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José Avalos

José L. Avalos

Assistant Professor in Chemical and Biological Engineering and the Andlinger Center for Energy and the Environment

B.S.E., Chemical Engineering / Biotechnology, Universidad Iberoamericana. Mexico City, Mexico, 1996
M.Sc., Biochemical Research, Imperial College, University of London. London, UK, 1998
Ph.D., Biochemistry, Cellular and Molecular Biology, Johns Hopkins University, School of Medicine 2004

Room: A313 Engineering Quad
Phone: 609-258-9881

Honors and Awards

  • Ruth L. Kirschstein National Research Service Award (NRSA), 2012-2013
  • Damon Runyon Cancer Research Foundation Fellowship, 2005-2008
  • Merck Fellowship of the Damon Runyon Cancer Research Foundations, 2005-2008
  • Harold M. Weintraub Graduate Student Award, Fred Hutchinson Cancer Research Center, 2004

Concurrent University Appointments

  • Andlinger Center for Energy and the Environment


Research Areas

Research Interests

The mission of the lab is to use biotechnology to address important problems in sustainable energy, the environment, industry and human health.

Synthetic biology and metabolic engineering are rapidly expanding fields of bioengineering that involve the development of biological pathways, systems, or organisms with synthetic biological behaviors (analogous to synthetic chemistry being the design of series of chemical reactions to produce synthetic molecules). We are interested in engineering microorganisms with new desirable traits of environmental, industrial, and medical importance. The scale of our bioengineering efforts spans microbial consortia, cellular engineering, organelle engineering, and protein engineering (Figure 1).

Figure 1. The scales of bioengineering projects in the lab span from microbial consortia, to protein engineering.

The approach in the lab is to integrate principles from microbiology, cellular biology, genetics, biochemistry, biophysics, and engineering, to the application and further development of technologies in synthetic biology and metabolic engineering. We are interested in designing microorganisms for the following applications:

  • Production of advanced biofuels, including drop-in fuels that can substitute gasoline, diesel, or jet fuel, using existing infrastructure; as well as biofuels derived from sources that do not compete with food production (such as cellulosic biomass or CO2).
  • Production of commodity chemicals currently derived from petroleum, which would reduce the carbon footprint of their industrial production, and increase their sustainability.
  • Production of specialty chemicals, including drugs and drug precursors, which are currently difficult, costly, or environmentally damaging to produce.
  • Production of bioplastics, which are biodegradable polymers with multiple applications, ranging from consumable bioplastics to tissue engineering and other biomedical applications.
  • Development of platforms for new drug discovery, using engineered microorganisms.
  • Bioremediation, to degrade and remove contaminants from the environment.

The central area of research in the lab is metabolic engineering, supported by mitochondrial engineering, biosensors, genetic circuits, systems biology, structural biology, and protein engineering (Figure 2).

Figure 2. The areas of research in the lab include metabolic engineering, organelle engineering (mitochondrial engineering), synthetic biology (biosensors and genetic circuits), systems biology, structural biology, and protein engineering.

Metabolic engineering

Metabolic engineering involves the discovery, assembly, and optimization of heterologous metabolic pathways in host microorganisms, with two possible goals: 1) to produce molecules of commercial value, such as biofuels, bioplastics, commodity chemicals, or specialty chemicals (drugs, pigments, flavorants, etc.) from renewable sources, (including cellulosic biomass); or 2) to degrade and remove contaminants from the environment (bioremediation).

Organelle/Mitochondrial Engineering

Figure 3. Confocal fluorescence microscopy image of yeast mitochondria.

Subcellular engineering is an emerging and exciting field in bioengineering, in which metabolic pathways are targeted to specific organelles in the cell, in order to benefit from their unique environments, metabolites, and enzymes, as well as from their physical separation from other compartments in the cell. We are particularly interested in mitochondrial engineering. We recently demonstrated that targeting metabolic pathways to yeast mitochondria is an effective strategy to improve the production of advanced biofuels. In addition, we are interested in engineering the mitochondrial physiology to enhance the metabolic pathways targeted to this highly dynamic, and versatile organelle (Figure 3).

Synthetic Biology

Synthetic biology includes the development of biosensors or genetic circuits to assist in the design and optimization of metabolically engineered strains. Biosensors and genetic switches are invaluable tools that help monitor or control cellular functions. In general, biosensors consist of a receptor (of a molecule or condition related to the engineered function), linked to a reporter via various possible mechanisms. Biosensors can be used to either monitor, screen, or select for a desired function (Figure 4). On the other hand, genetic switches have receptors linked to the regulation of specific genetic programs, including metabolic pathways, intercellular communication, or kill-/suicide-programs.

Figure 4. Biosensors enable the easy detection of desirable traits. Colonies seemingly identical (left), are easily screened using a biosensor that controls a fluorescent reporter protein that responds to a desirable trait (right).

Metabolic engineering is hindered by the lack of high throughput technologies. The application of biosensors to metabolic engineering is a powerful strategy to overcome this limitation. Thus, the main motivation to develop biosensors in the lab is to enable high throughput technologies to accelerate strain development, and optimization, and that confer the ability to use tools in modern biotechnology for metabolic engineering purposes.

Systems Biology

To achieve the levels of production of fuels and chemicals required for economic viability, it will be necessary to understand the effects that complex whole-cell biological systems have on their production, and take them into consideration when engineering strains. Our strategy is to use various methods of detection, including biosensors, to run genome-wide screens and measure the effects of different perturbations, on the production of molecules of interest. The goal is to use this data to identify computationally the cellular networks (metabolic, regulatory, signaling, etc.) involved in the production of fuels and chemicals, and the cellular tolerance of host organisms to these products.

Structural Biology and Protein Engineering

Our efforts in synthetic biology and metabolic engineering are complemented by fundamental studies on the molecular structure and function of the proteins involved, such as enzymes, transmembrane transporters, receptors, and transcription factors. To study these proteins in molecular detail we use different biophysical and biochemical methods, including X-ray crystallography. Understanding the relationship between the structure and the function of these proteins significantly enhances our ability to do protein engineering in order to confer new functions of interest and relevance to metabolic engineering (Figure 5).

Figure 5. After solving the crystal structure of an NAD+-dependent protein deacetylase (sirtuin), we engineered this enzyme to alter its cofactor specificity and inhibitor susceptibility from NAD+ to NAAD (nicotinic acid adenine dinucleotide), and from nicotinamide to nicotinic acid, respectively.