Navigation Links
Molecular economics: New computer models calculate systems-wide costs of gene expression
Date:8/8/2012

Bioengineers at the University of California, San Diego have developed a method of modeling, simultaneously, an organism's metabolism and its underlying gene expression. In the emerging field of systems biology, scientists model cellular behavior in order to understand how processes such as metabolism and gene expression relate to one another and bring about certain characteristics in the larger organism.

In addition to serving as a platform for investigating fundamental biological questions, this technology enables far more detailed calculations of the total cost of synthesizing many different chemicals, including biofuels. Their method accounts, in molecular detail, for the material and energy required to keep a cell growing, the research team reported in the journal Nature Communications.

"This is a major advance in genome-scale analysis that accounts for the fundamental biological process of gene expression and notably expands the number of cellular phenotypes that we can compute," said Bernhard Palsson, Galetti Professor of Bioengineering, at the UC San Diego Jacobs School of Engineering.

"With this new method, it is now possible to perform computer simulations of systems-level molecular biology to formulate questions about fundamental life processes, the cellular impacts of genetic manipulation or to quantitatively analyze gene expression data," said Joshua Lerman, a Ph.D. candidate in Palsson's Systems Biology Research Group.

The team's method can be compared to understanding both the chemical reactions and the machinery that are required to refine crude oil into petrol in a large, industrial factory. Modeling metabolism tells you what biochemical reactions need to take place. Modeling the organism's gene expression tells you what kind of machinery you need. The team's method specifically accounts for the expression of enzymes, which are the molecular machines responsible for the biochemical processes of life. With this knowledge, it is possible to explore how an organism distributes its resources to promote growth and how genetic manipulation of these organisms alters this distribution.

"What you could hypothetically do with our model is simulate the total cost of producing a value-added product, such as a biofuel. That includes all the operating and maintenance costs," said Daniel Hyduke, a project scientist in Palsson's lab. Hyduke said the method has the potential to help streamline industrial metabolic engineering efforts by providing a near complete accounting of the minimal material and energy costs associated with novel strain designs for biofuel, commodity chemicals, and recombinant protein production.

Hyduke and Lerman prototyped the method on the minimal, yet metabolically versatile, hyperthermophile Thermotoga maritima. Because T. maritima is not currently ready for use in industrial applications, Hyduke and Lerman are working as part of a larger team to produce similar models for industrially relevant microorganisms, such as E. coli.

"We've built a virtual reality simulator of metabolism and gene expression for Thermotoga maritima, and shown that it much better approximates phenotypes of cells than modeling metabolism in isolation," said Lerman.


'/>"/>
Contact: Catherine Hockmuth
chockmuth@yahoo.com
858-822-1359
University of California - San Diego
Source:Eurekalert

Related biology news :

1. Scientists discover molecular link between circadian clock disturbances and inflammatory diseases
2. The most celebrated lab manual in molecular biology has been updated and expanded
3. Delving into the molecular mechanism behind deep-sea bacterias pressure tolerance
4. Speed and power of X-ray laser helps unlock molecular mysteries
5. Highlighting molecular clues to the link between childhood maltreatment and later suicide
6. MARC travel award announced for the 2012 GSA Yeast Genetics and Molecular Biology Meeting
7. How bacteria change movement direction in response to oxygen: Molecular interactions unravelled
8. The activity of a bacterial effector protein seen in molecular detail
9. Hitting snooze on the molecular clock: Rabies evolves slower in hibernating bats
10. Molecular spectroscopy tracks living mammalian cells in real time as they differentiate
11. PNAS: Precise molecular surgery in the plant genome
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/2/2016)... -- Perimeter Surveillance & Detection Systems, Biometrics ... Support & Other Service  The latest report ... analysis of the global Border Security market . ... $17.98 billion in 2016. Now: In November ... software and hardware technologies for advanced video surveillance. ...
(Date:5/12/2016)... WearablesResearch.com , a brand of Troubadour Research & ... Q1 wave of its quarterly wearables survey. A particular ... a program where they would receive discounts for sharing ... "We were surprised to see that so many ... CEO of Troubadour Research, "primarily because there are segments ...
(Date:4/26/2016)... and LONDON , ... Finacle, part of EdgeVerve Systems, a product subsidiary ... Onegini today announced a partnership to integrate the ...      (Logo: http://photos.prnewswire.com/prnh/20151104/283829LOGO ) ... provide their customers enhanced security to access and ...
Breaking Biology News(10 mins):
(Date:6/23/2016)...  The Prostate Cancer Foundation (PCF) is pleased to announce 24 ... for prostate cancer. Members of the Class of 2016 were selected from a ... Read More About the Class of 2016 PCF Young Investigators ... ... ...
(Date:6/23/2016)... , June 23, 2016   EpiBiome , a ... $1 million in debt financing from Silicon Valley Bank ... automation and to advance its drug development efforts, as ... facility. "SVB has been an incredible strategic ... services a traditional bank would provide," said Dr. ...
(Date:6/23/2016)... , ... June 23, 2016 , ... STACS DNA Inc., ... Leader at the Arkansas State Crime Laboratory, has joined STACS DNA as a Field ... DNA team,” said Jocelyn Tremblay, President and COO of STACS DNA. “In further expanding ...
(Date:6/23/2016)... , June 23, 2016 Apellis Pharmaceuticals, ... 1 clinical trials of its complement C3 inhibitor, ... and multiple ascending dose studies designed to assess ... of subcutaneous injection in healthy adult volunteers. ... either as a single dose (ranging from 45 ...
Breaking Biology Technology: