Slideshows:Research Opportunities in Biosciences for 2013 (PDF)
Research Groups:Ayoub Lab: Molecular genetics of spider silk synthesis
Ayoub Research Lab
Research in the Ayoub lab will focus on two related projects during the summer of 2012. The first will involve describing (e.g. sequencing and annotating) genes involved in silk synthesis three species of cob-web weaving spiders, the black widow, Latrodectus hesperus, the brown widow, L. geometricus, and the false black widow, Steatoda grossa. We will also determine expression levels of the genes described using high throughput sequencing data and computational methods.
Recommended courses: BIOL220 and BIOL221 (Genetics and Genetics Lab). Suggested courses: Any computer science or computational biology course.
Number of students: 2-3. One student will work collaboratively with an experienced student in the wet lab. One or two students are needed for computational analysis of high-throughput sequencing data. Performing a combination of wet lab and computational analyses is also an option.
Blythe Research Lab
This summer my research team will explore the relationship between obesity and ADHD. Students will gain experience in animal care and handling, behavioral testing, blood sampling, histology, and conducting a variety of bioassays.
One or two student student positions available.
Cabe Research Lab
My research projects all fall under the heading of molecular ecology: we use modern DNA-based techniques to answer questions about wild populations of animals and plants. This summer, I am going to explore a new research question: Can DNA sequencing provide an attractive way to identify species of crayfish? Crayfish are notoriously difficult to identify with traditional morphological approaches (which are nearly useless for females and juveniles), and as a result, the distribution of species and the composition of aquatic communities are relatively poorly known. This is unfortunate, since crayfish diversity is high in eastern North America, and species and aquatic communities are threatened by invasive introduced crayfish species. I intend to see if standard or modified "DNA Barcoding" approaches can provide species discrimination. Barcoding is well established, and uses sequence from the COX1 mtDNA gene as an aid in species identification. As part of this, we will also be working to complete an entire mtDNA sequence from a local species. Students working on this project will get experience with basic DNA techniques including DNA extraction, gel electrophoresis, PCR, and DNA sequencing, as well as learning tools to work with and analyze DNA sequence data. Most of the time will be spent in the lab, though some field work may be included.
One to two student positions available.
Greer Research Lab
Greer's research focuses on characterization of ecosystem dynamics and reef health of a coral reef system dominated by an endangered coral species in Belize. Projects will include quantification of photographic data, urchin and fish surveys, and characterization of genetic and symbiotic algal variability across the reef system. One to two student positions available.
Hamilton Research Lab
The first project focuses on vegetation restoration and management in Yellowstone National Park while the second is local and focuses on sources of bacterial contamination and Nitrogen loading in our local watershed. While these two systems may appear to be quite different they both share a centralized theme of addressing a hypothesis at several levels of analysis (molecular to evolutionary) and/or multiple levels of biological organization (molecules to ecosystems). In these projects I utilize a variety of techniques ranging from molecular and biochemical assays to physiological and observational measures in the field.
Two student positions available.
Humston Research Lab
Robert's research focuses on understanding the ecology of fishes to better manage fisheries. His main interest is in fish movement and the spatial dynamics of populations. Right now he is using multiple methods, including chemical ‘tags' and population genetics, to examine how dispersal and migration shape spatial dynamics in river-tributary networks.
One student position available.
Hurd Research Lab
We will work on stable isotope analysis of the trophic structure of arthropod communities this coming summer. This work employs a novel approach to analyzing the predator/prey relationships among arthropod species in diverse communities such as old fields and forests where the top predators are praying mantids and spiders.
One student position available.
Johnson Research Lab
Dr. Johnson's research focuses on investigating the underlying cognitive mechanisms of narrative fiction's impact on prejudice and empathy. Students will learn specialized software for creating computerized cognitive tasks in addition to advanced statistics including math modeling and programming in SAS, SPSS and HTML.
One student is needed for Fall 2013
LaRiviere Research Lab
Research in the LaRiviere lab is aimed at understanding novel or fundamental aspects of ribosome metabolism in eukaryotes. Currently, the major focus of the lab is to uncover the mechanistic details of non-functional ribosomal RNA decay (NRD), a newly discovered ribosome quality control pathway in yeast. NRD effectively removes translationally defective ribosomes from the cell by specific degradation of mature, yet, non-functional rRNAs. One of the most important issues concerning the mechanism of NRD regards the trans-acting factors involved in this process. In other words, what factors are responsible for recognizing defective ribosomes and what factors are responsible for the actual degradation of the defective rRNA? To this end, we are developing a synthetic lethal screen in Saccharomyces cerevisiae to identify factors involved in NRD. We are also using DNA microarrays to determine which genes are up-regulated in response to NRD. Once NRD factors are identified, we will study their role(s) in NRD. Other ongoing projects are involved with determining the exact biological function of NRD and the conservation of NRD in other eukaryotes.
One to two student positions available.
Levy Research Lab
Prof. Levy has two kinds of projects: (1) developing iOS applications (iPhone, iPad, iPod touch) in collaboration with W&L researchers and other end-users; (2) developing software for controlling small unmanned aerial vehicles (UAV). For the iOS apps projects, students should have taken CSCI 251 (iPhone Application Programming) or otherwise have experience using Xcode and Objective-C for the iOS platform. For the UAV projects, experience programming in Python is essential.
Four student positions available.
Toporikova Research Lab
Two projects available:
1. Computational modeling of sighs: Most of the time when you wake up at night - you wake up with a sigh. When your emotions change - in pain or in love - you sigh. When you get hypoxic during sleep, sighs are initiated and are the first activities before you arouse. Sighs are large amplitude breaths that are also critical to prevent your alveoli from collapsing. If you don't sigh for a long time, you develop atelectasis. Hence it is important that we all sigh spontaneously. Sighs are typically triggered by a normal breath and followed by a brief period of post-sigh apnea. While sensory inputs from the lung can trigger sighs, the sighs are generated within the central nervous system. Sighs are centrally generated within the ventrolateral medulla in the area called the pre-Bötzinger complex. Isolated in a slice preparation the pre-Bötzinger complex continues to generate sighs. The goal of this project is to develop a computational model which would help to understand the cellular mechanisms that are responsible for the generation of the sigh on the level of the pre-Bötzinger complex.
2. Computational modeling of prolactin secretion during the pregnancy and early lactation: Breast milk provides the ideal nutrition for infants. It has the perfect mix of vitamins, protein, and fat -- everything a young infant needs to grow. However, between 5 and 10% of new mothers cannot take advantage of these health benefits because they cannot produce enough milk for their newborns. Lactation is regulated by the hormone prolactin, which is released in response to suckling, promoting the milk production. During the last part of pregnancy, prolactin level increases by 10 to 20 times. This dramatic increase in prolactin is required to prepare the body for lactation. The goal of this project is to develop a computational model for the prolactin release during the pregnancy and early lactation and use this model to determine the optimal conditions for successful lactation.
Three student positions available.
Uffelman Research Lab
• Projects in the investigation of cultural heritage objects (mostly paintings, some
• Projects at W&L and Winterthur
• Projects probably also involving Lunder Center, NCMA, and Frans Hals Museum
• Projects in inorganic and organic synthesis and spectroscopy.
Project duration 8-9 weeks.
Two to four students sought (although there may only be funding for two, so that might be the limit).
Watson Research Lab
Howe Hall room #413/ email@example.com
My lab is interested in studying the visual system of the frog to identify molecular signaling pathway differences in axon growth, protection, and optic nerve recovery following injury.
Three Main projects in the lab:
1. Using a line of transgenic frogs that express a green fluorescent protein (GFP) fused to a ribosomal protein (rpl10a) exclusively in eye retinal ganglion cells, students will use a translational profiling technique (TRAP) to compare nascent mRNAs extracted from adult frogs during various phases of recovery following optic nerve injury. We are currently collecting samples and will be sending them for RNA sequencing (RNAseq). By the summer, we will have the RNAseq data needed to begin examining the collections of genes that are upregulated and downregulated in response to optic nerve injury. Students working on this project are expected to manipulate large sets of data, help compile a list of genes and conduct literature searches to help determine candidate genes for validation.
2. Characterize the recovery of axons following optic nerve crush to examine differences between myelinated and non-myelinated axons. We are collecting samples from the eye, optic nerve, and tectum from transgenic and non-transgenic animals and will use a combination of immunostaining and in situ hybridization techniques to characterize the degeneration and subsequent reinnervation of the optic tectum. To determine the amount of cell death in the retina following optic nerve crush, we will flatmount the retina of eyes from transgenic frogs, treat flatmount sections with TUNEL and then count the number of GFP-positive RGCs and number of cells undergoing apoptosis. To assess and characterize what is occurring locally at the crush site, we will immunostain optic nerve sections with antibodies to different populations of retinal ganglion cells, antibodies to astrocytes as well as to microglia. Finally, in transgenic animals expressing GFP in the axons, we can use the fluorescence to quantify the amount of GFP in the tectum and use this as a measure of synaptic recovery in the tectum following deinnervation. Students working on this project will be expected to participate on all components of this project and help with the analysis.
3. Examine the effects of organopesticides on the development of embryonic frogs. We are currently treating embryonic frogs (tadpoles) with Chlorpyrifos and characterizing gross anatomical malformations, heart rate and startle behavior. Students working on this project are expected to image embryos and catalog any abnormalities. Students will also be expected to care for the tadpoles and monitor heart rates at specific times during the experimental period.
I plan on taking one or two students this summer.
Whiting Research Lab
The Cognition Lab focuses on the question of why attention and cognition changes as we age. Our current project examines the role of neural noise as an explanation of the general slowing of cognitive processes as adults age. The theory is that as we age neural circuitry in the brain begins to break down to some degree, and as a result, neural connections may be lost resulting in slower cognitive processing speeds. Recent work in our lab has focused on mechanisms allowing older adults to suppress neural noise. Using visual search paradigms, we have recently shown that older adults can enhance their search efficiency for targets by using top-down knowledge of a target's features to guide search to that target. Specifically, it seems that top-down processes may enable older adults to enhance target signal, while at the same time inhibiting distractor noise.
Two student positions available
Whitworth Research Lab
I am interested in understanding the ways in which gene expression in eukaryotes can be regulated post-transcriptionally to respond to changing cellular demands. There are many essential processing steps which eukaryotic mRNA must undergo to become competent for translation, each of which is carried out by complex molecular machines. In comparison to our understanding of transcriptional regulation, however, we know relatively little about how these complexes are modulated to affect the timing or diversity of gene expression. In our lab we use Bakers yeast (Saccharomyces cerevisiae) to study the mechanics of post-transcriptional regulation because, at the cellular and molecular level, these cells function very similarly to our own and offer us a host of powerful genetic, biochemical and cell biological tools. There are currently two projects in the lab. The first project is an ongoing collaboration investigating the regulation of pre-mRNA splicing in response to environmental stress. Student involvement in this project would be focused on using computational and statistical tools to explore a large-scale microarray-based data-set describing the regulation of pre-mRNA splicing in yeast in response to a broad range of environmental stresses. The second project in the lab is focused on understanding a provocative link between mRNA export from the nucleus and regulation of apoptosis, or programmed cell death. Student work on this project would primarily involve bench work, using genetics, biochemistry and cell biology to better understand how apoptotic regulation is modulated by the mRNA localization machinery.
Winder Research Lab
My broad interests are in the ecology, evolution, and conservation of rare plants of the Appalachians. My current work aims to characterize population-level genetic variation in three rare species of leatherflower (genus Clematis), and use this information to conserve the species and learn about their evolutionary history. I'm looking for two students interested in performing standard molecular techniques such as DNA extraction, PCR amplification, cloning, and sequencing, as well as data analysis. There would also be opportunities to perform a limited amount of fieldwork such as locating and mapping of plant populations, sampling of leaf tissue, and taking simple demographic measurements.
Two student positions available