Research Streams
Rather than placing individual students with individual faculty, or integrating parts of research into traditional laboratory courses, the FRI revolves around the "Research Stream,"a fully functional research laboratory in which students do cutting edge research supplemented by weekly lectures that are organized around the work being done in the lab.
Each research stream is led by a faculty member who has designed a program of research using our educational model to pursue their fundamental research questions. These faculty provide guidance to their respective Research Streams, set goals and directions, and develop and teach the Research Experience course to the students within their stream. The research labs themselves are each run by a Research Educator (RE), a Ph.D. research scientist dedicated to each Research Stream.
Students have the option to continue through the summer and will return in the fall to receive research credit for continued work in their lab.
For a PDF introducing these streams, click here.
**Please note that stream meeting times are subject to change**
Current Research Streams
Antibiotics: Discovery and Function
Marvin Whiteley
Gregory Palmer
Gregory Palmer
Can we discover new antibiotics, and what effects do antibiotic-producing bacteria have on other members of a microbial community?
As the numbers of antibiotic-resistant bacterial strains like methicillin-resistant Staphylococcus aureus (MRSA) are increasing, we are rapidly running out of last line drugs to treat infections. Nearly all of the antibiotics currently used in hospitals and clinics come from microorganisms that are commonly found in the soil. Students in this stream will isolate new antibiotic-producing bacteria from the soil right here on campus, determine the chemical nature of the drug(s) they produce, and use next generation sequencing technology to find out how the presence of antibiotic producers affects other bacteria in the community. At the stream’s conclusion it is possible that students will have both discovered a new antibiotic and determined its role in shaping the soil microbiome.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 2-3
Aptamers
Andrew Ellington
Gwen Stovall
Gwen Stovall
How can we use biochemistry and nucleic acids for drug development and sensor applications?
Simply put, we develop things that bind to things. More specifically, we develop nucleic acid oligonucleotides “aptamers” that can bind tightly and specifically to targets of interest.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: F 1-2 pm
Autonomous Intelligent Robotics
Peter Stone
Todd Hester
Todd Hester
Can intelligent robots effectively coordinate to aid humans?
The goal of this stream is to create a system of fully autonomous robots inside the new Gates complex to aid people inside the building. Students will learn about and contribute to cutting-edge research in artificial intelligence and robotics.
Credit Options: CS 378 Lab Meeting Times: Tu & Th 12:30–2 PM
Biobricks
Karen Browning
Grace Choy
Grace Choy
How do cells make proteins?
This Research Stream involves synthesizing genes or gene fragments and piecing them together like Legos (Biobricks) with molecular cloning tools. The genes or gene fragments will be used to explore how proteins are synthesized from mRNA templates. Students will receive training in all aspects of molecular cloning as well as recombinant protein expression in bacteria.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 1-2 PM
Biology of Biofuels
Tom Juenger and Christine Hawkes
This stream will not be taking new FRI students during the spring of 2013.
Can we use plants for energy instead of oil?
Almost seven billion humans live on Earth, supported by finite planetary resources that are being affected by global climate change. Biofuels are an alternative energy source that could be both sustainable and help minimize climate change. The benefits of growing plants for fuel will, however, depend upon both natural limits to plant productivity and competition for space between biofuel crops, food crops and natural ecosystems. This FRI stream will investigate the physiology, genetics/genomics, breeding and ecology of Switchgrass (Panicum virgatum), a promising biofuel species, comparing it with other potential biofuel sources.
Credit Options: BIO 205L/BIO 170C Lab Meeting Time: W 11 AM–12 PM
Bioprospecting; Isolation of Biologically Active Natural Products from Endophytes
Dr. Dionicio Siegel
Marsha Jane Lewis
Marsha Jane Lewis
What biologically active compounds can be obtained from endophytes present in native Texas plants?
The primary objective of the Bioprospecting stream is to isolate, characterize, cultivate, process and screen unique fungal endophytes from Central Texas for the discovery of compounds with potential therapeutic applications.
The stream will span multiple sub-disciplines of biology and chemistry. Our primary focus is mycology, molecular biology, and organic chemistry.
While working towards the primary objective, we also investigate questions regarding the ecology of fungal endophtyes.
Credit Options: BIO 205L/BIO 170C or CH 204/CH 108 Lab Meeting Time: W 4-5 PM
Brain Pathology
Jeff Luci
Mithra Sathishkumar
Mithra Sathishkumar
Can we develop new diagnostic techniques for use on the brain?
The Brain Pathology stream is concerned with the causes and effects of chronic diseases and acute conditions that affect the brain and central nervous system. We use genetic analysis, MR imaging, and standard clinical diagnostics to probe things like oncogenesis, white matter diseases, and traumatic brain injury. The students enrolled will learn skills routinely used in computational biology, biomedical imaging processing, functional brain mapping, biostatistics and other related fields of neuroscience. It will be common to work with both academic and clinical researchers in neurosurgery, genetics, psychology, and neuroscience.
Credit Option: NSC 309 Lab Meeting Time: M 4-5 PM
Cell Signaling and Signal Transduction
Stan Roux
Greg Clark
Greg Clark
How does the environment impact what cells do?
A recent exciting discovery in plants is that ATP is released into the cell wall during plant growth where it plays a major role in controlling how fast cells grow. Students in this stream carry out never-done-before experiments on this topic and discover significant new findings on how extracellular ATP controls growth. They learn methods of experimental design, data gathering, data interpretation, and data presentation, and they learn principles of stimulus-response coupling that apply equally well to animals and plants. Specifically, students will do their experiments on extracellular ATP signaling in root hairs, an agriculturally important model system for studying plant growth.
Credit Options: BIO 205L/BIO 170C Lab Meeting Time: Th 2:30-3:30 pm
Computational Evolution
Claus Wilke
Art Covert
Art Covert
What can the evolution of self-replicating computer programs tell us about evolution in nature?
Research on self-replicating computer programs (digital organisms) enables students to experience evolution in action and to perform evolutionary experiments that would take years to complete with natural organisms. Digital organisms evolve to perform computational tasks. Completion of these tasks rewards the organisms with resources they can use to replicate faster and gain a competitive edge. Over time, faster-replicating organisms out-compete slower-replicating ones. Hence, the organisms evolve to complete increasingly complex tasks, in a manner that parallels the evolution of natural organisms. This stream is a good option for students who want to learn about computer science and evolutionary biology.
Credit Options: BIO 321 or CS 378 Lab Meeting Time: M 4–5 PM
Computational Intelligence in Game Design
Risto Miikkulainen
Joel Lehman
Joel Lehman
How do you integrate trainable AI into a game platform?
In this class, you will learn about different aspects of video game technology and will get hands on experience in working with a real game engine. You will also be exposed to cutting-edge AI research that may play a central role in the next generation of video games.
Credit Option: CS 378 Lab Meeting Time: Tu & Th 3:30–5 PM
Computational Nanoparticles
Graeme Henkelman
Juliana Duncan
Juliana Duncan
Can we design better catalysts from nanoparticles?
This stream uses computation models to calculate the properties of nanoparticles and the chemical reactions that they catalyze. Students will be able to construct their own particles, each with a different composition and structure, and use quantum chemistry calculations to evaluate their properties in order to design new catalysts. Students may also design and investigate novel methods for finding the most stable configuration of atoms in nanoparticles. This stream also works in conjunction with an experimental nanoparticle stream. Students who find particularly promising catalytic nanoparticles will have the opportunity to synthesize their particles in the lab.
Credit Option: CH 204/CH 108 Lab Meeting Time: M 3-4 pm
Cosmic Dawn: How the first galaxies formed, ended the dark ages, and reionized the Universe
Paul Shapiro
Anson D'Aloisio
Anson D'Aloisio
What are the differences between galaxies born and raised in regions of space that were either crowded or sparse, and how did these differences affect the end of the cosmic dark ages?
Prof. Shapiro's group studies the first billion years of cosmic time when the first galaxies and stars were born, the last window of cosmic time accessible to direct observation. To test current theory, they use supercomputers to simulate the formation of galaxies and large-scale structure in the expanding universe. When these galaxies formed stars, starlight escaped into the surrounding gas, heating and ionizing it. This "feedback" impacted future galaxy and star formation and left observable imprints on the universe which astronomers are just now beginning to detect. Students will help make new discoveries with the most advanced simulations in the world, performed at the Texas Advanced Computing Center at UT.
Credit Options: PHY 101L/AST 210K or CS 378 or AST375K Lab Meeting Times: M & W 2–3 PM
Electronic and Magnetic Materials Research
John Markert
Jeremy Paster
Jeremy Paster
How do you create materials with new electronic and magnetic properties and structures?
This Research Stream focuses on materials physics and the design and development of materials for use in data storage, optics, sensors, and optical and infrared astronomy. Students will learn new materials synthesis via solid state reaction, followed by structural, microscopic, magnetic, thermal, and superconducting characterization of the materials. Students may also perform cantilever micromagnetometry, interferometry, and magnetic resonance microscopy.
Requirements: Concurrent enrollment/credit in PHY 301 or 316 Credit Options: PHY 101L & PHY 108 or PHY 116L & PHY 108 Lab Meeting Time: M 4-5 pm
Epidermal Cell Fates and Pathways
Alan Lloyd
Antonio Gonzalez
Antonio Gonzalez
How is a cell’s fate determined?
This stream uses a comprehensive genetics approach to investigate developmental mechanisms that lead to cell fate decision events and the regulation of organ differentiation pathways. Students will design and pursue experiments using a broad range of genetic strategies such as classical, molecular, forward and reverse genetics. In the process students will learn how to clone genes, engineer DNA, generate mutant and transgenic organisms, document and analyze data, and more. While this lab focuses on a plant molecular/genetic model, all the technologies learned in this stream are common to research in all modern molecular/genetic model organisms.
Credit Options: BIO 205L/BIO 170C Lab Meeting Time: W 4-5 pm
Exploring the Universe with White Dwarf Stars
Don Winget
Mike Montgomery
Mike Montgomery
What can white dwarfs tell us about exotic processes in stars?
Students in this stream will make astronomical observations of pulsating white dwarf stars and those in close binary systems. They will analyze the data and participate in building theoretical models through which we will explore physical processes in stars (e.g., convection, crystallization, and diffusion) as well as various relativistic effects (gravitational radiation, doppler beaming). In addition they will perform numerical experiments to study how pulsations allow us to “see beneath the surface” of these stars. Go here for stream video.
Credit Option: PHY 101L & AST 210K Lab Meeting Time: M 3-4 pm
Frontiers of Linear Algebra Library Development
Robert van de Geijn
Linear algebra is not just a subject in mathematics, it is a fundamental tool of scientific computing since many applications at their core require compute intensive matrix operations to be performed. In this course we examine new techniques for developing high-performance libraries for these operations, targeting modern architectures including processors with multiple cores. Importantly, these techniques allow novices with little background in linear algebra and computer science to develop algorithms and implementations that outperform traditional libraries.
Credit Options: To be determined depending on the student Lab Meeting Time: To be determined with each student
Functional Genomics Research
Vishy Iyer
Gregory Hatlestad
Gregory Hatlestad
How can we use genome sequences to better understand the function and evolution of organisms at the molecular level?
Next generation sequencing technologies explore the molecular biology of organisms on a genomewide scale. These cutting edge methods enable high resolution inspection of whole-genome regulatory interactions and gene expression. The Functional Genomics Research Stream combines molecular experimentation and creative computational analysis to engage significant novel research into the mechanistic understanding of transcriptional regulation as well as the evolutionary underpinnings of molecular behavior.
Credit Options: CH 204/CH 108 or BIO 205L/BIO170C Lab Meeting Time: Tu 3:30-4:30 PM
Functional Materials Based on Metal Complexes
Richard Jones and Brad Holliday
Xiaoping Yang
Xiaoping Yang
How do we make and characterize new metal-containing compounds that have useful properties?
Some chemical compounds that contain metal atoms have useful properties such luminescence, or the ability to “glow in the dark”. The efficiency or brightness of these compounds is related to the specific arrangement of the atoms within the chemical structure. In this research stream, students will learn to make new luminescent compounds and using state-of-the-art techniques explore both the exact chemical structure (X-ray diffraction) and luminescence properties (fluorescence, phosphorescence, and luminescence). The relationship between chemical structure and physical properties will be studied to develop new functional materials.
Credit Option: CH 204/CH 108 Lab Meeting Time: F 2-3 PM
Genome Evolution in Plants
Robert Jansen
How do nuclear encoded proteins influence organelle genome stability in plants?
Plant cells are unique in having genomes in three distinct compartments, the nucleus and two organelles – the mitochondrion and plastid. Since their establishment by endosymbiosis thousands of genes have been transferred from the organelle genomes to the nucleus. Extensive communication among the compartments has resulted in considerable conservation of the organellar genomes across the evolutionary tree of plants except in the geranium family, which has remarkably accelerated rates of change. Students in this stream will utilize molecular, genomic, evolutionary and bioinformatic approaches to identify and characterize the genes involved in inter-compartmental crosstalk within plant cells, which is critical to the development and growth of plants.
Credit Options: BIO 205L/BIO 170C or CH 204/CH 108 Lab Meeting Time: F 3–4 PM
Linear Algebra – Constructions and Applications
Ronny Hadani
Why is it useful to think without coordinates? How can we generalize Euclidian geometry and why is a tensor product the single most important operation in modern mathematics?
Linear algebra is a mathematical language which lies at the heart of almost every discipline of mathematics, physics, chemistry and engineering. A thorough understanding of its basic constructions and techniques is indispensable for serious study of any one of these fields. In particular, the fundamental ideas underlying linear algebra serve as a prototype for many modern mathematical theories. In this stream, we will cover some of the core topics of linear algebra, taking a slightly more sophisticated point of view: emphasizing the coordinate free formulation of the theory.
Credit Option: M 341 Lab Meeting Time: MWF 11 AM–12 PM
Mitochondrial Transporters
Dean Appling
This stream will not be taking new FRI students during the spring of 2013.
How are compounds critical for nucleic acid and amino acid biosynthesis transported across the mitochondrial inner membrane?
Tetrahydrofolate is the biologically active form of the vitamin folic acid, and is required for cellular synthesis of critical biological compounds such as purine nucleotides, thymidylate, and the amino acids serine, glycine and methionine. Folic acid deficiency or impaired folic acid metabolism can severely affect human health. Folic acid metabolic pathways involve both mitochondrial and cytoplasmic enzymes, and therefore, tetrahydrofolate and other key compounds must be transported across the mitochondrial inner membrane. This Research Stream will use the power of yeast genetics to identify the mitochondrial carrier proteins responsible for transport of these compounds.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 2-3 pm
Nanomaterials for Chemical Catalysis
Keith Stevenson, Co-PIs David Vanden Bout and Richard Crooks
Stacia Rodenbusch
Stacia Rodenbusch
How do you make new types of nanoreactors?
In this Research Stream, students use cutting edge technology to synthesize nanoparticles using combinations of metals including copper, gold, platinum, palladium, and nickel. The particles act like “nanoreactors” to catalyze chemical reactions. Nanoparticles are tiny, around one billionth of a meter across, but they hold huge potential for use in biosensors, drug synthesis, fuel production, environmental remediation, and specialty chemical production. Our goal is to identify the best chemical catalysts that could eventually be used in these applications.
Credit Options: CH 204/CH 108 Lab Meeting Time: M 3-4 PM
Neuroscience of Synapses
Kristen M. Harris
Jared B. Bowden
Jared B. Bowden
How do brain cells (neurons) and their connections (synapses) mediate learning and memory?
Synapses form neural circuits in the brain. Nanoscale imaging in the electron microscope is needed to determine where synapses are located and whether changes in synapse structure and composition are associated with learning and memory. Students engaged in this stream learn to identify, reconstruct in 3D, measure and analyze neuronal structures including: dendrites, axons, synapses, and subcellular components involved in synapse function. Opportunities exist to engineer improved computer imaging tools. Projects provide a strong foundation for understanding fundamental brain mechanisms.
Credit Options: NSC 309 Lab Meeting Time: Tu 4 PM
Supramolecular Sensors
Eric Anslyn
Eman Ghanem
Eman Ghanem
Can we fingerprint complex mixtures using arrays of sensors?
The stream goal is to mimic the mammalian sense of taste by creating sensor arrays that can “fingerprint” complex mixtures, a technology that has potential environmental and clinical diagnostic applications. Currently, the stream uses peptide based sensing ensembles to differentiate wine varietals, a complex mixture composed of metabolic products from grapes. In order to increase the diversity of peptides used in the sensing ensembles, the stream will apply the technology of phage display. Students in the stream practice research skill in organic and analytical chemistry, including solid phase peptide synthesis, high-pressure liquid chromatography, UV-vis spectrophotometry, and indicator displacement assays in addition to basic and advanced biology and virology techniques.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 3-4 PM
Synthesis and Biological Recognition
Stephen Martin
Kristen Procko
Kristen Procko
As the demand for therapeutic drugs increases, how are researchers working to better understand molecular interactions?
The design of small organic molecules that bind tightly and selectively to proteins is essential for the development of potent drugs that have minimal side effects. In this multidisciplinary stream, student researchers design and synthesize novel molecules that bind to proteins and learn to express, purify, and test the proteins of interest. The strength of binding between the protein and small molecule is tested by a technique called ITC, which provides data that can be used to elucidate the chemical features that allow for stronger intermolecular interactions, contributing to the field of drug discovery.
Credit Option: CH 204/CH 108 Lab Meeting Time: W 1-2 PM
Vertebrate Interactome Mapping
Scott Stevens
Albert MacKrell
Albert MacKrell
How do complexes of macromolecules control gene expression?
Students in the stream explore the nature of RNA-protein complexes that mediate gene expression, and coordinate transcription and RNA processing. Students engineer DNA molecules in E. coli using PCR, molecular cloning techniques and targeted recombination, and use these DNAs to alter specific genes in cultured vertebrate cells, tagging them with an added protein sequence. This tag allows native complexes to be isolated intact and purified from nuclei. These complexes allow us to map the interactome or “social network” of the nucleus, and gain insight into the function of proteins about which little is known.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: M 3-4 PM
Virtual Drug Screening
Jon Robertus
Josh Beckham
Josh Beckham
Can new drugs be identified from virtual libraries of drug-like molecules?
Identifying new drug leads using traditional methods is an expensive and time consuming process. This research stream uses both computational and wet lab techniques to discover new drugs. First, a molecular docking program is used to sift through libraries of chemical structures and predict which ones may bind to a protein that is a potential drug target. Results are analyzed with a molecular graphics program. Students will learn how to run Virtual Drug Screening software and will use molecular graphics programs to interpret the results. Then DNA cloning and protein expression protocols are implemented in the lab to test the top potential drugs in enzyme assays.
Credit Options: CH 204/CH 108 or BIO 205L/BIO 170C Lab Meeting Time: T 3:30-4:30 PM
