LIVIVO - Search results -

Search results

Result 1 - 8 of total 8

Search options

Article ; Online: Dissecting knowledge, guessing, and blunder in multiple choice assessments.

Abu-Ghazalah, Rashid M / Dubins, David N / Poon, Gregory M K

2023 Volume 36, Issue 1, Page(s) 80–98

Abstract: Multiple choice results are inherently probabilistic outcomes, as correct responses reflect a combination of knowledge and guessing, while incorrect responses additionally reflect blunder, a confidently committed mistake. To objectively resolve knowledge ...

Abstract	Multiple choice results are inherently probabilistic outcomes, as correct responses reflect a combination of knowledge and guessing, while incorrect responses additionally reflect blunder, a confidently committed mistake. To objectively resolve knowledge from responses in an MC test structure, we evaluated probabilistic models that explicitly account for guessing, knowledge and blunder using eight assessments (>9,000 responses) from an undergraduate biotechnology curriculum. A Bayesian implementation of the models, aimed at assessing their robustness to prior beliefs in examinee knowledge, showed that explicit estimators of knowledge are markedly sensitive to prior beliefs with scores as sole input. To overcome this limitation, we examined self-ranked confidence as a proxy knowledge indicator. For our test set, three levels of confidence resolved test performance. Responses rated as least confident were correct more frequently than expected from random selection, reflecting partial knowledge, but were balanced by blunder among the most confident responses. By translating evidence-based guessing and blunder rates to pass marks that statistically qualify a desired level of examinee knowledge, our approach finds practical utility in test analysis and design.
Language	English
Publishing date	2023-02-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2008021-9
ISSN	1532-4818 ; 0895-7347
ISSN (online)	1532-4818
ISSN	0895-7347
DOI	10.1080/08957347.2023.2172017
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: Structural polymorphism of the four-repeat Oxytricha nova telomeric DNA sequences.

Abu-Ghazalah, Rashid M / Macgregor, Robert B

Biophysical chemistry

2009 Volume 141, Issue 2-3, Page(s) 180–185

Abstract: G-quadruplexes are four-stranded nucleic acid complexes that exhibit a great deal of polymorphism. Recently a group described the polymorphism exhibited by the four-repeat of the Oxytricha nova telomeric sequences (Lee, J.Y., Yoon, J., Kihm, H.W., Kim, D. ...

Abstract	G-quadruplexes are four-stranded nucleic acid complexes that exhibit a great deal of polymorphism. Recently a group described the polymorphism exhibited by the four-repeat of the Oxytricha nova telomeric sequences (Lee, J.Y., Yoon, J., Kihm, H.W., Kim, D.S., Biochemistry 2008, 47, 3389-3396). In this study we evaluated the effects of G-tract and loop lengths on this behaviour using circular dichroism (CD) and gel electrophoresis. The largest changes were detected for oligonucleotides with different numbers of consecutive G residues. Furthermore, decreasing the number of residues between the G runs, the loops, from four to three only results in minor alteration in the polymorphism. However, the shortening of the G-tract from four to three guanine residues led to characteristically anti-parallel G-quadruplex CD spectra. Finally, we show that adenine bases in the loop sequences are less likely to form G-quadruplexes in the presence of Na(+) cations than those comprised of thymine residues. The results presented here are an addition to the modest information available for predicting the type of G-quadruplex to be formed from G-rich sequences in aqueous solutions containing sodium or potassium ions.
MeSH term(s)	Adenine/chemistry ; Animals ; Autoradiography ; Circular Dichroism ; DNA, Protozoan/chemistry ; Electrophoresis, Polyacrylamide Gel ; G-Quadruplexes ; Guanine/chemistry ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry ; Oxytricha/chemistry ; Phosphorus Radioisotopes ; Sodium/chemistry ; Thymine/chemistry
Chemical Substances	DNA, Protozoan ; Oligodeoxyribonucleotides ; Phosphorus Radioisotopes ; Guanine (5Z93L87A1R) ; Sodium (9NEZ333N27) ; Adenine (JAC85A2161) ; Thymine (QR26YLT7LT)
Language	English
Publishing date	2009-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2009.01.013
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1147: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Folding thermodynamics of the hybrid-1 type intramolecular human telomeric G-quadruplex.

Shek, Yuen Lai / Noudeh, Golamreza Dehghan / Nazari, Mozhgan / Heerklotz, Heiko / Abu-Ghazalah, Rashid M / Dubins, David N / Chalikian, Tigran V

Biopolymers

2014 Volume 101, Issue 3, Page(s) 216–227

Abstract: Guanine-rich DNA sequences that may form G-quadruplexes are located in strategic DNA loci with the ability to regulate biological events. G-quadruplexes have been under intensive scrutiny owing to their potential to serve as novel drug targets in ... ...

Abstract	Guanine-rich DNA sequences that may form G-quadruplexes are located in strategic DNA loci with the ability to regulate biological events. G-quadruplexes have been under intensive scrutiny owing to their potential to serve as novel drug targets in emerging anticancer strategies. Thermodynamic characterization of G-quadruplexes is an important and necessary step in developing predictive algorithms for evaluating the conformational preferences of G-rich sequences in the presence or the absence of their complementary C-rich strands. We use a combination of spectroscopic, calorimetric, and volumetric techniques to characterize the folding/unfolding transitions of the 26-meric human telomeric sequence d[A3G3(T2AG3)3A2]. In the presence of K+ ions, the latter adopts the hybrid-1 G-quadruplex conformation, a tightly packed structure with an unusually small number of solvent-exposed atomic groups. The K+-induced folding of the G-quadruplex at room temperature is a slow process that involves significant accumulation of an intermediate at the early stages of the transition. The G-quadruplex state of the oligomeric sequence is characterized by a larger volume and compressibility and a smaller expansibility than the coil state. These results are in qualitative agreement with each other all suggesting significant dehydration to accompany the G-quadruplex formation. Based on our volume data, 432±19 water molecules become released to the bulk upon the G-quadruplex formation. This large number is consistent with a picture in which DNA dehydration is not limited to water molecules in direct contact with the regions that become buried but involves a general decrease in solute-solvent interactions all over the surface of the folded structure.
MeSH term(s)	DNA/chemistry ; G-Quadruplexes ; Guanine ; Humans ; Nucleic Acid Conformation ; Telomere ; Thermodynamics
Chemical Substances	Guanine (5Z93L87A1R) ; DNA (9007-49-2)
Language	English
Publishing date	2014-03
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.22317
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 77: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: A study of the interactions that stabilize DNA frayed wires.

Abu-Ghazalah, Rashid M / Irizar, Juan / Helmy, Amr S / Macgregor, Robert B

Biophysical chemistry

2010 Volume 147, Issue 3, Page(s) 123–129

Abstract: Oligodeoxyribonucleotides (ODNs) with long, terminal runs of consecutive guanines, and either a dA or dT tract at the other end form higher-order structures called DNA frayed wires. These aggregates self-assemble into species consisting of 2, 3, 4, 5, ... ...

Abstract	Oligodeoxyribonucleotides (ODNs) with long, terminal runs of consecutive guanines, and either a dA or dT tract at the other end form higher-order structures called DNA frayed wires. These aggregates self-assemble into species consisting of 2, 3, 4, 5, ... associated strands. Some of the remarkable features of these structures are their extreme thermostability and resistance to chemical denaturants and nucleases. However, the nature of the molecular interactions that stabilize these structures remains unclear. Based on dimethyl sulfate (DMS) methylation results, our group previously proposed DNA frayed wires to be a unique set of nucleic-acid assemblies in which the N7 of guanine does not participate in the guanine-guanine interactions. To probe the hydrogen bonding involved in the stabilization of d(A(15)G(15)) frayed wires, we used Raman spectroscopy in which the DNA sample is held in photonic crystal fibers. This technique significantly enhances the signals thus allowing the use of very low laser power. Based on our results for d(A(15)G(15)) and those of incorporating the isoelectronic guanine analog pyrazolo[3,4,-d]pyrimidine or PPG, into a frayed wire-forming sequence, we provide evidence that these structures are based on the G-quadruplex model. Furthermore, from the Raman spectrum, we observed markers that are consistent with the presence of deoxyguanosine residues in the syn conformation, this suggests the presence of anti-parallel G-quadruplexes. To identify the species that contain syn guanine residues, we used circular dichroism and gel electrophoresis to study an ODN in which all of the guanine residues were brominated, d(A(15)(8-Br)G(15)). In the presence of potassium, d(A(15)(8-Br)G(15)) forms what appears to be an anti-parallel dimeric G-quadruplex. To our knowledge, this is the first report of a DNA sequence having all its guanine residues replaced by 8-bromo-guanine and maintaining its ability to form a G-quadruplex structure.
MeSH term(s)	DNA Methylation ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Oligodeoxyribonucleotides/chemistry ; Temperature ; Thermodynamics
Chemical Substances	Oligodeoxyribonucleotides
Language	English
Publishing date	2010-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2010.01.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1147: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Concentration-dependent structural transitions of human telomeric DNA sequences.

Abu-Ghazalah, Rashid M / Rutledge, Steve / Lau, Lewis W Y / Dubins, David N / Macgregor, Robert B / Helmy, Amr S

Biochemistry

2012 Volume 51, Issue 37, Page(s) 7357–7366

Abstract: Oligodeoxyribonucleotides (ODNs) that have four repeats of the human telomeric sequence d(TTAGGG)(n) can assume multiple monomolecular G-quadruplex topologies. These are determined by the cation species present, the bases at the 5' or 3' end, and the ... ...

Abstract	Oligodeoxyribonucleotides (ODNs) that have four repeats of the human telomeric sequence d(TTAGGG)(n) can assume multiple monomolecular G-quadruplex topologies. These are determined by the cation species present, the bases at the 5' or 3' end, and the sample preparation technique. In this work, we report our studies of the concentration dependence of the circular dichroism (CD) and the vibrational modes probed by Raman scattering of three previously characterized monomolecular G-quadruplexes: H-Tel, d[5'-A(GGGTTA)(3)GGG-3']; hybrid-1, d[5'-AAA(GGGTTA)(3)GGGAA-3']; and hybrid-2, d[5'-TTA(GGGTTA)(3)GGGTT-3']. At high (millimolar) ODN concentrations, we observed a transformation of the CD spectrum of H-Tel, with a relaxation time on the order of 10 h. Analysis of the kinetics of this process is consistent with the formation of an aggregated complex of folded H-Tel monomers. Upon dilution, the aggregates dissociate rapidly, yielding spectra identical to those of monomeric H-Tel. Both hybrid sequences undergo a similar transition under high-salt (1 M) conditions. The measurements suggest that for these ODN concentrations, which are typically used in high-resolution spectroscopies, the monomolecular G-quadruplex structures undergo a transition to multimolecular structures at room temperature. Guided by our findings, we propose that the terminal bases of the hybrid-1 and hybrid-2 ODNs impede the formation of these aggregates; however, in solutions containing 1 M salt, the hybrid oligonucleotides aggregate.
MeSH term(s)	Base Sequence ; Chromosomes, Human/chemistry ; Humans ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry ; Telomere/chemistry
Chemical Substances	Oligodeoxyribonucleotides
Language	English
Publishing date	2012-09-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi300689t
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 217: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Concentration-Dependent Structural Transitions of Human Telomeric DNA Sequences

Abu-Ghazalah, Rashid M / Rutledge Steve / Lau Lewis W. Y / Dubins David N / Macgregor Robert B / Helmy Amr S

Biochemistry. 2012 Sept. 18, v. 51, no. 37

2012

Abstract: Oligodeoxyribonucleotides (ODNs) that have four repeats of the human telomeric sequence d(TTAGGG)â can assume multiple monomolecular G-quadruplex topologies. These are determined by the cation species present, the bases at the 5â² or 3â² end, and the ...

Abstract	Oligodeoxyribonucleotides (ODNs) that have four repeats of the human telomeric sequence d(TTAGGG)â can assume multiple monomolecular G-quadruplex topologies. These are determined by the cation species present, the bases at the 5â² or 3â² end, and the sample preparation technique. In this work, we report our studies of the concentration dependence of the circular dichroism (CD) and the vibrational modes probed by Raman scattering of three previously characterized monomolecular G-quadruplexes: H-Tel, d[5â²-A(GGGTTA)âGGG-3â²]; hybrid-1, d[5â²-AAA(GGGTTA)âGGGAA-3â²]; and hybrid-2, d[5â²-TTA(GGGTTA)âGGGTT-3â²]. At high (millimolar) ODN concentrations, we observed a transformation of the CD spectrum of H-Tel, with a relaxation time on the order of 10 h. Analysis of the kinetics of this process is consistent with the formation of an aggregated complex of folded H-Tel monomers. Upon dilution, the aggregates dissociate rapidly, yielding spectra identical to those of monomeric H-Tel. Both hybrid sequences undergo a similar transition under high-salt (1 M) conditions. The measurements suggest that for these ODN concentrations, which are typically used in high-resolution spectroscopies, the monomolecular G-quadruplex structures undergo a transition to multimolecular structures at room temperature. Guided by our findings, we propose that the terminal bases of the hybrid-1 and hybrid-2 ODNs impede the formation of these aggregates; however, in solutions containing 1 M salt, the hybrid oligonucleotides aggregate.
Keywords	DNA ; Raman spectroscopy ; ambient temperature ; cations ; circular dichroism spectroscopy ; humans ; nucleotide sequences ; oligodeoxyribonucleotides ; telomeres
Language	English
Dates of publication	2012-0918
Size	p. 7357-7366.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021%2Fbi300689t
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.A 217: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Ionic mobilities of duplex and frayed wire DNA in discontinuous buffer electrophoresis: evidence of interactions with amino acids.

Poon, Gregory M K / Abu-Ghazalah, Rashid M / Macgregor, Robert B

Biochemistry

2004 Volume 43, Issue 51, Page(s) 16337–16347

Abstract: Nucleic acid-amino acid interactions are fundamental to understanding higher-order interactions made by nucleic acid-binding proteins. Here we employ electrophoresis to investigate DNA-amino acid interactions by using a set of amino acids (Ala, Gln, Gly, ...

Abstract	Nucleic acid-amino acid interactions are fundamental to understanding higher-order interactions made by nucleic acid-binding proteins. Here we employ electrophoresis to investigate DNA-amino acid interactions by using a set of amino acids (Ala, Gln, Gly, Met, Phe, Val, bicine and tricine) as trailing ions in a discontinuous buffer, and monitoring their interactions with duplex (from 12 to 3000 bp) and frayed wire [a set of self-assembled superstructures arising from d(A(15)G(15)) oligodeoxyribonucleotides] DNA by the change in their ionic mobility (in terms of %R(f)) as a function of amino acid concentration in a polyacrylamide matrix. By titration of the pH of Tris-HCl polyacrylamide gels (from 7 to 10), a span of steady-state amino acid concentrations and extents of ionization can be maintained. We found that with a decrease in pH (thereby increasing amino acid concentrations and the extent of ionization of the alpha-amino group), both the %R(f) and stacking limit were increased, but the extent varied among the trailing ions, resulting in an induced dispersion of %R(f) values for a given analyte. Using singular-value analysis to take into account the %R(f) dependence on fragment size (i.e., the %R(f) distribution), the degree of dispersion was found to be positively correlated with the accumulation of N-protonated trailing ions in the resolving phase. These results indicate that the modification of %R(f) of DNA is a mass-action effect involving DNA-amino acid interactions under essentially aqueous conditions.
MeSH term(s)	Amino Acids/metabolism ; DNA/metabolism ; Data Interpretation, Statistical ; Electrophoresis ; Hydrogen-Ion Concentration ; Ions/metabolism
Chemical Substances	Amino Acids ; Ions ; DNA (9007-49-2)
Language	English
Publishing date	2004-12-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi0480786
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 217: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Concentration-Dependent Structural Transitions of Human Telomeric DNA Sequences

Abu-Ghazalah, Rashid M. / Rutledge SteveauthorEdward S. Rogers Department of Electrical and Computer Engineering, Faculty of Applied Science and Engineering, University of Toronto, Toronto, Ontario, Canada / Lau Lewis W. Y.authorDepartment of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada / Dubins David N.authorDepartment of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada / Macgregor Robert B.authorDepartment of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada / Helmy Amr S.authorEdward S. Rogers Department of Electrical and Computer Engineering, Faculty of Applied Science and Engineering, University of Toronto, Toronto, Ontario, Canada

Language	English
Document type	Article
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

To top

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Inter-library loan at ZB MED