FRESHMAN RESEARCH INITIATIVE 2011–2012 ......stars, starlight escaped into the surrounding gas,...

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F R E S H M A N R E S E A R C H I N I T I AT I V E2 0 1 1 – 2 0 1 2 R E S E A R C H S T R E A M S

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INTRODUCTION

RESEARCH STREAMSAutonomous VehiclesBiobricksBiology of BiofuelsBioprospectingBrain PathologyCell Signaling and Signal TransductionComputational EvolutionComputational Intelligence in Game DesignComputational NanoparticlesCosmic DawnElectronic and Magnetic Materials ResearchEpidermal Cell Fates and PathwaysExploring the Physics of the Universe with White Dwarf StarsFrontiers of Linear Algebra Library DevelopmentFunctional GenomicsFunctional Materials Based on Metal ComplexesGenome Evolution in PlantsInfinite Uniqueness—Democratizing DesignLinear Algebra—Constructions and ApplicationsMitochondrial TransportersNanomaterials for Chemical CatalysisNucleic Acid Aptamer SelectionSupramolecular SensorsSynthesis and Biological RecognitionVertebrate Interactome MappingVirtual Drug Screening

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The Freshman Research Initiative offers first year students the opportunity to engage in authentic research experiences in chemistry, biochemistry, nanotechnology, molecular biology, physics, computer sciences, astronomy, mathematics and textiles and design while being supported and mentored by faculty and graduate students. Students emerging from this program, which spans three semes-ters of integrated coursework and laboratory research, will have considerable lab experience, an exposure to cutting edge research, and a deep understanding of the scientific process. Many students will have publications and letters of recommendation as well.

Students who complete the program will be ideally situated to: * Join a research group for the rest of their undergraduate time * Find a job or internship * Get into graduate school / medical school * Have a lifelong career in the sciences * Do research abroad

REQUIRED COURSE SEQUENCE

YEAR SEMESTER COURSE

Freshman Fall Research Methods

Spring Research Experience

Summer Optional research (volunteer or fellowship)

Sophomore Fall Advanced Research Experience

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The FRI course sequence begins in the first semester of freshmanyear, when students take a Research Methods course, and continues through two semesters in one of the Research Experi-ence courses. Each Research Experience course is tailored to one of the Research Streams, which are designed by faculty to integrate our educational model with the pursuit of 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 PhD research scientist dedicated to each Research Stream. In the first semester of their junior year, interested students will be matched into faculty research laboratories for their remaining two years, and select students can also continue in the program past the sophomore year, doing research with their Research Stream, either as a peer mentor TA for the next class of students entering the Research Stream, or on a volunteer or fellowship basis.

CREDIT

NSC 302 (3 hours) or equivalent course

Lower-division lab credit

Upper-division research credit

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2 0 1 1 – 2 0 1 2 R E S E A R C H S T R E A M S

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Autonomous Vehicles

Dr. Peter StonePiyush [email protected]

Can a car be built that drives itself?

The goal of this stream is to create a fully autonomous vehicle that can drive in traffic. Students will learn about and contribute to cutting-edge research in artificial intelligence and robotics.

FACULTY STREAM LEADER

EDUCATOR/CONTACT

>> COMPUTER SCIENCES

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Biobricks

Dr. Karen BrowningDr. Grace Choy [email protected]

How do cells make proteins?

This Research Stream involves syn-thesizing 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 tem-plates. Students will receive training in all aspects of molecular cloning as well as recombinant protein expres-sion in bacteria.


EDUCATOR/CONTACT

>> BIOLOGY >> BIOCHEMISTRY>> PRE-MED

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Biology of Biofuels

Dr. Thomas JuengerDr. Christine HawkesDr. Samuel [email protected]

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.

FACULTY STREAM LEADERS

RESEARCH EDUCATOR

CONTACT

>> BIOLOGY>> ECOLOGY>> GENETICS>> BIOCHEMISTRY

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Bioprospecting

Dr. Dionicio SiegelDr. Marsha Jane [email protected]

What biologically active compounds can be obtained from fungal endophytes present in native central 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.


RESEARCH EDUCATOR

CONTACT

>> BIOCHEMISTRY>> PRE-MED>> BIOLOGY>> CHEMISTRY

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Brain Pathology

Dr. Matt [email protected]. Jeff [email protected]

Can we develop new diagnostictechniques 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.


CONTACT

>> BIOLOGY>> CHEMISTRY>> PRE-MED>> BIOCHEMISTRY

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Cell Signaling and Signal Transduction

Dr. Stan Roux Dr. Greg Clark [email protected]

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 find-ings on how extracellular ATP controls growth. They learn methods of experi-mental 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 sys-tem for studying plant growth.

>> BIOLOGY >> PRE-MED


EDUCATOR/CONTACT

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Computational Evolution

Dr. Claus WilkeDr. Art [email protected]

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.


EDUCATOR/CONTACT

>> COMPUTER SCIENCES>> BIOLOGY>> MATHEMATICS

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Computational Intelligence in Game Design

Dr. Risto MiikkulainenDr. Uli [email protected]

How do you integrate trainable AI into a game platform?

In this stream, 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.

>> COMPUTER SCIENCES


EDUCATOR/CONTACT

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Computational Nanoparticles

Dr. Graeme HenkelmanLiang [email protected]

Can we design better catalysts from nanoparticles?

This stream uses computation models to calculate the properties of nanopar-ticles 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 proper-ties in order to design new catalysts. Students may also design and inves-tigate novel methods for finding the most stable configuration of atoms in nanoparticles. This stream also works in conjunc-tion with an experimental nanoparticle stream. Students who find particularly promising catalytic nanoparticles will have the opportunity to synthesize their particles in the lab.


EDUCATOR/CONTACT

>> COMPUTER SCIENCES>> MATHEMATICS>> PRE-MED>> PHYSICS>> CHEMISTRY

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Cosmic Dawn

Dr. Paul ShapiroDr. Anson D’[email protected]

Cosmic Dawn: How the First Galaxies Formed, Ended the Dark Ages, and Reionized the Universe” 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 thesurrounding 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.


EDUCATOR/CONTACT

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Electronic and Magnetic Materials Research

Dr. John MarkertIsaac [email protected]

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, and sensors. Students will learn new materials synthesis via solid state reaction, followed by structural, microscopic, magnetic, thermal, and superconduct-ing characterization of the materials. Students may also perform cantilever micromagnetometry, interferometry, and magnetic resonance microscopy.


CONTACTS

>> PHYSICS>> ASTRONOMY>> CHEMISTRY

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Epidermal Cell Fates and Pathways

Dr. Alan LloydDr. Antonio [email protected]

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.

>> BIOLOGY>> PRE-MED


CONTACT

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Exploring the Physics of the Universe with White Dwarf Stars

Dr. Don WingetDr. Mike [email protected]

What can white dwarfs tell us about exotic processes in stars?

Students in this stream will make astronomical observations of isolated pulsating white dwarf stars and those in close binary systems. They will analyze the data and participate in building theoretical models through which they 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.

>> ASTRONOMY>> PHYSICS>> COMPUTER SCIENCE>> MATHEMATICS


CONTACT

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Frontiers of Linear AlgebraLibrary Development

Dr. Robert van de [email protected]

How can we develop software that takes greater advantage of the extraordinary potential of high performance computers?

Linear algebra is not just a subject in mathematics, it is a fundamental tool of scientific computing. Many applications at their core require intensive matrix operations to be performed. In this stream we examine new techniques for developing high-performance libraries for these operations, targeting in particular modern architectures with 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.

>> COMPUTER SCIENCES>> MATHEMATICS>> PHYSICS


CONTACT

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Functional Genomics

Dr. Vishy IyerDr. Travis [email protected]

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 genome-wide 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.

>> BIOLOGY>> PRE-MED>> COMPUTER SCIENCES>> BIOCHEMISTRY


CONTACT

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Functional Materials Based on Metal Complexes

Dr. Richard JonesDr. Brad HollidayDr. Xiaoping [email protected]

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 spe-cific 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 proper-ties (fluorescence, phosphorescence, and luminescence). The relationship between chemical structure and physi-cal properties will be studied to develop new functional materials.

>> CHEMISTRY>> PRE-MED>> ENGINEERING


CO-PI

CONTACT

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Genome Evolution in Plants

Dr. Robert K. JansenDr. Tracey [email protected]

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.


CONTACT

>> BIOLOGY>> CHEMISTRY>> PRE-MED>> BIOCHEMISTRY

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Infinite Uniqueness—Democratizing Design

Dr. Zack Booth SimpsonDr. Leah [email protected] [email protected]

How can personalized fabrication create a world full of uniqueness?

The new field of personalized fabrication technology allows consumers to design and order their own unique products. Exploiting this technology will require development of ways to help consumers make pleasing designs, without training them to be designers. This stream will be a unique collaboration between designers and programmers to develop a computational design model that builds principles of good design into the programming behind fabric customization, using scientifically based evolutionary principles and genetic algorithms. Programmers and design students will be paired to develop their computational design models

– models which will develop pattern and color and ultimately result in a finished textile.

FACULTY STREAM LEADERS

CONTACT

>> COMPUTER SCIENCES>> TEXTILES AND APPAREL

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Linear Algebra—Constructions and Applications

Dr. Ronny [email protected]

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


CONTACT

>> MATH>> COMPUTER SCIENCES

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Mitochondrial Transporters

Dr. Dean ApplingDr. Anne [email protected]

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.

>> BIOLOGY >> BIOCHEMISTRY>> PRE-MED


EDUCATOR/CONTACT

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Nanomaterials for Chemical Catalysis

Dr. Keith StevensonDr. Stacia [email protected]

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. Nanopar-ticles are tiny, around one billionth of a meter across, but they hold huge potential for use in biosensors, drug synthesis, fuel production, environ-mental remediation, and specialty chemical production. Our goal is to identify the best chemical catalysts that could eventually be used in these applications.

>> CHEMISTRY>> COMPUTER SCIENCES>> NANOTECHNOLOGY>> PRE-MED


EDUCATOR/CONTACT

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Nucleic Acid Aptamer Selection

Dr. Andrew EllingtonDr. Gwen [email protected]

How can we use nucleic acid structural interactions for drug development and sensor applications?

Nucleic acids (DNA/RNA) have long been known to encode and express cellular information. In addition, oligonucleotides can control gene expression (siRNA), detect environments (riboswitches), and cure diseases (Macugen). This research stream interfaces biochemistry and biotechnology to produce nucleic acid

“aptamers” which function with similar specificity and affinity to antibodies. We perform in vitro selections against target molecules for biosensor and therapeutic applications. Students learn about oligo-nucleotide structure, causes of human disease, and bioengineering strategies. In the lab, students perform molecular biology techniques such as bead sieving, PCR and gel electrophoresis. Students use their knowledge to develop new biotechnology or therapeutics.


EDUCATOR/CONTACT

>> BIOLOGY>> BIOCHEMISTRY>> CHEMISTRY>> PRE-MED>> BIOENGINEERING

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Supramolecular Sensors

Dr. Eric V. AnslynDr. Eman [email protected]

Can we fingerprint complex mixtures using arrays of sensors?

The stream goal is to mimic the mam-malian 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 organic and ana-lytical chemistry, including solid phase peptide synthesis, high-pressure liquid chromatography, UV-vis spectrophotom-etry, and indicator displacement assays. Students will also be using basic and advanced biology and virology techniques.

>> CHEMISTRY>> PRE-MED>> BIOLOGY>> BIOCHEMISTRY


EDUCATOR/CONTACT

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Synthesis and Biological Recognition

Dr. Stephen MartinDr. Kristen [email protected]

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.

>> CHEMISTRY>> BIOCHEMISTRY>> PRE-MED>> PRE-PHARMACY


CONTACT

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Vertebrate Interactome Mapping

Dr. Scott StevensDr. Albert MacKrell [email protected]

How do complexes of macromolecules control gene expression?

Gene expression machinery mal-function is linked to a wide variety of diseases including cancer. Students in this stream will study individual genes implicated in mammalian gene expression whose precise functions are not yet known. They will employ RNA interference (RNAi) to “knock down” the expression of their gene of interest, and will use a wide variety of molecular techniques including PCR, cloning in bacteria, fluorescent microscopy, and mammalian tissue culture. Students will then measure the effect of their

“knock down” on gene expression, providing insight into the functions of these specific proteins and the process of RNA processing as a whole.


EDUCATOR/CONTACT

>> BIOCHEMISTRY>> BIOLOGY >> PRE-MED

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Virtual Drug Screening

Dr. Jon RobertusDr. Josh [email protected]

Can new drugs be identified from libraries of drug-like molecules?

Identifying new drug leads using traditional methods is an expensive and time consuming process. This research stream uses both com-putational 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. Then DNA cloning and protein expression protocols are implemented in the lab to test the top potential drugs in enzyme assays.


CONTACT

>> BIOCHEMISTRY>> COMPUTER SCIENCES>> CHEMISTRY>> PRE-MED

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CONTACT

Dr. Sarah Simmons – Assistant Dean

Freshman Research Initiative

Office for Honors, Research, and International Study

Painter Hall 3.04

512 232 9358

The University of Texas at Austin

College of Natural Sciences – Office of the Dean

1 University Station G2550

Austin, TX 78712

This program funded in part by the Howard Hughes Medical Institute,

the National Science Foundation and the College of Natural Sciences.

FRESHMAN RESEARCH INITIATIVE 2011–2012 ......stars, starlight escaped into the surrounding gas,...

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