Spring BIO 199 Research

The spring one-credit hour course, BIO 199, will give you early exposure to research.  Students will learn from authentic research in this first year course.  Students will meet in a laboratory which is mentored by one or several faculty members.  Students will have the opportunity to present their work at the UK Showcase of Undergraduate Scholars. All STEMCats students will be required to do research projects. 

Research Projects for Spring 2020  [Project descriptions are below the table]









Joao Costa


4-7 pm

400 WP Garrigus

Animal behavior and precision technologies: animal research in the XXI century


Mark Prendergast


1-3 pm


Neuroscience majors only: Neuroplasticity in Alcohol Dependence


David Atwood


3-5 pm

JSB 304

Honey Bees and Pesticides


Vincent Cassone



THM 302

The Effect of Melatonin Supplements on Blood Melatonin Levels


(Stephen) Randal Voss


5-7 pm


Analysis of Gene Expression During Salamander Tail Regeneration


Nicholas McLetchie


2-4:50 pm

MDR3, Room 202

The Acclimating Leaf


Peter Mirabito


10 am-12:50pm

JSB 304

Studying Genes and Drugs that Caused Defects During Embryonic Development


Yang Jiang


3-4:50 pm

132 Medical Behavioral Science Building

Research experience in human behavioral neuroscience


Stephen Testa


1-2:50 pm 

Chem-Phys 236

Improving the "Strawberry DNA" Experiment


Melody Danley


9-11:50 am

JSB 104

Crayfish social behavior and aggression


Douglas Harrison & Bruce O'Hara


4- 4:50 pm

JSB 158

Genetic Regulation of Sleep


Edmund Rucker



THM 313

Effect of Autophagy on the Growth of Tumors in a 3D Environment


Kaylynne Glover


11-11:50 am


Do Men Repond to Female Fertility?


Vincent Cassone &  Clif Harpole


1-4 pm

JSB 304

How to Speak Sparrow


Emily Croteau


9 am-12 pm

JSB 304

Biological Monitoring using Environmental DNA 


Cagney Coomer



JSB 158

Genetic Mutant Analysis in Zebrafish 


Stephen Ferguson


10 am-12 pm

JSB 304

Kegs and Eggs: An Avian Model of Prenatal Alcohol Exposure


Drs. Aardra and Pradeep Kachroo



3:30-6:30 pm

Plant Science Bldg room 309


Molecular and genetic analysis of plant defense signaling pathways



Dr. Subba Reddy Palli




S224 Ag Science North


Want to be a Bug Doctor?



Dr. Levi Gray





Lizard Signals and Parasites


94 Katie Everson TBD TBD THM 205 Museum Underground: Using specimen collections to study life on Earth


Lab Course Descriptions

BIO 199-073        Dr. Joao Costa, Animal behavior and precision technologies: animal research in the XXI century; Ever wonder how we will feed 9 billion people in the future? Technology... Also, ever wonder how dairy cattle spend their time? Is she spending most of her day walking around or eating? Why is she lying down for so long? Producers utilize precision technologies to determine the behavioral activities of their animals. They use this information to answer many questions regarding the animals’ health and productivity. Perhaps they are notified via the activity monitoring software that one cow has spent a significant amount of time that day lying down and being unusually inactive. The producer may investigate this alert further by looking in on the cow in person and finding that she has become ill. Precision technologies allow producers to monitor the behavioral activity and health status of cattle. The information gathered can be used by producers and researchers alike to make inferences on what underlying factors may be causing the behaviors in question. Students in this course will learn to design an experiment to test a specific hypothesis about dairy cattle behavior utilizing precision technology tools. Students will understand how precision technology is used to monitor the behavioral activity of dairy cattle and use the data collected to test their hypothesis. Overall, students will learn how to conduct a scientific experiment following protocols necessary for working with vertebrate animals, and ultimately understand the importance of ethical research conduct.

BIO 199-074        Dr. Mark Prendergast, Neuroplasticity in Alcohol Dependence; Development of alcohol dependence requires neuroplasticity of hippocampus glutamate systems. Students working on this project will employ a neuronal cell culture model to examine neuroplasticity in the hippocampus caused by binge-like exposure to alcohol. Students will be trained to perform sterile rodent brain surgery; fluorescent microscopy and histology to assess the extent of neuroplasticity resulting from alcohol exposure. This section is reserved for Neuroscience majors in the STEMCats program.

BIO 199-075        Dr. David Atwood, Honey Bees and Pesticides; Bees produce three biological products, honey, beeswax, and propolis that have nutritional and cosmetic value to humans. As pollinators, honey bees are the foundation of global agriculture. Pesticides, herbicides, and fungicides are commonly used in agricultural production. These products kill bacteria, fungi, and unwanted pests, but can have harmful biological effects. Bees can internalize pesticides during pollen and nectar collection and transfer pesticide-related chemicals into honey, beeswax, and propolis in the hive. Bees. The confluence of bees, honey, and pesticides has significant detrimental outcomes, from Colony Collapse Disorder (CCD) to human pesticide consumption. Despite the immediacy and importance of the bee-honey-pesticide relationship there has been a surprisingly modest scientific and public response. This transdisciplinary research project will develop methods for detecting pesticides in commercially available honey. With new knowledge of pesticide levels in honey, students in this course will develop a plan for continuing research and public education on the problem of pesticides in honey.

BIO 199-076        Dr. Vincent Cassone, The Effect of Melatonin Supplements on Blood Melatonin Levels; Melatonin is a hormone that is produced by the pineal gland during the night. It has been shown to decrease sleep latency (the time it takes to fall asleep) and decrease sleep fragmentation (stops waking up at night). It has also been used to help with jetlag and to synchronize sleep patterns in blind patients. However, as a dietary supplement, albeit a very safe dietary supplement, it is not regulated by the FDA, and very little is known about the pharmacokinetics of the widely varying dosages available in supermarkets and health food stores. This project will test the effects of 4 oral dosages of melatonin (0 mg (control), 300 mg (.3 mg), 1 mg, and 5 mg) manufactured by Sundown Naturals, on the salivary concentrations of melatonin, on the self-reported level of sleepiness, and on a psychomotor test to determine reaction times. The subjects will be students in a Bio 199 course. Students will spit into a labelled collection tube at 8 pm on a weekend and then take 1 of the 4 dosages at 9 pm and spit into labelled collection tubes every hour for the next 4 hrs (9 pm, 10 pm, 11pm, 12 am and 1 am). Then, subjects will spit into a collection tube every 2 hrs for the next 6 hrs (3 am, 5 am, 7 am, 9 am, 11 am and 12 pm). Samples will be placed immediately in the freezer for later assay.At each time, students will do a short psychomotor vigilance task available for their iPads (http://www.sleepdisordersflorida.com/pvt1.html) and take a short survey to assess students sleepiness. This survey, the Epworth Sleepiness Scale, is a very simple and recognized method for quickly assessing sleepiness. Students will then learn how to conduct a biochemical assay for melatonin, using an enzyme-linked immunosorbent assay (ELISA) for salivary melatonin (IBL International). Data will be collected and analyzed. The results will be reported at the Showcase for Undergraduate Scholars.

BIO 199-077        (Stephen) Randal Voss, Analysis of Gene Expression During Salamander Tail Regeneration; Salamanders are remarkable in their ability to regenerate damaged or missing body parts, including limbs and tail. Students will perform tail amputation surgeries on axolotl embryos and then rear these in the presence or absence of a chemical that is known to inhibit the function of a specific molecular signaling pathway. After the class establishes that the chemical alters tail regeneration, the tail amputation experiment will be repeated and regenerating tissue collected for RNA isolation and gene expression analysis. The data from the gene expression analysis will be used to identify when and where the targeted molecular signaling pathway functions during regeneration, and to identify down-stream gene expression targets. Overall, the exercise will introduce students to experimental approaches and data analysis techniques that are currently being used to resolve the molecular basis of tissue regeneration.

BIO 199-079        Dr. Nicholas McLetchie, The Acclimating Leaf; The leaf is the primary organ contributing to global terrestrial productivity, removal of carbon dioxide from the air, and production of the oxygen we breath.  The overall goal of this project is to examine how leaves can alter their physical and chemical characteristics (shape, thickness, cell structure, pigments, etc.) across variation in external stimuli (light, relative humidity, temperatures, air movement) occurring at the scale of the leaf.  Changes in leaf characteristics affect the level of photosynthesis at the leaf level and eventually scale up to the whole plant and ecosystem levels.  This years project will investigate changes in color that occur among and within leaves of the same plant.  Students will focus on a particular stimulus that might affect leaf color, design the experimental setup to manipulate the stimulus at the level of the leaf, and test a leaf’s relevant responses to this stimulus.

BIO 199-080        Dr. Peter Mirabito, Studying Genes and Drugs that Caused Defects During Embryonic Development

BIO 199-081        Dr. Yang Jiang, Research experience in human behavioral neuroscience; The project is designed for students who are interested in research on neural basis of human behavior.  Students will learn behavioral neuroscience approaches through hands-on laboratory experience (e.g. recording brain activity using wireless EEG headsets). Students will be involved in investigation of neuromarkers underlying alterations of human cognition, affect, or motivation.

BIO 199-082        Dr. Stephen Testa, Improving the "Strawberry DNA" Experiment; Oftentimes, the first hands-on experience children have with DNA is when they isolate DNA from strawberries. This ‘Strawberry DNA’ experiment is simple enough that it can be performed in an elementary school classroom, or even at home, using common household chemicals. At this educational level, DNA is usually framed in a purely biological context, and the experimental method is thought of as an inflexible, almost magical recipe. This approach downplays the importance of DNA as a useful chemical entity which can be subjected to experimental analyses after it has been isolated. In this 1 credit research course, students will attempt to redress these limitations by developing new and improved methods for the classic ‘Strawberry DNA’ experiment. The focus this year will be on developing age-appropriate methods for the visualization of isolated strawberry DNA, for example via fluorescence.

BIO 199-083        Dr. Melody Danley, Crayfish social behavior and aggression; Fight to the death?  Eat your own siblings?  Live in a dark muddy cave for 3 months out of the year? Come investigate the fascinating world of crayfish behavior and physiology!  Design your own project and conduct original research using crayfish, their interactions with each other, and their interactions with their environment as the basis of your project. 

BIO 199-084        Drs. Douglas Harrison & Bruce O'Hara, Genetic Regulation of Sleep; Sleep is a critical biological process that occurs in almost all animals, yet there are still many questions about why we sleep and how sleep is controlled.  In this project, we will use the fruit fly, Drosophila melanogaster, to investigate the role of specific candidate genes in sleep.  Genetic tools will be used to manipulate gene activities and effects on sleep will be observed and analyzed using an automated monitoring system.  We expect to identify specific genes that are needed for proper control of sleep and that these genes are likely to have similar roles in sleep in other animals. Additional required hours will be TBD, based on student schedule(s).

BIO 199-085        Dr. Edmund Rucker, Effect of Autophagy on the Growth of Tumors in a 3D Environment; Description: Tumor size progression is dependent upon vascularization in order to provide cancer cells needed nutrients to sustain their high metabolize. Prior to this recruitment of new blood vessels, the tumor can undergo nutrient stress and become dependent on the process of autophagy to recycle long-lived proteins and damaged organelles to maintain energy homeostasis. We have previously demonstrated in cell culture experiments that cancer cells (e.g. breast and cervical cancer cells) can be induced to undergo cell death when exposed to chemotherapeutic drugs and autophagy inhibitors. As an extension, the next phase is to interrogate the effects of this induced cell death on the growth potential of cancer cells in a 3D environment. The effects of two chemotherapeutic drugs, cycloheximide and camptothecin, will be tested for their efficacy at inducing cell death in three cell lines in a soft agar assay to examine 3D growth: 1) MDA-MB-231, a triple negative breast cancer cell line, 2) HeLa, a cervical cancer cell line, and 3) L929, a mouse fibroblast cell line. Additionally, the effect of autophagy induction or suppression on the efficacy of the chemotherapeutic drugs will be tested on all three cell lines.  Meeting times will be flexible (around students' class schedules).

BIO 199-086        Kaylynne Glover, Do Men Respond to Female Fertility?; How much does biology contribute to reproductive behavior in humans? This question is hard to answer, but in this class, we're going to do our best. After learning some background information, you'll help analyze data taken from survey responses and biological samples. 

BIO 199-087        Dr. Vincent Cassone & Clif Harpole, How to Speak Sparrow; Due to the earth's tilt on its axis, seasons exist. Animals have adapted to this through evolution and concentrate their breeding behavior to certain times of year, so that their young are reared at a time when resources are abundant and the climate is mild. Our lab has identified a part of the brain, the pineal gland, that helps convey seasonal information to the birds, specifically related to their vocalizations. This laboratory will record house sparrow vocalizations in different conditions, and learn to analyze the "meanings" behind the various types produced, learning about neuroscience and animal behavior.

BIO 199-088        Dr. Emily Croteau, Biological Monitoring using Environmental DNA; Environmental DNA (eDNA) is organismal DNA isolated from environmental samples such as, water or soil.  Aquatic environments can suspend sloughed organismal tissue providing a source of organismal DNA.  Typically, eDNA methodologies focus on monitoring amphibians or fish, but in this study we will isolate eDNA from ponds to ascertain if mammal DNA can be detected.

BIO 199-089        Cagney Coomer, Genetic Mutant Analysis in Zebrafish;  Students will track the effects of Thyroid hormone on sox10 expressing neural crest cells in the her9 mutant using dissecting, light and confocal microscopy. Students will develop an understanding of the effects of thyroid hormone during vertebrate development and the role of Her9 in neural crest cells.

BIO 199-090        Dr. Stephen Ferguson, Kegs and Eggs: An Avian Model of Prenatal Alcohol Exposure; Prenatal alcohol exposure has notable effects on the facial and neural structure of developing young. High doses of alcohol may result in fetal alcohol spectrum disorders (FASD), which can cause learning disabilities and behavioral problems. FASD are prevalent and costly in humans, and are studied using a variety of model species including rats, mice, frogs, and even C. elegans. Though animal models are an important tool in studying the consequences of many diseases they differ anatomically and behaviorally from humans, making direct comparisons sometimes difficult. Students will learn the basics of experimental design and analysis to investigate behavioral data from a model of FASD using the zebra finch, a common laboratory bird. A number of tests will be performed to investigate activity patterns, fearfulness, and learning and memory to draw clinical parallels with human FASD.

BIO 199-091        Dr. Aardra Kachroo and Dr. Pradeep Kachroo , Molecular and genetic analysis of plant defense signaling pathways; Students will learn to extract plant DNA and RNA, conduct PCR analysis and pathogenicity tests on wild type and mutant lines and learn to relate plant genotype with disease phenotype. Students will also have the opportunity to observe how analytical methods such as liquid/gas chromatography are used to detect plant metabolites that are important for plant defense to microbes.

BIO 199-092        Dr. Subba Reddy Palli, Want to be a Bug Doctor?; You will be working as a member of a team conducting tick surveillance, speciation, and pathogen diagnosis in  Kentucky. Ticks are primary vectors for many human diseases, including Lyme disease, Rocky Mountain Spotted Fever, Anaplasmosis, Tularemia, and Powassan encephalitis virus. Lyme disease is the most commonly reported tick-borne disease in the US. The research involves dragging for ticks in the forest, identifying species, isolation of genomic DNA, and conducting PCR to identify pathogens they carry.  Field trips will be times depending on weather conditions and availability of team members.  Some travel is required to conduct tick drags.

BIO 199-093               Dr. Levi Gray, Lizard Signals and Parasites; Anoles are a diverse group of lizards that use a cool trait to communicate with each other: the dewlap, a flag-like structure that can be extended below their chin for display or folded back and hidden when not in use. Dewlaps tend to be colorful and effective for signaling to other lizards and competitors, but there are also some costs that go along with having them. Maintaining a “pocket” for folded up dewlaps creates space for ectoparasites to exploit. In this course, we will investigate patterns of ectoparasite abundance in a dataset for over 40 species of anoles. Meeting times will be flexible based on student schedules. Logistics permitting, we are planning an optional trip to Miami over Spring Break to get hands-on experience generating a new dataset on the native and non-native anole species in Florida. Participation in the Spring Break trip will require additional funds, but we are aiming to keep costs at $400-500 per person.

BIO 199-094               Katie Everson, Museum Underground: Using specimen collections to study life on Earth; Most natural history museums have one area for the public and a second area that is off-limits except to professional researchers. These underground collections can house hundreds, thousands, or even millions of real specimens. Students will learn about the various ways that scientists use natural history collections to understand life on Earth, including discovering new species, tracking parasites, or studying anatomy and physiology. The students will then have the opportunity to develop an independent research project using a collection of small mammal specimens here at UK. Students can choose to focus their research on genetics, anatomy, parasitology, or conservation biology. Class times will be set based on student schedules.

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