Navigation Links
Math modeling integral to synthetic biology research
Date:4/4/2014

HOUSTON, April 4, 2014 A long-standing challenge in synthetic biology has been to create gene circuits that behave in predictable and robust ways. Mathematical modeling experts from the University of Houston (UH) collaborated with experimental biologists at Rice University to create a synthetic genetic clock that keeps accurate time across a range of temperatures. The findings were published in a recent issue of the Proceedings of the National Academy of Sciences.

"Synthetic gene circuits are often fragile, and environmental changes frequently alter their behavior," said Kreimir Josić, professor of mathematics in UH's College of Natural Sciences and Mathematics. "Our work focused on engineering a gene circuit not affected by temperature change."

Synthetic biology is a field in which naturally occurring biological systems are redesigned for various purposes, such as producing biofuel. The UH and Rice research targeted the bacterium E. coli.

"In E. coli and other bacteria, if you increase the temperature by about 10 degrees the rate of biochemical reactions will double and therefore genetic clocks will speed up," Josić said. "We wanted to create a synthetic gene clock that compensates for this increase in tempo and keeps accurate time, regardless of temperature."

The UH team, led by Josić and William Ott, an assistant professor of mathematics, collaborated with the lab of Matthew Bennett, assistant professor of biochemistry and cell biology at Rice. Josić, Bennett and Ott have been working together on various research projects for three years. The team also included UH postdoctoral fellow Chinmaya Gupta.

According to Bennett, the ability to keep cellular reactions accurately timed, regardless of temperature, may be valuable to synthetic biologists who wish to reprogram cellular regulatory mechanisms for biotechnology.

The work involved engineering a gene within the clock onto a plasmid, a little piece of DNA that is inserted into E. coli. A mutation in the gene had the effect of slowing down the clock as temperature increased.

UH researchers created a mathematical model to assess the various design features that would be needed in the plasmid to counteract temperature change. Gupta showed that the model captured the mechanisms essential to compensate for the temperature-dependent changes in reaction rates.

The computational modeling confirmed that a single mutation could result in a genetic clock with a stable period across a large range of temperatures an observation confirmed by experiments in the Bennett lab. Josić's team then confirmed the predictions of the models using real data.

"Having a mechanistic model that allows you to determine which features are important and which can be ignored for a genetic circuit to behave in a particular way allows you to more efficiently create circuits with desired properties," Gupta said. "It allows you to concentrate on the most important factors necessary in the design."

"Throughout this work, we used mathematical models to find out what is important in designing robust synthetic gene circuits," Josić said. "Computational and mathematical tools are essential in all types of engineering. Why not for biological engineering?"

Josić, Ott and Bennett's research is funded by the National Institutes of Health through the joint National Science Foundation/National Institute of General Medical Sciences Mathematical Biology Program.


'/>"/>

Contact: Lisa Merkl
lkmerkl@uh.edu
713-743-8192
University of Houston
Source:Eurekalert

Related biology news :

1. 3-D RNA modeling opens scientific doors
2. Patel recognized with NSF Career Award for computer-modeling research on cell membranes
3. 50 Years of Watershed Modeling -- Past, Present and Future
4. Geosphere: How geology, technology, modeling, and mapping see into Earths past and present
5. Modeling metastasis
6. Research finds heart remodeling rapidly follows cardiac injury
7. New modeling approach transforms imaging technologies
8. Computer modeling reveals how surprisingly potent hepatitis C drug works
9. Color in fossil insects, diamonds from the ancient ocean floor and modeling the worlds largest rivers
10. Computer modeling technique goes viral at Brandeis
11. Sugar-burning in the adult human brain is associated with continued growth, and remodeling
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:5/23/2017)... GENOA, Italy , May 23, 2017  Hunova, the first robotic ... and trunk, has been officially launched in Genoa, Italy ... Europe and the USA . The ... launched on the market by the IIT spin-off Movendo Technology thanks to ... view the Multimedia News Release, please click: ...
(Date:4/24/2017)... , April 24, 2017 ... and partner with  Identity Strategy Partners, LLP (IdSP) ... "With or without President Trump,s March 6, 2017 ... Terrorist Entry , refugee vetting can be instilled with ... resettlement. (Right now, all refugee applications are suspended ...
(Date:4/13/2017)... , April 13, 2017 UBM,s Advanced ... will feature emerging and evolving technology through ... Innovation Summits will run alongside the expo portion of ... sessions, panels and demonstrations focused on trending topics within ... advanced design and manufacturing event will take place June ...
Breaking Biology News(10 mins):
(Date:6/22/2017)... ... June 22, 2017 , ... RURO, Inc., a leading ... 6.5, a content-packed update to the Limfinity® framework. , LimitLIS® and other RURO ... diverse base of customers among labs and other businesses. Limfinity® 6.5 adds new ...
(Date:6/20/2017)... Pa. , June 20, 2017  Kibow Biotech ... pleased to announce the issuance of a new patent ... or hyperuricemia by the U.S. Patent and Trademark Office ... a winner of the Buzz of Bio award in ... is akin to developing non-drug approaches to chronic disease. ...
(Date:6/19/2017)... ... June 19, 2017 , ... ... clinical development reported today that it is launching two new additions of its ... be demonstrating new capabilities at the DIA 2017 Annual Meeting in Chicago, IL, ...
(Date:6/16/2017)... ... June 16, 2017 , ... CTNext , Connecticut’s go-to resource ... held at The LOFT at Chelsea Piers in Stamford. , Nine finalists, all of ... of judges for an opportunity to secure $10,000 awards to help support business growth. ...
Breaking Biology Technology: