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E 3 Summer Project “Exploring Research in Engineering and Science”

E 3 Summer Project “Exploring Research in Engineering and Science”. Presentor : Jesus A. Hernandez Gregory-Portland High School Dr. Kung- Hui Chu Assistant Professor, Department of Civil Engineering. The TEAM. Working along side Armando Vital, Brownsville, TX

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E 3 Summer Project “Exploring Research in Engineering and Science”

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  1. E3 Summer Project“Exploring Research in Engineering and Science” Presentor: Jesus A. Hernandez Gregory-Portland High School Dr. Kung-Hui Chu Assistant Professor, Department of Civil Engineering

  2. The TEAM • Working along side Armando Vital, Brownsville, TX • Working under Dr. Kung-Hui Chu, Environmental Engineering/Civil Engineering • Working in Dr. Ry Young’s Lab, Center for Phage Technology (CPT) under direction of Dr. Jason Gill • Working with assistance from Myunghee Kim and Do Gyun Lee, both PhD. Students in Dr. Chu’s Lab

  3. Dr. Kung-Hui Chu • Biodegradation and bioremediation of priority pollutants and emerging contaminants • Molecular quantification of microbial risk in water • Optimization of bioenergy production • Application of bioretention for stormwater runoff management • Advancing knowledge on microbial ecology of nitrogen and carbon cycles

  4. The Laboratory Work • Techniques used in molecular biology for working with the phages • This is a collaborative effort in the disciplines of applied microbiology, virology, and environmental engineering

  5. Research Question A tale of two phages: Does high degree of phage gene homology exist? Significance: Phage Genome Evolution

  6. Background on Phages • Phages or bacteriophages are viruses that infect bacterial cells. They are found everywhere. • Phages, like any other virus, cannot reproduce on their own. • The phage hijacks the cell’s machinery to reproduce progeny. • Phages are specific for their host bacteria.

  7. Lysis via a 3 component system in Mycobacteria • Aholin protein opens a pore in the cytoplasmic membrane • Thecreation of the pore triggers the release of endolysin • An esterase enzyme is also released that degrades the outer mycolic acid cell wall layer • YouTube - T4 Virus infecting a bacteria.

  8. What do we know about these two phages? • A phage , Phage RopaN4, was isolated in Germany 20 years ago • Threephages (Ropa1, Ropa2, Ropa3) were recently isolated from Chu’s laboratory • To our surprise, we found that 2 of 3 of these phages have high similarity in their DNA sequences to N4.99.99% Identical!!!  The other was very closely related.

  9. Discovery => If this is true, it would be a new finding in “Phage Genome Evolution” Approach:new personnel to repeat our work at other laboratory in order to rule out any cross contamination during isolation phages in Dr. Chu’s laboratory. 

  10. Primary Objective • Isolate and characterize phages that infect Rhodococcusopacus. • Collect activated sludge and soil samples that may contain phage. • Secondary Objective: • Collect some DNA

  11. Rhodococcusopacus • Rhodococcusopacusis a specific bacteria • Belongs to the family Actinomycetes, related to Mycobacterium • R. opacusis a rod, nonmotile, mycobacterium • This bacteria was used as the host to isolate phage in Chu’s laboratory

  12. Relevance/Impact of the Research • Potentially open a new research direction in phage genomics. • Some Rhodococcus species are pathogens. A better understanding of phages specific to Rhodococcus can enhance the development of phage therapy. • Phage treatment might be possible to minimize common sludge bulking problem in treatment plants.

  13. The Challenge for Science • The cell wall of the bacteria is difficult to disrupt. • First step is to see which phages can actually infect R. opacus • Rhodococcus-specific phages can lyse the cell.

  14. Research Work • Collecting soil samples • Learn aseptic techniques • Preparing media (broth/food) • Enriching samples for phage • Growing liquid cultures of bacteria • Plating out phage • Collecting plaques of phage on petri dishes

  15. Flow Chart of Lab Work

  16. Data to be Generated • Data that will help characterize the phages from our collection sites. • Comparing the characteristics of new phages to the ones currently available. • Finding phages that will successfully infect R. opacus

  17. Future Implications • Does the high similarity of phage sequences unique to Rhodococcusspecies? • Does the high similarity of phage sequences present concern G+ pathogens? • What are the implications of high conservation of phage sequences?

  18. Summary • Phages infect bacterial cells • Focus on phage that infect Rhodococcusopacus • Isolate and characterize phages • Further exploration

  19. Classroom Lesson/Activities • Physics • Chemistry & Biology

  20. Acknowledgements • TAMU E3 Program • National Science Foundation (NSF) • Nuclear Power Institute (NPI) • Texas Workforce Comission • Dr. Kung-Hui Chu and her lab • Dr. Ry Young and CPT • Dr. Jason Gill • Myunghee Kim and Do Gyun Lee • Armando Vital (partner)

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