| 1. |
- Beech, Jason P., et al.
(author)
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Sample preparation for single-cell whole chromosome analysis
- 2012
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In: Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012. - 9780979806452 ; , s. 998-999
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Conference paper (peer-reviewed)abstract
- In this work we present an integrated system for whole chromosome analysis of single bacterium. Using whole genome barcoding techniques, which offer direct and rapid microscopic visualization of the entire genome in one field-of-view, we aim to rapidly identify individual bacterium. We are developing our device to achieve the crucial, and difficult process of isolating a bacterium, removing the DNA in one piece and transferring it to a nano-channel for visualisation. In order to achieve control over the bacteria we encapsulate them in agarose, using flow focusing. The encapsulated bacteria can then be transported in microchannels to proximity with the nanochannels and then chemically lysis can be performed. Following lysis the intact genome can be extracted and transferred to the meandering nanochannel for analysis. We believe this device holds the potential to significantly decrease analysis times for single cell, whole genome analysis with the potential of opening up for automated, high-throughput genome analysis in microfluidic systems.
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| 2. |
- Frykholm, Karolin, 1977, et al.
(author)
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Probing concentration-dependent behavior of DNA-binding proteins on a single-molecule level illustrated by Rad51
- 2013
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In: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 443:2, s. 261-268
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Journal article (peer-reviewed)abstract
- Low throughput is an inherent problem associated with most single-molecule biophysical techniques. We have developed a versatile tool for high-throughput analysis of DNA and DNA-binding molecules by combining microfluidic and dense DNA arrays. We use an easy-to-process microfluidic flow channel system in which dense DNA arrays are prepared for simultaneous imaging of large amounts of DNA molecules with single-molecule resolution. The Y-shaped microfluidic design, where the two inlet channels can be controlled separately and precisely, enables the creation of a concentration gradient across the microfluidic channel as well as rapid and repeated addition and removal of substances from the measurement region. A DNA array stained with the fluorescent DNA-binding dye YOYO-1 in a gradient manner illustrates the method and serves as a proof of concept. We have applied the method to studies of the repair protein Rad51 and could directly probe the concentration-dependent DNA-binding behavior of human Rad51 (HsRad51). In the low-concentration regime used (100 nM HsRad51 and below), we detected binding to double-stranded DNA (dsDNA) without positive cooperativity. (C) 2013 Elsevier Inc. All rights reserved.
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| 3. |
- McGinn, Steven, et al.
(author)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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In: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Research review (peer-reviewed)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 4. |
- Noble, Charleston, et al.
(author)
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A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings.
- 2015
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:4
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Journal article (peer-reviewed)abstract
- Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge for this technique is thermal motion of the DNA as it undergoes imaging; this blurs fluorescent patterns along the DNA and results in information loss. Correcting for this effect (a process referred to as kymograph alignment) is a common preprocessing step in nanochannel-based optical mapping workflows, and we present here a highly efficient algorithm to accomplish this via pattern recognition. We compare our method with the one previous approach, and we find that our method is orders of magnitude faster while producing data of similar quality. We demonstrate proof of principle of our approach on experimental data consisting of melt mapped bacteriophage DNA.
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| 5. |
- So, Martin, et al.
(author)
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DEVELOPMENT OF A SYSTEM FOR COLLECTION OF POSITIONAL-BASED DATA FOR HORSES
- 2017
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In: Proceedings of the 13th INTERNATIONAL EQUITATION SCIENCE CONFERENCE.
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Conference paper (peer-reviewed)abstract
- Data gathering is a crucial part in many Equitation Science related projects, and this can be a very resource-intensive and time-consuming process. This project aimed to develop a tool to aid Equitation Science researchers in gathering positional-based data of horses. A prototype data collection system was developed, designed to enable cost-effective data acquisition, storage and presentation. The prototype system includes a GPS-enabled collar for collection of positional data, as well as a platform for presenting the gathered data online. Interviews were conducted with Equitation Science researchers in order to determine the requirements of such a system and to ensure that data obtained would be of sufficient quality. The GPS collar developed incorporates a microcontroller which allows tracking of horses within one metre. Furthermore, it is possible to extend the capabilities of the device using appropriate hardware to gather different types of equine data. The data gathered by the GPS collar are uploaded to a server where data are stored in a relational database ready for access by the scientist via a graphical user interface using a dedicated website. The user interface was developed using commonly practised interaction design methods such as user studies, heuristic evaluation and cognitive walkthroughs to ensure a user-friendly experience. Equitation Science experts contributed to both the design of the systems software in addition to the design and placement of the collar. It is anticipated that the GPS collar system can be used in Equitation Science projects that require identification of movement patterns of both individual horses as well as groups of horses, and will be able to provide measures such as distance moved and speed of movement. The system is designed to be future proof and able to be easily adapted according to the requirements of specific studies. For the Equitation Scientist in practice, the system provides the possibility to collect objective data from horses’ activities by removing the effect of the potentially biased human observer, and might thereby improve the quality of the conclusions in the scientific study. Lay person message: An electronic system has been developed to simplify the collection of positional-based data for equine research. The system consists of a GPS collar which collects data from horses and associated software accessed through a website for analysing and presenting the data. The system can be used in many different types of horse-based projects and will allow more objective data to be collected that can be used to understand horses and to improve horse welfare by removing the effect of the potentially biased human observer.
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