calcium. Axon maintenance also involves specialised cytoskeleton including the cortical actin-spectrin corset, and bundles of microtubules that provide the highways for motor-driven transport of components and organelles for virtually all the above-mentioned processes. Here, we aim to provide a conceptual overview of key aspects of axon biology and physiology, and the homeostatic networks they form. This homeostasis can be derailed, causing axonopathies through processes of ageing, trauma, poisoning, inflammation or genetic mutations. To illustrate which malfunctions of organelles or cell biological processes can lead to axonopathies, we focus on axonopathy-linked subcellular defects caused by genetic mutations. Based on these descriptions and backed up by our comprehensive data mining of genes linked to neural disorders, we describe the 'dependency cycle of local axon homeostasis' as an integrative model to explain why very different causes can trigger very similar axonopathies, providing new ideas that can drive the quest for strategies able to battle these devastating diseases.
Language	English
Publishing date	2023-07-26
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2411902-7
ISSN	1662-453X ; 1662-4548
ISSN (online)	1662-453X
ISSN	1662-4548
DOI	10.3389/fnins.2023.1236815
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Article: Sampling and Analysis of Low-Molecular-Weight Volatile Metabolites in Cellular Headspace and Mouse Breath.

Issitt, Theo / Sweeney, Sean T / Brackenbury, William J / Redeker, Kelly R

Metabolites

2022 Volume 12, Issue 7

Abstract: Volatile compounds, abundant in breath, can be used to accurately diagnose and monitor a range of medical conditions. This offers a noninvasive, low-cost approach with screening applications; however, the uptake of this diagnostic approach has been ... ...

Abstract	Volatile compounds, abundant in breath, can be used to accurately diagnose and monitor a range of medical conditions. This offers a noninvasive, low-cost approach with screening applications; however, the uptake of this diagnostic approach has been limited by conflicting published outcomes. Most published reports rely on large scale screening of the public, at single time points and without reference to ambient air. Here, we present a novel approach to volatile sampling from cellular headspace and mouse breath that incorporates multi-time-point analysis and ambient air subtraction revealing compound flux as an effective proxy of active metabolism. This approach to investigating breath volatiles offers a new avenue for disease biomarker discovery and diagnosis. Using gas chromatography mass spectrometry (GC/MS), we focus on low molecular weight, metabolic substrate/by-product compounds and demonstrate that this noninvasive technique is sensitive (reproducible at ~1 µg cellular protein, or ~500,000 cells) and capable of precisely determining cell type, status and treatment. Isolated cellular models represent components of larger mammalian systems, and we show that stress- and pathology-indicative compounds are detectable in mice, supporting further investigation using this methodology as a tool to identify volatile targets in human patients.
Language	English
Publishing date	2022-06-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo12070599
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Article: GC/MS analysis of hypoxic volatile metabolic markers in the MDA-MB-231 breast cancer cell line.

Issitt, Theo / Reilly, Matthew / Sweeney, Sean T / Brackenbury, William J / Redeker, Kelly R

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1178269

Abstract: Hypoxia in disease describes persistent low oxygen conditions, observed in a range of pathologies, including cancer. In the discovery of biomarkers in biological models, pathophysiological traits present a source of translatable metabolic products for ... ...

Abstract	Hypoxia in disease describes persistent low oxygen conditions, observed in a range of pathologies, including cancer. In the discovery of biomarkers in biological models, pathophysiological traits present a source of translatable metabolic products for the diagnosis of disease in humans. Part of the metabolome is represented by its volatile, gaseous fraction; the volatilome. Human volatile profiles, such as those found in breath, are able to diagnose disease, however accurate volatile biomarker discovery is required to target reliable biomarkers to develop new diagnostic tools. Using custom chambers to control oxygen levels and facilitate headspace sampling, the MDA-MB-231 breast cancer cell line was exposed to hypoxia (1% oxygen) for 24 h. The maintenance of hypoxic conditions in the system was successfully validated over this time period. Targeted and untargeted gas chromatography mass spectrometry approaches revealed four significantly altered volatile organic compounds when compared to control cells. Three compounds were actively consumed by cells: methyl chloride, acetone and n-Hexane. Cells under hypoxia also produced significant amounts of styrene. This work presents a novel methodology for identification of volatile metabolisms under controlled gas conditions with novel observations of volatile metabolisms by breast cancer cells.
Language	English
Publishing date	2023-05-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1178269
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Article ; Online: Retrovirus reactivation in CHMP2BIntron5 models of frontotemporal dementia.

Fort-Aznar, Laura / Ugbode, Chris / Sweeney, Sean T

Human molecular genetics

2020 Volume 29, Issue 16, Page(s) 2637–2646

Abstract: Frontotemporal dementia (FTD) is the second most prevalent form of pre-senile dementia after Alzheimer's disease. Amyotrophic lateral sclerosis (ALS) can overlap genetically, pathologically and clinically with FTD indicating the two conditions are ends ... ...

Abstract	Frontotemporal dementia (FTD) is the second most prevalent form of pre-senile dementia after Alzheimer's disease. Amyotrophic lateral sclerosis (ALS) can overlap genetically, pathologically and clinically with FTD indicating the two conditions are ends of a spectrum and may share common pathological mechanisms. FTD-ALS causing mutations are known to be involved in endosomal trafficking and RNA regulation. Using an unbiased genome-wide genetic screen to identify mutations affecting an FTD-ALS-related phenotype in Drosophila caused by CHMP2BIntron5 expression, we have uncovered repressors of retrovirus (RV) activity as modifiers of CHMP2BIntron5 toxicity. We report that neuronal expression of CHMP2BIntron5 causes an increase in the activity of the endogenous Drosophila RV, gypsy, in the nervous system. Genetically blocking Drosophila gypsy activation and pharmacologically inhibiting viral reverse transcriptase activity prevents degenerative phenotypes observed in fly and rat neurons. These findings directly link endosomal dysfunction to RV de-repression in an FTD-ALS model without TDP-43 pathology. These observations may contribute an understanding to previous discoveries of RV activation in ALS affected patients.
MeSH term(s)	Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/pathology ; Animals ; DNA-Binding Proteins/genetics ; Disease Models, Animal ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Endosomal Sorting Complexes Required for Transport/genetics ; Endosomes/genetics ; Frontotemporal Dementia/genetics ; Frontotemporal Dementia/pathology ; Gene Expression Regulation/genetics ; Humans ; Introns/genetics ; Mutation ; Neurons/metabolism ; Neurons/pathology ; Protein Transport/genetics ; RNA/genetics ; Rats ; Retroviridae/genetics ; Vesicular Transport Proteins/genetics
Chemical Substances	CHMP2B protein, Drosophila ; CHMP2B protein, human ; DNA-Binding Proteins ; Drosophila Proteins ; Endosomal Sorting Complexes Required for Transport ; TBPH protein, Drosophila ; Vesicular Transport Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2020-07-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddaa142
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Article ; Online: Volatile compounds in human breath: critical review and meta-analysis.

Issitt, Theo / Wiggins, Laura / Veysey, Martin / Sweeney, Sean T / Brackenbury, William J / Redeker, Kelly

Journal of breath research

2022 Volume 16, Issue 2

Abstract: Volatile compounds contained in human breath reflect the inner workings of the body. A large number of studies have been published that link individual components of breath to disease, but diagnostic applications remain limited, in part due to ... ...

Abstract	Volatile compounds contained in human breath reflect the inner workings of the body. A large number of studies have been published that link individual components of breath to disease, but diagnostic applications remain limited, in part due to inconsistent and conflicting identification of breath biomarkers. New approaches are therefore required to identify effective biomarker targets. Here, volatile organic compounds have been identified in the literature from four metabolically and physiologically distinct diseases and grouped into chemical functional groups (e.g. methylated hydrocarbons or aldehydes; based on known metabolic and enzymatic pathways) to support biomarker discovery and provide new insight on existing data. Using this functional grouping approach, principal component analysis doubled explanatory capacity from 19.1% to 38% relative to single individual compound approaches. Random forest and linear discriminant analysis reveal 93% classification accuracy for cancer. This review and meta-analysis provides insight for future research design by identifying volatile functional groups associated with disease. By incorporating our understanding of the complexities of the human body, along with accounting for variability in methodological and analytical approaches, this work demonstrates that a suite of targeted, functional volatile biomarkers, rather than individual biomarker compounds, will improve accuracy and success in diagnostic research and application.
MeSH term(s)	Biomarkers/analysis ; Breath Tests ; Discriminant Analysis ; Humans ; Neoplasms/diagnosis ; Volatile Organic Compounds/analysis
Chemical Substances	Biomarkers ; Volatile Organic Compounds
Language	English
Publishing date	2022-02-23
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2381007-5
ISSN	1752-7163 ; 1752-7155
ISSN (online)	1752-7163
ISSN	1752-7155
DOI	10.1088/1752-7163/ac5230
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Article ; Online: The Putative Drosophila TMEM184B Ortholog Tmep Ensures Proper Locomotion by Restraining Ectopic Firing at the Neuromuscular Junction.

Cho, Tiffany S / Beigaitė, Eglė / Klein, Nathaniel E / Sweeney, Sean T / Bhattacharya, Martha R C

Molecular neurobiology

2022 Volume 59, Issue 4, Page(s) 2605–2619

Abstract: TMEM184B is a putative seven-pass membrane protein that promotes axon degeneration after injury. TMEM184B mutation causes aberrant neuromuscular architecture and sensory and motor behavioral defects in mice. The mechanism through which TMEM184B causes ... ...

Abstract	TMEM184B is a putative seven-pass membrane protein that promotes axon degeneration after injury. TMEM184B mutation causes aberrant neuromuscular architecture and sensory and motor behavioral defects in mice. The mechanism through which TMEM184B causes neuromuscular defects is unknown. We employed Drosophila melanogaster to investigate the function of the closely related gene, Tmep (CG12004), at the neuromuscular junction. We show that Tmep is required for full adult viability and efficient larval locomotion. Tmep mutant larvae have a reduced body contraction rate compared to controls, with stronger deficits in females. In recordings from body wall muscles, Tmep mutants show substantial hyperexcitability, with many postsynaptic potentials fired in response to a single stimulation, consistent with a role for Tmep in restraining synaptic excitability. Additional branches and satellite boutons at Tmep mutant neuromuscular junctions are consistent with an activity-dependent synaptic overgrowth. Tmep is expressed in endosomes and synaptic vesicles within motor neurons, suggesting a possible role in synaptic membrane trafficking. Using RNAi knockdown, we show that Tmep is required in motor neurons for proper larval locomotion and excitability, and that its reduction increases levels of presynaptic calcium. Locomotor defects can be rescued by presynaptic knockdown of endoplasmic reticulum calcium channels or by reducing evoked release probability, further suggesting that excess synaptic activity drives behavioral deficiencies. Our work establishes a critical function for Tmep in the regulation of synaptic transmission and locomotor behavior.
MeSH term(s)	Animals ; Drosophila/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/metabolism ; Larva/metabolism ; Locomotion/genetics ; Mice ; Neuromuscular Junction/metabolism ; Presynaptic Terminals/metabolism ; Synaptic Transmission/physiology
Chemical Substances	Drosophila Proteins
Language	English
Publishing date	2022-02-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	645020-9
ISSN	1559-1182 ; 0893-7648
ISSN (online)	1559-1182
ISSN	0893-7648
DOI	10.1007/s12035-022-02760-3
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Zs.A 2411: Show issues

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Article ; Online: Leaky endosomes push tau over the seed limit.

Ugbode, Chris / Fort-Aznar, Laura / Sweeney, Sean T

The Journal of biological chemistry

2019 Volume 294, Issue 50, Page(s) 18967–18968

Abstract: The inter- and intracellular propagation of aggregated proteins like tau is emerging as a central mechanism behind progression of various neurodegenerative diseases. The steps by which tau aggregates and propagates is currently unclear. ... ...

Abstract	The inter- and intracellular propagation of aggregated proteins like tau is emerging as a central mechanism behind progression of various neurodegenerative diseases. The steps by which tau aggregates and propagates is currently unclear. Chen
MeSH term(s)	Cells, Cultured ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Endosomal Sorting Complexes Required for Transport/metabolism ; Endosomes/metabolism ; Humans ; Protein Aggregates ; tau Proteins/metabolism
Chemical Substances	Endosomal Sorting Complexes Required for Transport ; MAPT protein, human ; Protein Aggregates ; tau Proteins
Language	English
Publishing date	2019-11-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.H119.011687
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Article: The small G protein Arl8 contributes to lysosomal function and long-range axonal transport in

Rosa-Ferreira, Cláudia / Sweeney, Sean T / Munro, Sean

Biology open

2018 Volume 7, Issue 9

Abstract: The small GTPase Arl8 has emerged as a major regulatory GTPase on lysosomes. Studies in mammalian cells have shown that it regulates both fusion with late endosomes and also lysosomal motility. In its active GTP-bound state, it recruits to lysosomes the ... ...

Abstract	The small GTPase Arl8 has emerged as a major regulatory GTPase on lysosomes. Studies in mammalian cells have shown that it regulates both fusion with late endosomes and also lysosomal motility. In its active GTP-bound state, it recruits to lysosomes the HOPS (homotypic fusion and protein sorting) endosomal tethering complex and also proteins that link lysosomes to microtubule motors such as the kinesin adaptor PLEKHM2. To gain further insights into Arl8 biology, we examined the single
Language	English
Publishing date	2018-09-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2632264-X
ISSN	2046-6390
ISSN	2046-6390
DOI	10.1242/bio.035964
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Article ; Online: Ik2/TBK1 and Hook/Dynein, an adaptor complex for early endosome transport, are genetic modifiers of FTD-associated mutant CHMP2B toxicity in Drosophila.

Lu, Yubing / West, Ryan J H / Pons, Marine / Sweeney, Sean T / Gao, Fen-Biao

Scientific reports

2020 Volume 10, Issue 1, Page(s) 14221

Abstract: Mutations in CHMP2B, encoding a protein in the endosomal sorting complexes required for transport (ESCRT) machinery, causes frontotemporal dementia linked to chromosome 3 (FTD3). FTD, the second most common form of pre-senile dementia, can also be caused ...

Abstract	Mutations in CHMP2B, encoding a protein in the endosomal sorting complexes required for transport (ESCRT) machinery, causes frontotemporal dementia linked to chromosome 3 (FTD3). FTD, the second most common form of pre-senile dementia, can also be caused by genetic mutations in other genes, including TANK-binding kinase 1 (TBK1). How FTD-causing disease genes interact is largely unknown. We found that partial loss function of Ik2, the fly homologue of TBK1 also known as I-kappaB kinase ε (IKKε), enhanced the toxicity of mutant CHMP2B in the fly eye and that Ik2 overexpression suppressed the effect of mutant CHMP2B in neurons. Partial loss of function of Spn-F, a downstream phosphorylation target of Ik2, greatly enhanced the mutant CHMP2B phenotype. An interactome analysis to understand cellular processes regulated by Spn-F identified a network of interacting proteins including Spn-F, Ik2, dynein light chain, and Hook, an adaptor protein in early endosome transport. Partial loss of function of dynein light chain or Hook also enhanced mutant CHMP2B toxicity. These findings identify several evolutionarily conserved genes, including ik2/TBK1, cut up (encoding dynein light chain) and hook, as genetic modifiers of FTD3-associated mutant CHMP2B toxicity and implicate early endosome transport as a potential contributing pathway in FTD.
MeSH term(s)	Animals ; Disease Models, Animal ; Drosophila ; Drosophila Proteins/genetics ; Dyneins/genetics ; Endosomes/physiology ; Frontotemporal Dementia/genetics ; I-kappa B Kinase/genetics ; Microtubule-Associated Proteins/genetics ; Vesicular Transport Proteins/genetics
Chemical Substances	CHMP2B protein, Drosophila ; Drosophila Proteins ; Microtubule-Associated Proteins ; Spn-F protein, Drosophila ; Vesicular Transport Proteins ; ctp protein, Drosophila ; hook protein, Drosophila ; I-kappa B Kinase (EC 2.7.11.10) ; IKKepsilon protein, Drosophila (EC 2.7.11.10) ; Dyneins (EC 3.6.4.2)
Language	English
Publishing date	2020-08-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-71097-5
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Article ; Online: RNA-binding protein DDX3 mediates posttranscriptional regulation of androgen receptor: A mechanism of castration resistance.

Vellky, Jordan E / McSweeney, Sean T / Ricke, Emily A / Ricke, William A

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

2020 Volume 117, Issue 45, Page(s) 28092–28101

Abstract: Prostate cancer (CaP) driven by androgen receptor (AR) is treated with androgen deprivation; however, therapy failure results in lethal castration-resistant prostate cancer (CRPC). AR-low/negative (ARL/-) CRPC subtypes have recently been characterized ... ...

Abstract	Prostate cancer (CaP) driven by androgen receptor (AR) is treated with androgen deprivation; however, therapy failure results in lethal castration-resistant prostate cancer (CRPC). AR-low/negative (ARL/-) CRPC subtypes have recently been characterized and cannot be targeted by hormonal therapies, resulting in poor prognosis. RNA-binding protein (RBP)/helicase DDX3 (DEAD-box helicase 3 X-linked) is a key component of stress granules (SG) and is postulated to affect protein translation. Here, we investigated DDX3-mediated posttranscriptional regulation of AR mRNA (messenger RNA) in CRPC. Using patient samples and preclinical models, we objectively quantified DDX3 and AR expression in ARL/- CRPC. We utilized CRPC models to identify DDX3:AR mRNA complexes by RNA immunoprecipitation, assess the effects of DDX3 gain/loss-of-function on AR expression and signaling, and address clinical implications of targeting DDX3 by assessing sensitivity to AR-signaling inhibitors (ARSI) in CRPC xenografts in vivo. ARL/- CRPC expressed abundant AR mRNA despite diminished levels of AR protein. DDX3 protein was highly expressed in ARL/- CRPC, where it bound to AR mRNA. Consistent with a repressive regulatory role, DDX3 localized to cytoplasmic puncta with SG marker PABP1 in CRPC. While induction of DDX3-nucleated SGs resulted in decreased AR protein expression, inhibiting DDX3 was sufficient to restore 1) AR protein expression, 2) AR signaling, and 3) sensitivity to ARSI in vitro and in vivo. Our findings implicate the RBP protein DDX3 as a mechanism of posttranscriptional regulation for AR in CRPC. Clinically, DDX3 may be targetable for sensitizing ARL/- CRPC to AR-directed therapies.
MeSH term(s)	Animals ; Cell Line, Tumor ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; Male ; Mice ; Mice, Nude ; Prostate/chemistry ; Prostate/pathology ; Prostatic Neoplasms, Castration-Resistant/chemistry ; Prostatic Neoplasms, Castration-Resistant/genetics ; Prostatic Neoplasms, Castration-Resistant/metabolism ; Prostatic Neoplasms, Castration-Resistant/pathology ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Receptors, Androgen/genetics ; Receptors, Androgen/metabolism
Chemical Substances	AR protein, human ; RNA, Messenger ; Receptors, Androgen ; DDX3X protein, human (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2020-10-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; 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.2008479117
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