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Article ; Online: The effect of DNA CpG methylation on the dynamic conformation of a nucleosome.

Jimenez-Useche, Isabel / Yuan, Chongli

2012 Volume 103, Issue 12, Page(s) 2502–2512

Abstract: DNA methylation is an important epigenetic mark that is known to induce chromatin condensation and gene silencing. We used a time-domain fluorescence lifetime measurement to quantify the effects of DNA hypermethylation on the conformation and dynamics of ...

Abstract	DNA methylation is an important epigenetic mark that is known to induce chromatin condensation and gene silencing. We used a time-domain fluorescence lifetime measurement to quantify the effects of DNA hypermethylation on the conformation and dynamics of a nucleosome. Nucleosomes reconstituted on an unmethylated and a methylated DNA both exhibit dynamic conformations under physiological conditions. The DNA end breathing motion and the H2A-H2B dimer destabilization dominate the dynamic behavior of nucleosomes at low to medium ionic strength. Extensive DNA CpG methylation, surprisingly, does not help to restrain the DNA breathing motion, but facilitates the formation of a more open nucleosome conformation. The presence of the divalent cation, Mg(2+), essential for chromatin compaction, and the methyl donor molecule SAM, required for DNA methyltransferase reaction, facilitate the compaction of both types of nucleosomes. The difference between the unmethylated and the methylated nucleosome persists within a broad range of salt concentrations, but vanishes under high magnesium concentrations. Reduced DNA backbone rigidity due to the presence of methyl groups is believed to contribute to the observed structural and dynamic differences. The observation of this study suggests that DNA methylation alone does not compact chromatin at the nucleosomal level and provides molecular details to understand the regulatory role of DNA methylation in gene expression.
MeSH term(s)	Base Sequence ; CpG Islands/genetics ; DNA/genetics ; DNA Methylation/drug effects ; Magnesium/pharmacology ; Molecular Sequence Data ; Movement/drug effects ; Nucleosomes/chemistry ; Nucleosomes/drug effects ; Nucleosomes/metabolism ; Protein Conformation/drug effects ; S-Adenosylmethionine/pharmacology
Chemical Substances	Nucleosomes ; S-Adenosylmethionine (7LP2MPO46S) ; DNA (9007-49-2) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2012-12-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2012.11.012
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Article ; Online: Unmethylated and methylated CpG dinucleotides distinctively regulate the physical properties of DNA.

Jimenez-Useche, Isabel / Shim, Daphne / Yu, Jianger / Yuan, Chongli

Biopolymers

2014 Volume 101, Issue 5, Page(s) 517–524

Abstract: In eukaryotic cells, DNA has to bend significantly to pack inside the nucleus. Physical properties of DNA such as bending flexibility and curvature are expected to affect DNA packaging and partially determine the nucleosome positioning patterns inside a ... ...

Abstract	In eukaryotic cells, DNA has to bend significantly to pack inside the nucleus. Physical properties of DNA such as bending flexibility and curvature are expected to affect DNA packaging and partially determine the nucleosome positioning patterns inside a cell. DNA CpG methylation, the most common epigenetic modification found in DNA, is known to affect the physical properties of DNA. However, its detailed role in nucleosome formation is less well-established. In this study, we evaluated the effect of defined CpG patterns (unmethylated and methylated) on DNA structure and their respective nucleosome-forming ability. Our results suggest that the addition of CpG dinucleotides, either as a (CG)n stretch or (CGX8 )n repeats at 10 bp intervals, lead to reduced hydrodynamic radius and decreased nucleosome-forming ability of DNA. This effect is more predominant for a DNA stretch ((CG)5) located in the middle of a DNA fragment. Methylation of CpG sites, surprisingly, seems to reduce the difference in DNA structure and nucleosome-forming ability among DNA constructs with different CpG patterns. Our results suggest that unmethylated and methylated CpG patterns can play very different roles in regulating the physical properties of DNA. CpG methylation seems to reduce the DNA conformational variations affiliated with defined CpG patterns. Our results can have significant bearings in understanding the nucleosome positioning pattern in living organisms modulated by DNA sequences and epigenetic features.
MeSH term(s)	DNA/chemistry ; DNA Methylation ; Electrophoresis, Polyacrylamide Gel ; Models, Molecular ; Nucleosomes/metabolism ; Oligodeoxyribonucleotides/metabolism
Chemical Substances	CPG-oligonucleotide ; Nucleosomes ; Oligodeoxyribonucleotides ; DNA (9007-49-2)
Language	English
Publishing date	2014-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1123-x
ISSN	1097-0282 ; 0006-3525
ISSN (online)	1097-0282
ISSN	0006-3525
DOI	10.1002/bip.22411
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Article: The Effect of DNA CpG Methylation on the Dynamic Conformation of a Nucleosome

Jimenez-Useche, Isabel / Yuan, Chongli

Biophysical journal. 2012 Dec. 19, v. 103, no. 12

2012

Abstract	DNA methylation is an important epigenetic mark that is known to induce chromatin condensation and gene silencing. We used a time-domain fluorescence lifetime measurement to quantify the effects of DNA hypermethylation on the conformation and dynamics of a nucleosome. Nucleosomes reconstituted on an unmethylated and a methylated DNA both exhibit dynamic conformations under physiological conditions. The DNA end breathing motion and the H2A-H2B dimer destabilization dominate the dynamic behavior of nucleosomes at low to medium ionic strength. Extensive DNA CpG methylation, surprisingly, does not help to restrain the DNA breathing motion, but facilitates the formation of a more open nucleosome conformation. The presence of the divalent cation, Mg2+, essential for chromatin compaction, and the methyl donor molecule SAM, required for DNA methyltransferase reaction, facilitate the compaction of both types of nucleosomes. The difference between the unmethylated and the methylated nucleosome persists within a broad range of salt concentrations, but vanishes under high magnesium concentrations. Reduced DNA backbone rigidity due to the presence of methyl groups is believed to contribute to the observed structural and dynamic differences. The observation of this study suggests that DNA methylation alone does not compact chromatin at the nucleosomal level and provides molecular details to understand the regulatory role of DNA methylation in gene expression.
Keywords	DNA ; DNA methylation ; epigenetics ; fluorescence ; gene expression ; gene silencing ; ionic strength ; magnesium ; nucleosomes ; observational studies ; salt concentration
Language	English
Dates of publication	2012-1219
Size	p. 2502-2512.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2012.11.012
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Article ; Online: Clipping of flexible tails of histones H3 and H4 affects the structure and dynamics of the nucleosome.

Nurse, Nathan P / Jimenez-Useche, Isabel / Smith, Ian Tad / Yuan, Chongli

Biophysical journal

2013 Volume 104, Issue 5, Page(s) 1081–1088

Abstract: Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to ... ...

Abstract	Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to partake in intranucleosomal interactions by restricting the DNA breathing motion and compacting the nucleosome. The H3 tail effects were mostly independent of the ionic strength and valency of the ions. The H4 tail was shown to not greatly affect the nucleosome conformation, but did slightly influence the relative population of the preferred conformation. The role of the H4 tail varied depending on the valency and ionic strength, suggesting that electrostatic forces play a primary role in H4 tail interactions. Interestingly, despite the H4 tail's lack of influence, when H3 and H4 tails were simultaneously clipped, a more dramatic effect was seen than when only H3 or H4 tails were clipped. The combinatorial effect of H3 and H4 tail truncation suggests a potential mechanism by which various combinations of histone tail modifications can be used to control accessibility of DNA-binding proteins to nucleosomal DNA.
MeSH term(s)	Amino Acid Sequence ; Animals ; DNA/chemistry ; Fluorescence Resonance Energy Transfer ; Histones/chemistry ; Nucleosomes/chemistry ; Osmolar Concentration ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Sequence Deletion ; Static Electricity ; Xenopus laevis
Chemical Substances	Histones ; Nucleosomes ; Recombinant Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2013-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2013.01.019
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Article ; Online: DNA methylation effects on tetra-nucleosome compaction and aggregation.

Jimenez-Useche, Isabel / Nurse, Nathan P / Tian, Yuqing / Kansara, Bhargav S / Shim, Daphne / Yuan, Chongli

Biophysical journal

2014 Volume 107, Issue 7, Page(s) 1629–1636

Abstract: DNA CpG methylation has been associated with chromatin compaction and gene silencing. Whether DNA methylation directly contributes to chromatin compaction remains an open question. In this study, we used fluorescence fluctuation spectroscopy (FFS) to ... ...

Abstract	DNA CpG methylation has been associated with chromatin compaction and gene silencing. Whether DNA methylation directly contributes to chromatin compaction remains an open question. In this study, we used fluorescence fluctuation spectroscopy (FFS) to evaluate the compaction and aggregation of tetra-nucleosomes containing specific CpG patterns and methylation levels. The compactness of both unmethylated and methylated tetra-nucleosomes is dependent on DNA sequences. Specifically, methylation of the CpG sites located in the central dyad and the major grooves of DNA seem to have opposite effects on modulating the compactness of tetra-nucleosomes. The interactions among tetra-nucleosomes, however, seem to be enhanced because of DNA methylation independent of sequence contexts. Our finding can shed light on understanding the role of DNA methylation in determining nucleosome positioning pattern and chromatin compactness.
MeSH term(s)	Animals ; Base Sequence ; CpG Islands/genetics ; DNA Methylation/drug effects ; Gene Expression Regulation ; Magnesium/pharmacology ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosomes/chemistry ; Nucleosomes/drug effects ; Nucleosomes/genetics ; Protein Aggregates/drug effects ; Protein Conformation ; Spectrometry, Fluorescence
Chemical Substances	Nucleosomes ; Protein Aggregates ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2014-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2014.05.055
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Article ; Online: Elucidating internucleosome interactions and the roles of histone tails.

Howell, Steven C / Andresen, Kurt / Jimenez-Useche, Isabel / Yuan, Chongli / Qiu, Xiangyun

Biophysical journal

2013 Volume 105, Issue 1, Page(s) 194–199

Abstract: The nucleosome is the first level of genome organization and regulation in eukaryotes where negatively charged DNA is wrapped around largely positively charged histone proteins. Interaction between nucleosomes is dominated by electrostatics at long range ...

Abstract	The nucleosome is the first level of genome organization and regulation in eukaryotes where negatively charged DNA is wrapped around largely positively charged histone proteins. Interaction between nucleosomes is dominated by electrostatics at long range and guided by specific contacts at short range, particularly involving their flexible histone tails. We have thus quantified how internucleosome interactions are modulated by salts (KCl, MgCl2) and histone tail deletions (H3, H4 N-terminal), using small-angle x-ray scattering and theoretical modeling. We found that measured effective charges at low salts are ∼1/5th of the theoretically predicted renormalized charges and that H4 tail deletion suppresses the attraction at high salts to a larger extent than H3 tail deletion.
MeSH term(s)	Animals ; Chickens ; Histones/chemistry ; Histones/metabolism ; Magnesium Chloride/pharmacology ; Nucleosomes/metabolism ; Potassium Chloride/pharmacology ; Protein Binding/drug effects ; Scattering, Small Angle ; Static Electricity ; X-Ray Diffraction
Chemical Substances	Histones ; Nucleosomes ; Magnesium Chloride (02F3473H9O) ; Potassium Chloride (660YQ98I10)
Language	English
Publishing date	2013-07-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2013.05.021
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Article ; Online: Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal.

Andresen, Kurt / Jimenez-Useche, Isabel / Howell, Steven C / Yuan, Chongli / Qiu, Xiangyun

PloS one

2013 Volume 8, Issue 11, Page(s) e78587

Abstract: Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from ... ...

Abstract	Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.
MeSH term(s)	DNA/chemistry ; Dose-Response Relationship, Drug ; Fluorescence Resonance Energy Transfer ; Histones/chemistry ; Models, Molecular ; Nucleosomes/chemistry ; Nucleosomes/drug effects ; Potassium Chloride/pharmacology ; Protein Conformation/drug effects ; Scattering, Small Angle ; Solutions ; X-Ray Diffraction
Chemical Substances	Histones ; Nucleosomes ; Solutions ; Potassium Chloride (660YQ98I10) ; DNA (9007-49-2)
Language	English
Publishing date	2013-11-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0078587
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DNA methylation regulated nucleosome dynamics.

Jimenez-Useche, Isabel / Ke, Jiaying / Tian, Yuqing / Shim, Daphne / Howell, Steven C / Qiu, Xiangyun / Yuan, Chongli

Scientific reports

2013 Volume 3, Page(s) 2121

Abstract: A strong correlation between nucleosome positioning and DNA methylation patterns has been reported in literature. However, the mechanistic model accounting for the correlation remains elusive. In this study, we evaluated the effects of specific DNA ... ...

Abstract	A strong correlation between nucleosome positioning and DNA methylation patterns has been reported in literature. However, the mechanistic model accounting for the correlation remains elusive. In this study, we evaluated the effects of specific DNA methylation patterns on modulating nucleosome conformation and stability using FRET and SAXS. CpG dinucleotide repeats at 10 bp intervals were found to play different roles in nucleosome stability dependent on their methylation states and their relative nucleosomal locations. An additional (CpG)5 stretch located in the nucleosomal central dyad does not alter the nucleosome conformation, but significant conformational differences were observed between the unmethylated and methylated nucleosomes. These findings suggest that the correlation between nucleosome positioning and DNA methylation patterns can arise from the variations in nucleosome stability dependent on their sequence and epigenetic content. This knowledge will help to reveal the detailed role of DNA methylation in regulating chromatin packaging and gene transcription.
MeSH term(s)	CpG Islands ; DNA Methylation ; Fluorescence Resonance Energy Transfer ; Nucleosomes/metabolism ; Scattering, Small Angle
Chemical Substances	Nucleosomes
Language	English
Publishing date	2013-07-02
Publishing country	England
Document type	Journal Article ; 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/srep02121
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Article ; Online: Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal.

Kurt Andresen / Isabel Jimenez-Useche / Steven C Howell / Chongli Yuan / Xiangyun Qiu

PLoS ONE, Vol 8, Iss 11, p e

2013 Volume 78587

Abstract	Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Elucidating Internucleosome Interactions and the Roles of Histone Tails

Howell, Steven C / Andresen, Kurt / Jimenez-Useche, Isabel / Yuan, Chongli / Qiu, Xiangyun

Biophysical journal. 2013 July 2, v. 105, no. 1

2013

Abstract	The nucleosome is the first level of genome organization and regulation in eukaryotes where negatively charged DNA is wrapped around largely positively charged histone proteins. Interaction between nucleosomes is dominated by electrostatics at long range and guided by specific contacts at short range, particularly involving their flexible histone tails. We have thus quantified how internucleosome interactions are modulated by salts (KCl, MgCl2) and histone tail deletions (H3, H4 N-terminal), using small-angle x-ray scattering and theoretical modeling. We found that measured effective charges at low salts are ∼1/5th of the theoretically predicted renormalized charges and that H4 tail deletion suppresses the attraction at high salts to a larger extent than H3 tail deletion.
Keywords	DNA ; X-radiation ; eukaryotic cells ; genome ; histones ; magnesium chloride ; models ; nucleosomes ; potassium chloride
Language	English
Dates of publication	2013-0702
Size	p. 194-199.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2013.05.021
Database	NAL-Catalogue (AGRICOLA)

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