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Bioenergy & Defense

Anne M. Ruffing, Ph.D.

Biographical Information - Select Research Projects - Publications
Photo of Anne Ruffing

Senior Member of the Technical Staff
Bioenergy and Defense Technologies Department

(505) 844-9334

Research Interests

Metabolic engineering



Algal and cyanobacterial physiology

Omics (genomics, transcriptomics, metabolomics)

Metabolic modeling

Polysaccharide and oligosaccharide production in bacteria

Engineering, genetics, and metabolism of Agrobacterium ATCC 31749

Biographical Information

Anne Ruffing joined the Bioenergy & Defense Technologies department at Sandia in early 2010. As a Truman Fellow, Anne led her own research project on the Genetic Engineering of Cyanobacteria for Biodiesel Feedstock Production (see below). In February of 2013, Anne converted to a technical staff position, in which she continues to research cyanobacteria and algae for biofuel production. Recent research in Anne's laboratory has expanded to include genetic engineering for bioremediation and biosensing applications.

Anne earned a bachelor's degree in Chemical Engineering at the University of Dayton in 2004. During her graduate studies at the Georgia Institute of Technology, Anne worked with a polysaccharide-producing soil bacterium, Agrobacterium sp. ATCC 31749. Her thesis included metabolic engineering of the Agrobacterium for the production of medically-important oligosaccharides, investigation of Agrobacterium physiology, and genomic and transcriptomic studies of polysaccharide production. Upon completing this work, Anne received her Ph.D. in Chemical Engineering from Georgia Tech in 2010.

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Select Research Projects

Systems-Level Synthetic Biology for Advanced Biofuel Production

Strain development for applications using unconventional microorganisms, such as those used for microalgal fuel production, are currently limited by low-throughput methods for genetic engineering. This project aims to develop advanced genetic engineering methods and standardized synthetic biology parts and tools for engineering a model cyanobacterium, Synechococcus sp. PCC 7002, for advanced biofuel production. High-throughput methods for screening engineered strains are also being explored in this project. This work was funded by the Early Career LDRD program at Sandia.

Genetic Engineering of Cyanobacteria for Biodiesel Feedstock Production

This work is funded by the President Harry S. Truman Fellowship in National Security Science and Engineering through Sandia's Laboratory Directed Research and Development (LDRD) program. The main goal of this project is to investigate the development of genetically modified cyanobacteria for production of a biodiesel feedstock. Unlike eukaryotic algae, cyanobacteria are not natural lipid producers, yet cyanobacteria can be easily manipulated through genetic modification. In this work, the metabolism of a model cyanobacterium, Synechococcus elongatus PCC 7942, will be engineered for the production of free fatty acids, a precursor for biodiesel production. Furthermore, the engineered strains will be characterized using Sandia's hyperspectral fluorescence imaging technology in addition to other traditional techniques to assess the effect of free fatty acid production on the cyanobacterium's physiology and metabolism.


hyperspectral fluorescence images of cyanobacteria
Figure: Hyperspectral fluorescence images of cyanobacteria engineered for free fatty acid biosynthesis.

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Journal Articles

Ruffing AM and Trahan CA. Biofuel toxicity and mechanisms of biofuel tolerance in three model cyanobacteria. Algal Research. 2014. 5:121-132.

Ruffing AM. Improved free fatty acid production in cyanobacteria with Synechococcus sp. PCC 7002 as host. Frontiers in Bioengineering and Biotechnology. 2014.2:17.

Ruffing AM. RNA-Seq analysis and targeted mutagenesis for improved free fatty acid production in an engineered cyanobacterium. Biotechnology for Biofuels. 2013. 6:113.

Ruffing AM. Borrowing genes from Chlamydomonas reinhardtii for free fatty acid production in engineered cyanobacteria. Journal of Applied Phycology. 2013. In Press.

Ruffing AM and Jones HDT. Physiological effects of free fatty acid production in genetically engineered Synechococcus elongatus PCC 7942. Biotechnology and Bioengineering. 2012. 109(9): 2190-2199. (Cover, Spotlight)

Reichardt TA, Garcia OF, Collins AM, Jones HDT, Ruffing AM, and Timlin TA. Spectroradiometric monitoring of Nannochloropsis salina growth. Algal Research. 2012. 1(1): 22-31.

Ruffing AM, Chen RR. Transcriptome profiling of a curdlan-producing Agrobacterium reveals conserved regulatory mechanisms of exopolysaccharide biosynthesis. Microbial Cell Factories. 2012. 11:17.

Ruffing AM, Castro-Melchor M, Hu WS, and Chen RR. Genome sequencing of the curdlan-producing Agrobacterium sp. ATCC 31749. Journal of Bacteriology. 2011. Epub June 17.

Ruffing AM. Engineered Cyanobacteria: Teaching an old bug new tricks. Bioengineered Bugs. 2011. 2(3).

Ruffing AM and Chen RR. Citrate stimulates oligosaccharide synthesis in metabolically engineered Agrobacterium sp. Applied Biochemistry and Biotechnology. 2011. 164(6):851-866.

Ruffing AM and Chen RR. Metabolic engineering of Agrobacterium sp.strain ATCC 31749 for production of an alpha-gal epitope. Microbial Cell Factories. 2010. 9:1.

Ruffing AM and Chen RR. Metabolic engineering of microbes for oligosaccharide and polysaccharide synthesis. Microbial Cell Factories. 2006. 5: 25-33.

Ruffing AM, Mao Z, and Chen RR. Metabolic engineering of Agrobacterium sp. for UDP-galactose regeneration and oligosaccharide synthesis. Metabolic Engineering. 2006. 8(5): 465-473.

Book Chapters

Ruffing AM. Metabolic Engineering of Hydrocarbon Biosynthesis for Biofuel Production. Book chapter in Liquid, Gaseous and Solid Biofuels - Conversion Techniques. Fang Z (ed). InTech. 2013. ISBN 978-953-51-1050-7.

Ruffing AM and Chen RR. Metabolic Engineering and Other Methods of Strain Improvement. Book chapter in Advances in Fermentation Technology. Asiatech Publishers, Inc. New Delhi. 2008. p119-144.

Ruffing AM and Chen RR. Metabolic Engineering of Microorganisms for Oligosaccharide and Polysaccharide Production. Book chapter in Microbial Production of Biopolymers and Polymer Precursors: Applications and Perspectives. Horizon Bioscience, Wymondham, UK. 2009. p197-228.

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