Mark R. Riley

Associate Professor

Department of Agricultural and Biosystems Engineering

Shantz Bldg. Room 504a,

The University of Arizona; Tucson, AZ 85721-0038

(520) 626-9120 (Phone)

(520) 621-3963 (FAX)




My research involves the application of engineering principles to biological systems. Much of our current work derives from our studies of animal cell metabolism using near infrared spectroscopy. These methods have evolved into other approaches to monitor cell stress, to sense volatile compounds, and to detect pathogenic organisms.


Sensor development

We are designing devices to respond to gaseous materials such as ethylene released from ripening fruits. This work has been supported by the Washington Tree Fruit Research Commission and an SBIR from the USDA. Our goal is to develop a simple, inexpensive device that changes color in response to fugitive gases. A patent has been filed and a new company (RediRipe, LLC 2004-2006) developed around this technology.


These ethylene detecting stickers have use in evaluating the ripeness of climacteric fruits and vegetables. Examples include apples, peaches, pears, and some varieties of melons. The devices change from a pale yellow to a dark blue when the fruit has a high rate of ethylene release indicative of a late stage of maturation.


Field trials run in the summer/fall of 2005 were successful for apples, but we have been undergoing further development to improve the stability of the device. Plans are to run more extensive trials in apple orchards in Arizona, Washington, and New Mexico in the summer/fall of 2006. If successful, the device would then be distributed in a limited manner to growers and packing houses for further testing. Our goal is to have a commercially marketable device in the spring of 2008.


Figure: Color change for stickers on 3 varieties of apples (left to right, Control on a Gala, Gala (24 hours), Golden delicious (24 hours), and Fuji (24 hours)). The white membrane on the control apple was placed on apples immediately before the picture was taken and shows the typical white starting point for all of these membranes.


Stickers placed on Rome and Golden Delicious variety during the harvesting stage.


Ethylene release is autocatalytic, that is, one fruit releasing ethylene encourages neighboring fruit to mature - "one bad apple spoils the bunch".




Cell culture

We use animal cell cultures as the recognition elements in biosensors to detect chemical toxins and pathogenic organisms. When a cell is subjected to a stress it can respond by altering its metabolism and function, changing shape and structure, or dying. Each of these processes is distinct for the type of stressor. For example, some microbial toxins such as cholesterol binding cytolysins damage primarily the cell membrane. These damage and response mechanisms can be detecting using non-invasive methods such as infrared or Raman spectroscopy. This has been the focus of much of our recent work for detecting genotoxins, cytotoxins, metals, and combustion derived particulate matter.

Lung cells grown on a glass surface. Note the strong connections between neighboring cells.



Fluorescence microscopy images of lung cells showing actin (green, left) and vinculin (red, right) connections on a permissive substrate.




Spectroscopy for pathogen detection

We are using the non-invasive techniques of near infrared and Raman spectroscopy to quantify and identify bacteria and viruses in a variety of environmental samples. This technique provides rapid quantitation, allows measurement of many compounds at once. We have successfully characterized different responses to sterilization methods demonstrating path-dependent cell damage.




Bio-based products

We have several projects within this area to convert waste of undesirable materials into value added products. One project utilizes a unique organism to convert waste cellulose into valuable bioplastics in one step. It is unusual for an organism to be able to meet both challenges without the need for added enzymatic processing. We are also exploring the production of fuel materials (biodiesel and ethanol) in efficient and cost-effective ways.


S. degradans growth on insoluble fibers (avicel on the left and bagasse fibers on the right).




We also participate in the international Genetically Engineered Machine competition coordinated by the synthetic biology group at MIT. The goal of this program is to design, produce, and characterize a machine constructed using interchangeable genetic elements introduced to bacteria. Our project for 2006 is to design a watercolor system in which color paintings may be made on a bacterial lawn. The program has 9 UA students and is supported by bio5, CALS, ABE, and SWES.



My research group


Crystal Vargas, MS candidate in ABE

Walter Diaz, MS candidate in ABE

Peggi Cross, PhD candidate in MSE

Shanaz Sikder, BS in BE

Joseph Bitz, BS in BE

David Whitlach, BS in BE

Megan Coe, BS in BE

Mariah Bossardet, Pima CC

Dominic DeCianne, Research Technician






BE sophomore seminar, ABE 296.

Engineering of biological processes, ABE / CHEE 481a



Applications of bioprocess engineering, ABE / CHEE 481b

Research methods in ABE, ABE 601





Updated 8/1/06