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1. Gümüscü, B. Lab-on-a-chip devices with patterned hydrogels.

Degree: 2016, University of Twente

Hydrogels are considered to be in the class of smart materials that find application in diagnostic, therapeutic,and fundamental science tools for miniaturized total analysis systems. In this thesis, the focus is on three major applications of patterned hydrogels, which are explored as an alternative strategy to expensive and low throughput systems for preparative DNA fractionation, in vitro compartmentalization of human gut epithelium, and desalination by microelectrodialysis. The use of patterned hydrogels in closed fluidic microchips or different research fields depends crucially on the ease and accessibility of their fabrication technology. In this work, two simple fabrication procedures are developed to pattern hydrogel microarrays. First, intermittent illumination is applied on mechanically polished microchips or the photopatterning of hydrogels. Second, capillary pressure barriers are used for controlling the position of the liquid-air meniscus in microchip channels, allowing the subsequent patterning of hydrogels by photopolymerization and thermo-gelation. Both fabrication techniques differ from previous studies in terms of versatility and high reproducibility. Preparative fractionation and purification of small-sized DNA fragments play an important role for second-generation sequencing and personalized medicine, and it is the first major application of hydrogels explored. We describe a novel method for concurrent continuous flow fractionation and purification of DNA fragments in a microfluidic device filled with agarose gel. The innovation of this work is twofold. Firstly, a new principle for continuous flow DNA fractionation is demonstrated. We exploit the variation in the field-dependent mobility of DNA molecules with DNA length for the fractionation, which is a separation mechanism that has hitherto gone unnoticed. Secondly, since this new mechanism can be applied using agarose gel, it provides a low-cost, robust, and versatile separation matrix. The theoretical advancement in combination with the practical advantages can lead to new developments in the gield of sample preparation of biological samples. Baseline fractionation of a 0.5-10 kbp DNA ladder is achieved within 2 minutes, which is ~15 times faster than in commercially available devices. Furthermore, the gel technology is easily adaptable; for example, changing the gel type can enable the fractionation of protein molecules. Thus, the microfluidic device is of broad interest for second generation sequencing and clinical diagnosis applications. The second major application of hydrogels reported in this thesis is the use of multicompartmental hydrogel arrays for 3D culturing of human intestine epithelial cells. Engineering in vitro microenvironments that mimic in vivo tissue systems is crucial for improving our understanding of tissue physiology, as well as curtailing the high costs and complexities associated with the existing techniques. We propose and demonstrate an in vitro microfluidic cell culture platform that consists of periodic 3D hydrogel… Advisors/Committee Members: van den Berg, Albert, Eijkel, Jan C.T..

Subjects/Keywords: IR-101009; METIS-318547; EWI-27288

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APA (6th Edition):

Gümüscü, B. (2016). Lab-on-a-chip devices with patterned hydrogels. (Doctoral Dissertation). University of Twente. Retrieved from https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html ; urn:nbn:nl:ui:28-101009 ; b2dc0768-23da-4e21-9603-5162ffe7c7ea ; 10.3990/1.9789036541916 ; urn:isbn:978-90-365-4191-6 ; urn:nbn:nl:ui:28-101009 ; https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html

Chicago Manual of Style (16th Edition):

Gümüscü, B. “Lab-on-a-chip devices with patterned hydrogels.” 2016. Doctoral Dissertation, University of Twente. Accessed July 04, 2020. https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html ; urn:nbn:nl:ui:28-101009 ; b2dc0768-23da-4e21-9603-5162ffe7c7ea ; 10.3990/1.9789036541916 ; urn:isbn:978-90-365-4191-6 ; urn:nbn:nl:ui:28-101009 ; https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html.

MLA Handbook (7th Edition):

Gümüscü, B. “Lab-on-a-chip devices with patterned hydrogels.” 2016. Web. 04 Jul 2020.

Vancouver:

Gümüscü B. Lab-on-a-chip devices with patterned hydrogels. [Internet] [Doctoral dissertation]. University of Twente; 2016. [cited 2020 Jul 04]. Available from: https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html ; urn:nbn:nl:ui:28-101009 ; b2dc0768-23da-4e21-9603-5162ffe7c7ea ; 10.3990/1.9789036541916 ; urn:isbn:978-90-365-4191-6 ; urn:nbn:nl:ui:28-101009 ; https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html.

Council of Science Editors:

Gümüscü B. Lab-on-a-chip devices with patterned hydrogels. [Doctoral Dissertation]. University of Twente; 2016. Available from: https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html ; urn:nbn:nl:ui:28-101009 ; b2dc0768-23da-4e21-9603-5162ffe7c7ea ; 10.3990/1.9789036541916 ; urn:isbn:978-90-365-4191-6 ; urn:nbn:nl:ui:28-101009 ; https://research.utwente.nl/en/publications/labonachip-devices-with-patterned-hydrogels(b2dc0768-23da-4e21-9603-5162ffe7c7ea).html

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