1. Case Study on San Jacinto Basin
This is our generic title slide. Not sure what to place for the title so its left blank atm.
Case Study on San Jacinto Basin
Rupa Iyer Ph.D. Founding Director, Biotechnology Programs Director, Center for Life Sciences Technology
University of Houston

2. Biotechnology Medicine Food Pharmaceutical Agriculture Environmental
• improving human, animal, and plant health;
• increasing the availability of nutritious food products
• reducing our reliance on chemical pesticides
Agriculture
Environmental

3. Environmental Sampling Remediation of OP Compounds
UH Interdisciplinary Research Based Laboratory Curriculum
Discovery
R & D
Production
Applications
Environmental Sampling
Remediation of OP Compounds
Biomanufacturing
Module I
Sample Collection & Screening
Module II
Cloning & Transformation of OP Genes
Module III
Upstream & Downstream Processing of OP Hydrolase
Bioremediation
Biosecurity
Energy
Health
Entrepreneurship
Infused 20 years of research in biotechnology laboratory curriculum
Pesticide degrading bacteria as a model to demonstrate the life cycle of a biotech product
Modular format , ease of integration in a variety of courses
Seed Funding NSF*, TWC
Model for interdisciplinary Education

4. Environmental Sampling
Research & Education
No comments.
A hands-on research experience for undergraduates with real world applications

5. Database of Environmental Contamination Activity – Research Collaboration Network
A hands-on research experience for undergraduates with real world applications engages students in an authentic,
ongoing research activity to populate a database of the geographic distribution of environmental contamination
Electronic archive of experimental data – *Students contributing and mining their own research data to enhance STEM skills

6. A Database of Environmental Activity
The ESRM database around the Houston-metropolitan area. AN old picture, doesn’t appear to include SJR sites. Discuss in context of the ESRM before our extended focus on the SJR.

7. Integration of Education and Research - Outcomes
60+ bacterial strains
Map of location and distribution pesticide degradation activity
2 distinct organophosphate (OP) degradation genes
*Genetic Map of 8 bacteria
Check font and formatting for consistency.

8. Platform for Education and Research Collaboration
Students: Hands-on STEM activities and Research Experiences
Faculty: Implications and applications in biotechnology
Government and Community : Location, monitoring, and remediation efforts
Commercial: Diverse collection of bacteria available for purchase- bioremediation, enhanced oil recovery, antibiotic resistance
Consider switching this with the slide below.

9. Platform for Education and Research Collaboration
Local
UH BTEC
Prairie View A&M
Alvin Community College
National
BYU-Hawaii
Louisiana Tech
RIT
SUSU
Global
St. Xavier's (India)
Morocco
Fulbright Specialist (5 years)
No comments.
Addressing two social Issues : STEM & the Environment

10. San Jacinto Waste Pits – Case study
Location – Two pits: Consists of two pits under 1-10 overpass as it crosses the San Jacinto River
14 acres total in size
Pits partially submerged releasing contamianants into and across the SJR.
Location
Consists of two pits under 1-10 overpass as it crosses the San Jacinto River
Purpose
Champion Paper Mill dumping ground for paper mill waste in the 1960’s
Contaminants
Polychlorinated organics
Dibenzo-p-dioxins
Dibenzofurans
Biphenyls

11. San Jacinto Waste Pits - History
Location
Consists of two pits under 1-10 overpass as it crosses the San Jacinto River
14 acres total in size
Purpose
Champion Paper Mill dumping ground for paper mill waste in the 1960’s
Contaminants
Polychlorinated organics
Dibenzo-p-dioxins
Dibenzofurans
Biphenyls
Location – Two pitsConsists of two pits under 1-10 overpass as it crosses the San Jacinto River
14 acres total in size

12. San Jacinto Waste Pits - History
1990
First dioxin based consumption advisory for fish and shellfish for HSC and Galveston Bay
2005
San Jacinto Waste pits superfund site was rediscovered.
2011
Waste Management temporary cap to minimize release
Location – Two pitsConsists of two pits under 1-10 overpass as it crosses the San Jacinto River
14 acres total in size

13. San Jacinto Waste Pits - Legacy
Areial Map; Red is the superfund and immediate surrounding area. Yellow, census tracks representing cancer cluster. Official report does not exist.
TDSHS Report: Noted increased incidences in cancer in various eastern Harris county census tracts. Three of those tracts overlap on top of the Superfund and extend downstream towards Galveston Bay. Widespread contamination of sediment, surface water, soil, and aquatic wildlife downstream of waste pits
San Jacinto River
Houston Ship Channel
Buffalo Bayou
Galveston Bay
Health risks
Texas Department of State
Health Services Cancer
Report

14. Map of Dioxin Monitoring Stations
Shows the location of dioxin monitoring stations across the SJR and down into Galveston Bay. Pins are color coded based on the area not concentration. Colors do not correspond to TEQs on next slide.
Yellow – Buffalo Bayou
Pink – Bear Lake
Light blue surrounded by red outline – Superfund
Blue – Lost Lake
Light pink – Burnet Bay
Green – Scott Bay
Red – Upper SJR Bay
Light blue – Black duck Bay
Dark blue – Tabbs bay
Purple – Mouth of SJR
Orange – Galveston Bay

15. San Jacinto River Collection - Project Rationale
Detect Pollution
Bacteria as biomarkers
Remediation
In situ bioremediation
No comments. Develop a distribution map of xenobiotic-degrading activity across SJR
Dioxins
Furans
Biphenyls
Petroleum Hydrocarbons
Pesticides
Other Organic Waste
Biomarkers
Degradation Activity
Development of bacterial biosensorsAdd to a collection of xenobiotic degrading bacteria that can be utilized for environmental cleanup of these pollutants
SJR
Superfunds

16. Project Goals (1) Collect environmental samples from San Jacinto River
Soil and sediment
Project Goals
Samples were taken at multiple locations along the San Jacinto river in Fall 2016 – Spring 2017.
- Samples are color coded as follows: Blue – No isolate obtained from sample. Yellow – Positive isolate (paraoxon). Purple – Positive isolate (methyl parathion). Green – Positive isolate (dioxin/dibenzofuran). Orange – Positive isolate (1,4 dioxane). Brown – Positive isolate (biphenyl). Light green – Positive (paraoxon/dioxin)
Blue – No isolate obtained from sample. Yellow – Positive (paraoxon).
Purple – Positive (methyl parathion). Green – Positive (dioxin).
Brown – Positive (biphenyl). Light green – Positive (paraoxon/dioxin)

17. Project Goals
(2) Screen collected environmental samples for dioxin and other xenobiotic degrading bacteria
Ops on the top. Central phosphorus atom.
Dioxins Furans and Biphenyls. Very similar structures. Many degradation genes exhibit cross activity especially in the presence of a preferred co-substrate.
1,4 Dioxane and a similar compound. Tetrahydrofuran monooxygenase is the enzyme that targets 1,4 dioxane.

18. Preliminary Project Results: Identification of SJR Bacterial Isolates
Genera + species screened out on specific substrates from areas along the SJR.
Updated Table. This is in picture form. See supplementary slide for editable table.

19. Project Goals
(3) Identify dioxin degradation biomarker genes and functional degradation pathways
Whole genome sequencing
Data analysis
Characterization
Genomics – DNA sequencing (Represents the biological potential of your organism(s))
Transciptnomics – RNA sequencing, Microarray (Represents gene expression of different biological activities)
Proteomics – Protein modeling (Represents actual biological activity taking place inside of organism)
Metablomics – Degradation kinetics (The end result of biological activity in your organism)
Together this data allows you to determine what your organism can do and how you can improve upon it.
Potential
Function
Activity
DNA
RNA
Protein
Metabolites

20. Project Goals
(4) Map spatial-genomic distribution of dioxin degrading activity
Phylogeographic analyses
(5) Engineer bacteria for improved degradation of dioxin compounds
Last goal slide. Analysis of degradation activity and directed improvement to degradation enzymes.
Genomic insertion, deletion, or editing
Mutagenesis
CRISPR-Cas

21. Preliminary Project Results:
General Trends
Many isolated bacteria so far are noted opportunistic pathogens or known pathogens
Polluted environments are hotspots for later transfer
SJR may be a breeding ground for antibiotic resistance
Data mirrors previous results taken over 8 years of undergraduate environmental sampling in agricultural soils for organophosphate degradation
High incidence of opportunistic pathogens as OP degraders
Evidence of lateral transfer of antibiotic resistance genes observed in a subset of collected isolates
Manure was a likely source of resistance genes in these instances
No comments.

22. Environmental Ideals
Not too sure about slide title. Meant to depict a pristine river devoid of pollution.