Graduate Mentor Research Projects - 2008
This year we have 9 mentors who are currently seeking undergraduate fellows and high school students to join their teams.
Seth Bybee, Entomology
Clayton Cox, SNRE, Interdisciplinary Ecology
Charlotte Germain-Aubrey, Botany
Jorge Gomez, Environmental Engineering
Mohammad Reza Hossein Zadeh, Plant Pathology
Barbara Smith, Rehabilitation Science
Danielle Watts, SNRE, Wetland Ecology
Frank Wessels, Entomology
Jada-Simone White, Zoology
Link to previous projects, 2007
Seth Bybee
PhD Student – Entomology and Nematology
Project Area: The Evolution of flight within Dragonflies and Damselflies (Insecta: Odonata)
Email: sbybee@ufl.edu
My research focuses on fossil and living dragonflies and damselflies and their more than 300 million years of flight adaptations. I am looking for students eager to work on two smaller questions within dragonflies. One involves the phylogeny of Helicopter damselflies, a charismatic group of endangered insects containing the insect with the world’s largest wingspan (~190 mm). Helicopter damselflies carry out their entire life-cycle in the forest canopy and feed on spiders plucked directly from their webs. This research will provide baseline data for conservation work within the group and an improved classification scheme in which to explore the group’s flight adaptations.
The second research project is a museum based project in the world’s largest dragonfly collection in Gainesville, FL. This project focuses on the variation in overall dragonfly wing area between individuals of a single species that inhabit both high and low elevations. Due to varying levels of oxygen at different elevations, it is predicted that individuals living at higher elevations will have a larger wing area than those individuals from lower elevations. Using label data and Google Earth we can identify the elevation at which each specimen was caught and correlate this data with total wing area.
Students working on these projects will learn how to use the scientific method and formulate research questions. They will gain valuable experience in generating and analyzing both morphological and molecular data. They will also learn to conduct both collection and laboratory based research. I plan to work side by side with students so that they can present their findings at a national scientific meeting and publish their results in peer-reviewed journals.
Clayton Cox
Ph.D. Student – School of Natural Resources and Environment
Project Area: Investigation of resilience mechanisms of oyster-associated microbial communities
Email: cec9@ufl.edu
My research focuses on the role of community-wide bacterial cell-to-cell communication in the resilience of oyster-associated microbial communities and their resistance to invasion by a model pathogen, Salmonella enterica. Bacteria are omni-present in nature and often exist in complex, multi-species communities which are capable of communication and coordinated activity. Bacteria constantly sense their external environment and are capable of perceiving complex chemical cues from animals, plants and other bacteria which regulate bacterial behaviors such as motility, surface colonization, biofilm formation and virulence in a process called Quorum Sensing.
There are two aspects to my project; dissecting the genetic regulation of colonization of established microbial communities by an opportunistic pathogen using a S. enterica gfp labeledpromoter-probe library and determining the role of the GacS/GacA regulatory system in surface colonization and persistence on oysters. The characterization of interactions between host-associated microbiota and “invaders” can serve as a model for dissecting evolutionarily conserved mechanisms of microbe-microbe and host-microbe interactions which are central to understanding the ecology of host-associated microbiota.
The surface of an oyster harbors many species of bacteria, most of which are harmless to humans. However, little is known about the composition of these communities. Characterizing the wild type community composition and shifts in community composition in response to specific treatments under controlled laboratory conditions allows studying microbe-microbe and host-microbe interaction in greater depth. These analyses are a central element to this project which will augment the genetic analyses.
Characterization will be achieved primarily through 16s rDNA analysis. This will be done by extracting total microbial DNA from oysters and amplifying the 16s rDNA by PCR for sequencing using commercially available kits which are straightforward and easy to use. These are important tools for environmental microbiological research, as many bacteria species can not be cultured in the lab. Other techniques such as selective media, BIOLOG plates and biofilm assays will be used as necessary. These are standard experiments which are routine in our lab and may be used in any bacteriological laboratory.
Projects such as characterizing shifts in the wild type population after exposure to invading pathogens (S. enterica) or characterizing wild type population shifts in response to treatment with small molecule GacA inhibitors would be appropriate for an undergraduate student. Characterizing shifts with seasonal variations such as temperature, salinity, etc. utilizing commercially harvested oysters from Apalachicola Bay prior to any treatment can be performed by a high school student
Interested applicants are encouraged to speak with me as individual projects can be tailored to interest and background.
Charlotte Germain-Aubrey
PhD student- Botany
Project area: Conservation genetics of endangered plant species in Florida.
My research project is looking at one of the diversity hotspots in the US, the highly threatened central Florida scrub. This unique ecosystem, which used to be an island in the geological past when the sea level was higher, has many endemic species and my project is focusing on 5 plants that are typical of this region. I want to look at their genetic diversity in order to better understand the origin of the central Florida scrub, but also to give a scientific base to their conservation. My research would involve some field work in the summer in the form of multiple collection trips in central Florida, but also more locally, and an extensive lab experience in the summer and fall.
I foresee students to take on their own part within my dissertation work. Each student will be responsible for the work of one particular species, so that they would experience every step of the process, from collecting the data and processing voucher specimens for the herbarium, to doing the lab work and finally analyzing, interpreting and writing up the results. The lab component of this research will familiarize them with the latest molecular tools such as microsatellites and primer design, and a pilot study will also be undertaken for the possible development of new molecular markers that have never been used in plants before. I am planning on being in the field, and then in the lab with my students in order to supervise them and guide them in every step.
The last part of the project will involve interpreting these results for conservation purposes. I will familiarize the students with some very recent statistical programs that will help to build a strong case for a management plan. Each student will present their work in the form of a poster to a national conference and probably talks in more local meetings to help raise awareness on these species. They will also co-author papers in peer-reviewed papers. This experience will be very valuable to any motivated student wanting to go into botany, research and/or a conservation-related field in the future.
Jorge Gomez
PhD student- Environmental Engineering
Project area: Molecular characterization of bacteria living in polluted aquatic sites
My research project involves the characterization of the bacterial populations present in groundwater contaminated with chlorinated hydrocarbons using molecular techniques. Understanding how the microbial populations present in groundwater contaminated with chlorinated hydrocarbons changes over time is of paramount importance, particularly when designing the treatment strategies to be implemented. The main objective is to characterize the composition of the microbiological population on a lower surficial aquifer that is contaminated with chlorinated hydrocarbons, using molecular genetics techniques. The site for the study is a Florida Department of Transportation (FDOT) property located in Fairbanks, which is relatively close to some of the groundwater intakes that supply the City of Gainesville. The site is currently being treated, mainly for 1,1-dichlorethene (DCE), by using a combination of air sparging and bioaugmentation. Groundwater samples are routinely analyzed for the bacterial population’s composition.
Students will be working directly with all the microbiology and molecular biology techniques that we currently use in our lab. Including but not limited to: solid and liquid bacterial culture media preparation, maintenance of pure and enriched cultures, isolation of pure cultures form environmental samples, Polymerase Chain Reaction (PCR) of the 16S rDNA region using universal primers, agarose gel electrophoresis, polyacrylamide denaturing gradient gel electrophoresis (DGGE), construction of phylogenetic trees, as well as the main statistical methods pertinent to the work we do. I firmly do believe that a hands on approach, it is by far the best way to learn. Most of the work for the students will be based on the laboratory; however some field sampling events will also be included, where groundwater samples will be collected. Regular lab meetings will be held to present partial results and discuss relevant papers to their work.
Additionally, the possibility of working with Life Cycle Assessment (LCA) and/or heavy metals toxicity will be also available, to tailor specific preferences of the students, so they can develop their own senior honor thesis in a subject that will match their interest. Students will be also encouraged to participate in the writing, reporting and publication of the results of the work, as well as presenting it on national scientific conferences. That way, they not only will get a very nice set of research tools that can be applied to almost any other field, whatever career path they choose to purse. But also, they will start building their CV with publications, and will get the experience of attending a scientific meeting and presenting their work.
Mohammad Reza Hossein Zadeh
PhD Student – Plant Pathology
Project Area: Identification and molecular pathology of viral diseases in turf grass
I am working on a new disease of St. Augustine grass which is characterized by a systemic necrosis and death of the plant during the cool season in Florida. The causal agent is suspected to be one or more viruses. My objectives are to identify the causal agent(s) of this disease, characterize the virus or viruses both biologically and molecularly, to determine if there are any St. Augustine grass genotypes that are resistant to the virus(es) and to understand more about how the virus(es) cause the necrosis. Since my research plan comprises a lot of work in the field of molecular plant virology and as well as plant virus biology and ecology, this project provides a great opportunity for the mentees to gain technical skills as well as an understanding of the research process. Specifically they will learn how to interpret and use published scientific papers; learn basic molecular techniques that can be used in many research areas, learn how to work as part of a team; learn how to use the computer for data organization, analysis and presentation; learn how to communicate their results both informally and formally.
Undergraduate student involvement in the research plan:
The undergraduate students will be taught and guided in the cloning and sequencing of the new virus(es) which I have found in the St.Augustine grass. This section of the research will include several molecular techniques including PCR, genomic-segment cloning and sequencing, nucleic acid hybridization and construction of full length infectious clones, sequence analysis using proper computer software.
RT-PCR: To do cloning, fragments of the viral genome must be amplified using this molecular technique. Since the viral agent(s) of the disease is/are RNA virus(es), Therefore a specific method of PCR called RT-PCR is used to amplify the genomic fragment. In this method first genomic RNA is converted into DNA called c-DNA .In the next step the c-DNA is used as a template for degenerate and/or specific primers for amplification. The most important part of the successful PCR is the appropriate primer sets designed before. The students will be taught how to design the accurate primers to target the wanted fragment of the viral Genome.
Cloning and Sequencing: After amplification of each fragment the amplified fragment would be isolated and cleaned up from the Agarose gel to get ready for ligation into an appropriate plasmid, usually p-Drive plasmid as a vector, and then the transferred plasmid would be transformed into E.coli competent cells by a process called chemical transformation. The transferred E.coli will be screened after culturing on the selective media. The individual white colonies will be chosen having the amplified segment of the genome and will be cultured in liquid medium to create high population of the transferred bacteria. Finally using appropriate procedure the wanted plasmid with the amplified segment is purified and sent to DNA sequencing lab to be sequenced. The result from sequencing is analyzed using proper computer software such as DNA MAN. Finally the full-length infectious clones are constructed using the amplified fragment and the infectivity test is conducted on the healthy plant to prove the virus as a pathogen for the plant.
High school student involvement in the research:
The high school student will work as a research team assistant in the biological characterization of the virus. The host range of this new virus will be established (as well as the type of symptoms that it causes in the various hosts). This will involve using insects to move the virus from plant to plant, as well as detection of the virus in inoculated host using appropriate laboratory assays such as PCR. This project will give the student an opportunity to set up experiments, learn to work with plants, learn to work with insects as vectors, learn to collect, organize and analyze data, and learn a fundamental molecular technique. Since the students will be working with the same virus, they will be a team each generating complementary data and will need to share their findings with each other on a regular basis. I plan to have regular lab meetings with the students to allow a frequent exchange of information.
I hope that after completion of this program that the students will have enjoyed their experiences and that they will be excited about pursuing a career in research in some aspect of biology or agriculture
Barbara Smith
PhD Student – Rehabilitation Science
Project Area: Lower extremity strength training in recipients of lung transplantation
The goal of my doctoral research is to examine the role of strength training on muscle, from molecules to movement. I am especially interested in how illness or disease affect respiratory or limb muscle strength. During illness, skeletal muscles may undergo structural and functional adaptations due to disease, administration of powerful medications, or a decline in overall activity. Muscle degeneration can not only result in weakness, but may diminish ability to perform work or self-care activities. Students who are interested in a career in healthcare or the biomedical sciences would particularly benefit from a research experience with our lab.
Two current projects would provide an enriching and rewarding research experience. First, for my doctoral thesis work, I am studying the effects of lower extremity strength training in adults who are hospitalized for lung transplantation. After transplantation, breathing function improves, but transplant recipients continue to demonstrate a reduced exercise capacity. Prior research reports that lower extremity weakness is an important contributor to this post-transplant exercise limitation. My research looks at both laboratory and clinical measurements of strength, following 4 weeks of strength training. It is hoped that this study will help describe the strength deficits present in recipients of lung transplantation and define training protocols to improve the outcome of care.
In an additional project, I am measuring the function of the lungs and strength of the respiratory muscles in children with muscular dystrophy. This is one component of a large, multi-center study. We track this data over time, to determine how respiration changes with growth and disease progression. It is hoped that this project will help researchers understand relationships between changes in disease activity and strength, as they explore future treatments for muscular dystrophy.
Students who join the research team will gain experience in scientific inquiry, including research design, data collection and analysis. In addition, we will aim to enhance scientific writing and presentation skills at both informal and professional settings. Clinical and laboratory safety will be emphasized at all times, and students collaborate with our research team throughout the process. Although undergraduate researchers cannot provide direct treatments to our research subjects, they would develop mastery of the testing equipment and analysis software. Students will receive support and guidance as they build a related research question of their own, gaining valuable critical thinking skills. I hope this affiliation will provide practical research applications for students and establish a foundation for future graduate work.
Danielle Watts
PhD Student - SNRE, Wetland Ecology
Project Area: Nutrient and Carbon Dynamics in the Central Everglades
I am interested in discovering how the ridge and slough mosaic in the central Everglades formed and is maintained. This involves multiple scales, from spatial distribution of nutrients in individual ecosystem patches, to whole-ecosystem carbon exchange, to landscape-scale variations in plant communities as they relate to water depth. These studies have two objectives: first, to contribute to theoretical ecology via an application of alternative stable state theory to the ridge and slough portion of the Everglades; and second, to provide diagnostic methodology to contribute to restoration goals in the central Everglades. My research has both a field and laboratory component.
Since my research program encompasses several broad topics, there are a number of opportunities for smaller-scale, related research projects. Potential student projects include a study of nitrogen on tree islands, soil and plant nutrients in marsh communities, vegetation community analyses, carbon sources and fluxes in wetlands, among many other possibilities. I foresee the students spending approximately 25% of their summer research time in the field. Understanding wetland ecology requires spending time in a wetland, and there is no experience like spending time in the Everglades for a student to appreciate the importance of these ecosystems.
Students would be expected to work in the field as a team, providing valuable experience not only for sample collection, but also for designing and preparing field research trips, a key skill to have for ecological studies. Field training will include airboat safety and use, plant identification, sample collection, as well as collection design. More individually, students will also learn many laboratory protocols, including sample preparation, soil, plant, and water nutrient analyses, as well as training on gas chromatograph analyzers.
Frank Wessels
PhD Student - Entomology and Nematology
Project Area: Plasticity and Energetics of Insect Reproduction and Diapause
My research investigates the diversification of life history strategies in insects from a mechanistic point of view. Characterizing the plasticity of life history traits in response to environmental hardships is fundamental to understanding the evolution of life history traits. Insects are ideal models for studying life history plasticity because they display a wide variety of developmental, reproductive, and overwintering strategies. My research focuses on the energetics of reproduction and diapause in the flesh fly, Sarcophaga crassipalpis. I have two areas of ongoing research with the flesh fly. First, I am looking at the contribution stored resources and available income nutrients to reproduction and how allocation patterns vary with environmental stress. Secondly, I am characterizing nutrient metabolism and periodical arousal during pupal diapause. Documenting the underlying physiological and biochemical machinery that controls the phenotypic plasticity of resource allocation in flesh flies can help us understand the diversification of life history strategies in insects and other animals.
I will involve my students in this area of research by developing individual projects within my graduate research. This will allow them to be involved in every aspect of the research process. My students will be supervised and guided in experimental design, experimental assays, data collection and data analysis. In addition to the high level of involvement with their individual experiments, the students will be instructed in safety procedures and laboratory etiquette. Our lab has a solid history of building long-term productive relationships with undergraduate researchers. We operate under the philosophy of providing valuable real world experience in return for hard work and commitment. My students will become full interactive members of our research group and will play a critical role in our laboratory.
Jada-Simone S. White
Ph.D. Candidate – Department of Zoology
Project Area: Community effects of habitat modification by farmerfish
Website: http://www.flmnh.ufl.edu/malacology/white.htm
Email: jswhite@zoology.ufl.edu
In my study system, an abundant algal-farming fish, the dusky farmerfish Stegastes nigricans, modifies the coral reef community by farming algal turf and exerting resource control through territorial defense. These behaviors indirectly affect other species by changing their interactions with two guilds of community members: 1) increased interactions with farmed algal turf; and 2) decreased interactions with mobile grazers and predators due to reduced reef access. I seek to understand the relative impact of these processes on the community structure. My research explores how this habitat modifying speciesaffects the strength of a given interaction (e.g., competition, predation, or facilitation) between other community members by combining demographic monitoring, experimental manipulations, and population modeling. Ultimately, I wish to test the extent to which differences in these relationships account for the observed variation in the abundance or distribution of organisms.
Students who join my research team will be involved in all aspects of the scientific endeavor – from idea formation and sampling design, to project funding, data collection and organization, statistical analyses and, finally, dissemination. Because this project has a large remote field component, students will be responsible for collecting digital data, i.e., from field photographs, and / or processing taxonomic specimens of algae, corals, and invertebrates in conjunction with the Florida Museum of Natural History. Undergraduate students will be encouraged to undertake a component of the research as a senior honors thesis. Available projects include quantifying differences in population parameters (e.g., growth, survival, etc.) in the presence, removal, and absence of this common farmerfish for one of a variety of guilds of community members, e.g., algae, corals, urchins, fishes, vermetid snails, or micro-invertebrates. These projects will generate novel findings which we will develop into a manuscript and submit to a reputable journal. Throughout the process, we will train our high school student by actively involving them in all aspects of research.
