University of Florida

Research: Biological Engineering

Research projects in Biological Engineering

Linking Genes And Gene Expression To Crop Models: A Genotype To Phenotype Approach

Investigator: Correll, M.J.

Existing crop models are used extensively around the world to predict the yield of crops based on a variety of inputs including environmental conditions (Boote et al., 1998; Jones et al., 2003). However, these models do not include sufficient information about genes or gene pathways that are involved in regulating specific traits that are used in the models (Boote et al., 2001, 2003; Messina et al., 2005; 2006). For example, the genes and/or expression of genes involved in flowering are not included in the model to predict time-to-flowering. In order to increase the efficiency of breeding programs for high yielding genotypes that are adapted for specific environments, a fundamental knowledge of the genetic changes in response to the environment is required. The improvement in sequencing technology and gene expression arrays has identified many of the genes and gene pathways involved in many traits under various environmental conditions. However, the interation of the physiological data into genetic models and vice versa are lacking. This project will be a critial step toward linking genetic information into crop models to improve the prediction of plant growth and development in response to varying environments.


The overall objective of this project is to identify the genes that influence plant growth and development in response to varying environmental stimuli. To accomplish this objective the following specific objectives will be performed.

  • Characterize the growth and development of plants from different genotypes in varying environmental conditions.
  • Identify genes or genetic loci involved in differential plant adaptation to environmental conditions using gene expression analyses or Quantitative Trait Loci identification techniques.
  • Link this genetic data with existing crop models to provide a more gene-based approach for predicting plant growth and development.

Through the completion of these objectives a more comprehensive prediction of plant growth to environmental conditions will be possible. Breeders will be able to develop geneotypes that are optimized for challenging environmental conditions such as drought or increased temperatures. Farmers will be able to apply the improved models to better predict the effects of different environments on crop yields and select optimal genotypes for their field conditions.

Impact Of Emerging Bio- And Nanotechnologies On Water Resources

Investigator: Gao, B.

Emerging technologies may present a double-edged sword to the water resources. On one hand, emerging technologies such as nanotechnology, biotechnology, and information technology hold great promise for end-of-pipe treatment (e.g., Wu et al. 2005), in-situ remediation (e.g. Elliott and Zhang 2001; Kim et al. 2004; Cao et al. 2005; Waychunas et al. 2005), pollution control (e.g. Diallo et al. 1999; Fujishima et al. 2000; Long and Yang 2001; Yue and Economy 2005), and pollutant detection (e.g., Kong et al. 2000; Cui et al. 2001; Nicewarner-Pena et al. 2001). On the other hand, some of the technologies such as nanotechnology and biotechnology may present health and contamination risks to the water resources and ecosystems because they introduce new materials to the environment (e.g., Dreher 2004; Halford 2004; Renwick et al. 2004). The State of Florida is facing many water issues that can be solved with the emerging technologies. However, there are still knowledge gaps in how to properly apply these technologies to water bodies without damaging the aquatic ecosystems and natural environment. These knowledge gaps have impeded the applications of emerging technologies and the development of new solutions to Florida and global water problems. This project is designed as a critical step towards filling the knowledge gaps by informing the development of science-based strategies to best utilize the emerging technologies to solve water problems.


  • Apply emerging technologies (e.g. nanotechnology and computing technology) to advance current knowledge of water quality modeling and monitoring.
  • Develop alternative low-cost materials for water treatment/remediation using emerging technologies (e.g. nanotechnology and biotechnology), particularly with respect to biochar/agrichar/charcoal adsorbents treated with bio- and nanotechnologies.
  • Apply emerging technologies (e.g. biotechnology and nanotechnology) to develop new methods to reclaim biomass residues and wastewater, particularly with respect to residues and wastewater from the biofuel productions.
  • Investigate the fate and transport of byproducts of emerging technologies (e.g. engineered nanomaterials and incidental biomaterials) in hydrologic pathways.
  • Investigate the fate and transport of fine particles (e.g. pathogens, natural nanoparticles, and colloidal particles) and particle-contaminant complexes (e.g. heavy metals, nutrients, and organic pollutants) in hydrologic pathways.

Based on the objectives, we expect to achieve the following: 1)The applications and benefits of emerging technologies to water pollution control will be better understood. 2)Water quality models and water quality monitoring methods will be improved. 3)Low-cost water treatment and remediation technology (e.g. modified biochar) will be developed. 4)New methods to reclaim biomass residues and wastewater will be designed. 5)New strategies of sustainable biofuel production and carbon sequestration (e.g. biochar land application) will be evaluated. 6)The risks of emerging technologies to water resources and the environment will be better understood. 7)The capacity to predict and monitor the fate and transport of contaminants in water bodies will be enhanced.

Management Strategies For Category I Invasive Weeds In Florida: Potential For Carbon Sequestration And Bioenergy

Investigators: Rathinasabapathi, B.; Gao, B.; Ma, L. Q.

Category I invasive plants have caused tens of millions of dollars in economical and ecological damages in Florida. It is therefore imperative to control Category I weeds to protect the fragile Florida ecosystems. Among the 67 plants listed under Category I invasive weeds by Florida Exotic Pest Council, many are woody species, which are fast-growing with abounding biomass. Our overall objective is to evaluate the ecological, environmental, and economic benefit of using invasive weeds as feed stocks for the biochar and bioenergy productions. Our central hypothesis is that the application of biochar technology to invasive weed management is not only feasible but also preferable to that of the other traditional methods.


Our overall objective is to evaluate the ecological, environmental, and economic benefit of using invasive weeds as feed stocks for the production of biochar and bioenergy. Our central hypothesis is that the application of biochar technology to invasive weed management is not only feasible but also preferable to that of the other traditional methods. This hypothesis is formulated based on our previous research experience in invasive plant control and biochar technology. We anticipate that this new strategy will not only reduce the impact of invasive plants to the ecosystem, but also provide new solutions to carbon sequestration (biochar) and new sources of energy. We will accomplish the overall objective and test our central hypothesis by pursuing the following three specific objectives:

  • To compare and optimize the pyrolysis processes of biochar production from selected invasive weeds considering feedstock material, biochar mass and quality, and energy production and consumption.
  • To characterize the physicochemical properties (i.e. total carbon content, black carbon content, density, surface charge density, surface area to mass ratio, water holding capacity, and cation exchange capacity) of biochar from invasive weed biomass.
  • To evaluate feasibility of land application of biochar from invasive weeds as sequestered carbon and as a soil amendment.

Integrated Agro-Ecological and Hydrological Modeling for Analysis of Complex, Adaptive and Environmental Decisions

Investigator: Kiker, G.A..

Computer simulation models and interactive decision tools/games coupled with human interaction methodologies have been suggested as one solution to create adaptive learning environments. In addition, scenario analysis provides a powerful way to think about uncertainty and risk. Scenarios are sets of possible future worlds in which strategic options provide storylines for these envisioning futures to be played out under social, political and economic realities.


Objectives of this research effort include the construction of a flexible framework for scoping problems in a systematic method, the creation of viable integrated simulation, decision and scenario tools for managing the various elements of complex environmental challenges (namely interaction, visualization and calculation) and the application at sites of various scales and locations.

  • Construct an overall methodological framework to integrate model creation, model simulation, decision/scenario analysis and adaptive learning..
  • Develop computer programs for the construction and use of simulation models and scenarios for scale-varied, complex environmental challenges.
  • Explore and test the scenario model framework on different case study areas to illustrate adaptive learning and management with different scenarios, models and scales.