MURI Project Proposal Form
Section I: Proposal Cover Page
Date of submission: ___April 21, 2014________________________
Proposed project title: __Developing a microfluidic device for in situ water column
profiling of phototrophic sulfur bacteria ________________________
Principal Mentor
Name: William P. Gilhooly III
Phone number: 317-278-6319
Department: Earth Sciences
Title: Assistant Professor
Email: wgilhool@iupui.edu
School: Science
Co-mentor
Name: Horia I. Petrache
Phone number: 317-278-6521
Department: Physics
Title: Associate Professor
Email: hpetrach@iupui.edu
School: Science
Co-mentor
Name: Merrell A. Johnson
Phone number: 317-278-0159
Department: Physics
Title: Visiting Research Associate
Email: mermejoh@iupui.edu
School: Science
Proposals must include at least two faculty mentors from more than one discipline.
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Section II: Student Request Page
Total number of students requested: 6
(Note: The total number of students must exceed by two the number of mentors)
Total Number of freshmen and/or sophomores to be recruited: 3
(Note: Preference will be given to projects that include at least one freshman and/or sophomore)
Disciplines or majors of students (preference will be given to projects that include at least two disciplines
or majors): Geology, Environmental Science, Physics, Chemistry, Biology
Skills expected from students: Basic chemistry; laboratory experience in geology, physics, chemistry, or
biology; willingness to work outside to collect field samples
__________________________________________________________________________________
Names of students you request to work on this project.
(Mentors are invited to recommend students that they would prefer to work on the proposed project.
Please provide an email address and a rationale; for example, a student may have an essential skill, may
already be working on a similar project, or may be intending to apply to graduate school to pursue the
same area of research.)
The Center for Research and Learning will consider the students requested below, but cannot guarantee
placement of specific students on teams.
Name of Student:
1) Simran Gurdasani
Student’s Email:
simran5396@hotmail.com
Rationale:
Has experience with the biophysics lab
2) Hannah Caito
hlcaito@iupui.edu
Has experience with the biophysics lab
3) Eric Alt
ealt@umail.iu.edu
has experience in biogeochemistry lab
4) John Byer
jwbyer@iupui.edu
freshman Geology student
5) Alyssa Henke
henkea@indiana.edu
freshman Geology student
6) Kyle Puls
pulsk@iupui.edu
freshman Geology student
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Section III: Body of Proposal
(A maximum of 5 pages is allowed for answers to questions 1-13.)
Pigment analysis can be used to determine the taxonomic diversity of photosynthetic microorganisms in
situ because, i) phytoplankton and photosynthetic bacteria use specific light harvesting chlorophylls or
carotenoids, and ii) these light harvesting pigments have unique spectral signatures (Hubas et al., 2011).
We propose to develop an in situ device to measure the spectral composition of photosynthetic bacteria
in anoxic lakes. Unlike plants that produce oxygen during photosynthesis, phototrophic sulfur bacteria use
sulfide and sunlight to produce carbohydrates and elemental sulfur. These unique phototrophs live in
close association with sulfate reducing bacteria, which generate hydrogen sulfide during organic matter
decomposition (Gilhooly et al., 2014, in revision). Northern Indiana has many anoxic lakes and one such
location is Lake of the Woods (Figure 1). This lake hosts a purple bacterium, the water column is anoxic,
and the sulfur chemistry suggests that dissolved sulfide is actively produced in the water column
(Gilhooly, unpublished data). These redox conditions and light availability suggest that the Lake of the
Woods water column is conducive to blooms of phototrophic sulfur bacteria. Other anoxic lakes in Indiana
that are likely candidates for supporting the growth of these bacteria include Smith Hole, Pretty Lake and
Martin Lake. Although there are likely many local study areas, sampling these organisms tends to be
problematic because: i) measurement devices tend to be large and prone to physically mixing the water
column, and ii) the thickness of the bacterial plate is usually very thin (cm’s) relative to the sampling
resolution (m’s). Microfluidics is a novel technology for developing small volume, continuous-flow devices
that can be used to deploy instrumentation natural environmental settings without disturbing the in situ
conditions (e.g. temperature and oxygen concentrations) (Di Caprio et al., 2013). The project will develop
and test various microfluidic devices to measure the spectral signatures of photosynthetic bacteria in
anoxic lakes.
Figure 1. Preliminary data from an anoxic lake, Lake of the Woods, Indiana (41°25’23.96”N,
86°13’47.18”W). An unidentified (A) purple bacterium was deposited along the shoreline. Sulfur
chemistry (B) shows sulfate concentrations decrease with depth and sulfur isotope values increase
with depth, consistent with microbial sulfate reduction, and sulfide production. Water column data (C)
indicates oxygen and solar radiation are consumed within the upper 4 m of the lake.
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1) What are the research objectives for the proposed project?
This multidisciplinary project will develop a robust analytical device for measuring the in situ spectra
of phototrophic microorganisms within anoxic lakes. These measurements can potentially provide
qualitative information about the identity and abundance of phototrophic bacteria with the lakes.
The objectives are as follows:
1. Design and build a microfluidic device that can be attached to a pump sampler, deployed
underwater, and used to measure the in situ spectra of phototrophic sulfur bacteria.
2. Perform tests to streamline the shape of the device to prevent turbulent mixing within the water
column when the device is deployed in the water.
3. Perform bench-top spectral analyses with the device on environmental samples and microbial
cultures.
4. Deploy the device in a number of lakes with known phototrophic sulfur microbial plates and
perform spectral analysis. Also collect chemical and environmental data to provide context of redox
conditions, light availability, and nutrients.
5. Compare spectra of bench-top measurements and in situ measurements with spectra published
in the literature.
2) What specific research question(s) will your proposed project address?
1. What are the spectra that can be used to uniquely identify the presence of purple sulfur bacteria
and green sulfur bacteria?
2. What is the vertical distribution of phototrophic sulfur bacteria within the lake?
3. What environmental conditions promote the growth of purple sulfur bacteria and green sulfur
bacteria? Are there specific levels of sulfide, nutrients, and light that enhance the productivity of
these phototrophs?
4. Can the relative predominance or presence of either purple sulfur bacteria or green sulfur
bacteria be used to determine the chemical and redox composition of the water column?
5. How does the vertical distribution of phototrophic sulfur bacteria change diurnally and
seasonally?
3) What is the significance of this research?
Several lines of geochemical evidence suggest that the coastal margins during the Cretaceous
(145-66 million years ago) were anoxic and sulfidic (Owens et al., 2013). Known as ocean anoxic
events, these periods of low oxygen are expected to occur again given the current pace of climate
change, as dissolved oxygen solubility decreases with increasing seawater temperatures
(Falkowski et al., 2011). Phototrophic sulfur bacteria sulfur bacteria grow where water column
sulfide migrates into the photic zone, a region known as ‘photic zone exunia’. Studying the growth
of purple and green sulfur bacteria in modern anoxic lakes can provide better constraints on
environmental conditions that may have prevailed in the past and are projected outcomes of
climate change.
Pigment analysis has been used to quantify population dynamics of microscopic phytoplankton in
lakes and the ocean. The chlorophyll content of a natural sample can be measured by standard
spectrophotometric techniques; however the method requires several milliliters of water and the
sample collection tends to mix and disturb the redox conditions of the lake. The method is also time
consuming, and of low spatial resolution relative to the centimeter thickness of the microbial plate.
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Designing a new, flow-through, method to determine the in situ microbial composition of
phototropic sulfur bacteria will enable a more accurate and less invasive assessment of the
anoxygenic photosynthesizers.
4) Why does this proposal offer a good opportunity for undergraduate researchers to gain
substantive research skills?
The undergraduate students will have the unique opportunity to participate in a project that
combines lab work and fieldwork. Such projects tend to be mutually exclusive; however,
environmental studies such as these are best informed by both approaches. The students will learn
about microbial metabolisms, ecological constraints on microbial activity, and the use of stable
isotopes as environmental tracers. In addition to this knowledge, the students will develop a skill
set in designing and making microfluidic devices, collecting environmental samples in the field, and
measuring the stable isotope compositions. The students will benefit from this interdisciplinary
collaboration between Petrache’s physics laboratory and Gilhooly’s biogeochemistry laboratory
with the assistance of Merrell Johnson, a visiting research associate with experience on microfluidic
devices. Combined, these laboratories have 2 graduate students and 4 undergraduate students
with research experience with whom the MURI students will interact with. Students will be
mentored and trained jointly by Petrache, Gilhooly, and Johnson.
5) What research methodology and specific tasks will students and mentors undertake?
1. In accordance with EHS guidelines, mentors will provide laboratory safety training for all
students involved in the research project. Lab methods will be demonstrated to all students to
ensure that the entire research group is familiar with the full range of skills and procedures used for
the project. All students will be encouraged to participate in the field sampling of the lakes. Prior to
the fieldwork, Gilhooly will confirm whether the students can swim, and will give a safety lecture
about working on small boats and with field equipment.
2. Sample preparation and analysis will be conducted on lab equipment in Petrache’s and
Gilhooly’s labs. Students will be responsible for sample preparation under the supervision of
Petrache, Gilhooly, and Johnson.
3. Microfluidic devices will be designed and made by the students in Petrache’s laboratory under
the supervision of Petrache and Johnson.
4. Field samples will be collected by the students and under the supervision of Gilhooly.
5. Students will prepare and analyze samples for stable isotope composition in Gilhooly’s lab.
6. Students will present their research at university meetings such as IUPUI Research Day and at
national meetings.
6) What plan has been designed to ensure effective communication with all co-mentors and
undergraduate researchers on the MURI team?
Weekly group meetings will be held in the Geology conference room, SL118, which is in a
convenient location for both lab groups. The conference room has a computer and projector for
displaying Powerpoint presentations and dry-erase boards for writing out problems and ideas.
Students will provide updates on the research progress and the group as a whole will have roundtable discussion of results and modifications of the experimental design. An Oncourse project site
will be created and access provided to team members in order to share and exchange data.
7) What measureable outcomes and benefits will this research provide to the students, you
and your co-mentor(s), your department, and your school?
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The students will gain extensive experience in laboratory and field-based research, and develop
the critical thinking skills needed to succeed in graduate studies. Involvement in active scientific
research expands students’ horizons by making them aware of the range of possibilities in science
inquiry, and makes them aware of their own academic abilities. Gaining familiarity with lab and field
science helps develop self-confidence and has encouraged students in both the Petrache and
Gilhooly laboratories to go on to prestigious graduate programs.
Mentors Petrache and Gilhooly will benefit from having additional help in conducting idea-driven
research. Introducing students with fresh questions and ideas to active research often leads to new
directions and observations. These students also add an infectious energy to research projects that
helps propel the research forward. Outcomes from this study will also provide a preliminary dataset
for a collaborative research proposal to an external funding agency.
The Physics and Earth Sciences departments will benefit from the recognition of research
presented at university-wide meetings, such as IUPUI Research Days, and national meetings.
8) What is the timeline for the major tasks associated with this proposal?
Week 1:
Training and introduction to methods
Week 2:
Collect environmental samples from anoxic lakes in Indiana
Week 3-5:
Measure chemistry of environmental samples; initial microfluidics designs
Week 6-8:
Measure spectra of environmental samples with microfluidic proto-type; continue
chemical analyses
Week 9-11:
Spectral analysis and bench-top tests of device; continue chemical analyses
Week 12-14:
Spectral analysis, data analysis, work on research reports and manuscript drafts
Week 15-17:
Deploy microfluidic device in anoxic lakes, measure in situ spectra, collect
environmental data.
Week 18-20:
Data analysis; finalize research reports; present at Research Days
9) Please provide a rationale for your budget request. (NOTE: The maximum budget
allowance is $2,000 for equipment and/or supplies needed for the research team. Generally
speaking, expenditures for computers and/or travel are not approved by the review
committee at this time due to financial constraints.)
Funds are requested for isotopic and chemical analyses ($1000), and for microfluidics preparation
and fabrication ($1000).
10) Please describe your plan for sustaining your research beyond the funding that MURI is
able to provide. (For example, please list other external grants that have been or will be
submitted as a follow-up to your MURI funding.)
This research project is appropriate for proposal submissions to NSF Geobiology and LowTemperature Geochemistry (06030000 EAR) and NASA Astrobiology: Exobiology and Evolutionary
Biology (NNH14ZDA001N-EXO). The methodology developed herein is appropriate for a
publication in journals such as Geobiology, or Limnology and Oceanography.
11) Please identify any areas relevant to risk management.
The students will receive proper laboratory training for physics and biogeochemistry. The project
will not involve the use of animals, human subjects, DNA, human pathogens, or radiation.
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Please check any risk assurances that apply to this proposal:
Animals (IACUC Study #): _________________
Human Subjects (IRB Study #): ____________________
r-DNA (IBC Study #): _____________________
Human Pathogens, Blood, Fluids, or Tissues must be identified if used: ______
Radiation : ______
Other : ______
12) The Center for Research and Learning generally shares the text of funded proposals on the
web so that prospective students can learn about available MURI projects. Please let us
know if it is OK with you to post your proposal on the CRL MURI webpage by checking one
of the following answers:
YES
NO
NOTE: If you indicated that it is not OK to share your full proposal via the web, you will be
asked to send us a few short summary paragraphs that can be used to describe your project to
potential undergraduate scholars. These will be posted on the MURI website and attached to
the application for the students to review.
13) Please indicate any dates that mentors will not be available for students during the summer
such as planned vacations, conferences, etc.
Section IV: References/Bibliography (insert 1-2 pages as needed)
Di Caprio G, Schaak D, Schonbrun E (2013) Hyperspectral fluorescence microfluidic (HFM) microscopy.
Biomed. Opt. Express, 4, 1486-1493.
Falkowski PG, Algeo T, Codispoti L, Deutsch C, Emerson S, Hales B, Huey RB, Jenkins WJ, Kump LR,
Levin LA, Lyons TW, Nelson NB, Schofield OS, Summons R, Talley LD, Thomas E, Whitney F,
Pilcher CB (2011) Ocean deoxygenation: Past, present, and future. Eos, Transactions American
Geophysical Union, 92, 409-410.
Gilhooly WP, Reinhard C, Lyons TW (2014, in revision) A comprehensive sulfur and oxygen isotope study
of sulfur cycling in a shallow, hyper-euxinic meromictic lake. Geochimica et Cosmochimica Acta.
Hubas C, Jesus B Fau - Passarelli C, Passarelli C Fau - Jeanthon C, Jeanthon C (2011) Tools providing
new insight into coastal anoxygenic purple bacterial mats: review and perspectives. Research in
Microbiology, 162, 858-868.
Owens JD, Gill BC, Jenkyns HC, Bates SM, Severmann S, Kuypers MMM, Woodfine RG, Lyons TW
(2013) Sulfur isotopes track the global extent and dynamics of euxinia during Cretaceous
Oceanic Anoxic Event 2. Proceedings of the National Academy of Sciences, 110, 18407-18412.
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Section V: CVs/Resumes (insert 2 pages per mentor for a maximum of 6 pages)
See attached pdfs.
Section VI: Support Letters (insert 1- 2 pages as needed)
Section VII: Appendix (Title of and information on the status and outcomes of the past Student
Multidisciplinary Research Team projects received by the Principal Mentor and/or any of the Co-Mentors
must be detailed here. Please insert 1-3-page summary per previous MURI project as needed according to
template below.)
Section VII: Appendix -- Part I
Title of Past MURI Project:
Electrical properties of biological materials under DC and AC applied signals
Date Awarded:
Summer 2013
Date Completed:
August 2013
Description of Project:
In this multidisciplinary project we investigated electrical properties of a series of biological
materials, primarily lipid membranes with and without ion channels and protein networks made of
fibrinogen molecules found in blood.
Mentors Involved in Project:
Horia I. Petrache, Elliot D. Rosen, and Yogesh N. Joglekar
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Students Involved in Project:
Vannara Chhim, Yuncong Hao, Qurat-ul-Ann Mirza, Dan Preston, Alexander Walls,
Raquel Zacherl
Description of Basic Project-related Student Learning Outcomes:
Vannara Chhim worked on ion current measurements and on computer programming
Yuncong Hao worked primarily on measurements of electrical properties of samples used for ion
current measurements
Quarat-ul-Ann Mirza worked on theoretical calculations
Dan Preston worked on measurements of electrical properties of solutions and membranes under
DC signals
Alexander Walls worked on AC measurements
Raquel Zacherl worked on NMR measurements of solutions used for DC and AC studies
Three posters were presented at IUPUI at the end of the summer program in 2013 and two posters
were presented at the Biophysical Society meeting in San Francisco (February 2014). Alexander
Walls was the first author on one of these posters at the Biophysical Society meeting. He could
not attend but my other students presented the poster for him.
Section VII: Appendix -- Part II
NOTE: MURI receives funding for a INSCG, and we are required to report on the following outcomes
for projects:
Publications/Presentations
# Faculty Mentors
How many authors have
published results of this
research/activity?
How many authors have
submitted manuscripts on
this research/activity that are
not yet published?
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# Undergraduate
Scholars
Names of Participating
Mentors/Undergraduate
Scholars
How many invited papers
were presented based on
this research/activity?
How many peer-reviewed
presentations at
conferences were based on
this research/activity?
Proposal Development
# Faculty Mentors
How many proposals for
additional funding based on
this research/activity were
submitted this year?
Total dollar value of the
amount requested on
submitted proposals?
How many of these
proposals were funded this
year?
Total dollar value of the
amount received through
funded proposals?
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# Undergraduate
Scholars
Names of Participating
Mentors/Undergraduate
Scholars
Patents
# Faculty Mentors
# Undergraduate
Scholars
Names of Participating
Mentors/Undergraduate
Scholars
How many related patents
have been applied for?
How many related patents
have been granted?
How many patent licenses
have been issued based on
this research/activity?
Technology Transfer
# Faculty Mentors
# Undergraduate
Scholars
Names of Participating
Mentors/Undergraduate
Scholars
How many technology
transfer activities resulted
from this research/activity?
Section VIII: Signature
Name and Signature of the Principal Mentor:
(typing in the full name suffices as signature for electronic copies)
William P. Gilhooly III
Name
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William P. Gilhooly III
Signature
4/21/14
Date