Examples of tiered mentoring research projects
Below are research statements written by some of the students who participated in the 26 STEM projects in the Tiered Mentoring program.
Student 1: I was involved with a research team working on the cultivation and processing of algae as a renewable feedstock to bio-diesel fuel. In addition to helping with the waste water system, I designed and carried out multiple experiments on the effects of ethylene glycol, sodium acetate, and xylose on algae. There was interest in the possibility of our algal species to metabolize ethylene glycol or xylose, along with any possible inhibitory effects they may have. Sodium acetate was studied to see if it possessed inhibitory effects, and if so, at what concentration, out of interest for using it as a pH buffer. Many side studies and projects were carried out in addition to these.
Student 2: I was heavily involved with a waste water system to feed algae to create Biodiesel using a system of tanks with different retention times. The other project I was involved with was trying to separate the algae from the lipids.
This summer I was involved with the development of a combustion facility for studying flame propagation of aerosol fuels.
This summer I worked on a telemetry study of coyotes in the Cuyahoga Valley in partnership with MetroParks, Serving Summit County. The bulk of the project involved tracking five coyotes fitted with radio collars. Each coyote was located once a week during the day and tracked overnight once a month. The purpose of the project is to determine their home ranges and movement patterns as well as analyze how much time they spend in urban vs. rural areas. As part of a diet analysis being completed by Cleveland Metroparks, I also collected and processed scat twice a month.
Student 1: Bacterial infections in the form of biofilms exhibit increased tolerance or resistance to antibiotics. This can be explained in part by the presence within the biofilm of persister cells, a small sub-population of antibiotic-tolerant cells. Antibiotic tolerance in persisters is non-heritable and reversible, and is currently believed to be the result of a stochastic switch in the expression of toxin-antitoxin modules within each cell. This summer we continued work on a mathematical model of the gene regulatory network controlling the toxin-antitoxin modules associated with the persister state. Recent discoveries on genes associated with persister formation were used along with gene expression data of Escherichia coli to derive equations representing the regulation of these genes. A larger goal of our work is to couple this intracellular modeling of persister formation with dynamical models of cell populations in order to describe the overall growth and treatment of biofilm infections.
Student 2: I was involved with the biofilm project in Dr. Wilber's group. I was basically like a student in this group as they taught me a lot about biofilms and the application of mathematics applied to situations in which biofilms were related. I would often get mini-assignments for research, but it was mostly for my own understanding, rather than for contributions to the group project. I did learn a lot throughout the summer though. I had never really had any experience applying high-level mathematics to real life situations, so it was a good experience for me.
The main project I was involved culturing and observing cell growth, and the effect environment has on cell growth. Beginning with a pre-patterned silicon wafer, with different arrays of grooves on micrometer wide and deep, I mixed a clear polymer and let it set over the wafer, molding a microgrooved surface. I then cut and sterilized the surface, and cultured bovine endothelial cells on it. Every few days I observed cell morphology under a microscope and changed media. Grooved helped facilitate tube structures to grow, the first step to growing veins and arteries essential to complete organ synthesis.
Student 1: Over the past summer I was involved in research with the lab of Dr. Mitchell. As this was my second year in the program I spent the majority of the time conducting field work on a project that I designed with the help of Dr. Mitchell. The project that I was investigating was the grooming behavior of Bombus bees visiting the flower Mimulus ringens. The observations were conducted mostly in an area at the Bath Nature Preserve with some work also being conducted at the Panzner Farm Wetlands. Observations of Bombus bee grooming was conducted with a high speed video camera which was able to record behavior at 300 fps. The analysis of these videos is still ongoing and I am preparing the data for the October presentations. Other projects I worked on this summer were assisting Heath Garris with setting up areas for his studies at the Bath Nature Preserve and this was mostly done in the late spring. I also assisted Dr. Mitchell in looking at the effect of bee visits to pollen removal from Mimulus ringens. Predominantly most of my time spent on research was during the last weeks of July and through the month of August.
Student 2: For the first part of the summer I did a lot of just skipping around and helping out Dr. Mitchell with pollen counting as well as I help Matt out with his project dealing with the landfill. As for the pollen counting, Dr. Mitchell and I were having problems with finding clumps of pollen being hard to count and we found out a new way of counting them that made it easier. We put the test tubes in a ultra sonic cleaner and we found out that this made it so the pollen broke apart from each other a lot better than just shaking them. Later in the season I helped Heath out by setting up his experiment where he was testing the difference temperature had on some of the wetland environment. He put of 3 of these sites but I only helped him out with 2 of them. One was at bath and the other was at Twinsburg. I helped Heath several times recording data he got and also took pictures for him. I also helped Sean out with filming bees with the high speed camera. After Sean got enough film we were looking at bee pollen baskets and was trying to determine how much bigger of a basket a bigger bombos Impatient basket was compared to a early season Bombos impatient had. We measured a lot of bees lengths and found out that they only varied a little bit. I forgot to mention but Sean’s experiment was about if bees had a set cleaning routine or if they varied the number of times they used there legs to clean off the pollen. Also I forget when but i went down to a place like hour and a half south of Akron with Dr. Mitchell to talk to another professor about bee behavior as well. She had some very interesting ideas about how pollination was better closer to forests because of the amount of bees that nest there rather than the open meadow. I also watched videos Dr. Mitchell had recorded when there were a bee sightings for him so he could go back and review them. The only sad thing I had for this summer was the fact that I had to go on vacation with my family around August, and I missed a bunch of stuff that happened for that week.
Student 1: I assisted Timothy Astrop with his research on the evolution of sexual systems of clam shrimp by imaging preserved clam shrimp specimens and helping rear tanks of living clam shrimp. Also, I participated in a field trip to Pennsylvania where we collected fossils of clam shrimp.
Student 2: I am involved in an ongoing project studying sexual dimorphism in Eulimnadia. I hypothesized that Eulimnadia become dimorphic during a definitive morphological event within 4 days of soil hydration. To test this I hydrated two samples of WAL dirt from New Mexico and sampled 5 specimens per day per tank beginning 3 days after hydration. I sampled at this constant rate per day for 8 days and imaged each specimen with light microscopy and the ProgRes camera in the Ecology Commons. Once each specimen was imaged I used Adobe Photoshop's magnetic lasso tool to outline the carapace of each specimen. Once the outlining stage was completed I used a program named TPSdig to turn the outline of the carapaces into 500 coordinates of a graph. Once all of the outlines were digitized I exported them to an online program on the Morpho tools website which gave a standard carapace shape per day per tank. I am currently involved in re imaging and digitizing more specimens and will soon begin the third and final stage of the WAL soil hydration, which will offer 10 samples per tank per day and a larger amount of husbandry to pinpoint the dimorphic event, and reduce error by capturing second and third generations of Eulimnadia of the same hydration. As a second year student I also, taught the new students microscopy technique and hydration/ husbandry techniques of Eulimnadia. I also participated in a field trip to PA for the purpose of fossil collection
Student 3: The Project that I was involved with was with clam shrimp. I organized the clam shrimp specimens that were in vials that were filled with EtOH. I organized them by species. I did this by looking into past papers that Dr. Weeks had published. In these published papers there were locations that had known species at them. Some of the specimens also came from rehydrated soil samples. I went through these samples and was able to match some of the specimens with known species from the same soil sample at different locations. I was able to identify almost all of the unknown species vials and place them with other specimens of the same species. I then placed the vials in the preserved specimens locker with other specimens of the same species. This helped clear out space in the lab and should help future projects find specimens easier. I also did imaging of specimens. This required me to use the imaging setup that is located in the wet lab in the old biology department. I did this by suspending specimens in ethanol and then taking a picture with the camera. The goal of this was to try to get as clear of an outline of the carapace of the clam shrimp so that Tim Astrop could use a program that allows him to compare the differences in shape of the carapaces. I also used the new camera setup that is located in the Ecology commons once that setup was finished about halfway through the summer. The weekly maintenance of the tanks that contained rehydrated soil from various places was also something that I did. This required me to feed the clam shrimp and to observe the tanks and remove any other organisms that could be in the tank to eliminate competition of food for the clam shrimp. In August we went on a trip to Pennsylvania to a site where there was possible clam shrimp fossils. We were taught basic dig techniques like how to remove specimens, how to create a overview of the area, and labeling and collecting of specimens.
The identification of a compound in Black Raspberry which is thought to help in the treatment of cancer.
Student 1: Studies have shown that soaking gecko setae in water has no effect on their frictional forces (Pesika et al, 2009). Early data from our lab indicates that a gecko’s frictional strength decreases dramatically when made to walk on glass coated with a thin film of water. For my experiment, I soaked the feet of Tokay geckos in water then tested their frictional strength while submerged in water. We took measurements at the initial cling, and then allowed the gecko to take steps, measuring frictional forces after each step. The results showed that the gecko’s frictional strength was lower than dry trials at each measurement. As a control, we tested dry geckos submerged in water. The results were very similar to those from the soaked geckos. Further experiments are needed to fully evaluate what exactly is causing the inhibition of the geckos’ frictional strength. Some ideas for these experiments are: to do trials with soaked gecko feet on a misted glass, and to do trials with soaked gecko feet on a dry glass.
Student 2: Based on a study done by Pesika et al (Gecko adhesion pad: a smart surface? 2009) there is evidence that a patch of gecko setae that has been submerged in water for 1.5 hours then pulled to test frictional forces shows the same results as trials done under dry conditions. The data indicate that water has no significant effect on the frictional forces of gecko setae. Initial data from experiments conducted within our lab shows that when a gecko is placed on glass misted with water then pulled to test frictional forces, the results match those of the same force test under dry conditions. However, after the gecko is allowed to take 1 or more steps the frictional forces decrease significantly. According to the data from Pesika’s experiment, we would not expect this sort of result to happen. Their conclusion was that frictional forces are load dependent and are unaffected by water; the contact region of the spatulae excludes water. Continuing with these findings, the assumption could be made that having the gecko take steps under the previously described conditions would not affect frictional force. This assumption contradicts the results we have seen.
Student 1: Over the summer I worked with the invasive Eurasian watermilfoil and the weevils that consume this plant. We were getting the DNA out of the weevils. We used gels and the PCR machine
Student 2: This is the second time that I have participated in the Tiered Mentoring Research Program under Lara Rocketenetz. The research was focused on the Milfoil Weevil (Euhrychiopsis Lecontei). The goal of the research was to prove that the eastern weevils and the western weevils are two different species. Necessary procedures were followed to obtain DNA from the collected weevils and analyze the obtained data. Several methods were put to test in order to determine the best solvent to be used to store the weevils once they have been collected. Storing the weevils in ATL buffer at room temperature yielded the best results. After the best method of storage was determined the research was carried on to obtain more data on the Milfoil Weevil.
This summer my research focused on the manganese concentration in the 196 acre Barberton Reservoir in Norton Township. We collected from three different sample sites along the reservoir. We then took samples from each site at three different depths; the surface, the middle, and the bottom.
Each sample was taken back to the lab for multiple tests. The sample was tested for pH, Fluorescence’s, TOC, and manganese. My focus was on manganese in which I took readings for each sample both soluble and insoluble. We were able to map the manganese concentration per depth and location over a period of time and begin to predict how and why each sample had the concentrations it had.
They will be continuing this study through-out the next year in order to get a better read-out of the concentrations; this will allow us to determine solutions to the amount of manganese in the reservoir.
This summer I worked with Doctor Newby under the Grad student Jia Fang on two projects. One was to produce scaffolds to grow stem cells and implant them into the body with the aim of deep wound healing. This was for Dr. Yin of NEOMED. However, I eventually stopped working on this project as a new grad student came into the lab and instead focused on my second project which I had also been working on in collaboration with the Biomedical Engineering Department's Dr. Zhang and her grad student Nikul. My focus was to find an alternative surface to produce cell sheets using a thermoresponsive polymer, thus providing a scaffoldless implantable supply of tissue for various regenerative pupose. Both projects focused on using micropatterns produced from fracture of cured PDMS (polydimethylsiloxane) strips from glass which spontaneously produce micropatterns 5-30 microns in length, perfect for certain types of cells to grow and align. I spent my time mixing solutions and duplicating these micropatterned strips of pdms and then modifying them with various polymers to meet our goals. I also learned how to do basic characterization of the thin polymer films using ellipsometry, contact goniometry, and using various settings on the microscope in the lab.
Although we haven't found success in finding an alternative method for cell sheets, we're still moving forward with different approaches.
Tiered Mentoring (TM) students went to both RoboGames in San Francisco, and the NASA Lunar Mining Competition at Kennedy Space Center. One TM student’s robot at RoboGames was the 340-lb combat-bot. The TM student was responsible for command and control. The team got second place. Our Lunar Mining robot was one of only six robots out of 29 that was able to load lunar regolith. We got 5th place honorable mention, the TM student was again responsible for command and control. The TM student mostly used his TM funds to go to improving our general command and control capability.
Additional TM students have been working hard on their quadrotor for this next year. It will be a robot that uses four rotors to hover and maneuver. It is more stable and maneuverable than a helicopter. One TM student used his opportunity to get involved with the IEEE Aerospace Systems - Gyro Committee. He was even able to get them to meet on campus, and he acted as their host. The TM students mostly used their TM funds to develop their quadrotor hardware.
This summer, I was involved in two different projects with Vasav. All of the research I assisted in was concerning a species of orb-weaving spiders, Lariniodies cornutus. I learned how to dissect spiders in order to extract the aggregate glands, which contain glue that could potentially be used for a medical adhesive. I also did experiments with the spider silk, exposing it to different humidities and measuring how the glue droplets increased or decreased in size.
Working with my graduate mentor, Donnie Copeland, over the summer, I learned a lot about various lab techniques including PCR, gel electrophoresis, plating, growing cultures and conducting protein assays. I am continuing to work on my project throughout this semester to be used for my Honors Thesis. I am working to identify the exact number of mRNA copies of leptin that are expressed in carp tissues including liver, brain, heart, and testes. Leptin is a protein hormone that plays a key role in a number of metabolic and biological processes throughout the body. So far, in working to create a standard to eventually compare leptin I and II quantitations of these different tissues to, and under the direction of my mentor, I have successfully cloned leptin I, and leptin II into vectors that were transformed and grown in E.Coli bacterial cultures. After several weeks of trial and error and trying to verify that my clones were in fact expressing the leptin sequence I was hoping for, we deemed the cloning to be a success. We ran several PCRs followed by gel electrophoresis to determine this, and then purified the plasmid DNA on the clones, to be able to isolate it. We will now continue with quantitative PCR. This will then be our standard, and we will be able then to use different carp tissues that we suspect to contain leptin and quantify the number of mRNA copies being produced in each tissue. This will greatly contribute to our understanding of leptin expression and will allow us to compare with other species, leading to a better understanding of this protein’s role in the metabolic processes of carp and different species.
I worked as a research assistant for Dr. Mittal and his Graduate Assistant, Anveeksh. The project we are in the process of working on is a Rapid Compression Machine. The goal of our project is to control the combustion of bio-diesel fuel in order to obtain information on this type of fuel. We will be using a two step process to determine the fuel concentration and flame propagation rate of the fuel. The first step, obtaining the concentration, utilizes a preexisting combustion chamber that will be retrofitted with quartz glass windows to allow a He-Ne laser to pass through the chamber and ultimately determine the fuel concentration. A second chamber will be used to combust the same fuel concentration in a controlled setting. A spark will be used to initiate combustion and a high speed camera will be used to capture images of the flame as it expands through the gas.
Student 1: This summer I was involved with the Co-op working in the Fetal Treatment Center at Akron Children's Hospital. We entered closed patients' cases into a database, and then narrowed down our sample to only include those patients who were prenatally diagnosed with gastroschisis. Gastroschisis is an abnormality involving the herniation of the contents of the baby’s abdomen, and can most often be treated effectively and efficiently. We also received lists of babies who were transported to the NICU (Neonatal Intensive Care Unit) with this disorder, and we were able to separate them into three groups: Babies prenatally diagnosed with the abnormality and having had received services from the FTC, babies prenatally diagnosed and not seen in the FTC, and babies who were not prenatally diagnosed. We compared averages for the first two groups (with and without FTC services) based on several variables which included: birth weight, apgar score at 1 and 5 minutes, whether or not the baby was transported to the NICU and if so what day they were transported and how many days they spent there, postnatal diagnosis, postnatal procedures, pediatric management plan made, psychosocial concerns, male/female, the follow up known on the baby (premature, live born, spontaneous/terminated abortion, stillborn or newborn death), type of surgery, days until surgery, additional complications (bowel peel, short gut syndrome, atresia, necrotizing entercolitis), days on ventilator, days to oral feed and newborn death. We were not able to achieve statistical confirmation that babies seen in the treatment center did better after birth, and the project is going to be continued from a different angle to better support the work that the treatment center does for it's patients.
Student 2: I continued my research at Children's Hospital this past summer. My partner and I finished work that I started the previous summer with a different partner. We compiled a database of all the patients seen by the fetal treatment center. This database included high amounts of information on the patients. Once the database was completed, we chose one disorder as our focal point. We compiled more information on the patients with this disorder (gastroschisis) and then did a statistical study to determine if visiting the FTC was beneficial to patients. (We had a separate list of patients with gastroschisis who did not visit the FTC.) Unfortunately, it was determined that the patients w/gastroschisis who came to the FTC were significantly "sicker" (had other disorders) and therefore could not be compared to the other patients. We determined this right at the end of summer and there was no time to put together another study and obtain some results. However, the database (which we spent two summers putting together) still exists and can be used for future studies
With an increase in medical technology and science, medical product development has also increased. Being responsible for evaluating and predicting the safety effectiveness and manufacturing process of all medical devices, the Food and Drug Administrating (FDA) launched the Critical Path Initiative (CPI) to drive innovation in the scientific processes through which FDA-regulated products are developed, evaluated, and manufactured. The CPI covers a broad range of medical devices and drugs. The main goal of the CPI’s focus on medical devices is to accelerate the safety assessment of medical devices in the preclinical stage, with particular attention paid to blood damage, and to standardize computational fluid (CFD) dynamics techniques for such use.
CFD programs have been created to predict flow and fluid forces and calculate physical parameters such as shear stress. However, no CFD program has been created to predict blood damage in medical devices. To create such a program, baseline testing of blood damage will need to be completed. In the CFD field, benchmark tests are used to evaluate the ability of an algorithm to correctly solve the field equations. If a CFD algorithm correctly handles the benchmark cases, considered to be known results, it is assumed that predictions in unknown cases with similar fluid mechanics conditions will be correct. The FDA will use such a program to model blood damage in medical devices. Since data ranges can vary due to a number of external conditions, baseline data will be collected by at least three different labs to insure quality of the CFD program. The University of Pittsburgh, the Cleveland Clinic Foundation, and the FDA will be conducting round robin testing of models to assure quality. Cleveland Clinic Foundation’s (CCF) Biomedical Engineering Department and the University of Pittsburgh are solely responsible for collecting and sending baseline data to the FDA.
Hemolysis is defined as the rupture or breakage of the red blood cell membrane, causing the release of hemoglobin, also called free hemoglobin, and other internal cellular components into the surrounding fluids. The rate of change of free hemoglobin in a system is a measure of device quality. Hemolysis is the main type of blood damage that will be documented in the testing. Because baseline testing for the CFD program requires precise documentation of levels of hemolysis, defined objects will be used to create blood damage. The FDA selected a nozzle model with a defined geometry to create hemolysis in a closed loop system. The closed loop system used to create and sample blood damage consisted of pressure ports, a temperature port, a blood pump, reservoir, and heat exchanger.
The student was to take lead in hemolysis testing for the Cleveland Clinic. After weekly testing had been completed, data processing began. Once all data was processed, it was sent to the FDA for analysis. Purchasing supplies for testing and shipping supplies to separate labs was also conducted. Since the student was directing hemolysis testing, he was allowed to hire a student from the Tiered Mentoring Program to aid him in testing. The student got to experience research first hand in a state-of-the-art facility under direction of some of the world’s best researchers.