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:
Dept. Chair:
Murphey, Rodney K.
Local IT:
N/A
Dean:
Ivy, Russell L.
Facilities:
N/A
OIT:
Bagdonas, Joseph A.
Year 1:
$ 34,495.95
Year 2:
$ 0.00
Year 3:
$ 0.00
Total:
$ 34,495.95
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.
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.
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.
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.
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 |
Filename | Size | Description |
---|---|---|
JS20141113A_Ebanks_xxpress.pdf | 387,215b | Quote |
Ryan Tech Fee support.pdf | 162,177b |