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 2019  [Project descriptions are below the table]

BIO 199-







Dr. Randal Voss




Salamander Tail Regeneration


Dr. Joao Costa and Melissa Cornett



W.P. Garrigus 4th Floor Conference Room

Precision Dairy Farming: the Relationship Between Animal Behavior and Digital Image Processing


Dr. Vincent Cassone and Dr. Jiffin Paulose


2:00 pm-4:50pm

THM 302

What makes a clock tick? Characterizing a bacterial clock through random mutagenesis


Dr. Vincent Cassone and Clifford Harpole



JSB 304

How to Speak Sparrow


Dr. Aardra Kachroo and Dr. Pradeep Kachroo



Plant Science Bldg room 309

Molecular and genetic analysis of plant defense signaling pathways


Kaylynne Glover



JSB 304

Female Fertility and Perception Ability


Kaylynne Glover



The90 room 219

Do Men Respond to Female Fertility?


Dr. Mark Prendergast




Neuroplasticity in Alcohol Dependence


Dr. Ann Morris and  Cagney Coomer



JSB 158

Genetic Mutant analysis in Zebrafish


Dr. Elizabeth Debski



MDR#3 201

Exploring the Axolotl Nervous System


Drs. Peter Mirabito



JSB 304

Studying genes and drugs that caused defects during embryonic development. 


Dr. Catherine Linnen



JSB 304

Genetic basis of adaptation in plant-feeding insects


Dr. Yang Jiang



Medical Behavioral Science Bldg #116, Aging Brain and Cognition Lab

Human Behavioral Science


Dr. Stephen Testa



Chem-Phys 236

Improving the 'Strawberry DNA' Experiment


Dr. Rebecca Kellum



THM 300E

Green Fluorescent Proteins in Studies of Sex lethal gene regulation


Dr. Rebecca Kellum



THM 300E

Green Fluorescent Proteins in Studies of Sex lethal gene regulation


Dr. David Weisrock and Mariah Donohue


3:00pm-5:00pm THM 204

Feces fun: Exploring evolutionary and ecological dynamics driving variation in gut microbiome composition and diversity of wild lemurs


Drs. Douglas Harrison and Bruce O'Hara



JSB 158

Gene Regulation of Sleep


Dr. David Atwood



Chem-Phys 245

The Dangerous Confluence of Honey Bees, Pesticides, and Honey


Dr. Edmund Rucker



THM 313


Effect of autophagy on the growth of tumors in a 3D environment


Dr. Emily Croteau



JSB 304

Genetic Diversity in Jefferson salamanders


Dr. Julie Pendergast

WED 1:00pm- 2:50pm THM 316

Circadian Rhythms in College Students


Lab Course Descriptions


BIO 199-069        Dr. Randal Voss, Salamander Tail Regeneration: Students will investigate salamander tail regeneration using an axolotl embryo model and chemicals that modify molecular mechanisms.

BIO 199-070        Dr. Joao Costa and Melissa Cornett, Precision Dairy Farming: the Relationship Between Animal Behavior and Digital Image Processing: With changes in dairy farm management systems shifting towards an individual-based and data-driven approach, there are more opportunities for farmers to make decisions using on-farm diagnosis. The use of digital image processing is an underused tool in the dairy industry. The objective of this study was to develop and validate an automated recordings system of grooming brush use in dairy calves utilizing digital image processing technology.

BIO 199-071        Dr. Vincent Cassone and Dr. Jiffin Paulose, What makes a clock tick? Characterizing a bacterial clock through random mutagenesis: The human gut is home to tens of trillions of microorganisms, including bacteria, fungi, and viruses.  Recently, the Cassone lab discovered that one bacterium in the human gut, Enterobacter aerogenes, possesses a self-sustaining circadian rhythm (or a "clock") that responds to the hormone melatonin.  This is only the second bacterium shown to have a circadian rhythm, and the genetic basis for this rhythm is still unknown.  Our project this semester will be to apply "Wreck and Check" genetic screening: we will randomly mutate bacteria that have been engineered to light up when a clock-controlled gene is activated.  If the "clock" stops in any of the mutants, we can get the sequence of the mutated gene and, hopefully, begin to construct the gene network that keeps our novel clock ticking.  In addition to being part of our gut microbiome, E. aerogenes is a well-known source of hospital-borne infections, so our project has fundamental, clinical, and epidemiological importance.

BIO 199-072       Dr. Vincent Cassone and Clifford 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 199-073        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 199-074        Kaylynne Glover, Female Fertility and Perception Ability: Just how well can a woman tell when she's fertile? Is there anything that changes in her behavior when she's fertile? This class will seek to answer these questions by collecting and analyzing data taken from women who answered surveys and provided biological samples. 

BIO 199-075        Kaylynne Glover, Do Men Respond to Female Fertility?: How much does biology contribute to behavior? Does a woman's behavior change when she's fertile - and does a man's change in response to a woman's fertility? We'll try to answer these questions by analyzing the data taken from survey responses and hands-on experiments. 

BIO 199-076        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 only*

BIO 199-077        Dr. Ann Morris and  Cagney Coomer, Genetic Mutant analysis in Zebrafish: Students will use a combination of dissecting, light, and confocal microscopy to characterize the mutant phenotype of the Her9 1bp deletion mutant. The Her9 mutant was generated using CRISPR/Cas9 technology, students will develop an understanding about CRISPR/Cas9 works and the role of Her9 during vertebrate development.  Will be scheduled around students' availability. 

BIO 199-078        Dr. Elizabeth Debski, Exploring the Axolotl Nervous System: The axolotl salamander has extensive regenerative capabilities that are not found in mammalian systems.   Students will learn and use histological and immunocytochemical techniques to explore the nervous system organization of this animal at the cellular level.  Our goal will be identify cell types and/or particular molecules that might be involved in directing repair of axolotl central nervous system tissue.  

BIO 199-079        Drs. Peter Mirabito & Ann Morris, Studying genes and drugs that caused defects during embryonic development: Animal development is among the coolest things to study in all of biology.  Students in this course will use zebrafish as an experimental system to design and conduct experiments testing the effects of genetic mutations and selected drugs on the early stages of embryonic development.  No prior lab skills are needed to be part of this study: the only requirement is a love of science and a curious mind.

BIO 199-080        Dr. Catherine Linnen , Genetic basis of adaptation in plant-feeding insects: Over 25% of all described species on the planet are plant-feeding insects. Why are these organisms so unusually diverse? And how do they adapt to so many different environments? In this course, we will attempt to answer these questions using a species of insect that feeds on pine trees. This species can be found throughout eastern North America, but individuals collected from different locations differ in many different characteristics. Students will develop their own hypotheses about how and why individuals sampled from different locations vary.  To test these hypotheses, students will then use a combination of genome annotation, PCR, and gene sequencing to characterize genetic differences between sampling locations. If successful, these projects have the potential to shed light on the genetic underpinnings of adaptation.

BIO 199-081        Dr. Yang Jiang, Human Behavioral Science: This project is designed for students who are interested in research on brain and human behavior.  Students will learn behavioral neuroscience approaches through hands-on laboratory experience (e.g. recording brain activity using wireless EEG headsets; Using neurofeedback to improve performance during a cognitive task). Students will be involved in investigation of neural mechanisms underlying alterations of human performance in cognition and emotion.

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 chemical, and of the use of common chemical separation procedures, for example solubility and filtration, in DNA isolation. Finally, and perhaps most restraining, is the general lack of experimental options for what can be done with DNA once isolated. In this 1 credit research course, students will attempt to redress these limitations by developing new and improved methods for the classical ‘Strawberry DNA’ experiment.  

BIO 199-083 and -084     Dr. Rebecca Kellum, Green Fluorescent Proteins in Studies of Sex lethal gene regulation: Students will study Sex lethal gene regulation in Drosophila.  This gene is needed for proper sexual differentiation and viability in the fruit fly.  We will use classical genetics in combination with a Drosophila stock carrying a transgene for the Sex lethal gene promoter fused to the Green Fluorescent Protein to examine the roles of other genes in regulating the activity of this promoter.

BIO 199-085        Dr. David Weisrock and Mariah Donohue, Feces fun: Exploring evolutionary and ecological dynamics driving variation in gut microbiome composition and diversity of wild lemurs: This research aims to understand prokaryotic diversity in the gastrointestinal tract of wild lemurs. Fecal samples were collected from 5 lemur genera (9 species) across diverse habitats (dry forest, rainforest, unprotected forest fragment, protected continuous forest). Students will gain experience extracting DNA from feces, amplifying variable regions of the 16S gene, and analyzing data to evaluate hypotheses about the relative contributions of ecology and evolution in microbiome patterning.”

BIO 199-086        Drs. Douglas Harrison and Bruce O'Hara, Gene 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.

BIO 199-087        Dr. David Atwood, The Dangerous Confluence of Honey Bees, Pesticides, and Honey: 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 199-088        Dr. Edmund Rucker, Effect of autophagy on the growth of tumors in a 3D environment: 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.

BIO 199-089        Dr. Emily Croteau, Genetic Diversity in Jefferson salamander: This research aims to identify the influence of genetic diversity on survival and body size in Jefferson salamanders, a species that exhibits considerable size variation.  Students will gain experience in DNA extraction, PCR and primer optimization, and genetic analyses to examine the parental contributions of genetic variation on body size variation and rates of survival.

BIO 199-090        Dr. Julie Pendergast, Circadian Rhythms in College Students: Have you ever wondered why you are so sleepy for your 8am class? Or why you are starving at noon? Your daily, or circadian, rhythms are controlled by a network of clocks in your body. In this course, we will explore non-invasive methods for measuring human circadian rhythms of physiology and behavior. We will develop research questions to elucidate factors that impact circadian rhythms in college students. We will then perform the experiments and analyze the rhythmic data.

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