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Article ; Online: Breakthrough instruments and products: DriveAFM for high-performance atomic force microscopy.

Adams, Jonathan D / Frederix, Patrick L T M / Bippes, Christian A

2021 Volume 92, Issue 12, Page(s) 129503

Abstract: Atomic force microscopy is a powerful technique for measurement and mapping of nanoscale topography and electrical and mechanical sample properties. The Nanosurf DriveAFM is a new generation instrument that combines ease of use and high performance ... ...

Abstract	Atomic force microscopy is a powerful technique for measurement and mapping of nanoscale topography and electrical and mechanical sample properties. The Nanosurf DriveAFM is a new generation instrument that combines ease of use and high performance through full motorization, CleanDrive photothermal excitation, and a mechanical and electrical design that allows for both high-resolution and large-range imaging.
MeSH term(s)	Microscopy, Atomic Force
Language	English
Publishing date	2021-12-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/5.0081190
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Article ; Online: Reference-free alignment and sorting of single-molecule force spectroscopy data.

Bosshart, Patrick D / Frederix, Patrick L T M / Engel, Andreas

Biophysical journal

2012 Volume 102, Issue 9, Page(s) 2202–2211

Abstract: Single-molecule force spectroscopy has become a versatile tool for investigating the (un)folding of proteins and other polymeric molecules. Like other single-molecule techniques, single-molecule force spectroscopy requires recording and analysis of large ...

Abstract	Single-molecule force spectroscopy has become a versatile tool for investigating the (un)folding of proteins and other polymeric molecules. Like other single-molecule techniques, single-molecule force spectroscopy requires recording and analysis of large data sets to extract statistically meaningful conclusions. Here, we present a data analysis tool that provides efficient filtering of heterogeneous data sets, brings spectra into register based on a reference-free alignment algorithm, and determines automatically the location of unfolding barriers. Furthermore, it groups spectra according to the number of unfolding events, subclassifies the spectra using cross correlation-based sorting, and extracts unfolding pathways by principal component analysis and clustering methods to extracted peak positions. Our approach has been tested on a data set obtained through mechanical unfolding of bacteriorhodopsin (bR), which contained a significant number of spectra that did not show the well-known bR fingerprint. In addition, we have tested the performance of the data analysis tool on unfolding data of the soluble multidomain (Ig27)(8) protein.
MeSH term(s)	Algorithms ; Bacteriorhodopsins/chemistry ; Bacteriorhodopsins/ultrastructure ; Computer Simulation ; Microscopy, Atomic Force/methods ; Models, Molecular ; Molecular Probe Techniques ; Molecular Probes/chemistry ; Reference Values
Chemical Substances	Molecular Probes ; Bacteriorhodopsins (53026-44-1)
Language	English
Publishing date	2012-07-23
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.2012.03.027
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Article ; Online: Atomic force microscopy of biological membranes.

Frederix, Patrick L T M / Bosshart, Patrick D / Engel, Andreas

Biophysical journal

2008 Volume 96, Issue 2, Page(s) 329–338

Abstract: Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, ...

Abstract	Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes.
MeSH term(s)	Algorithms ; Cell Membrane/ultrastructure ; Elasticity ; Image Processing, Computer-Assisted ; Interferometry ; Membrane Proteins/chemistry ; Membrane Proteins/ultrastructure ; Microelectrodes ; Microscopy, Atomic Force/instrumentation ; Microscopy, Atomic Force/methods ; Microscopy, Electron, Scanning/methods ; Models, Biological ; Protein Structure, Quaternary ; Spectrum Analysis/methods
Chemical Substances	Membrane Proteins
Language	English
Publishing date	2008-12-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2008.09.046
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Article: Reference-Free Alignment and Sorting of Single-Molecule Force Spectroscopy Data

Bosshart, Patrick D / Frederix, Patrick L.T.M / Engel, Andreas

Biophysical journal. 2012 May 2, v. 102, no. 9

2012

Abstract	Single-molecule force spectroscopy has become a versatile tool for investigating the (un)folding of proteins and other polymeric molecules. Like other single-molecule techniques, single-molecule force spectroscopy requires recording and analysis of large data sets to extract statistically meaningful conclusions. Here, we present a data analysis tool that provides efficient filtering of heterogeneous data sets, brings spectra into register based on a reference-free alignment algorithm, and determines automatically the location of unfolding barriers. Furthermore, it groups spectra according to the number of unfolding events, subclassifies the spectra using cross correlation-based sorting, and extracts unfolding pathways by principal component analysis and clustering methods to extracted peak positions. Our approach has been tested on a data set obtained through mechanical unfolding of bacteriorhodopsin (bR), which contained a significant number of spectra that did not show the well-known bR fingerprint. In addition, we have tested the performance of the data analysis tool on unfolding data of the soluble multidomain (Ig27)8 protein.
Keywords	algorithms ; cluster analysis ; data collection ; principal component analysis ; proteins ; sorting ; spectroscopy
Language	English
Dates of publication	2012-0502
Size	p. 2202-2211.
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.2012.03.027
Database	NAL-Catalogue (AGRICOLA)

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Article: Characterization of microfabricated probes for combined atomic force and high-resolution scanning electrochemical microscopy.

Gullo, Maurizio R / Frederix, Patrick L T M / Akiyama, Terunobu / Engel, Andreas / deRooij, Nico F / Staufer, Urs

Analytical chemistry

2006 Volume 78, Issue 15, Page(s) 5436–5442

Abstract: A combined atomic force and scanning electrochemical microscope probe is presented. The probe is electrically insulated except at the very apex of the tip, which has a radius of curvature in the range of 10-15 nm. Steady-state cyclic voltammetry ... ...

Abstract	A combined atomic force and scanning electrochemical microscope probe is presented. The probe is electrically insulated except at the very apex of the tip, which has a radius of curvature in the range of 10-15 nm. Steady-state cyclic voltammetry measurements for the reduction of Ru(NH3)6Cl3 and feedback experiments showed a distinct and reproducible response of the electrode. These experimental results agreed with finite element simulations for the corresponding diffusion process. Sequentially topographical and electrochemical studies of Pt lines deposited onto Si3N4 and spaced 100 nm apart (edge to edge) showed a lateral electrochemical resolution of 10 nm.
Language	English
Publishing date	2006-08-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac0521495
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Article: Conductive supports for combined AFM-SECM on biological membranes.

Frederix, Patrick L T M / Bosshart, Patrick D / Akiyama, Terunobu / Chami, Mohamed / Gullo, Maurizio R / Blackstock, Jason J / Dooleweerdt, Karin / de Rooij, Nico F / Staufer, Urs / Engel, Andreas

Nanotechnology

2008 Volume 19, Issue 38, Page(s) 384004

Abstract: Four different conductive supports are analysed regarding their suitability for combined atomic force and scanning electrochemical microscopy (AFM-SECM) on biological membranes. Highly oriented pyrolytic graphite (HOPG), MoS(2), template stripped gold, ... ...

Abstract	Four different conductive supports are analysed regarding their suitability for combined atomic force and scanning electrochemical microscopy (AFM-SECM) on biological membranes. Highly oriented pyrolytic graphite (HOPG), MoS(2), template stripped gold, and template stripped platinum are compared as supports for high resolution imaging of reconstituted membrane proteins or native membranes, and as electrodes for transferring electrons from or to a redox molecule. We demonstrate that high resolution topographs of the bacterial outer membrane protein F can be recorded by contact mode AFM on all four supports. Electrochemical feedback experiments with conductive cantilevers that feature nanometre-scale electrodes showed fast re-oxidation of the redox couple Ru(NH(3))(6)(3+/2+) with the two metal supports after prolonged immersion in electrolyte. In contrast, the re-oxidation rates decayed quickly to unpractical levels with HOPG or MoS(2) under physiological conditions. On HOPG we observed heterogeneity in the re-oxidation rate of the redox molecules with higher feedback currents at step edges. The latter results demonstrate the capability of conductive cantilevers with small electrodes to measure minor variations in an SECM signal and to relate them to nanometre-scale features in a simultaneously recorded AFM topography. Rapid decay of re-oxidation rate and surface heterogeneity make HOPG or MoS(2) less attractive for combined AFM-SECM experiments on biological membranes than template stripped gold or platinum supports.
Language	English
Publishing date	2008-09-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1362365-5
ISSN	1361-6528 ; 0957-4484
ISSN (online)	1361-6528
ISSN	0957-4484
DOI	10.1088/0957-4484/19/38/384004
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Article: High-throughput single-molecule force spectroscopy for membrane proteins.

Bosshart, Patrick D / Casagrande, Fabio / Frederix, Patrick L T M / Ratera, Merce / Bippes, Christian A / Müller, Daniel J / Palacin, Manuel / Engel, Andreas / Fotiadis, Dimitrios

Nanotechnology

2008 Volume 19, Issue 38, Page(s) 384014

Abstract: ... were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L ... between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D ...

Abstract	Atomic force microscopy-based single-molecule force spectroscopy (SMFS) is a powerful tool for studying the mechanical properties, intermolecular and intramolecular interactions, unfolding pathways, and energy landscapes of membrane proteins. One limiting factor for the large-scale applicability of SMFS on membrane proteins is its low efficiency in data acquisition. We have developed a semi-automated high-throughput SMFS (HT-SMFS) procedure for efficient data acquisition. In addition, we present a coarse filter to efficiently extract protein unfolding events from large data sets. The HT-SMFS procedure and the coarse filter were validated using the proton pump bacteriorhodopsin (BR) from Halobacterium salinarum and the L-arginine/agmatine antiporter AdiC from the bacterium Escherichia coli. To screen for molecular interactions between AdiC and its substrates, we recorded data sets in the absence and in the presence of L-arginine, D-arginine, and agmatine. Altogether ∼400 000 force-distance curves were recorded. Application of coarse filtering to this wealth of data yielded six data sets with ∼200 (AdiC) and ∼400 (BR) force-distance spectra in each. Importantly, the raw data for most of these data sets were acquired in one to two days, opening new perspectives for HT-SMFS applications.
Language	English
Publishing date	2008-09-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1362365-5
ISSN	1361-6528 ; 0957-4484
ISSN (online)	1361-6528
ISSN	0957-4484
DOI	10.1088/0957-4484/19/38/384014
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Article ; Online: Pediatric HIV Treatment Gaps in 7 East and Southern African Countries: Examination of Modeled, Survey, and Routine Program Data.

Saito, Suzue / Chung, Hannah / Mahy, Mary / Radin, Anna K / Jonnalagadda, Sasi / Hakim, Avi / Awor, Anna C / Mwila, Annie / Gonese, Elizabeth / Wadonda-Kabondo, Nellie / Rwehumbiza, Patrick / Ao, Trong / Kim, Evelyn J / Frederix, Koen / Nuwagaba-Biribonwoha, Harriet / Musuka, Godfrey / Mugurungi, Owen / Mushii, Jeremiah / Mnisi, Zandile /

Munthali, Gloria / Jahn, Andreas / Kirungi, Wilford L / Sivile, Suilanji / Abrams, Elaine J

Journal of acquired immune deficiency syndromes (1999)

2018 Volume 78 Suppl 2, Page(s) S134–S141

Abstract: Background: Remarkable success in the prevention and treatment of pediatric HIV infection has been achieved in the past decade. Large differences remain between the estimated number of children living with HIV (CLHIV) and those identified through ... ...

Abstract	Background: Remarkable success in the prevention and treatment of pediatric HIV infection has been achieved in the past decade. Large differences remain between the estimated number of children living with HIV (CLHIV) and those identified through national HIV programs. We evaluated the number of CLHIV and those on treatment in Lesotho, Malawi, Swaziland, Tanzania, Uganda, Zambia, and Zimbabwe. Methods: We assessed the total number of CLHIV, CLHIV on antiretroviral treatment (ART), and national and regional ART coverage gaps using 3 data sources: (1) Joint United Nations Programme on HIV/AIDS model-based estimates and national program data used as input values in the models, (2) population-based HIV impact surveys (PHIA), and (3) program data from the President's Emergency Plan for AIDS Relief (PEPFAR)-supported clinics. Results: Across the 7 countries, HIV prevalence among children aged 0-14 years ranged from 0.4% (Uncertainty Bounds (UB) 0.2%-0.6%) to 2.8% (UB: 2.2%-3.4%) according to the PHIA surveys, resulting in estimates of 520,000 (UB: 460,000-580,000) CLHIV in 2016-2017 in the 7 countries. This compared with Spectrum estimates of pediatric HIV prevalence ranging from 0.5% (UB: 0.5%-0.6%) to 3.5% (UB: 3.0%-4.0%) representing 480,000 (UB: 390,000-550,000) CLHIV. CLHIV not on treatment according to the PEPFAR, PHIA, and Spectrum for the countries stood at 48% (UB: 25%-60%), 49% (UB: 37%-50%), and 38% (UB: 24%-47%), respectively. Of 78 regions examined across 7 countries, 33% of regions (PHIA data) or 41% of regions (PEPFAR data) had met the ART coverage target of 81%. Conclusions: There are substantial gaps in the coverage of HIV treatment in CLHIV in the 7 countries studied according to all sources. There is continued need to identify, engage, and treat infants and children. Important inconsistencies in estimates across the 3 sources warrant in-depth investigation.
MeSH term(s)	Adolescent ; Africa, Eastern/epidemiology ; Africa, Southern/epidemiology ; Anti-Retroviral Agents/therapeutic use ; Child ; Child, Preschool ; Female ; HIV/isolation & purification ; HIV Infections/diagnosis ; HIV Infections/drug therapy ; HIV Infections/epidemiology ; Humans ; Infant ; Male ; Prevalence ; Surveys and Questionnaires ; United Nations
Chemical Substances	Anti-Retroviral Agents
Language	English
Publishing date	2018-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	645053-2
ISSN	1944-7884 ; 1077-9450 ; 0897-5965 ; 0894-9255 ; 1525-4135
ISSN (online)	1944-7884 ; 1077-9450
ISSN	0897-5965 ; 0894-9255 ; 1525-4135
DOI	10.1097/QAI.0000000000001739
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Article: Reference-Free Alignment and Sorting of Single-Molecule Force Spectroscopy Data

Bosshart, Patrick D. / Frederix, Patrick L.T.M. / Engel, Andreas

Biophysical journal

Volume v. 102,, Issue no. 9

Abstract	Single-molecule force spectroscopy has become a versatile tool for investigating the (un)folding of proteins and other polymeric molecules. Like other single-molecule techniques, single-molecule force spectroscopy requires recording and analysis of large data sets to extract statistically meaningful conclusions. Here, we present a data analysis tool that provides efficient filtering of heterogeneous data sets, brings spectra into register based on a reference-free alignment algorithm, and determines automatically the location of unfolding barriers. Furthermore, it groups spectra according to the number of unfolding events, subclassifies the spectra using cross correlation-based sorting, and extracts unfolding pathways by principal component analysis and clustering methods to extracted peak positions. Our approach has been tested on a data set obtained through mechanical unfolding of bacteriorhodopsin (bR), which contained a significant number of spectra that did not show the well-known bR fingerprint. In addition, we have tested the performance of the data analysis tool on unfolding data of the soluble multidomain (Ig27)₈ protein.
Keywords	data collection ; principal component analysis ; sorting ; algorithms ; spectroscopy ; proteins ; cluster analysis
Language	English
Document type	Article
ISSN	0006-3495
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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