Proposal

Name:

Enriching Undergraduate Educational and Professional Experience In Biotechnology And Molecular Biology

FiscalYear:

2014

Audience:

Science, College of

Submitter:

Ebanks, Ryan

Budget Manager:

Blanchard, Dominique

Project Manager:

Proposal Approvers

Dept. Chair:

Murphey, Rodney K.

Local IT:

N/A

Dean:

Ivy, Russell L.

Facilities:

N/A

OIT:

Bagdonas, Joseph A.

Proposal Funding

Year 1:

$ 34,495.95

Year 2:

$ 0.00

Year 3:

$ 0.00

Total:

$ 34,495.95

Proposal Funding versus Average

Questionnaire

Narrative

This proposal requests $34,495.95 to fund a student projects to provide over 2908 undergraduate students with interdisciplinary research experience. The research projects will utilize modern molecular biology techniques to address ecological and environmental research questions.  Many ecological research projects advance to a point where molecular biology techniques are required to address the mechanisms involved. However, most students in environmental sciences and ecology do not have the training to employ such methods. I propose to educate and train these students in molecular biology techniques. All current studies are concentrated within the Florida Atlantic University Preserve (FAUP) on the Boca Raton Campus, and Jonathan Dickinson State Park (JDSP). The research projects objectives are 1) to foster and expand undergraduate education via applied professional research, 2) to provide undergraduates with additional research opportunities that will be available annually and 3) to train environmental science students in molecular biology techniques and to the expansion of information on decomposition rates and training in forensic sciences (forensic ecology): as there is diminutive research in Florida (a humid subtropical climate and tropical wet/dry seasonal climate). It will also enhance knowledge of specific topics in forensics, ecology, geoscience, biotechnology and molecular biology. The scientific findings and data generated from these ecological and forensic studies will also be utilized by Florida Fish and Wildlife, United States Department of Agriculture, and by the FAU Conservation Committee, to aid in the management of the health of the gopher tortoises at the preserve. The funding provided to these research projects will propel FAU into the future a trendsetter in the cutting edge biological education by providing new skills to our undergraduates.

qPCR: A Cutting Edge Molecular Biological And Biotechnological Technique For the Identification And Quantification Of Rare Microbial Species.

 

qPCR thermal cycling—a laboratory technique of molecular biology—is established on the polymerase chain reaction (PCR), which is used to amplify and simultaneously identify and quantify a targeted DNA molecule. qPCR is frequently used for both diagnostic and rudimentary research. Scientists in all areas of life science—rudimentary research (biotechnology, medicine, forensics, diagnostics etc.,) utilize these methods. This technique can be used for the quantification and genotyping of human and nonhuman viral pathogens and presently used to detect viral load. qPCR used clinical microbiological laboratory has significantly improved the diagnosis of infectious diseases and as a device to detect newly discovered diseases. These projects introduce two novel approaches to the analysis of ecological species with cutting edge molecular biological and biotechnological techniques. The two projects described in this proposal have already been established within the FAUP and JDSP. The first project addresses forensic ecology and the second project addresses the health of gopher tortoises as listed below:

 

1) Forensic Ecological Study of The Microorganisms In The Soil Under Decomposing Carrions:

 

Forensic Science has often been used in medicolegal investigation to elucidate the conditions under which a person was killed.  Coroners, police investigators, and medical examiners use the information gathered by forensic scientists to determine how, when and where a person may have been killed. Forensic scientists commonly investigate the postmortem interval (PMI), “the time of death,” in cadavers (carcasses) via the life cycle of specific groups of arthropods and aerobic and anaerobic decomposition rate. This is crucial in homicide cases when there are no witness testimonies. It is impossible to accurately reproduce the exact conditions present during the time of death, but these studies on soil microbes shade light on the approximate the time of death and the environmental conditions, under which the body was originally placed. Soil analysis provides information about specific factors that relate to the rate of decomposition (i.e., microbial and protozoan habitation).  Microbial-ingesting microbes/micro-fauna (bacteria, fungi, nematodes and protozoa) are part of the lithosphere. Studies have shown a measurable relevance of micro-fauna in ecosystem budgets of nitrogen mineralization in the ecological consumer-resource systems. This can be identified and quantified by an analysis of the microbial population’s 16S rRNA and 18S rRNA sequencing: via real-time polymerase chain reaction (qPCR). For example, 16S rRNA sequencing is especially essential with regard to bacteria with unknown phenotypic profiles, rare bacteria, slow-growing bacteria and uncultivable bacteria as an identification tool. Certain groups of bacteria and fungi are dif?cult to identify and only a tiny percentage of total bacteria, <1% of bacterial species, can be cultivated in a laboratory. Metagenomics is capable of investigate the ecological characteristics of either whole communities or individual microbial taxa (Caporaso et al., 2011, p. 4516) Through 16S rRNA and 18S rRNA gene sequence informatics, it is possible to provide genus and species identification, for isolates (microorganisms) that do not fit any standard biochemical profiles (Janda & Abbott, 2007, p. 2761)

 

2) The Health Of Gopher Tortoises In Populations In South Florida:

 

The gopher tortoise, Gopherus polyphemus, is currently threatened in Florida. It is endangered in Georgia, Alabama and Louisiana. This is primarily due to the loss of natural habitat, from increased human development. Habitat loss also leads to habitat fragmentation and isolation of populations. Populations may become overcrowded due to any or a combination of these spatial restricting factors. Common pathogens described from G. polyphemus include ectoparasite  (e.g. ticks), various blood pathogens, intestinal parasites, and mycoplasma, a pulmonary pathogen and the cause of Upper Respiratory Tract Disease (Gopher Tortoise Council). Intestinal parasites are known to be detrimental to their hosts; this is especially true when parasitic infections occur simultaneously with other infectious diseases and amidst poor habitat quality. Intestinal parasite include Cryptosporidium, a pathogen found in human and many animals, indicates potential risk of human and domestic infections. The goal of this project is to expand on existing research projects to identify intestinal, blood and ectoparasite species, and establish infection intensities, of several G. polyphemus populations. For each intestinal, blood and tick sample, DNA will be isolated through qPCR analysis, using 16S rRNA and 18S rRNA gene sequence informatics. Also, we aim to expand on current long term research projects that identified a novel Rickettsia (prokaryote) species on the gopher tortoise tick Amblyoma tuberculatum.

 

Outreach:

Goal I: Enrich the Educational Experience

This first goal is in compliance to the Florida Atlantic University’s current Strategic Plan, this grant accentuates, “enriching the educational experience” of students. This includes the universities determination to inspire research, scholarship and creative activity within the university. Through practical laboratory and theoretical lecture these research projects will impact over 2,908 students each year in the courses below:

BSC 1011 – Biodiversity (800 students per academic year).

BSC 1010L- Bio-principles Lab (800 students per academic year).

BSC 4905 – Life of a Scientist (30 students per academic year).

BSC 4430L – Biotechnology lab I  (64 students per semester).

BSC 4448L- Biotechnology lab II  (64 students per semester).

MCB 3020 General Microbiology (590 students per academic year).

MCB 3020L General Microbiology Laboratory (590 students per academic year).

MCB 4203 Medical Bacteriology (200 students per academic year).

PCB 3352 - Issues in Human Ecology (200 students per academic year).

PCB 3063 Genetics (1024 students per academic year).

 

Goal II: Inspire Research, Scholarship and Creative Activity

 

The research will directly and indirectly benefits FAU by bringing recognition and prestige to the university, promoting educational understanding, guidance and apprenticeship, by expanding on interdisciplinary skills and studies. Through the OURI, Distinction through Discovery Grant and the Quality Enhancement Plan (QEP), a program at FAU geared at professor, graduate, and undergraduate mentorship of undergraduate peers, students and volunteers will attain guidance in techniques of research methodology and grant writing. Thereby, students can reciprocate their training and knowledge to a future mentee. All research will educate research students and volunteers (i.e., non science and science majors) and affirm or reaffirm knowledge in the scientific method. Undergraduate students may apply and enhance knowledge for credit in the Introduction to Honors and Honors Thesis Programs in Biology (BSC 4917 and BCS 4918) and Direct independent Study (BSC 4905).

 

Goal III: Increase FAU’s Community Engagement:

The universities continued push towards research has facilitated an increase in undergraduate research via the Office of Undergraduate Research and Inquiry (OURI). The proposed research facilitates a continue research relationship between Florida Atlantic University, United States Department of Agriculture, Fish and Wildlife, and Jonathan Dickinson State Park. Research experiences will benefit by instilling a practical foundation. Students will be provided with direct practical or professional skills. This experiences will enhance their knowledge in diverse technological required to implement analyze data and access their findings, make them highly marketable. Also, students and volunteers will have access and guidance to JDSP state ranges and state biologist; this will help to foster relation between other state entities and the university. “Service learning and volunteerism help strengthen social capital in the community and enrich the education experience on campus.”

 

Once students are exposed to these projects in their classes, they will be motivated and guided to continue the projects for Undergraduate Direct independent Study (BSC 4905) credit.  All students will be trained and mentored by graduate and undergraduate students will be in the Terrestrial Ecology Laboratory, under the direction of Dr. Evelyn Frazier. 

 

Training of undergraduate students on molecular techniques—Real-time polymerase chain reaction (qPCR) training will be facilitated by Dr. David Binninger (molecular biology and biotechnology), and Dr. Joseph Caruso (Medical microbiology, immunology, parasitology).  Dr. David Binninger’s Laboratory will oversee qPCR analysis and molecular biology protocols. As a trained graduate student, I will serve as the proxy for undergraduate qPCR training.

Facilities
N/A
Hardware Requirements

xxpress qPCR system, 110V includes: xxpress®thermal cycler, ( XP-1003-011) xxsealer (HS-1003-01-1), xxcentrifuge (CF1003-01-1); One year subscription to qBASE+ analysis software and One year standard warranty, all parts and labor (estimated cost $34,495.95). This equipment will be used to run the qPCR analysis. 

Software Requirements
N/A
Personnel Costs
N/A
Other Costs
N/A
Timeline

Gopher Tortoise Health Survey - throughout Spring/Summer/Fall

August 2014

Learn field and lab techniques

September 2014

Begin field collections and analyses; continue to practice field and lab techniques.

October 2014

Continue field collections and analysis

November 2014

Field collection and analysis of data

December 2014

process data, preliminary results; continue collections.

January 2015

Preliminary results, continue collections

February 2015

Final data collections, results, prepare poster presentation

 

Anaerobic and Aerobic Soil Analysis - the wet and dry seasons1 (mid-season)(Kottek et al 2006).

 

Day 12  Professor accompanied

-document daily activity3

-gather temperature and moisture level of soil

-Soil sampling (9) and take fecal sample before it

touches the ground

-freeze sample to be taken to the lab.

-kill feral boars.

-first bow flies emerge (23 min)

 

Day 4-7

-document daily activity.

-collect sample of insects and maggots place in

80% ethanol.

-gather temperature and moisture level of soil

-Soil sampling (9)

-freeze sample to be taken to the lab.

 

 Day 7-14

-document daily activity.

-collect pupate, insects (other insect orders and

families).

-place a sample in 80% ethanol

-soil sampling (9)

-freeze sample to be taken to the lab.

 

Day 14-28

-Soil Analysis via qPCR

 

1Florida is classified as a humid subtropical climate (Cfa) and a tropical wet/dry seasonal climate (Aw) with changing weather patterns.

2 The days in bold are sample days. Sample should be taken to the lab for preservation, freezing or rearing

3 This includes standard measurement of ambient temperature, humidity, biomass, moisture etc.

Sustainability

There will be no recurring costs will arise after the initial procurement, and any additional purchases for reagents (primer and qPCR Master Mix etc.,) will obtained via external. Some primer have been already stored in Dr. Binninger and Terrestrial Ecology Laboratory.  

Resource Matching
N/A
Implementing Organization
All students will be trained and mentored by graduate and undergraduate students will be  in the Terrestrial Ecology Laboratory SC-225, under the direction of Dr. Evelyn Frazier.  Dr. David Binninger’s Laboratory (SC-223) will oversee qPCR analysis and molecular biology protocols.


Proposal Budget

Fiscal Year 1 Fiscal Year 2 Fiscal Year 3 Total
Hardware One-Time $ 34,495.95 $ 0.00 $ 0.00 $ 34,495.95
Hardware Recurring $ 0.00 $ 0.00 $ 0.00 $ 0.00
Software One-time $ 0.00 $ 0.00 $ 0.00 $ 0.00
Software Recurring $ 0.00 $ 0.00 $ 0.00 $ 0.00
Personnel One-time $ 0.00 $ 0.00 $ 0.00 $ 0.00
Personnel Recurring $ 0.00 $ 0.00 $ 0.00 $ 0.00
Other One-time $ 0.00 $ 0.00 $ 0.00 $ 0.00
Other Recurring $ 0.00 $ 0.00 $ 0.00 $ 0.00
Totals $ 34,495.95 $ 0.00 $ 0.00 $ 34,495.95

Supporting Documentation

Filename Size Description
JS20141113A_Ebanks_xxpress.pdf 387,215b Quote
Ryan Tech Fee support.pdf 162,177b