Participating Faculty for Summer 2014
- Dr. Preston Aldrich, Associate Professor and Chair, Biological Sciences:
My research lab deals with systems biology, specifically with the analysis of complex biological networks. I have ongoing projects in the following areas:
Typically a student will work in two of these areas over the summer with a primary and a secondary project. Which projects are active depend on my interests and the interests and aptitude of the student. Students use a variety of software packages allowing the visualization and analysis of networks. Students also learn to write computer programs in Python allowing more refined analyses and modeling of networks. No prior programming experience is required.
- Invasive plants - analysis and modeling of invasive plant spread using networks
- Genomics - study of promoter, gene and protein networks in bacteria
- Curricular dynamics - the use of networks to understand and revise academic curricula
- Linguistics of natural languages – using networks to understand the structure and evolution of natural systems of communication.
View Dr. Aldrich's home page.
- Dr. Tim Comar, Associate Professor, Mathematics:
- Biological Models using Impulsive Differential Equations. The dynamics of models for integrated pest management and epidemics are investigated. Attention is paid to finding conditions for the existence and stability of total pest eradication solutions/disease free solutions and permanent solutions. Stochastic effects and delays may be incorporated into these models
- Dynamics of Gene Regulatory Networks: We primarily study small gene regulatory network via Boolean models. We are interested in how the dynamics is determined by the structure of the network. We are also interested in the relationship between the dynamics in Boolean models using synchronous versus asynchronous update. Finally, we would like to continue the study of the relationships between Boolean dynamics and continuous dynamics these networks.
View Dr. Comar's home page.
- Dr. Pedro Del Corral, Associate Professor and Academic Program Director, Clinical Exercise Physiology:
- Our group works on the effects of exercise on energy metabolism and endocrinology in humans. It is well known that intense or prolonged endurance exercise activates the hypothalamic-pituitary –adrenal axis, leading to increases in plasma and salivary cortisol levels. Cortisol is the chief glucocorticoid in humans, it has a plethora of effects on energy metabolism, the immune and cardiovascular system, and the skeleton. The Clinical Exercise Physiology Laboratory is currently examining the effects of intense exercise on cortisol and other glucocorticoids (cortisone, corticosterone) and binding proteins (CBG) in plasma and saliva, in both men and women. We are currently analyzing data from men, and during the Spring we will analyze data collected in females. We have hypothesize that the glucocorticoid hormonal response to exercise is different between women on vs women off oral estrogens (ie., contraceptives) The findings of the female study will shape the research direction we take during the Summer 14’ and Fall 14’.
View Dr. Corral's home page.
- Dr. Anthony DeLegge, Assistant Professor, Mathematics and Computational Sciences:
- The Epidemic Spread of Facebook
Abstract: Since Facebook was launched in 2004, millions of people have joined the social networking site to interact with friends, share photos, and/or play interactive games. However, in recent years, due to constantly changing privacy settings and the novelty wearing off, people have started leaving Facebook. While Facebook’s popularity is still very high currently, is it possible that the social networking giant will go the way of MySpace, fading into obscurity? Or, will it have a strong fan base for generations to come?
We plan to answer this question by modeling the spread of Facebook as an epidemic disease. Specifically, one can think of the “infectious” group as those that are currently members of Facebook. In order for someone new to become “infected,” much like a disease, that person would have to be in contact with people already on Facebook, or who are already “infected.” And, similarly to a disease, there will be a group of people that are considered “immune” to Facebook, and will not join. Building off of current research, we will look at how people who are not on Facebook can influence those that are on Facebook currently to leave it, potentially setting up the demise of the site.
View Dr. DeLegge's home page
- Dr. Peter D. Dijkstra, Assistant Professor, Biological Sciences:
- Stress and body coloration in a polymorphic cichlid fish.
The melanocortin system regulates sexual behavior, aggression, pigmentation, and the stress response. The cichlid species Astatotilapia burtoni has two distinct color types (yellow and blue) and we have evidence that the melanocortin system regulates this color variation: yellow males are more aggressive and less sensitive to stress than blue males, and α-melanocyte stimulating hormone (α-MSH, a melanocortin hormone) changes behavior and increases yellow body coloration in A. burtoni. We are interested in testing the effects of α-MSH on the stress response using hormone manipulations followed by behavioral analysis and cortisol measurements. Students use a variety of approaches (hormone manipulations, hormone measurements, behavioral analysis, statistical analysis in R).
- Oxidative stress in East African cichlid fish.
Oxidative stress is an indicator of an imbalance between the production of reactive oxygen metabolites (reactive waste products resulting from normal metabolism) and the antioxidant system. The level of oxidative stress is an indicator of the rate of aging and general stress levels. Cichlids are the most diverse group of vertebrates on the planet and are an excellent system to test how oxidative stress varies across cichlid lineages that differ in behavior, body coloration and ecological specialization. Our goal is to measure both reactive oxygen metabolites and the antioxidant defense in blood plasma collected from four cichlid species from Lake Victoria.
View Dr. Dijkstra's home page
- Dr. Robert McCarthy, Assistant Professor, Biological Sciences:
- Comparative context of primate basicranial flexion. Compared to other mammals, primates have large brains and short, flexed cranial bases. In this project, students will be using phylogenetic comparative techniques to test the effects of brain size, body size, and cranial base length on basicranial flexion using a large dataset of extant and fossil primates.
- Mandibular variation and speech anatomy in non-human primates and the genus Homo. Recent evidence suggests that Neanderthals may have had a hyoid and larynx positioned high in the throat, a configuration not consistent with the production of fully modern human speech. To test this hypothesis, students will collect landmark data from the deep border of human and non-human primate mandibles (where tongue and suprahyoid muscles attach), and conduct a geometric morphometric analysis of mandibular shape variation using their data and data previously collected for Homo erectus, Homo heidelbergensis, Neanderthals, and early modern Homo sapiens.
View Dr. McCarthy's summer research page
- Dr. Scott Meyer, Assistant Professor, Physical Sciences:
- In vitro selection -
Knowledge about the relationship between a biological molecule’s structure and its functions is central to the understanding of biochemistry. In an effort to develop systems to study the structure/function relationships of proteins and their binding partners, we will use a method called in vitro selection to discover peptide ligands for various protein targets. In our research, we will develop new approaches to phage display, a type of in vitro selection, that will facilitate the discovery of novel protein/ligand pairs. These approaches include the development of novel library architectures and the development of a real-time monitoring system for phage display.
- Biosensors Development - Modifications to DNA, such as mutations and covalent modifications, are of intense interest in the biochemical and medical fields. We will use a method known as SEER (SEquence Enabled Reassembly of proteins) to develop biosensors to detect covalent modifications of DNA. Using SEER, we will be able to detect DNA damage (in the form of covalent modifications) adjacent to specific sequences of double stranded DNA. As an entry into this field, our goal is to detect DNA damage caused by the chemotherapeutic agent cisplatin. Once we construct a functional biosensor for cisplatin, we will look to develop biosensors for other kinds of DNA damage.
- Synthesis of Bile Acid Derivatives - In a collaboration with Dr. Jayashree Sarathy, we have begun the synthesis of bile acid derivatives to facilitate the study of this important class of biological molecules. The bile acid derivatives that we synthesize will be used to isolate the cellular targets of these compounds as well as tracking their interactions in isolated cell cultures.
View Dr. Meyer's home page
- Dr. Jeremy Nadolski, Associate Professor, Mathematics:
- A continued statistical look into the Tree of Heaven and possible eradication strategies.
This project is a continuation of summer research conducted two years ago in conjunction with Dr. Aldrich. Since that time, more variables and real data have been obtained to assist in judging validity of results.
- An investigation into the use of statistical trigonometry, phase and shift relationships, with emphasis on biological/physiological data.
This project will investigate how trigonometry and vectors can be used to analyze data. We will attempt to analyze two experiments conducted on crayfish (an experiment conducted at the University of Kentucky under Dr. Robin Cooper). One experiment was on the behavior of crayfish interactions and the second experiment was to look at the relationship between heart rate and ventral rate under different stimulus to determine synchronicity.
- An investigation into methods to detect outliers using Stalactite Plots and other mechanisms.
This project is a completion of a project started years ago. This project will involve programming and analysis of baseball data. The goal is to find and remove real outliers from the data based on an overall, multiple variable, approach.
View Dr. Nadolski's home page
- Dr. Pete Nelson, Associate Professor, Physics and Biology:
There is a growing movement to transform undergraduate science education. A major goal is for students to learn how think like a scientist. My contribution has been to develop learning modules that engage students in research activities using a “guided-inquiry” process. I have been pioneering this active-learning approach in my recent physics and biology courses (University Physics I and II, Biophysics and Physiological Modeling). This modular approach begins with a scientific investigation into the properties of a prototypical kinetic Monte Carlo simulation – “the marble game”. The marble game is a realistic simulation of Brownian motion and molecular diffusion that is inherently interdisciplinary. It provides a conceptual framework that can be applied to systems ranging from single molecules (ligand binding) to organisms (drug elimination) and entire ecosystems (population dynamics). The mathematical and computational framework provided by the marble game has universal applicability across all of science, technology, engineering and math (STEM). It can be applied to physics and engineering problems ranging from Newtonian mechanics and automotive engineering through to quantitative molecular biology and biomedical engineering. Students are engaged in an authentic research experience. They have gone on to graduate school at institutions such as Harvard, Yale, Georgetown and Northwestern. This summer, my plan is to focus on membrane transport and molecular dynamics.
- Two areas of membrane transport received the 2003 Nobel Prize in Chemistry – the transport of water molecules (osmosis) and potassium ions (ion channel permeation). These two processes are central to all life on earth. The marble game can be modified in a very simple way to model both of these processes in a quantitatively accurate manner at different levels of molecular detail. This project will focus on research activities that can be developed into guided-inquiry modules.
- Molecular dynamics (MD) simulations are the foundation of quantitative molecular biology (biophysics). Newton’s laws of motion are used to predict how the molecules of life behave. MD simulations can be applied to simple ions and molecules, enzymes, transporters and even small cellular machines such as ribosomes and motor proteins. This project will focus on engaging students in research activities about the fundamentals of molecular dynamics.
For more information, visit the Biophysics and Physiological Modeling web page http://circle4.com/biophysics or contact Dr. Nelson directly.
- Dr. Robin Rylaarsdam, Professor, Biological Sciences:
Title: G-protein related diseases: developing drugs to inhibit mutated G-proteins
- McCune-Albright Syndrome is a genetic disease caused by a mutation that permanently activates the Gs alpha protein in cells. Previous work in the laboratory identified several secondary mutations in the G alpha gene of yeast that can reverse the permanent activation caused by the MAS mutation and confirmed that four of these mutations suppress the human Gs activation. This summer we will investigate whether the suppressor mutations can block activation of other G-protein subtypes (Gq, G12, Go), mutations that are found in different cancers. The work will involve site-directed mutagenesis, mammalian cell culture and transfection, western blotting, ELISA assays, in vitro tumor formation assays, and microscopy.
View Dr. Rylaarsdam's home page
- Dr. Jayashree Sarathy, Assistant Professor, Biological Sciences:
- Bile acids and tight junctions: We are interested in studying the effects of conjugated vs unconjugated bile acids on colonic epithelial cells. We have shown that unconjugated bile acids increase paracellular permeability and allow luminal bile acids to access the basolateral membrane. This summer we would like to continue this study and determine what size molecules are able to move through the tight junctions. Cells will be grown on inserts to form a monolayer, challenged with various doses of bile acid. Transepithelial resistance will be measured using an electrical resistance system and paracellular permeability measured via mucosal to basolateral flux of 3-, 5 and 10-kDa fluorescence tagged dextran.
- Bile acids and Apoptosis: We have shown that bile acids show dose- and time-dependent cytotoxic effect using viability and lactate dehydrogenase assays. Does this cell death involve bile-acid induced apoptosis as well? This will be studied by Annexin V staining of T-84 cells following treatment with various doses of bile acids (different times) and Etoposide (1 – 10M) as positive control. Cell viability will be tested using propidium iodide. The percent of apoptotic cells will be identified using the Accuri Flow cytometer.
View Dr. Sarathy's home page
- Dr. Lee Ann Smith, Associate Professor, Biology:
- Using Drosophila melanogaster as a model, we studying how additives in energy drinks and sugar substitutes affect the long-term and short-term health of the flies. Using dose curves, life span studies, and preference tests, flies are subjected to these compounds, separately and in combination, to determine if there are any beneficial or adverse effects.
View Dr. Smith's home page
- Dr. Andrew Wig, Associate Professor, Physics:
- Optical Tweezers: Research will be conducted to use the BU optical tweezers instrument to study biological systems. Optical tweezers use focused light to trap and manipulate small objects. The initial study is focused on the trapping and analysis of E. coli bacteria. The project is experimental and involves learning about optics, lasers, and the interaction of light with matter.
- Scanning Probe Microscopy: A Scanning Tunneling Microscope (STM) is a device used to image surfaces of materials with atomic resolution. This project will involve building and testing an STM. It is an experimental project and will involve computer programming and electronics.
View Dr. Wig's home page
- Dr. Ellen Zilliak, Assistant Professor, Mathematics:
- Computing the Structure of Generalized Symmetric Spaces: For over 100 years symmetric spaces have been of interest to geometers, group theorists, physicists and topologists. These spaces have been generalized and many open questions exist concerning the characterization and classification of various symmetric spaces. In this project we will choose one of the open groups and classify the involutions, compute the fixed point group, generalized symmetric space and extended symmetric space. We will determine if our group follows the patterns that have been found for other groups. Finally we can study the orbit decomposition of the generalized symmetric space by various subgroups. The project will be computational by nature, using the software GAP to investigate and classify these groups.
- Cayley Graphs and Colored Graphs: A Cayley graph is a directed graph that encodes the multiplication table for an algebraic structure. These graphs can be used to study many interesting problems including constructing group extensions and cryptosystems based on algebraic structures. In this project I would like to study a related graph called a Colored graph which is a graph that generalizes the notion of distance. It was first introduced in the paper “Groups of graphs of groups” by Sibley, Byrne, and Donner. In this project we will investigate properties of these two graphs. Interesting questions include which Cayley graphs have the same Colored graph, and how this classification is related to the algebraic structure encoded by the graphs.
- Cryptography in Group Theory:
Public key cryptosystems have been used for secure communication between two parties. This system is used most often when the two individuals who wish to communicate have not met prior to the communication. It is used often in online transactions. Most of the algorithms currently used rely on modular arithmetic in Zp however the need to ensure security has led to explorations in the field of noncommutative groups. In this project we will study how noncommutative groups are used for developing new approaches and study several of the open questions associated with their use.
- The Algebra of Rewriting: In mathematics, one method of defining a group is by a presentation. Every group has a presentation. A presentation is often the most compact way of describing the structure of the group. However there are also some difficulties that arise when working with groups in this form. One of the problems is called the word problem which is an algorithmic problem of deciding whether two words represent the same element. I want to study the word problem on group extensions. Currently there is a procedure called coset enumeration which can be used to address this problem, however it has difficulties with memory when the groups reach a certain size. In this project we will continue the work of a former student to compute in the group extension using a modified coset enumeration technique. This method is derived using the Cayley graphs for the two smaller groups.
View Dr. Ziliak's home page