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You searched for +publisher:"Leiden University" +contributor:("van Noort, John"). Showing records 1 – 3 of 3 total matches.

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Leiden University

1. Botto, Margherita. Structural changes of chromatin fibers induced by variation of linker DNA length.

Degree: 2017, Leiden University

In this thesis we are going to study the mechanical properties of a chromatin fiber. Chromatin is the second compaction stage of DNA, after the wrapping of DNA around histones proteins to form nucleosomes. Specifically we are going to analyze how its behaviour under external stresses is going to change with the variation of the linker DNA length, the DNA segment that links two adjacent nucleosomes. We will be able to do it at a single-molecule level thanks to the use of magnetic tweezers, an apparatus that can exert forces and torques directly to individual molecules. Advisors/Committee Members: van Noort, John (advisor).

Subjects/Keywords: chromatin; nucleosomes; DNA

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APA (6th Edition):

Botto, M. (2017). Structural changes of chromatin fibers induced by variation of linker DNA length. (Masters Thesis). Leiden University. Retrieved from http://hdl.handle.net/1887/53213

Chicago Manual of Style (16th Edition):

Botto, Margherita. “Structural changes of chromatin fibers induced by variation of linker DNA length.” 2017. Masters Thesis, Leiden University. Accessed July 19, 2019. http://hdl.handle.net/1887/53213.

MLA Handbook (7th Edition):

Botto, Margherita. “Structural changes of chromatin fibers induced by variation of linker DNA length.” 2017. Web. 19 Jul 2019.

Vancouver:

Botto M. Structural changes of chromatin fibers induced by variation of linker DNA length. [Internet] [Masters thesis]. Leiden University; 2017. [cited 2019 Jul 19]. Available from: http://hdl.handle.net/1887/53213.

Council of Science Editors:

Botto M. Structural changes of chromatin fibers induced by variation of linker DNA length. [Masters Thesis]. Leiden University; 2017. Available from: http://hdl.handle.net/1887/53213


Leiden University

2. Culkin, Jamie. Simulations of Tracking Gold Nanorods with Two-Photon Scanning Microscopy in 3D.

Degree: 2016, Leiden University

Complex cellular processes can be characterised using single particle tracking techniques (SPT). ‘Labels’ such as metal nanoparticles are introduced into cells and tracked to reveal molecular trajectories. Many current techniques are based on fluorescence microscopy, and have nanometre-resolution. To accurately probe cellular processes, a technique must also have long-term 3D in-vivo observing capability with a minimal toxic effect. Gold nanorods (GNRs) in two-photon microscopy is a promising technique. GNRs are non-toxic, easily functionalisable, and exhibit a bright two-photon fluorescence. However, the theoretical positional accuracy for this technique is not yet known. Furthermore, the detailed trajectory data present statistical challenges. We have addressed these issues here numerically, using simulated image data. We found the accuracy to be between 5.2nm and 8.9nm for stationary GNRS, dependent on the separation between slices. We also found that diffusive movement of a nanorod lowers the accuracy, at worst case to 31.8nm. We have also investigated optimising the extraction of behaviour properties from MSD plots, and have used Welsh’s test to detect transitions. GNRs in two-photon microscopy has been shown to be a very accurate technique, and its trajectory data can yield accurate behavioural information. The fit of the PSF may be improved, but the techniques already compares well against others. Advisors/Committee Members: van Noort, John (advisor).

Subjects/Keywords: superresolution; tracking; gold nanorods; two-photon microscopy; simulation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Culkin, J. (2016). Simulations of Tracking Gold Nanorods with Two-Photon Scanning Microscopy in 3D. (Masters Thesis). Leiden University. Retrieved from http://hdl.handle.net/1887/39099

Chicago Manual of Style (16th Edition):

Culkin, Jamie. “Simulations of Tracking Gold Nanorods with Two-Photon Scanning Microscopy in 3D.” 2016. Masters Thesis, Leiden University. Accessed July 19, 2019. http://hdl.handle.net/1887/39099.

MLA Handbook (7th Edition):

Culkin, Jamie. “Simulations of Tracking Gold Nanorods with Two-Photon Scanning Microscopy in 3D.” 2016. Web. 19 Jul 2019.

Vancouver:

Culkin J. Simulations of Tracking Gold Nanorods with Two-Photon Scanning Microscopy in 3D. [Internet] [Masters thesis]. Leiden University; 2016. [cited 2019 Jul 19]. Available from: http://hdl.handle.net/1887/39099.

Council of Science Editors:

Culkin J. Simulations of Tracking Gold Nanorods with Two-Photon Scanning Microscopy in 3D. [Masters Thesis]. Leiden University; 2016. Available from: http://hdl.handle.net/1887/39099


Leiden University

3. Oikonomeas Koppasis, Nikolaos. Automation of identification and transformation of fluorescence images in CLEM data post-processing.

Degree: 2019, Leiden University

We introduce an open source, freely available algorithm for automatic correlation of fluorescence and electron microscopy images in Correlative Light-Electron Microscopy (CLEM). With a minimal amount of manual input, two custom modules perform an automatic identification of the fluorescent nuclei and the watershed nucleus of a TEM image and hence calculate the necessary affine transformation for accurate correlation. The process can be performed on a group of pre-processed images and allows for an efficient solution around the data handling bottleneck encountered in the technique. Advisors/Committee Members: van Noort, John (advisor).

Subjects/Keywords: CLEM; Automation; fluorescence; post-processing; transformation; identification

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Oikonomeas Koppasis, N. (2019). Automation of identification and transformation of fluorescence images in CLEM data post-processing. (Masters Thesis). Leiden University. Retrieved from http://hdl.handle.net/1887/74200

Chicago Manual of Style (16th Edition):

Oikonomeas Koppasis, Nikolaos. “Automation of identification and transformation of fluorescence images in CLEM data post-processing.” 2019. Masters Thesis, Leiden University. Accessed July 19, 2019. http://hdl.handle.net/1887/74200.

MLA Handbook (7th Edition):

Oikonomeas Koppasis, Nikolaos. “Automation of identification and transformation of fluorescence images in CLEM data post-processing.” 2019. Web. 19 Jul 2019.

Vancouver:

Oikonomeas Koppasis N. Automation of identification and transformation of fluorescence images in CLEM data post-processing. [Internet] [Masters thesis]. Leiden University; 2019. [cited 2019 Jul 19]. Available from: http://hdl.handle.net/1887/74200.

Council of Science Editors:

Oikonomeas Koppasis N. Automation of identification and transformation of fluorescence images in CLEM data post-processing. [Masters Thesis]. Leiden University; 2019. Available from: http://hdl.handle.net/1887/74200

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