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Article: A Student-Focused Lab Module To Investigate Single-Nucleotide Polymorphisms of Common Heritable Traits.

Shanle, Erin K / Trubitsyn, Denis

Journal of microbiology & biology education

2020 Volume 21, Issue 3

Language	English
Publishing date	2020-11-12
Publishing country	United States
Document type	Journal Article
ISSN	1935-7877
ISSN	1935-7877
DOI	10.1128/jmbe.v21i3.2173
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Article ; Online: A Student-Focused Lab Module To Investigate Single-Nucleotide Polymorphisms of Common Heritable Traits<xref ref-type="fn" rid="fn1-jmbe-21-70">†</xref>

Erin K. Shanle / Denis Trubitsyn

Journal of Microbiology & Biology Education, Vol 21, Iss

2020 Volume 3

Keywords	Special aspects of education ; LC8-6691 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	American Society for Microbiology
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Yeast-based screening of cancer mutations in the DNA damage response protein Mre11 demonstrates importance of conserved capping domain residues.

Harris, Caitlin / Savas, Jessica / Ray, Sreerupa / Shanle, Erin K

Molecular biology reports

2021 Volume 48, Issue 5, Page(s) 4107–4119

Abstract: DNA damage response (DDR) pathways are initiated to prevent mutations from being passed on in the event of DNA damage. Mutations in DDR proteins can contribute to the development and maintenance of cancer cells, but many mutations observed in human ... ...

Abstract	DNA damage response (DDR) pathways are initiated to prevent mutations from being passed on in the event of DNA damage. Mutations in DDR proteins can contribute to the development and maintenance of cancer cells, but many mutations observed in human tumors have not been functionally characterized. Because a proper response to DNA damage is fundamental to living organisms, DDR proteins and processes are often highly conserved. The goal of this project was to use Saccharomyces cerevisiae as a model for functional screening of human cancer mutations in conserved DDR proteins. After comparing the cancer mutation frequency and conservation of DDR proteins, Mre11 was selected for functional screening. A subset of mutations in conserved residues was analyzed by structural modeling and screened for functional effects in yeast Mre11. Yeast expressing wild type or mutant Mre11 were then assessed for DNA damage sensitivity using hydroxyurea (HU) and methyl methanesulfonate (MMS). The results were further validated in human cancer cells. The N-terminal point mutations tested in yeast Mre11 do not confer sensitivity to DNA damage sensitivity, suggesting that these residues are dispensable for yeast Mre11 function and may have conserved sequence without conserved function. However, a mutation near the capping domain associated with breast and colorectal cancers compromises Mre11 function in both yeast and human cells. These results provide novel insight into the function of this conserved capping domain residue and demonstrate a framework for yeast-based screening of cancer mutations.
MeSH term(s)	Adenocarcinoma/genetics ; Adenocarcinoma/pathology ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; DNA Damage/drug effects ; DNA Damage/genetics ; DNA Repair/genetics ; Early Detection of Cancer/methods ; Endodeoxyribonucleases/chemistry ; Endodeoxyribonucleases/genetics ; Exodeoxyribonucleases/chemistry ; Exodeoxyribonucleases/genetics ; Female ; Humans ; Hydroxyurea/pharmacology ; MCF-7 Cells ; MRE11 Homologue Protein/chemistry ; MRE11 Homologue Protein/genetics ; Methyl Methanesulfonate/pharmacology ; Microorganisms, Genetically-Modified ; Mutation Rate ; Protein Domains/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics
Chemical Substances	MRE11 protein, human ; Saccharomyces cerevisiae Proteins ; Methyl Methanesulfonate (AT5C31J09G) ; Endodeoxyribonucleases (EC 3.1.-) ; Exodeoxyribonucleases (EC 3.1.-) ; MRE11 Homologue Protein (EC 3.1.-) ; MRE11 protein, S cerevisiae (EC 3.1.-) ; Hydroxyurea (X6Q56QN5QC)
Language	English
Publishing date	2021-06-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-021-06424-8
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Article: Yeast-based screening of cancer mutations in the DNA damage response protein Mre11 demonstrates importance of conserved capping domain residues

Harris, Caitlin / Savas, Jessica / Ray, Sreerupa / Shanle, Erin K.

Molecular biology reports. 2021 May, v. 48, no. 5

2021

Abstract	DNA damage response (DDR) pathways are initiated to prevent mutations from being passed on in the event of DNA damage. Mutations in DDR proteins can contribute to the development and maintenance of cancer cells, but many mutations observed in human tumors have not been functionally characterized. Because a proper response to DNA damage is fundamental to living organisms, DDR proteins and processes are often highly conserved. The goal of this project was to use Saccharomyces cerevisiae as a model for functional screening of human cancer mutations in conserved DDR proteins. After comparing the cancer mutation frequency and conservation of DDR proteins, Mre11 was selected for functional screening. A subset of mutations in conserved residues was analyzed by structural modeling and screened for functional effects in yeast Mre11. Yeast expressing wild type or mutant Mre11 were then assessed for DNA damage sensitivity using hydroxyurea (HU) and methyl methanesulfonate (MMS). The results were further validated in human cancer cells. The N-terminal point mutations tested in yeast Mre11 do not confer sensitivity to DNA damage sensitivity, suggesting that these residues are dispensable for yeast Mre11 function and may have conserved sequence without conserved function. However, a mutation near the capping domain associated with breast and colorectal cancers compromises Mre11 function in both yeast and human cells. These results provide novel insight into the function of this conserved capping domain residue and demonstrate a framework for yeast-based screening of cancer mutations.
Keywords	DNA damage ; Saccharomyces cerevisiae ; breasts ; humans ; hydroxyurea ; methyl methanesulfonate ; models ; molecular biology ; mutants ; mutation rate ; yeasts
Language	English
Dates of publication	2021-05
Size	p. 4107-4119.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-021-06424-8
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Article ; Online: A course-based undergraduate research experience investigating p300 bromodomain mutations.

Shanle, Erin K / Tsun, Ian K / Strahl, Brian D

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology

2016 Volume 44, Issue 1, Page(s) 68–74

Abstract: Course-based undergraduate research experiences (CUREs) provide an opportunity for students to engage in experiments with outcomes that are unknown to both the instructor and students. These experiences allow students and instructors to collaboratively ... ...

Abstract	Course-based undergraduate research experiences (CUREs) provide an opportunity for students to engage in experiments with outcomes that are unknown to both the instructor and students. These experiences allow students and instructors to collaboratively bridge the research laboratory and classroom, and provide research experiences for a large number of students relative to traditional individual mentored research. Here, we describe a molecular biology CURE investigating the impact of clinically relevant mutations found in the bromodomain of the p300 transcriptional regulator on acetylated histone interaction. In the CURE, students identified missense mutations in the p300 bromodomain using the Catalogue of Somatic Mutations in Cancer (COSMIC) database and hypothesized the effects of the mutation on the acetyl-binding function of the domain. They cloned and purified the mutated bromodomain and performed peptide pulldown assays to define its potential to bind to acetylated histones. Upon completion of the course, students showed increased confidence performing molecular techniques and reported positively on doing a research project in class. In addition, results generated in the classroom were further validated in the research laboratory setting thereby providing a new model for faculty to engage in both course-based and individual undergraduate research experiences.
MeSH term(s)	Humans ; Models, Molecular ; Molecular Biology/education ; Mutation ; Research ; p300-CBP Transcription Factors/chemistry ; p300-CBP Transcription Factors/genetics
Chemical Substances	p300-CBP Transcription Factors (EC 2.3.1.48)
Language	English
Publishing date	2016-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1539-3429
ISSN (online)	1539-3429
DOI	10.1002/bmb.20927
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Article ; Online: Chromatin biochemistry enters the next generation of code 'seq-ing'.

Shanle, Erin K / Rothbart, Scott B / Strahl, Brian D

Nature methods

2014 Volume 11, Issue 8, Page(s) 799–800

MeSH term(s)	Chromatin/chemistry ; DNA Barcoding, Taxonomic
Chemical Substances	Chromatin
Language	English
Publishing date	2014-07-29
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/nmeth.3044
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Article ; Online: The essential role of acetyllysine binding by the YEATS domain in transcriptional regulation.

Andrews, Forest H / Shanle, Erin K / Strahl, Brian D / Kutateladze, Tatiana G

Transcription

2016 Volume 7, Issue 1, Page(s) 14–20

Abstract: The YEATS domains of AF9 and Taf14 have recently been found to recognize the histone H3K9ac modification. In this commentary, we discuss the mechanistic and biological implications of this interaction. We compare structures of the YEATS-H3K9ac complexes ... ...

Abstract	The YEATS domains of AF9 and Taf14 have recently been found to recognize the histone H3K9ac modification. In this commentary, we discuss the mechanistic and biological implications of this interaction. We compare structures of the YEATS-H3K9ac complexes the highlighting a novel mechanism for the acetyllysine recognition through the aromatic cage. We also summarize the latest findings underscoring a critical role of the acetyllysine binding function of AF9 and Taf14 in transcriptional regulation and DNA repair.
MeSH term(s)	Acetylation ; Binding Sites ; Gene Expression Regulation ; Humans ; Lysine/metabolism ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Nuclear Proteins/chemistry ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factor TFIID/chemistry ; Transcription Factor TFIID/genetics ; Transcription Factor TFIID/metabolism ; Transcription, Genetic
Chemical Substances	MLLT3 protein, human ; Nuclear Proteins ; Saccharomyces cerevisiae Proteins ; TAF14 protein, S cerevisiae ; Transcription Factor TFIID ; DOT1L protein, human (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2646974-1
ISSN	2154-1272 ; 2154-1264
ISSN (online)	2154-1272
ISSN	2154-1264
DOI	10.1080/21541264.2015.1125987
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Article ; Online: HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies.

Slaughter, Mariesa J / Shanle, Erin K / Khan, Abid / Chua, Katrin F / Hong, Tao / Boxer, Lisa D / Allis, C David / Josefowicz, Steven Z / Garcia, Benjamin A / Rothbart, Scott B / Strahl, Brian D / Davis, Ian J

Cell reports

2021 Volume 34, Issue 3, Page(s) 108638

Abstract: Histone acetylation levels are regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) that antagonistically control the overall balance of this post-translational modification. HDAC inhibitors (HDACi) are potent agents that ... ...

Abstract	Histone acetylation levels are regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) that antagonistically control the overall balance of this post-translational modification. HDAC inhibitors (HDACi) are potent agents that disrupt this balance and are used clinically to treat diseases including cancer. Despite their use, little is known about their effects on chromatin regulators, particularly those that signal through lysine acetylation. We apply quantitative genomic and proteomic approaches to demonstrate that HDACi robustly increases a low-abundance histone 4 polyacetylation state, which serves as a preferred binding substrate for several bromodomain-containing proteins, including BRD4. Increased H4 polyacetylation occurs in transcribed genes and correlates with the targeting of BRD4. Collectively, these results suggest that HDAC inhibition functions, at least in part, through expansion of a rare histone acetylation state, which then retargets lysine-acetyl readers associated with changes in gene expression, partially mimicking the effect of bromodomain inhibition.
MeSH term(s)	Acetylation ; Cell Cycle Proteins/metabolism ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylase Inhibitors/therapeutic use ; Histones/metabolism ; Humans ; Transcription Factors/metabolism
Chemical Substances	BRD4 protein, human ; Cell Cycle Proteins ; Histone Deacetylase Inhibitors ; Histones ; Transcription Factors
Language	English
Publishing date	2021-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2020.108638
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Article ; Online: Selectively targeting estrogen receptors for cancer treatment.

Shanle, Erin K / Xu, Wei

Advanced drug delivery reviews

2010 Volume 62, Issue 13, Page(s) 1265–1276

Abstract: Estrogens regulate growth and development through the action of two distinct estrogen receptors (ERs), ERα and ERβ, which mediate proliferation and differentiation of cells. For decades, ERα mediated estrogen signaling has been therapeutically targeted ... ...

Abstract	Estrogens regulate growth and development through the action of two distinct estrogen receptors (ERs), ERα and ERβ, which mediate proliferation and differentiation of cells. For decades, ERα mediated estrogen signaling has been therapeutically targeted to treat breast cancer, most notably with the selective estrogen receptor modulator (SERM) tamoxifen. Selectively targeting ERs occurs at two levels: tissue selectivity and receptor subtype selectivity. SERMs have been developed with emphasis on tissue selectivity to target ER signaling for breast cancer treatment. Additionally, new approaches to selectively target the action of ERα going beyond ligand-dependent activity are under current investigation. As evidence of the anti-proliferative role of ERβ accumulates, selectively targeting ERβ is an attractive approach for designing new cancer therapies with the emphasis shifted to designing ligands with subtype selectivity. This review will present the mechanistic and structural features of ERs that determine tissue and subtype selectivity with an emphasis on current approaches to selectively target ERα and ERβ for cancer treatment.
MeSH term(s)	Breast Neoplasms/drug therapy ; Breast Neoplasms/metabolism ; Estrogen Receptor alpha/chemistry ; Estrogen Receptor alpha/metabolism ; Estrogen Receptor beta/chemistry ; Estrogen Receptor beta/metabolism ; Female ; Humans ; Ligands ; Male ; Molecular Conformation ; Molecular Targeted Therapy ; Neoplasms/drug therapy ; Neoplasms/metabolism ; Selective Estrogen Receptor Modulators/chemistry ; Selective Estrogen Receptor Modulators/metabolism ; Selective Estrogen Receptor Modulators/therapeutic use ; Signal Transduction ; Structure-Activity Relationship
Chemical Substances	Estrogen Receptor alpha ; Estrogen Receptor beta ; Ligands ; Selective Estrogen Receptor Modulators
Language	English
Publishing date	2010-08-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	639113-8
ISSN	1872-8294 ; 0169-409X
ISSN (online)	1872-8294
ISSN	0169-409X
DOI	10.1016/j.addr.2010.08.001
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Article ; Online: Endocrine disrupting chemicals targeting estrogen receptor signaling: identification and mechanisms of action.

Shanle, Erin K / Xu, Wei

Chemical research in toxicology

2010 Volume 24, Issue 1, Page(s) 6–19

Abstract: Many endocrine disrupting chemicals (EDCs) adversely impact estrogen signaling by interacting with two estrogen receptors (ERs): ERα and ERβ. Though the receptors have similar ligand binding and DNA binding domains, ERα and ERβ have some unique ... ...

Abstract	Many endocrine disrupting chemicals (EDCs) adversely impact estrogen signaling by interacting with two estrogen receptors (ERs): ERα and ERβ. Though the receptors have similar ligand binding and DNA binding domains, ERα and ERβ have some unique properties in terms of ligand selectivity and target gene regulation. EDCs that target ER signaling can modify genomic and nongenomic ER activity through direct interactions with ERs, indirectly through transcription factors such as the aryl hydrocarbon receptor (AhR), or through modulation of metabolic enzymes that are critical for normal estrogen synthesis and metabolism. Many EDCs act through multiple mechanisms as exemplified by chemicals that bind both AhR and ER, such as 3-methylcholanthrene. Other EDCs that target ER signaling include phytoestrogens, bisphenolics, and organochlorine pesticides, and many alter normal ER signaling through multiple mechanisms. EDCs can also display tissue-selective ER agonist and antagonist activities similar to selective estrogen receptor modulators (SERMs) designed for pharmaceutical use. Thus, biological effects of EDCs need to be carefully interpreted because EDCs can act through complex tissue-selective modulation of ERs and other signaling pathways in vivo. Current requirements by the U.S. Environmental Protection Agency require some in vitro and cell-based assays to identify EDCs that target ER signaling through direct and metabolic mechanisms. Additional assays may be useful screens for identifying EDCs that act through alternative mechanisms prior to further in vivo study.
MeSH term(s)	Endocrine Disruptors/chemistry ; Endocrine Disruptors/toxicity ; Hydrocarbons, Chlorinated/chemistry ; Hydrocarbons, Chlorinated/toxicity ; Phenols/chemistry ; Phenols/toxicity ; Phytoestrogens/chemistry ; Phytoestrogens/toxicity ; Protein Structure, Tertiary ; Receptors, Estrogen/chemistry ; Receptors, Estrogen/metabolism ; Signal Transduction
Chemical Substances	Endocrine Disruptors ; Hydrocarbons, Chlorinated ; Phenols ; Phytoestrogens ; Receptors, Estrogen
Language	English
Publishing date	2010-11-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	639353-6
ISSN	1520-5010 ; 0893-228X
ISSN (online)	1520-5010
ISSN	0893-228X
DOI	10.1021/tx100231n
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