Source: UNIVERSITY OF ARIZONA submitted to
MONITORING PATHOGENS IN WATER SYSTEMS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0217990
Grant No.
(N/A)
Project No.
ARZT-1360440-H22-133
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jul 1, 2009
Project End Date
Sep 30, 2013
Grant Year
(N/A)
Project Director
An, LI.
Recipient Organization
UNIVERSITY OF ARIZONA
888 N EUCLID AVE
TUCSON,AZ 85719-4824
Performing Department
Agri & Biosystems Engineering
Non Technical Summary
The prevention of infectious disease from exposure to contaminated food, water, and air remains a major task for environmental health workers. Despite substantial efforts to ensure the safety of water supplies, outbreaks of infectious waterborne illnesses continue. The USA has an average of 4 reported outbreaks of infectious diseases affecting perhaps 10,000 people per year due to deficiencies in community water systems [Haas et al., 1999]. It has been estimated that nearly one-fourth of all hospital beds in the world are occupied by patients with complications arising from infection by waterborne organisms [Gerba, 1996]. Produce is the second most common food item associated with foodborne illness in the Unites States and has been on the increase in recent years. Methods for detecting microbial agents that cause disease typically involve extensive laboratory analyses that require from many days to several weeks to perform. This time is not suitable for early diagnostic and preventative purposes to ensure the safety of the water or food supply. Methods are needed that work much more quickly but still provide high specificity for certain organisms and provide an ability to quantify small amounts of potentially hazardous materials. There is no single method to analyze a water or food sample for the variety of pathogenic microorganisms of concern. Current technical problems limit our capabilities for monitoring high volume materials such as domestic drinking water for the presence of potentially pathogenic materials. There are a number of new commercial sensors with promise for continual monitoring, however, they have not been fully tested and vetted in an independent manner such that performance capabilities can be compared. Outcomes / impacts. The likely outcome of this work is the development of new methods that can detect pathogens in water. This fills an important niche between continual monitoring methods and time intensive laboratory work. The impact could be substantial in preventing and diagnosing the presence of active viral material in water and other systems.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
7230210100010%
7230210202015%
7234099100015%
7234099202015%
7235350100010%
7235350202010%
7237010100010%
7237010202015%
Knowledge Area
723 - Hazards to Human Health and Safety;

Subject Of Investigation
4099 - Microorganisms, general/other; 7010 - Biological Cell Systems; 5350 - Domestic and community water supply facilities and systems; 0210 - Water resources;

Field Of Science
2020 - Engineering; 1000 - Biochemistry and biophysics;
Goals / Objectives
Rationale and significance. The prevention of infectious disease from exposure to contaminated food, water, and air remains a major task for environmental health workers. Despite substantial efforts to ensure the safety of water supplies, outbreaks of infectious waterborne illnesses continue. The USA has an average of 4 reported outbreaks of infectious diseases affecting perhaps 10,000 people per year due to deficiencies in community water systems [Haas et al., 1999]. It has been estimated that nearly one-fourth of all hospital beds in the world are occupied by patients with complications arising from infection by waterborne organisms [Gerba, 1996]. Human enteric viruses are believed to be the major cause of foodborne disease in the United States [Gerba and Kayed, 2003], causing up to 67% of all cases [Mead 1999]. Produce is the second most common food item associated with foodborne illness in the Unites States and has been on the increase in recent years. Human caliciviruses are now believed to be the major cause of foodborne illness in the United States [Gerba and Kayed, 2003] and are estimated to be responsible for 40% of all cases of food borne illness. Methods for detecting microbial agents that cause disease typically involve extensive laboratory analyses that require from many days to several weeks to perform. This time is not suitable for early diagnostic and preventative purposes to ensure the safety of the water or food supply. Methods are needed that work much more quickly but still provide high specificity for certain organisms and provide an ability to quantify small amounts of potentially hazardous materials. There is no single method to analyze a water or food sample for the variety of pathogenic microorganisms of concern. Some of the difficulties in developing such a universal method include physical and biochemical differences between the major pathogen groups (viruses, bacteria, protozoa), the presence of compounds that inhibit the reverse transcriptase utilized in PCR, and the long times required for analysis through traditional microbiological techniques [Straub and Chandler, 2003]. Such problems limit our capabilities for monitoring high volume materials such as domestic drinking water for the presence of potentially pathogenic materials. There are a number of new commercial sensors with promise for continual monitoring, however, they have not been fully tested and vetted in an independent manner such that performance capabilities can be compared. Objectives. The overall objectives of this project are to develop and evaluate methods for detection of pathogenic organisms in drinking water systems. This objective will be met by addressing the following specific aims: Aim 1: Develop cell culture spectroscopy method to quantify the presence of infective materials. Aim 2: Evaluate commercial and developing technologies for continual monitoring of water systems for the presence of microorganisms.
Project Methods
Approach. To meet the objectives of this project will require significant progress in instrumentation development, applied microbiology, and real world testing. To address the first aim, we will build on our prior work to develop cell culture infrared spectroscopic measurements. This approach, described in more detail below, provides a means to quantify and differentiate between chemical and biological toxicants in water systems based on the response of a sacrificial cell layer. The cells are probed by infrared light which does not damage cell components, but rather provides a means to search for changes in cell physiology and function. We have used this approach to detect inhalation health hazards. Focus here will be on detecting infective viral particles and other related biological compounds. To address the second aim, we shall continue to construct and test a real-time testing facility for water monitoring utilizing a variety of commercial sensors operating in parallel such that injections of microorganisms can be delivered to each sensor at the same time. This allows rigorous testing of sensing performance capabilities, limits of detection, and sensitivity to interfering factors. This facility is under construction at the Environmental Research Laboratories at the UAs Water Village, approximately 10 miles south of main campus. The facility is unique in its design and capabilities and has been developed with significant support from our local water provider, Tucson Water.

Progress 07/01/09 to 09/30/13

Outputs
Target Audience:Researchers in biological systems engineering or related. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Fei Jia (MS, ABE), Jeerwan Chawhyaymak (MS, ABE), Felipe Lee-Montiel (PhD, ABE), Peggi Cross (PhD, MSE), Dianne Peterson (MS, ABE), Crystal Vargas (MS, ABE), Pryanca Sarkar (MS, ABE). Naruekamol Pookhao (PhD, ABE) and Isaac Jenkins (MS, STAT) How have the results been disseminated to communities of interest?The output from this project has been shared with the scientific community and the general public through publications in the peer reviewed literature and through formal and informal presentations at scientific meetings and at public venues. Software has been developed and this can download from http://cals.arizona.edu/~anling/sbg/software.htm What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Under this project was developed several experimental and computational methodologies for detection and assessment of biological systems. Advances include development of a new method for capture of pathogens followed by spectroscopic detection. Micro and nano-scale devices were developed for capture of pathogens. Computational and statistical methods were developed for detecting the genes with special pattern along time and estimating the species/gene abundance in a metagenomic sample.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Jiang H*, An *L, Lin SM, Feng G, Qiu Y (2012) A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads. PLoS ONE 7(10): e46450. doi:10.1371/journal.pone.0046450
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Tamimi E, Murat K, Choi C, An L (2013) Analysis of Microclimate Uniformity in a Naturally Vented Greenhouse with High Pressure Fogging System. Transactions of the American Society of Agricultural and Biological Engineers (ASABE). 56(3): 1241-1254
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Piegorsch W*, An L*, Wickens A, West W, Pe�a E, Wu W. (2013) Information-theoretic model-averaged benchmark dose analysis in environmental risk assessment. Environmetrics 24:143-157 (*: co-first author)
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Kadiyala V, Patrick N, Mathieu W, Jaime-Frias R, Pookhao N., An L, Smith C. (2013) Class I Lysine Deacetylases Facilitate Glucocorticoid-Induced Transcription. Journal of Biological Chemistry. 288: 28900-12
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Fei Jia, Jeerwan Chawhuaymak, Mark R. Riley, Werner Zimmt, Kimberly L. Ogden, Efficient extraction method to collect sugar from sweet sorghum, Journal of Biological Engineering, 7, 1, 1, (2013). www.jbioleng.org/content/7/1/; doi:10.1186/1754-1611-7-1.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Scholz M.J., M.R. Riley, and J.L. Cuello, "Acid hydrolysis and fermentation of algal starches to ethanol by the yeast Saccharomyces cerevisiae." Biomass & Bioenergy, 48, 59-65 (2013).
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Phat L Tran, Jessica R Gamboa, Katherine E McCracken, Mark R Riley, Marvin J Slepian, Jeong-Yeol Yoon, Nanowell-Trapped Charged Ligand-Bearing Nanoparticle Surfaces - A Novel Method of Enhancing Flow-Resistant Cell Adhesion, accepted for publication in Advanced Healthcare Materials, 2, 7, 1019-1027 (2013) doi: 10.1002/adhm.201200250
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: An L and Doerge RW (2012). Dynamic Clustering of Gene Expression. ISRN Bioinformaitcs. Vol (2012), Article ID 537217. Doi:10.5402/2012/537217
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: West W, Piegorsch W, Pe�a E, An L, Wu W, Wickens A, Xiong H, and Chen W. (2012) The Impact of Model Uncertainty on Benchmark Dose Estimation. Environmetrics. Environmetrics. 23(8): 706716


Progress 01/01/12 to 09/30/12

Outputs
Target Audience:researchers in the related research areas. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Fei Jia (MS, ABE), Jeerwan Chawhyaymak (MS, ABE), Felipe Lee-Montiel (PhD, ABE), Peggi Cross (PhD, MSE), Dianne Peterson (MS, ABE), Crystal Vargas (MS, ABE), Pryanca Sarkar (MS, ABE). Naruekamol Pookhao (PhD, ABE) and Isaac Jenkins (MS, STAT) How have the results been disseminated to communities of interest?The output from this project has been shared with the scientific community and the general public through publications in the peer reviewed literature and through formal and informal presentations at scientific meetings and at public venues. Software has been developed and this can be publicly available at the PI's webpage. What do you plan to do during the next reporting period to accomplish the goals?We plan to finish the remaining of the proposed tasks.

Impacts
What was accomplished under these goals? Under this project was developed several experimental and computational methodologies for detection and assessment of biological systems. Advances include development of a new method for capture of pathogens followed by spectroscopic detection. Micro and nano-scale devices were developed for capture of pathogens. Computational and statistical methods were developed for 1) studying the impact of model uncertainty on benchmark dose estimation and 2) accurate estimating the taxon abundance in a mixture of microbial sample.

Publications

  • Type: Journal Articles Status: Published Year Published: 2012 Citation: West W, Piegorsch W, Pe�a E, An L, Wu W, Wickens A, Xiong H, and Chen W. (2012) The Impact of Model Uncertainty on Benchmark Dose Estimation. Environmetrics. Environmetrics. 23(8): 706716
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: An L and Doerge RW (2012). Dynamic Clustering of Gene Expression. ISRN Bioinformaitcs. Vol (2012), Article ID 537217. Doi:10.5402/2012/537217
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Jiang H*, An L*, Lin SM, Feng G, Qiu Y (2012) A Statistical Framework for Accurate Taxonomic Assignment of Metagenomic Sequencing Reads. PLoS ONE 7(10): e46450. doi:10.1371/journal.pone.0046450


Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: This project has led to the development and testing of sensors to detect waterborne contaminants. One approach uses a cell culture based method for detecting infective viral particles. Measurements have been performed on the vaccine strain of the polio virus, echo virus and coxsackie virus using FTIR spectroscopy as the read out. A flow chamber for continuous measurements has been constructed thus permitting detection in an automated fashion. An extensive spectra database has been developed for healthy and infected cells. Performance is significantly better than the standard cell culture methods which often require 24-48 hours for detection. Statistical selection of spectra to include has been a key focal point. We are in the process of developing a related lab-on-a-chip method for rapid screening of liquid samples for the presence of active virus particles. We have also performed a number of tests using chemicals towards the development of a database on sensor response to organic solvents (such as TCE) which contaminate drinking water. PARTICIPANTS: Mark Riley, Lingling An, Priyanca Sarkar, Felipe Lee Montiel, Fei Jeff Jia, Ilsa Rojas. Partner organizations include Tucson Water, Pinal Energy, and BioVigilant. TARGET AUDIENCES: Target audience is quite varied and includes the scientific and engineering community, students and faculty, and the general public. Last year we published videos on water quality topics. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Project evaluation is still in progress and focuses on meeting detection limits needed for community based drinking water users. It is necessary to detect on the order of 1000 viral particles / mL. We have not reached that level, but are making progress. A more extensive spectral database has been developed and improved the detection limit. More work must be done to address non-target variability.

Publications

  • Zeng L, An L, Wu X. Modeling Drug-Carrier Interaction in the Drug Release from Nanocarriers. Journal of Drug Delivery. 2011, Article ID: 370308
  • Niu Y, Hao N, and An L. Detection of functional rare variants using Group ISIS. BMC proceedings, 2011, 5(Suppl 9):S108.
  • Lee-Montiel, F., K. A. Reynolds and M. R. Riley, "Detection and quantification of poliovirus infection using FTIR spectroscopy and cell culture", Journal of Biological Engineering, 5:16 (2011), doi:10.1186/1754-1611-5-16
  • Scholz, M., T. Hoshino, D. Johnson, M.R. Riley, J.L. Cuello, "Flocculation of wall-deficient cells of Chlamydomonas reinhardtii mutant cw15 by calcium and methanol," Biomass and Bioenergy 35, 12, 4835-4840, (2011), doi:10.1016/j.biombioe.2011.08.020.
  • Riley, M.R., C.P. Gerba, M. Elimelech, "Biological Approaches for Addressing the Grand Challenge of Providing Access to Clean Drinking Water," Journal of Biological Engineering, 5:2 (2011).
  • Miles, S.L., R. G.G. Sinclair, M. R. Riley, I. L. Pepper, "Evaluation of Select Sensors for Real Time Monitoring of E. coli in Water Distribution Systems," Applied and Environmental Microbiology, 2011,p. 2813-2816, Vol. 77, No. 8, doi:10.1128/AEM.02618-10.
  • Valerie H. Teetor, Denise V. Duclos, Elisabeth T. Wittenberg, Kelly M. Young, Jeerawan Chawhuaymak, Mark R. Riley, Dennis T. Ray, "Effects of planting date on sugar and ethanol yield of sweet sorghum grown in Arizona," Industrial Crops and Products, 34, 2, 1293-1300 (2011) DOI: 10.1016/j.indcrop.2010.09.010.


Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: This project has led to the development of a cell culture based method for detecting infective viral particles. Measurements have been performed on the vaccine strain of the polio virus, echo virus and coxsackie virus using FTIR spectroscopy as the read out. A flow chamber for continuous measurements has been constructed thus permitting detection in an automated fashion. An extensive spectra database has been developed for healthy and infected cells. Performance is significantly better than the standard cell culture methods which often require 24-48 hours for detection. Statistical selection of spectra to include has been a key focal point. The work in developing the water sensing laboratory has included designing and building the infrastructure for continual measurements in flowing water (with ranging qualities from standard drinking water to deionized water). We have also performed a number of tests using chemicals towards the development of a database on sensor response to organic solvents (such as TCE) which contaminate drinking water. PARTICIPANTS: Mark Riley, Lingling An, Ryan G.G. Sinclair, Syreeta Miles, Lucy Cheng, Priyanca Sarkar, Felipe Lee Montiel, Fei Jeff Jia, Ilsa Rojas. Partner organizations include Tucson Water, Pinal Energy, and BioVigilant. TARGET AUDIENCES: Target audience is quite varied and includes the scientific and engineering community, students and faculty, and the general public. Last year we published videos on water quality topics. This year we also published videos on water pathogen detection. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Project evaluation is still in progress and focuses on meeting detection limits needed for community based drinking water users. It is necessary to detect on the order of 1000 viral particles / mL. We are not quite at that level, but are making progress. A more extensive spectral database will help to achieve this goal. Published several videos on water quality, pathogen measurement, and energy requirements for water production. These are posted on the MIT Tech TV site.

Publications

  • Zhiyong Yang, Kelly A. Reynolds, Mark R. Riley, Bruno Bureau, and Pierre Lucas, "Opto-electrophoretic detection of bio-molecules using conducting chalcogenide glass sensors," Optics Express 18, 25, 26754-26759 (2010).
  • Valerie H. Teetor, Denise V. Duclos, Elisabeth T. Wittenberg, Kelly M. Young, Jeerawan Chawhuaymak, Mark R. Riley, Dennis T. Ray, "Effects of planting date on sugar and ethanol yield of sweet sorghum grown in Arizona," Industrial Crops and Products, Available online 25 October 2010.
  • P. Cross, P., N. Odegaard, M.R. Riley, "Lipoic Acid Formulations for the Removal of Arsenic and Mercury from Museum Artifact Materials," Journal of Archaeological Science, 37, 8, 1922-1928, August 2010. http://dx.doi.org/10.1016/j.jas.2010.02.018.
  • Peterson, D.E., J.M. Collier, M.E. Katterman, R.A. Turner, M.R. Riley, "Cytotoxicity of bacterial-derived toxins to transformed lung epithelial and macrophage cells," Applied Biochemistry and Biotechnology, 160:751-763 (2010).
  • A. Ashleigh Long, Cecon T. Mahapatra, Elvin A.Woodruff, III1, Jeff Rohrbough1, Hung-Tat Leung, Shikoh Shino, Lingling An, Rebecca W. Doerge, Mark M. Metzstein, William L. Pak and Kendal Broadie, "The nonsense-mediated decay pathway maintains synapse architecture and synaptic vesicle cycle efficacy," Journal of Cell Science 123 (2010) 3303-3315.
  • Videos published on the MIT Tech TV site (2010). The collection can be accessed from: http://techtv.mit.edu/collections/ibe


Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: Outputs of this project include developing a virus detection technique and building and testing a water contaminant sensing facility. Sensor development efforts have focused on detecting the vaccine strain of the polio virus which can infect a variety of laboratory cell cultures. The method uses a combination of cell culture and infrared spectroscopy. Our best measurements to date have shown a detection limit of 1000 pfu (plaque forming units) / mL of water in approximately 30 minutes. This performance is significantly better than the standard cell culture methods which often require 24-48 hours for detection. Our work in developing the water sensing laboratory has included designing and building the infrastructure for continual measurements in flowing water (with ranging qualities from standard drinking water to deionized water). We have performed a number of tests using bacteria and chemicals towards the development of a database on sensor response. Bacteria can be reliably detected at concentrations ranging from 10^4 to 10^6 / mL, but not at higher or lower levels. Chemical measurements are in development for TCE (trichloroethylene). PARTICIPANTS: Mark Riley, Lingling An, Ryan G.G. Sinclair, Syreeta Miles, Lucy Cheng, Priyanca Sarkar, Felipe Lee Montiel TARGET AUDIENCES: Teachers at the K-12 level were the targets for educational developments. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
We have published 10 short videos on water quality measurements (pH, chlorine, bacterial loads) as a component of training program. Impact has not been measured yet, but videos are being distributed to K-12 teachers as part of water and environment curriculum development.

Publications

  • Peterson, D.E., J.M. Collier, M.E. Katterman, R.A. Turner, M.R. Riley, "Cytotoxicity of bacterial-derived toxins to transformed lung epithelial and macrophage cells," Applied Biochemistry and Biotechnology, 160:751-763 (2010), DOI 10.1007/s12010-009-8526-y
  • Vargas, C. A., A. A. Wilhelm, J. Williams, P. Lucas, K. A. Reynolds, M. R. Riley, "Integrated capture and spectroscopic detection of viruses," Applied Environmental Microbiology, 6431-6440, 75, 20 (2009), doi:10.1128/AEM.02036-08.
  • Yoon, J.Y. and M. R. Riley, "Grand challenges for biological engineering," Journal of Biological Engineering 2009, 3:16; doi:10.1186/1754-1611-3-16.
  • Liu S, Kim H, Chen J, and An L. "Visualizing Desirable Patient Healthcare Experience". Health Marketing Quarterly. 27(1) (2009)
  • N. Riddle, H. Jiang, L. An, R.W. Doerge, J. Birchler. "Gene expression analysis at the intersection of ploidy and hybridity in maize". Theoretical and Applied Genetics. 120:341-353 (2009)