Please select the desired project time frame:
- July 2026
- January 2026
- July 2025
- January 2025
- July 2024
- January 2024
- July 2023
- January 2023
- July 2022
- January 2022
- July 2021
- January 2021
- July 2020
- January 2020
- July 2019
- January 2019
- July 2018
- January 2018
- July 2017
- January 2017
- July 2016
- January 2016
- July 2015
- January 2015
- July 2014
- January 2014
- July 2013
- January 2013
- July 2012
- January 2012
- July 2011
- January 2011
- July 2010
- January 2010
- July 2009
- January 2009
- July 2008
- January 2008
- July 2007
- January 2007
- July 2006
- January 2006
- July 2005
- January 2005
- July 2004
- January 2004
- July 2003
- January 2003
- July 2002
- January 2002
- July 2001
- January 2001
Start of funding 01.07.2016
Patterning gene expression with active fluctuations induced by surface acoustic waves
Prof. Dr. Christoph Westerhausen
University of Augsburg
Lehrstuhl für Experimentalphysik I
Dr. Omar A. Saleh
University of California, Santa Barbara
Materials Department
Over the past decade, it has become increasingly clear that active fluctuations, which are non-directed positional fluctuations attributable not to thermal energy but to active ATP-dependent processes, are central to biological processes in that they increase the mobility of biomolecules. A collaboration between the Saleh lab (UCSB) and the Westerhausen/Wixforth group (University of Augsburg) is focusing on the question of whether artificially induced active fluctuations correlate with elevated gene expression in a lab-on-a-chip-system. The Saleh lab can incorporate genetic DNA into hydrogels and, combined with cell-free in vitro transcription systems, quantify gene expression from these DNA hydrogels. The Westerhausen/Wixforth group, with their expertise on SAW, provides an effective means of generating tunable active fluctuations on a chip carrying a DNA hydrogel network. We envision creating standing wave patterns within a hydrogel where the nodes and antinodes are points of low and high fluctuations, respectively, and are correlated with transcriptional activity as measured via a fluorescent RNA reporter system.
Final report:
Activities
The project treats the question in how far artificially induced fluctuations in a lab-on-a-chip-system employing surface acoustic waves (SAW) correlate with gene expression. To do so, two research stays of the physicists of Augsburg University at the UCSB (Lukas Schnitzler, Nov.-Dec. 2016 and Nov.-Dec. 2017), as well as a return-visit of Mr. Dan Nguyen (Jan. – Feb. 2017) have so far been successfully completed. During these research visits we used so-called DNA-Nanostars1 to successfully create and control arrangements of DNA-hydro gel droplets on a SAW-chip. Moreover, by optimization of the experimental setup we were able to form DNA-hydrogel networks of the dimensions up to 600 µm x 600 µm x 25 µm on a SAW-chip. Active SAW irradiation then leads to a patterning of this thin hydrogel network according to the geometry of the applied standing wave field. Currently, we are optimizing the fluorescence based measurements of transcription activity to finally be able to make statements on the correlation of active fluctuations and gene expression. To do so, another visit of Dan Nguyen to Augsburg is scheduled for summer 2018.
Output
The obtained data will lead to at least two jointed publications in the near future. First, we will report on the gene expression in micro structured DNA-hydrogels, secondly, we will finally be able to report on the role of active and deliberate fluctuations for gene expression. Based on the initial and quick success, we were able to acquire further funding for this project (C. Westerhausen, „Support of interdisciplinary, international and regional collaborations“ from the Augsburg Competence Center for Innovative Technologies ACIT to support the project „Deliberate gene expression by means of fluctuations“, ca. 10k€).
Outlook
To reach the long term goal of this collaboration and to answer the exciting question on the role of active fluctuations for gene expression, we will draft a proposal based on the outcome of this BaCaTeC project and submit it to the DFG/NSF in the near future.
[1] Nguyen, D. T., & Saleh, O. A. (2017). Tuning phase and aging of DNA hydrogels through molecular design. Soft matter, 13(32), 5421-5427.