Internationally known scientists on the IU faculty have chosen to be mentors to undergraduates in the IU STARS and IFLE Programs. Students in the programs are paired with faculty members who direct their research.
To read about faculty mentors and their areas of research, select a field of study:
Susan Alt
I am an archaeologist studying Mississippian societies with a particular focus on the central Mississippi and lower Ohio valleys. My research is centered on the reconstruction of the histories of past peoples and places, utilizing social theory to understand those histories. I am fascinated by the relationships between material culture, and social process, and how as archaeologists we can best "read" patterns in the material world as representative of real people, their experiences and sensibilities. My goal is to understand how societies transform themselves, both intentionally and unintentionally, via processes involving gender, ritual, memory, traditions, identity formation and hybridity. My goal is to understand how historical events and social process combine to shape human society.
Frederika Kaestle
Molecular anthropology, molecular evolution, population genetics, ancient DNA
Stacie King
Ancient and Colonial Mexico, household archaeology, identity, food practices, soundscapes, social theory, colonialism, soil chemistry and microscale methods in archaeology
Anya Peterson Royce
Local and global identities, anthropology of dance, performance, popular theater, ethnic identity, aesthetics and creative processes, indigenous peoples of Mesoamerica, death belief and ritual, anthropological writing, anthropology of food
Laura Scheiber
Zooarchaeology, Faunal Analysis, North American Archaeology, Native American Ethnohistory, Culture Contact, Archaeological Theory and Practice, Historical Anthropology, Landscapes, Identity, Archaeological Fiction
Tom Schoenemann
Coevolution of brain and behavior, evolution of language, functional morphology of the brain, human variation, modeling evolutionary hypotheses, mathematical image analysis
Constantine Deliyannis
Big Bang cosmology and nucleosynthesis; stellar interiors, structure, evolution, and ages; star cluster photometry and spectroscopy; light element probes.
Caty Pilachowski
Professor Catherine A. Pilachowski investigates the evolution of stars and the chemical history of the Milky Way Galaxy from studies of chemical composition of stars and star clusters. As stars evolve, chemical elements are synthesized by nuclear processes in the stars' interiors. These newly created elements appear in the stars' outer layers, where we can observe them. Changes in the surface composition of stars help us to understand what's going on inside the star, and to understand the process of stellar evolution.
Professor Pilachowski also uses her data on the compositions of stars to explore the chemical history of the Milky Way Galaxy. Since its formation 13.8 billion years ago, the Galaxy has been gradually enriched in the abundance of chemical elements as these elements have been produced in stars. Studies of the abundances of the chemical elements in the oldest stars can reveal the nature of the first generation of stars formed in the Galaxy, and the compositions of old stars can also tell us about the history of the Galaxy.
Kathy Rhode
Dr. Rhode's primary research interest is the formation and evolution of galaxies and their stellar populations. She has ongoing projects to survey the globular cluster populations of massive galaxies in order to investigate the galaxies’ evolutionary histories. She is also leading a campaign to obtain WIYN 3.5-meter telescope imaging of gas-rich galaxies discovered in the ALFALFA radio survey; in 2013, as part of this campaign, she helped discover a new nearby galaxy called Leo P. In addition to her research on galaxies, Dr. Rhode has studied the evolution of young, low-mass stars in order to help understand the early evolution of the Solar System.
John Salzer
Professor Salzer has broad research interests in the area of extragalactic astronomy. His current research focuses are in the area of abundances in galaxies and star-formation in the nearby universe. His abundance research involves studying the metal content of hundreds of galaxies to understand the demographics of chemical enrichment as well as to measure the evolution of abundances to modest lookback times. His current star-formation studies focus on measuring the rate at which stars are being born in hundreds of nearby gas-rich galaxies, with the goal of carrying out an unbiased census of star formation in the local universe. In addition, he has ongoing interests in Seyfert Galaxies and AGN, Blue Compact Dwarf galaxies, and the spatial distribution of galaxies in the local universe, with an eye toward the affects that galaxian environment plays in shaping the properties of galaxies.
Liese van Zee
Professor van Zee is working on several projects related to understanding the links between star formation, elemental enrichment, and gas distribution and kinematics in star forming galaxies. Her work focuses on both the star formation history and evolution of dwarf galaxies (including stellar population models and regulatory mechanisms for star formation) as well as the elemental enrichment of spiral and irregular galaxies.
Matt Bochman
The work in the Bochman lab focuses on genome stability, i.e., the sum total of everything cells do to maintain their genetic material in a pristine state and pass it down to future generations. This is a broad area that allows us to follow the biology and biochemistry of the experiments we do into DNA metabolism (replication, recombination, and repair), telomere maintenance, and transcription in both the nucleus and mitochondria in a variety of different systems. Our main model organism is the budding yeast Saccharomyces cerevisiae, which is also the workhorse organism used to make beer, wine, mead, hard cider, kombucha, etc. As such, we're also notorious for our collaborations with Upland Brewing Company, Cardinal Spirits, and a variety of other industry partners. We have also gone "yeast hunting" to identify and characterize novel strains indigenous to the Midwest and beyond.
Lingling Chen
The theme of our laboratory is to study molecular mechanisms of how to interfere with bacteria, with the overarching aim to develop novel antimicrobial reagents to target bacterial infections. We work on essential bacterial processes and those nonessential for survival, with the latter having less selection pressure to develop resistance. To this end, we collaborate with microbiologists, chemical biologists, and biophysicists. Together, we employ a wide range of experimental approaches, including microbiology, genetics, chemical biology, molecular biology, combinatorial biology, biochemistry, biophysics, structural biology, and particularly protein crystallography
Susanne Ressl
The Ressl lab focuses on solving protein structures, in particular membrane proteins. Membrane proteins are a fascinating class of proteins. Embedded in the cell's membrane, they are the vital link between outside and inside world and facilitate various crucial physiological functions. Functions such as: 1) transporters, transporting molecules or ions across the membrane, 2) anchors, anchoring proteins and providing cell stability and interacting with cell matrix proteins, 3) receptors and enzyme that provide major signalling functions in the cell, such as G-protein coupled receptors that are involved in the majority of physiological functions.
Adam Zlotnick
Our broad goal is to examine the structure and assembly of protein oligomers, determining structures of products, reactants and intermediates, and correlating them with solution studies. A major focus of the lab is to understand the biophysics of virus capsid assembly. The capsid of a spherical of virus is assembled from multiples of 60 protein subunits, arranged with icosahedral symmetry. All projects in the lab involve multimeric viral proteins and enzymes.
Farrah Bashey-Visser
Currently, my work focuses on insect-parasitic nematodes (genus Steinernema) and their symbiotic bacteria (genus Xenorhabdus). We have used these organisms in experimental studies to examine how different selective pressures within and among hosts shape the evolution of parasite virulence and host exploitation. We have found that among-host selection can change the number, size, and timing of nematodes emerging from an infected insect. We have also found that greater migration of parasites among their insect hosts results in greater within-host competition. This competition is especially apparent among the bacteria, which produce allelopathic toxins (bacteriocins) to inhibit each other's growth. Conconmitent with the greater inhibition among the bacteria, these infections progress more slowly such that the insect takes longer to die and nematodes longer to emerge.
Brian Calvi
It is critical to discover the mechanisms of normal cell cycle regulation if we are to fully understand what goes awry in cancer cells. We focus on how cells coordinate the duplication of their genome with cell division. This is an important question because defects in this coordination cause genome instability and are common early events in carcinogenesis.
We use the genetic, molecular, and cell biological tools available in the fruitfly, Drosophila melanogaster, to study cell cycle regulation and to define DNA damage and the checkpoint responses in a developmental context. For example, we are asking how the eukaryotic cell tightly regulates the activity of origins of DNA replication so that the genome is duplicated exactly once per cell cycle.
Pranav Danthi
The Danthi laboratory investigates how mammalian reovirus interacts with host cells. Reoviruses infect a variety of mammals, including humans, and are known to produce neurological disease in young animals. These viruses serve as a versatile experimental system for studies of events at the virus-cell interface, including virus entry, activation of the innate immune response, and viral pathogenesis. We are specifically interested in understanding how reoviruses bypass host membranes to initiate infection and how infection of host cells by reovirus results in programmed cell death or apoptosis.
Lynda Delph
I am generally interested in evolutionarily based questions concerning various aspects of flowering plant reproduction from both ecological and genetic perspectives. At a more general level, my research focuses on understanding selective forces in natural populations and the extent to which adaptation is slowed or prevented by genetic constraints.
Greg Demas
The primary focus of our laboratory is in the general area of "ecological physiology." Specifically, we study of the interactions among the nervous, endocrine and immune systems and behavior in a variety of ecologically relevant environmental contexts.
Clay Fuqua
Research projects in the Fuqua laboratory utilize the model Alphaproteobacterium, Agrobacterium tumefaciens, a well-studied bacterial pathogen of plants that causes the disease crown gall. A. tumefaciens is best known for its ability to transfer DNA to plants during pathogenesis, via an interkingdom genetic transfer mechanism that has been extensively utilized to genetically engineer plants. We have discovered that this rod-shaped bacterium exhibits profound asymmetries at the subcellular level that are intimately tied to its cell biology, physiology, genetics and host interactions. One of these asymmetric activities is the production of an adhesive glue at one end of the cell, a structure we call the unipolar polysaccharide (UPP). The UPP is required to cement A. tumefaciens to biotic and abiotic surfaces during formation of the multicellular structures known as biofilms. A. tumefaciens forms robust biofilms on a variety of surfaces, and production of the UPP is a crucial first step in this process. The UPP adhesive is only produced once the cell contacts the surface, and as such is very tightly regulated. We are studying the mechanism of UPP production, its spatial and temporal regulation, and the complex control networks that coordinate attachment with other aspects of cellular physiology and the bacterial cell cycle. Other surface structures such as flagella and pili are also asymmetrically distributed on the cell surface, reflecting a discrete underlying cellular architecture. Recent work demonstrates that A. tumefaciens cells divide asymmetrically via a budding mechanism, in contrast to the standard paradigm of binary fission. We are interested in how the extensive asymmetric organization of the A. tumefaciens cell, its division, and all the activities that it contains, are coordinated. These basic properties are also shared with a growing range of different bacteria, including pathogens and commensals, and thus our fundamental work is broadly relevant.
Matthew Hahn
Our work focuses broadly on asking questions about organismal function and evolution using genomic data. The huge amount of data currently being produced allows us to ask and answer questions on a genomic scale that have never been possible before. Our questions largely revolve around the relative roles of natural selection and genetic drift in shaping nucleotide, gene family, and gene expression variation both within and between species. Although most of the empirical work has been on systems such as humans, flies and mosquitoes (and now tomatoes!), members of the lab can work on topics and organisms that appeal to them. This page covers several major topics currently being studied.
Spencer Hall
I study interactions between species and their environment at population, community, and ecosystem levels. I use freshwater plankton to study these interactions. Plankton provide an ideal system because they interact strongly, are readily manipulated in the lab and field, reproduce quickly, and supply crucial functioning to freshwater ecosystems.
My research program hinges on: (1) development of mathematical models; (2) experimental tests of those in both the laboratory and the field; and (3) surveys of natural systems. Combined, these approaches help me rigorously test logical, relevant ideas.
Ke Hu
Nearly 20% of the global population is permanently infected with Toxoplasma gondii, a unicellular parasite. Toxoplasmosis is an important cause of congenital neurological defects. To cause disease, Toxoplasma must reiterate its lytic cycle through host cell invasion, replication, and parasite egress, all of which rely on a functional cytoskeleton (the “backbone” of a cell). Furthermore, the parasite’s cytoskeleton is rich in novel features, which are highly attractive targets for designing parasite-specific drugs. Using molecular genetics and microscopy, the lab is trying to understand how the unique structures in Toxoplasma cytoskeleton are constructed and how they function in the lytic cycle.
Laura Hurley
Sensory systems demonstrate an amazing ability to filter environmental information depending on the prevailing context. This ability allows animals to act appropriately in situations such as interaction with members of their species, or in response to potential threats. Sensory filtering is also important in human perception, as in hearing and understanding speech during social interactions, and in disorders in such perceptual processes. Work in my lab explores a neurochemical signal, serotonin, which is one of the mechanisms allowing the auditory system to filter important information. We are interested in the function of serotonin-auditory interactions, how these are influenced by behavioral context, and how they change the way the auditory system interprets behaviorally relevant information. In order to address these issues, we use a range of techniques from analysis of social behavior and vocalizations in mice, to several types of electrophysiological measurements.
Roger Innes
Our primary interest is in understanding the genetic and biochemical basis of disease resistance in plants. Plants are able to specifically recognize pathogens and actively respond. We are investigating how this specific recognition is accomplished and how recognition is translated into a resistant response.
Daniel Kearns
The overall goal of the lab is to identify, characterize, and understand new genetic components of multicellular behavior in undomesticated B. subtilis. With this information, we hope to create a larger model that explains how swarming motility and biofilm formation interact and in which environments each is favored.
David Kehoe
My research group is broadly interested in uncovering the molecular mechanisms that control how organisms sense and respond to changes in their environment. Our primarily focus is on the cyanobacteria, oxygen producing microorganisms that are the progenitors of land plants and responsible for nearly one half of the Earth's current primary productivity. This group is excellent for our studies because they have successfully colonized nearly every type of habitat on Earth (and thus are capable of a wide range of responses to environmental change), have small genome sizes, grow rapidly, and many molecular genetic tools are available for their study. Our research efforts are providing important new insights into signal transduction pathways that are found in both bacteria and plants.
Ellen Ketterson
We take an experimental approach to life-history evolution that we call 'phenotypic engineering'. By treating birds with hormones, documenting the phenotypic consequences of hormonal treatment, and relating these consequences to fitness, we hope to understand how natural selection shapes organisms as integrated units. Our study animal is the dark-eyed junco, and we have found that testosterone affects numerous aspects of the male phenotype in free-living juncos, including song, parental behavior, home range size, attractiveness to females, immune capacity, corticosteroid responses to stress, regulation of body mass, and timing of molt, to name a few. With respect to fitness, males treated with testosterone are less successful at rearing offspring with their social mates but more successful at siring offspring by means of extra-pair fertilizations. Our current goals include investigation of the extended phenotypic effects of testosterone on a male's associates, including his mate and offspring. We are also investigating constraints on testosterone, including correlated responses in females and effects of testosterone on males during the non-breeding season.
Our studies of migration have focused on factors that promote site fidelity, the role of experience in regulating onset and termination of migration, and the relative importance of a series of selective factors in shaping the distance an individual migrates. These factors include dominance status in winter, arrival time at breeding areas in spring, risk of mortality during migration, and physiological adaptations (such as fattening) for coping with unpredictable environments.
Justin Kumar
Lab Website: www.indiana.edu/~kumarlab/. A crucial task for nearly all multicellular organisms is to create complex three-dimensional organs such as the brain, the eye, and the heart (just to name a few). The solution to this problem involves the tissue in question adopting the correct identity, growing to an appropriate size, dividing itself into required subdomains, and specifying all needed cell types. Failure to execute any of these processes correctly can be disastrous in that the organ may fail to develop or function properly. Such errors are the underlying cause of many human congenital disorders such as anencephaly, spina bifida, and anophthalmia.
We use the developing compound eye of the fruit fly, Drosophila melanogaster, as our experimental model system to study the above developmental processes. The eye is an ideal system because it contains a limited number of different cell types and its cellular architecture as well as its developmental history has been described in exquisite detail. In addition, we can take advantage of the fact that hundreds of genes and mutations that affect eye development have been identified over the last century. Our goals are to understand the molecular and developmental mechanisms that underlie tissue fate selection, growth, and pattern formation.
Jennifer Lau
Our work combines community ecology with evolutionary ecology—often capitalizing on long-term experiments—to study how human-caused global changes influence the ecology and evolution of plants and the insects and microbes with which they interact. Recent projects focus on: 1) the potential for rapid evolution and interactions with microorganisms to mitigate (or sometimes exacerbate) the effects of global change on plants, 2) the repeatability of evolutionary change in plant-microbe mutualisms, 3) the influence of genetic variation on prairie restorations, and 4) the effects of global warming on biological invasions.
Soni Lacefield
Lab Website: http://lacefieldlab.bio.indiana.edu. The goal of our research is to understand the cell cycle regulatory network leading to the segregation of chromosomes in mitosis and meiosis. Errors in chromosome segregation can have devastating consequences. In mitosis, chromosomal instability is a hallmark of cancer. In meiosis, chromosome mis-segregation can result in miscarriage, infertility, and trisomy conditions such as Down syndrome, the leading genetic cause of developmental disability. We are interested in understanding how the cell prevents errors in chromosome segregation by analyzing how the cell cycle progresses through a series of ordered events, how chromosomes properly attach to the spindle, and how this attachment is monitored by the spindle assembly checkpoint. Our primary model system is the budding yeast, S. cerevisiae, as it allows us to use powerful genetic, biochemical, and cell biological tools to address the mechanisms of how cell cycle proteins are regulated.
Jay Lennon
Microorganisms are the most abundant and diverse life forms on Earth. They have fast reproductive rates and evolve rapidly to changes in their environment. Microbes also carry out processes that are critical for the stability of natural and managed ecosystems.
We study the ecology and evolution of microbial communities. We are interested in the factors that generate and maintain microbial biodiversity. In turn, we seek to understand the implications of microbial diversity for ecosystem functioning. Our research uses various tools including molecular biology, simulation modeling, laboratory experiments, field surveys, and whole ecosystem manipulations in a wide range of habitats.
Curt Lively
Evolution and coevolution; sex, virulence and genetic diversity in host-parasite interactions.
Jake McKinlay
The vast majority of life on Earth is microbial. Within this microbial life is a profound diversity of lifestyles. Our lab studies the diverse ways that microbes convert simple forms of matter and energy into complex living cells that sense and respond to their environment. Areas actively under study include strategies that microbes use to thrive in the absence of oxygen, partnerships wherein microbes exchange essential nutrients to survive, and the microbial conversion of renewable resources into biofuels.
Scott Michaels
A longstanding interest in my laboratory is the regulation of flowering time. Understanding how undifferentiated cells make developmental decisions is a central challenge in biology. In the model plant Arabidopsis, stem cells in the shoot apical meristem (SAM) give rise to all of the above-ground parts of the plant. Early in development, the SAM gives rise to vegetative structures (e.g., leaves), but later switches to produce the reproductive structures (flowers). The timing of this transition is not predetermined and can be influenced by multiple pathways that integrate both endogenous signals and environmental cues. We are particularly interested in the role of that the floral repressor FLOWERING LOCUS C (FLC) plays in the regulation of flowering. FLC is the major target of the vernalization pathway (the promotion of flowering by cold). Vernalization results in a mitotically stable epigenetic repression of FLC that is mediated by repressive histone modifications, such as H3K27me3. Because of the epigenetic regulation of FLC, our work on flowering time has led to the discovery of a number of epigenetic regulators that play much broader roles in development.
Our current research combines flowering time, gene regulation, epigenetics, and chromatin structure/function. Our laboratory has discovered a previously undescribed class of Arabidopsis transcription factors, BORDER (BDR) proteins, that are providing insight into the relationship between the 3-dimensional arrangement of chromatin and transcription. Changes in gene expression play a central role in development, as well as responses to environmental stimuli/stress. Depending on the situation, hundreds to thousands of genes will show significant changes in expression. A major challenge during these large-scale changes in gene expression is to ensure that changes are restricted to target genes and do not affect the expression of neighboring genes. In animals, CCCTC-binding factor (CTCF) plays a critical role in the formation of chromatin loops and the activity of insulator sequences that separate transcriptional domains. Despite the fact that CTCF homologs are not found in plants, chromatin loops are a significant feature of the Arabidopsis genome, where intragenic “gene loops” often occur between the 5’ and 3’ regions of genes. The function of these gene loops, as well has how they are formed in the absence of CTCF-type insulator proteins, are currently unclear. Our work on BORDER (BDR) proteins are providing insight into the relationship between the 3-dimensional arrangement of chromatin and transcription. BDR proteins interact with RNA polymerase II (Pol II) and are overrepresented in the 5’ and 3’ regions of genes containing gene loops. In bdr mutants, the expression of the loop-containing gene is unaffected, however, the expression of genes that are located downstream on the same DNA strand from the loop-containing gene are downregulated. This suggests a model in which BDR interacts with gene loops to prevent the transcription of upstream genes from interfering with the expression of downstream neighbors. In our future research, will use a range of complementary approaches to investigate the role of BDR proteins in gene loops and transcriptional regulation. These will include using HiC and related techniques to determine the requirement for BDR proteins in the formation and/or function of gene loops, using biochemistry to determine the effect of BDR on Pol II elongation and/or pausing, and using the regulation of flowering time as a system to study the role of BDR proteins in development. Because proteins with BDR-like domain structures occur in plants, animals, and yeast, we believe the knowledge gained in these studies will have broad applications, including human health and food security.
Armin Moczek
Our lab addresses a fundamental question in biology: how do novel phenotypic traits originate and diversify in nature? We use a wide range of approaches to address this question from different perspectives, and on different levels of biological organization. We use behavioral and ecological approaches in the lab and field on experimental and natural populations to understand when and how ecological processes can drive phenotypic evolution. We employ standard developmental techniques and growth manipulations to address physiological mechanisms of phenotype formation and evolution. Lastly, we rely on an increasing range of developmental-genetic and molecular tools (gene expression, gene function analysis, genomic and proteomic approaches) to investigate the genetic and genomic regulation of phenotype expression and diversification.
Leonie Moyle
I am interested in the genetic basis of adaptation and speciation, and the evolutionary forces responsible for these processes. Despite more than a century and a half of research, we still understand little about Darwin's 'mystery of mysteries' - the origin of new species. Many basic questions remain: What drives diversification and speciation in natural systems? What is the genetic basis of reproductive incompatibility? How important are adaptive processes in the evolution of reproductive barriers? Do dominant modes of speciation differ among diverse biological systems?
Tuli Mukhopadhyay
Alphavirus Structure and Assembly My lab is focused on examining molecular interactions required for efficient assembly and release of infectious virus particles. We work with alphaviruses which are enveloped, positive-strand RNA viruses that are transmitted to a variety of hosts by mosquitoes. Their life cycle is comprised of receptor mediated host-cell infection, viral-host membrane fusion, genome replication, virus assembly and budding.
Irene Newton
My research interests span the areas of microbiology, genomics, and evolution. A common thread in my research is the following question: What is the molecular basis of interactions between bacteria and eukaryotes and ultimately, how do these interactions affect the diversity, population structure, and genomic evolution of bacteria? In order to answer these questions we use a series of molecular and bioinformatic techniques including functional genomics, computational evolutionary analyses, and genetic screens. We currently focus on two groups of insect-associated organisms: the ubiquitous reproductive parasite Wolbachia pipientis and the microbiota of honey bees. In the first project we're exploring the molecular interaction between Wolbachia and its insect hosts and how these interactions affect genomic evolution. In the second project, we work to understand how host genetic diversity affects bacterial diversity in the context of Apis mellifera, the honey bee.
Richard Phillips
My research broadly seeks to quantify and better understand how plants and soil microbes influence energy flow and nutrient cycling in terrestrial ecosystems in the wake of human-accelerated environmental change. Of particular interest is the degree to which plant-microbial interactions in soils influence feedbacks to regional and global change through their effects on ecosystem carbon storage and nitrogen and phosphorus retention. I use a complimentary suite of approaches that integrate field observations with novel techniques (e.g. stable and radioactive isotopes) and controlled environmental systems (e.g. growth chambers, FACE sites) to address questions that intersect plant physiological ecology and soil microbial ecology in an ecosystem context.
Kimberly Rosvall
Research in the Rosvall lab seeks to identify the genomic and physiological bases of behavioral adaptation and plasticity, and how these mechanisms change over evolutionary time. We approach these questions by combining conceptual and analytical tools from animal behavior, neuroendocrinology, evolutionary ecology, physiology, and genomics - almost entirely by studying free-living birds.
Sidney Shaw
The Shaw laboratory studies how the microtubule cytoskeleton organizes and influences cellular morphogenesis. We focus on the interphase microtubule arrays in Arabidopsis plants as a model for understanding how cells generate ordered patterns in acentriolar cells. If the randomly arranged microtubules in a growing plant cell organize into a co-aligned array, like hoops around a barrel, the cell will elongate into a rod shape instead of a sphere. The influence of the microtubules comes as a result of their ability to organize and reorganize in response to spatially defined cellular cues. The fundamental mechanisms by which the microtubules recognize the cell axis, become co-aligned, and alter the cell wall properties to influence cell expansion are not yet known.
Troy Smith
How does the nervous system control species-typical behavior and how do hormones influence neural physiology to modify behavior? Our laboratory addresses these questions by studying the neuroendocrine control of sexually dimorphic communication behavior in weakly electric fish.
Nicholas Sokol
MicroRNAs are a recently discovered class of small RNAs that regulate the expression of target genes. Some microRNAs have been highly conserved across millions of years of animal evolution, suggesting that their regulation of particular target genes plays an essential role in animal development and/or function. Yet, for many of these conserved microRNAs, their relevant gene targets as well as their developmental function are not known. We use the fruitfly Drosophila melanogaster to identify the molecular and cellular roles that evolutionarily conserved microRNAs play in the formation and function of complex organisms.
Jason Tennessen
Both cancer cells and embryonic stem cells rely on a specialized metabolic program known as aerobic glycolysis to support their rapid proliferation. Aerobic glycolysis, which is also known as the Warburg effect in the context of tumor metabolism, is characterized by the increased expression of glucose transporters, enzymes involved in glycolysis, and other proteins that promote glycolytic flux. This up-regulation of glycolysis, however, is not solely used to produce energy. Instead, the abundant supply of glucose-derived metabolites is used to generate the amino acids, nucleotides, and fatty acids required for rapid proliferation. Meanwhile, a significant quantity of the pyruvate generated during this process is not oxidized in the mitochondria, but rather is converted into lactate—a hallmark of aerobic glycolysis that is required for maximal glycolytic flux.
Dan Tracey
Research in the Tracey laboratory aims to understand the general principles that govern the specification and function of neuronal circuits. We study this problem using the fruitfly Drosophila melanogaster whose relatively simplified nervous system must perform many of the same computations that are carried out by our own. Despite its simplified brain,Drosophila perform an array of complex behaviors. Powerful genetic tools of Drosophilaenable the dissection of neural circuits with a precision that is not matched in any other model system. Genetically encoded calcium sensors allow us to measure the neuronal activity of identified neurons while neuronal silencers and activators allow us to determine the behavioral consequences of the same activity. Optogenetic tools allow us to activate behaviors via remote control by simply shining light on the animals. Our primary focus is to use the fly model to identify circuits and genes that function in nociception. These studies lead to a greater understanding pain signaling. In addition, we are attempting to identify the molecules that are used in neurosensory mechanotransduction, which underlies our sense of touch. Finally, we are attempting to build trans-synaptic tracers for use in Drosophila. These tools will enable visualization of interconnected circuits in the brain of flies and may eventually be extended to studies in mammals
Michael Wade
Evolution in Metapopulations; Genetic basis of speciation in Tribolium; Epistasis; Evolutionary genetics of maternal effects; Sexual selection and alternative male mating strategies; Coevolution of arthropod hosts and Wolbachia endosymbionts.
Malcom Winkler
The general goal of my research program is to understand signal transduction, regulatory mechanisms, and supramolecular complexes that mediate the stress responses, metabolism, cell structure, and pathogenesis of this bacterium. At one level, our work is providing fundamental information about the roles played by physiology, protein complexes, and metabolism in the pathogenesis of this bacterial species. At another level, we are gaining insights into the biology of S. pneumoniae, and by inference other Streptococcus species, which are distinctive, fascinating organisms that carry out many processes by mechanisms different from those of model bacteria like Bacillus subtilis. Therefore, besides understanding pathogenesis, there is the expectation of learning new biological principles from studies of S. pneumoniae.
Andrew Zelhof
Photoreceptor cell morphogenesis:
An essential feature of photoreceptor cells is the presence of an elaborate membrane structure that houses the millions of receptor proteins required for the detection of light. Whether it is the rhabdomeres of invertebrate photoreceptors, or the membrane discs of vertebrate photoreceptor cells, these sub-cellular compartments are fundamental not only for photon capture, but in addition for the functional integrity of the photoreceptor neuron. Surprisingly, in spite of their importance -and vital roles- in cell biology and sensory physiology, very little is known about the molecular events choreographing the biogenesis and maintenance of rhabdomeres or outer segments discs.
Lane Baker
Lane is interested in the electrochemical methods for analysis and imaging. Current work in his group is focused on applications of nanopores for the development of chemical and biochemically selective membranes, sensor development and electrochemical imaging.
David Clemmer
A major area of interest to our group is protein structure. Although the "native" solution structures of many proteins are known, little is known about how denatured forms fold into the native state. This is because isolating and determining structures for a large number of solutions-phase intermediates is difficult. We are approaching this problem quite differently by studying the structures of naked proteins in the gas phase. Although it seems unlikely that proteins in the gas phase will have structures that are identical to those found in solution, it is straightforward to separate gas-phase intermediates and follow the dynamics associated with folding.
A major area of interest to our group is protein structure. Although the "native" solution structures of many proteins are known, little is known about how denatured forms fold into the native state. This is because isolating and determining structures for a large number of solutions-phase intermediates is difficult. We are approaching this problem quite differently by studying the structures of naked proteins in the gas phase. Although it seems unlikely that proteins in the gas phase will have structures that are identical to those found in solution, it is straightforward to separate gas-phase intermediates and follow the dynamics associated with folding.
Silas Cook
Inspiration for research in the Cook lab derives from the complex challenges presented by natural products. Through the broad study of natural product synthesis, the group seeks to uncover new strategies in synthesis, catalysis and molecular pharmacology. Target molecules are selected for both their elaborate architecture and biological activity. Furthermore, the group's methodology program aims to discover new or improved methods and catalysts for application toward the synthesis of interesting chemical entities.
Charles Dann
The research in Dr. Dann's laboratory focuses on determining atomic resolution structures of RNA and protein macromolecules by X-ray crystallography. An emphasis is placed on cis-acting regulatory RNAs termed riboswitches and the gene products (proteins) that they regulate. In addition to structural biology, we are interested in both manipulating riboswitches to generate engineered molecular sensors (on/off switches) and testing riboswitches as targets in small molecule screens to discover new antibiotics. Projects in the laboratory afford the researcher opportunities to learn computational modeling, structural and biophysical techniques as well as general biochemistry and molecular biology in both RNA and protein systems.
Romualdo de Souza
The focus of our research is heavy-ion reaction dynamics spanning the range from the Coulomb barrier to intermediate energies (upto 200A MeV). Our research emphases are:
Trevor Douglas
Research in the Douglas Lab is focused on using natural biochemical structures, specifically protein-cages and viral capsids, to design functional nano-material systems. Protein-cages are molecular containers with three distinct interfaces that impart function. These are: the exterior surface, the interior surface, and the interface between the subunits that make up the overall architecture. Current work in the Douglas Lab is focused on developing both chemical and genetic methods for the development of protein cages for for applications in catalysis, medicine, nano-particle formation and higher-order materials construction. Current projects are primarily focused on the virus-like particle (VLP) from Salmonella typhimurium bacteriophage P22, a robust 60 nm diameter cage composed of 420 copies of a single coat protein and 100-300 copies of an accessory scaffolding protein that template self-assembly from the capsid interior.
Bogdan Dragnea
Exploring and emulating the synergies encountered in self-organizing biological matter has been a central theme of our research program. In terms of scope, our activities fit into four main categories:
Amar Flood
We think of chemical compounds as functional molecules that can serve as machines akin to those in the world around us. Our research focuses on molecular wires for use in electronic circuits and on molecular motors to power molecular machines. In practice, we use standard synthetic techniques in conjunction with self-assembly to make the compounds and incorporate them into hybrid devices that we then interrogate using electrochemistry, spectroscopy and probe microscopy.
Joseph P. Gerdt
Microorganisms are competing, cooperating, and communicating everywhere. We are fascinated by this and want to understand the molecules that regulate these interactions. We first grow mixtures of bacteria, fungi, protozoans, and viruses to see how they interact. Then we isolate the molecules they produce and use chemical characterization methods (e.g., mass spectrometry, nuclear magnetic resonance) to identify them. We use biological assays to uncover which molecules cause which interspecies interactions. We then apply these molecules as antimicrobial drugs, anticancer agents, or molecules that treat pain without addiction.
David Giedroc
Transcriptional metalloregulatory proteins, with a particular focus of zinc- and copper-specific metal sensor proteins from bacterial pathogens, translational frameshifting, and RNA structure and function in mammalian coronavirus replication.
Srinivasan Iyengar
We deal with the development of new theoretical and computational methods and the subsequent implementation of these into efficient computational models. The methods are derived with an aim to help solve problems in biophysical chemistry and the nano-material science. Our instrumentation is the computer and the mathematical and theoretical frameworks that we derive, and our field of study is the challenging and richly interesting world of chemistry.
Stephen C. Jacobson
Research in the Jacobson group is directed toward miniaturization of analytical instrumentation with an emphasis on developing micro- and nanofluidic devices for chemical and biological assays. His research group is currently working in the areas of microfluidic separations, nanofluidic transport, cancer screening, virus sensing and assembly, and bacterial development and aging.
Caroline Jarrold
All research projects in the CC Jarrold group are motivated by problems associated with energy and the environment. We have projects geared toward two classes of systems: (1) Design and optimization of heterogeneous catalysts with lower operating temperatures (and therefore, lower energy consumption) in common catalytic applications, or for photocatalytic fuel production from water or CO2, and (2) Atmospheric reaction complexes involving oxidation of volatile organic compounds. Our research "toolbox" includes gas-phase reactivity studies using high-pressure, fast flow reactors, mass spectrometry, anion spectroscopy (anion photoelectron spectroscopy and resonant two-photon detachment spectroscopy) and density functional theory calculations, in close collaboration with the Krishnan Raghavachari research group.
Liang-shi Li
We study molecular interactions, self-assembly, charge and energy transfer on multiple length scales (from nanoscale to macroscopic scale), and explore their applications in organic electronics, energy conversion, and biological imaging. Our work extends from synthesis of organic compounds, characterization of their properties, to making and testing functional devices.
Martha Oakley
Dr. Oakley and her research group have applied their coiled-coil expertise to a fascinating family proteins that contain a long (50 nm) antiparallel coiled coil. These structural maintenance of chromosomes (SMC) proteins are crucial for the faithful organization and segregation of chromosomes in essentially all organisms. The Oakley lab's initial work has focused on bacterial SMC proteins, with an emphasis on the E. coli condensin, MukB. Their contributions to the field have included mapping the structure of the coiled coil domains of MukB; solving the structure of the hinge domain of MukB, in collaboration with James Berger's lab at UC Berkeley; and identifying the topoisomerase IV subunit, ParC, as a new binding partner for MukB.
Peter Ortoleva
Our activities focus on research and education regarding the structure and function of living and non-living materials at scales from the atomic to the global.
We are developing the mathematical and computational methods needed to understand the physics and chemistry of these systems. The latter range from macromolecules, viruses and intelligent nanoparticles to supra-kilometer scale structures in the earth's sub-surface.
Applications range from the design of vaccines, nanocapsule drug delivery systems and a variety of nanomaterials, to the exploration and recovery of petroleum resources. Techniques used include multiscale theory, statistical mechanics for quantum and classical systems, and bioinformatics.
Dennis Peters
The Peters Group is a multidisciplinary, electrochemistry research group engaged in a variety of individual and collaborative efforts which can be classified into the broad areas of mechanistic organic, environmental, and biological electrochemistry.
Our research goals include:
Nicola Pohl
The Pohl research group is finding new ways to make and analyze sugars to dissect their important roles in plant, animal, and human biology and to design therapeutics.
One major long-term goal is to rationally design therapeutic interventions such as vaccines based on a deeper knowledge of these carbohydrate interactions. Most recently, we have created the first automated solution-phase method to readily synthesize oligosaccharides using methodologies that we are applying to other biologically active molecules. This automated method circumvents key problems encountered with the solid-phase approaches that allowed commercial automated synthesis of other biopolymers like DNA and peptides. We have also discovered that the same fluorocarbon tag that facilitates our automated synthesis can be used to directly surface-pattern these tagged molecules to form carbohydrate microarrays for screening against carbohydrate-binding proteins. In addition, the group has found several extremely heat-stable enzymes analyzed by mass-spectrometry-based assays to make carbohydrate structures.
Krishnan Raghavachari
Prof. Raghavachari is perhaps best known for his work on the development and applications of electron correlation techniques in computational quantum chemistry. His work covers a broad spectrum of problems ranging from chemical bonding in small clusters to computational investigations of semiconductor and nanoscale materials. Most recently, his group is also focused on the development of the new electronic embedding methods in quantum chemistry and the development of accurate methods for theoretical thermochemistry.
James Reilly
Our research group exploits the remarkable properties of laser light in various experiments in bioanalytical chemistry and high resolution mass spectrometry. We are interested in both the development of new techniques and in their application to solving scientific problems.
Sara Skrabalak
Research in the Skrabalak Laboratory aims to provide general design criteria and strategies for the rational synthesis of new nanomaterials with desirable properties. The area of nanoscience concerns itself with materials that are on the scale of one billionth of a meter. When an inorganic material is confined to this size regime in the form of nanocrystals, new and size-dependent properties often emerge. These properties can be used in new technologies with the potential to address critical social needs such as better tools for disease diagnosis and treatment and platforms for sustainable energy. Central to these new technologies is the ability to synthesize high-quality nanomaterials, where the composition, size, shape, and architecture of the nanocrystals are precisely controlled. Our research program provides general guidelines for nanomaterial synthesis by demonstrating new strategies that are connected to fundamental chemical and physical principles. These efforts are directed toward materials that are compositionally complex (and thus traditionally more challenging to achieve as high-quality samples) and toward the development of scalable routes to nanomaterials.
Michael VanNieuwenhze
The principal focus of our research is to use the power of organic synthesis to study problems of biological and medicinal interest.
Our research interests include: Synthesis, study, and design of antibiotics that inhibit bacterial cell wall biosynthesis; peptidoglycan biosynthesis and bacterial cell morphology; development of HBV capsid-binding probes and assembly-directed antivirals; oxidized phospholipids in disease and diagnostics.
Yan Yu
Research in the Yu laboratory is at the interface of materials, bioanalytical, and physical chemistry. The research vision is to quantify and control cell behavior with novel materials and chemical approaches. Specific research projects in the Yu group include: (1) self-assembly and interactions of lipid membranes; (2) biomaterials-cell interactions: develop biomimetic materials to manipulate cell behavior; and (3) cell-cell interactions: quantify how molecular interactions and dynamics in membranes determine cell functions.
Jeff Zaleski
Designing Biomedical Reagents for
Using Spectroscopy to Probe
Novel Inorganic/Organic Hybrid Materials
Jonathon Crystal
Research in my lab is focused on developing new animal models of cognition. One benefit of studying cognition in animals is that it may provide insight into impairments in cognition observed in people. Cognitive impairments in people are debilitating, and developing insight into the origins of such impairments offers a tool to improve the effectiveness of treatments. Significant obstacles nonetheless impede the development of animal models of disordered cognition. Although there is a long history of studying learning and memory in animals, these types of cognitive processes may not match those observed clinically (e.g., Alzheimer's disease features severe impairments in episodic memory). Thus, it is possible that drug-development programs may identify agents effective at the pre-clinical level that subsequently fail when translated to a clinical trial in people. Ultimately, the expansion of the suite of cognitive processes that may be modeled in animals may translate to improved therapies for debilitating memory impairments observed in humans. The long-range goal is to understand how animals process and remember events in time and provide a neuroanatomically guided theoretical framework for understanding memory disorders.
Current projects in the lab focus on: Animal models of episodic memory. Animal models of prospective memory. Animal models of retrieval practice.
Eduardo Izquierdo
Professor Izquierdo's main interest is in understanding how behavior arises from the interaction of the organism's brain, its body, and its environment. He approaches this from a theoretical perspective, analyzing artificially evolved, situated, and embodied agents using the tools of dynamical systems theory.
Ehren Newman
We study how neural circuits generate memory using methods from systems-, behavioral-, and computational- neuroscience. We use electrophysiology, optical recording and circuit manipulation techniques, and computer simulations to study how memories are formed and retrieved in freely behaving rats.
Franco Pestilli
The Cognitive and Computational Neuroscience lab lead by Dr. Pestilli works at the interface between computational neuroimaging, data science and neuroinformatics. Primary goal is to understand how human perception and cognition is implemented in the biological tissues properties and activity of the brain cells. Projects in the lab span among different topics such as perception, attention, and motivation as well as, Vision, clinical neuroscience, aging. Major effort in the lab is the development of the new generation cloud computing platform for neuroscience research: brainlife.io
Simon Brassell
Research focused on deciphering biogeochemical responses to climatic and environmental change that are preserved in the occurrence, abundance, and isotopic composition of organic matter in sediments.
Activities focused on the exploration and application of biomarkers, and their isotopic signatures, as environmental, paleoclimatic, stratigraphic and geochemical tools to better understand:
James Brophy
Research interest centers around the chemical and physical processes involved in magmatic differentiation. My work utilizes a wide range of techniques and approaches including geologic field mapping, petrologic and geochemical analysis (major and minor element geochemistry, electron micro-probe) and fluid dynamic modeling. Another area of interest is one-atmosphere experimental petrology.
Douglas Edmonds
My research focuses on the sedimentology, stratigraphy, and geomorphology of depositional sedimentary systems. Example projects and scales of interest range from: secondary circulation and turbulence to formation of reach-scale features such as levees, to whole system behavior of deltas and river belts. I use a combination of mathematical modeling, field observation, and occasionally experimentation to understand these systems. My research is generally directed toward understanding the coupled surficial and sedimentological evolution of these systems.
Michael Hamburger
Research interests include seismotectonics, dynamics of earthquake and volcanic processes, and application of satellite geodetic measurements to geodynamic problems. He currently has active research programs in the subduction zone environment of the Philippine island arc, as well as in zones of continental extension in the Long Valley Caldera region of California and the intraplate environment of the central U.S.
Claudia Johnson
The focus of my research is to evaluate evolutionary processes in the paleotropics. The tropical reef ecosystem provides the empirical database that I analyze using statistical methods. I then synthesize patterns and processes affecting reef evolution and demise, and evaluate the biotic changes in the context of the tropical ocean-climate system. At present, I examine reefs that evolved under Cretaceous "greenhouse", Pleistocene "icehouse" and Oligocene transitional climate states.
P. David Polly
We study vertebrate paleontology with a focus on how earth history, especially changing climates and geographies, has affected vertebrate evolution and community composition. Our work includes trait-based studies of community responses to environmental change, geometric morphometric analysis of evolution and morphology, phylogenetics, biogeography, and speciation. Our studies synthesize data from regional and continental geographic scales and across historical, Quaternary, and Cenozoic time scales.
Juergen Schieber
Early diagenetic mineral formation in shales. Preservation of microbes in mudstones. Provenance of quartz in mudstones.
Chen Zhu
We study the chemistry of water and its reactions with minerals and rocks. Through these reactions, water acquires chemical constituents and isotopic signatures. The chemical and isotopic signatures are useful to map the movement of fluid flow and allow us to calculate the in situ rates of chemical reactions under geological conditions. On a global scale, these chemical reactions are a key component of the interactions between the Earth’s hydrosphere, lithosphere, biosphere, and atmosphere. Many fundamental processes in Earth’s geological systems, such as chemical weathering, diagenesis, and the movement, distribution, and global cycling of chemical elements are related to these interactions.
How water reacts with minerals and rocks is not merely an intellectual curiosity, but is intimately related to societal needs.
Professor Zhu’s research has addressed water quality (what chemicals are in water, how did they get there, and where are they going to end up), water quantity (how much water recharges an aquifer and whether the amount of withdrawal is environmentally sustainable), arsenic, antimony, and uranium contamination of surface and ground water, and large scale numerical models of water flow and contaminant transport.
My research involves the analysis for food security, food sovereignty and food justice in the US.
Justin Maxwell
My research focuses on climate variability and change with a particular focus on drought conditions. I use both instrumentally record climate data (i.e., data from weather station and proxy data from tree-rings. I have a laboratory fully equipped to conduct tree-ring research to examine past climate and look at historic climatic variability to help put the modern climate in a historical context.
Claire Walczak
Our lab is interested in the fundamental mechanisms that cells use to accurately distribute their genetic material to the two daughter cells. Defects in this process lead to aneuploidy and genomic instability, which are hallmarks of cancer. Using a combination of biochemistry, biophysics, cell biology, genomics, and high resolution imaging techniques we ask fundamental questions about how cells maintain mitotic fidelity and how cell maintain proper ploidy.
John Beggs
Research combining biological experiments and computer simulations directed toward understanding fundamental emergent properties of living neural networks and how these properties may contribute to neural function.
Heather Bradshaw
During my graduate career, I studied behavioral responses to uterine and vaginal stimulation in rats in concert with neurophysiologic measurements in the brainstem in order to understand neuronal responses to stimulation of reproductive tissue. These studies identified novel processing of neuronal information from stimulation of the uterus, cervix, and vagina in the brainstem and showed that both the behavioral and neuronal responses changed with variations in circulating hormones.
To further understand neuronal processing at the cellular level I began work in the field of endogenous cannabinoid lipid signaling. My studies in this field are centered on the relationship of endogenous cannabinoids and uterine and vaginal neurophysiology. More specifically, our current work focuses on the regulation of uterine contractions by endogenous cannabinoid signaling lipids.
As a laboratory in both the department of Psychological and Brain Sciences and at the Kinsey Institute our focus will be to more fully understand how different chronic pain conditions in humans may be caused by the loss of the regulation of uterine and vaginal neurophysiology. There are very little data on vaginal neurophysiology in particular in humans, which is a direction of study that we will undergo within the Kinsey Institute. By crossing-over into human studies of the regulation of vaginal smooth muscle tone, our goal is to provide a better framework for understanding chronic conditions involving vaginal function.
Joshua Brown
My interests are wide-ranging but focus on the frontal lobes. How do people and animals learn, optimize, and control goal-directed behavior in complex and changing environments? These abilities entail reinforcement learning, planning, prediction, expectation, evaluation, and sequential ordering of movements, in addition to complex sensory processing. Currently I have three main research thrusts:
1) Develop computational models of brain circuitry involved in cognitive control. My recent model of the Anterior Cingulate Cortex, or ACC (Brown & Braver, 2005, Science), suggests that ACC is critically involved in predicting the likelihood of making a mistake. Current simulations further predict that ACC activity also depends on the predicted severity of the consequences of a mistake, should one occur.
2) Test computational model predictions with fMRI. Computational modeling often provides counter-intuitive, non-trivial predictions that strongly guide empirical investigations. We are beginning to test whether ACC activity in healthy individuals reflects perceived behavioral risk, as predicted by the computational modeling work.
3) Investigate the neural bases of cognitive impairment in clinical populations using fMRI and computational modeling. We are interested in how impairments in working memory interact with possible impairments in an individual's ability to monitor their own behavior. Computational modeling provides a framework for understanding the nature of information processing in both normal and pathological human brains.
Jonathon Crystal
Research in my lab is focused on developing new animal models of cognition. One benefit of studying cognition in animals is that it may provide insight into impairments in cognition observed in people. Cognitive impairments in people are debilitating, and developing insight into the origins of such impairments offers a tool to improve the effectiveness of treatments. Significant obstacles nonetheless impede the development of animal models of disordered cognition. Although there is a long history of studying learning and memory in animals, these types of cognitive processes may not match those observed clinically (e.g., Alzheimer's disease features severe impairments in episodic memory). Thus, it is possible that drug-development programs may identify agents effective at the pre-clinical level that subsequently fail when translated to a clinical trial in people. Ultimately, the expansion of the suite of cognitive processes that may be modeled in animals may translate to improved therapies for debilitating memory impairments observed in humans. The long-range goal is to understand how animals process and remember events in time and provide a neuroanatomically guided theoretical framework for understanding memory disorders.
Current projects in the lab focus on: Animal models of episodic memory. Animal models of prospective memory. Animal models of retrieval practice.
Greg Demas
The primary focus of our laboratory is in the general area of "ecological physiology." Specifically, we study of the interactions among the nervous, endocrine and immune systems and behavior in a variety of ecologically relevant environmental contexts.
Joseph Farley
Dr. Farley studies the cellular and molecular bases of behavioral and neural plasticity, particularly those which involve changes in the biophysical properties of excitable membranes. Using voltage- and patch-clamp recording techniques with native neuronal membranes and artificial bilayers, as well as site-directed mutagenesis studies of cloned ion channel subunits in heterologous expression systems (e.g., Xenopus oocytes), he studies the cellular and molecular bases of associative learning in invertebrates and cellular models of memory (e.g., LTP) in the mammalian brain. Changes in potassium and calcium ion channels, their contributions to cellular mechanisms of coincidence- and non-coincidence detection, and the molecular mechanisms underlying those changes, such as protein kinase C-, PKA, tyrosine kinase-, and phosphatase-dependent (PP1, PP2B) changes in channel activities are of current interest.
Andrea Hohmann
My research has focused on understanding pain modulation from a neurochemical perspective. The discovery of cannabinoid receptors and identification of brain constituents that act at these receptors established the existence of an endogenous cannabis-like (endocannabinoid) transmitter system. My research has identified functional roles of the endocannabinoid system in the nervous system and mapped it's distribution in sensory pathways. My research has identified enzymes implicated in endocannabinoid deactivation as novel therapeutic targets. My laboratory strives to maximize the therapeutic potential of endocannabinoid signaling systems while minimizing unwanted central nervous system side-effects (e.g. psychoactivity and addiction). My research program combines behavioral, drug self-administration, neuroanatomical, neurophysiological and molecular approaches to study cannabinoid mechanisms for suppression of pain and stress responsiveness.
Laura Hurley
Sensory systems demonstrate an amazing ability to filter environmental information depending on the prevailing context. This ability allows animals to act appropriately in situations such as interaction with members of their species, or in response to potential threats. Sensory filtering is also important in human perception, as in hearing and understanding speech during social interactions, and in disorders in such perceptual processes. Work in my lab explores a neurochemical signal, serotonin, which is one of the mechanisms allowing the auditory system to filter important information. We are interested in the function of serotonin-auditory interactions, how these are influenced by behavioral context, and how they change the way the auditory system interprets behaviorally relevant information. In order to address these issues, we use a range of techniques from analysis of social behavior and vocalizations in mice, to several types of electrophysiological measurements.
Ken Mackie
The Mackie lab examines the role and function of the endocannabinoid system by using a combination of electrophysiological, imaging, biochemical and immunological approaches. The endocannabinoid system is comprised of cannabinoid receptors, endogenous cannabinoids (endocannabinoids), and the enzymes that regulate the production and degradation of endocannabinoids. ?9THC, the principal psychoactive component of cannabis, interacts with this system to produce the classic effects of cannabis intoxication. In addition, this system is widely involved in multiple physiologically important processes including memory, motivation, movement, analgesia, and emesis. Through our studies, we hope to better understand the implications of social and therapeutic use of drugs that influence this fascinating system.
Ehren Newman
We study how neural circuits generate memory using methods from systems-, behavioral-, and computational- neuroscience. We use electrophysiology, optical recording and circuit manipulation techniques, and computer simulations to study how memories are formed and retrieved in freely behaving rats.
Franco Pestilli
The Cognitive and Computational Neuroscience lab lead by Dr. Pestilli works at the interface between computational neuroimaging, data science and neuroinformatics. Primary goal is to understand how human perception and cognition is implemented in the biological tissues properties and activity of the brain cells. Projects in the lab span among different topics such as perception, attention, and motivation as well as, Vision, clinical neuroscience, aging. Major effort in the lab is the development of the new generation cloud computing platform for neuroscience research: brainlife.io
Anne Prieto
The research in my laboratory focuses on understanding the signaling mechanisms that underlie the establishment and maintenance of mature neuronal phenotypes in the developing brain. In particular, we investigate the potential functional roles of receptor protein tyrosine kinases (RPTKs) and their ligands in the central nervous system. Currently, we study a novel RPTK family, the Axl subfamily, which includes at least 4 members, Tyro-3, Axl, Mer and Rek. They share a common ligand, the molecule Gas6 (for growth-arrest specific gene-6) capable of inducing receptor phosphorylation and thus initiating intracellular signaling events upon binding. Our current efforts are focused on possible roles for these receptors and their cognate ligand in promoting the survival or growth of subsets of neural cells, in mediating cell adhesion, and in modifying synaptic function and plasticity
Kimberly Rosvall
Research in the Rosvall lab seeks to identify the genomic and physiological bases of behavioral adaptation and plasticity, and how these mechanisms change over evolutionary time. We approach these questions by combining conceptual and analytical tools from animal behavior, neuroendocrinology, evolutionary ecology, physiology, and genomics - almost entirely by studying free-living birds.
Troy Smith
How does the nervous system control species-typical behavior and how do hormones influence neural physiology to modify behavior? Our laboratory addresses these questions by studying the neuroendocrine control of sexually dimorphic communication behavior in weakly electric fish.
Cara Wellman
My lab is examining the effects of chronic stress and stress hormones on behaviors mediated by prefrontal cortex, as well as the changes in neural pharmacology and morphology that underlie these effects. We have demonstrated that both chronic stress and exposure to the stress hormone corticosterone reorganize dendrites of neurons in prefrontal cortex. We are now beginning to more fully characterize these effects, assess their functional significance, and elucidate mechanisms underlying them.
The School of Optometry and vision science graduate program is a collaborative community of basic science researchers, clinicians and engineers who work together to better understand eye biology, development and disease in order to develop novel methods to diagnose, treat and prevent vision impairment.
My research has utilized the eye lens as model to study a variety of cell biology questions, including the roles of gap junction communication, the chaperone-like activity of small heat shock proteins, Eph-ephrin bidirectional signaling and cytoskeletal networks in normal cell functions. The goal of my work is to elucidate the mechanisms for establishing and maintaining lifelong homeostasis and transparency in the eye lens. Despite decades of research, there remain many unanswered questions about basic lens cell biology that hinder the development pharmaceuticals to prevent or delay age-related lens pathologies, including cataracts and presbyopia. The lab employs super-resolution microscopy, biomechanical testing, biochemistry and novel techniques to isolate and immunostain complex lens cells to link changes on the molecular and cellular level with alterations on the tissue level.
Through this program, students will learn standard cell and molecular biology techniques as well as microscopy and image analysis. Students will participate in experimental design and data analysis to develop project management skills. Co-author credit on publications will be given to those who make significant contributions to projects.
The Vision Science program at the School of Optometry is a community of vision scientists, clinicians and engineers working in the areas of eye development and function, eye biology, physiology, eye disease, visual perception, visual optics, optical imaging, etc. Ocer the years, we have had a variety of undergraduate, graduate, post-doctoral, and other trainees.
My research develops optical and software techniques to uncover the underlying causes of retinal disease and improve the management of patients. My group particularly focuses on developing cutting-edge optical imaging systems, particularly ones with low cost to enable more widespread use to combat blindness. We probe how human vision works, in both normal and diseased eyes, with the goal of maximizing visual function despite eye disease. Recently, we have begun using big data approaches to study eye movements.
Through this program, students will have the opportunity to develop and use a multidisciplinary approach, developing technical skills for a successful career. I was trained as a mathematician and science, with my initial interest in color vision spreading into clinical applications. A multidisciplinary approach has led me to applications such as laser development, use of novel wavelength ranges for biological imaging, studying light tissue interactions to obtain optical signatures of pathology, understanding the criteria that lead to being able to see specific sizes of objects, detection of previously undiscovered weak fluorophores, and processing image data in new ways to visualize the previously unseen.
The Vision Science program at the School of Optometry is a community of vision scientists, clinicians and engineers working in the areas of eye development and function, eye biology, physiology, eye disease, visual perception, visual optics, optical imaging, etc.
My research work lies at the frontier of optics, engineering and biology. My group particularly focuses on developing cutting-edge optical imaging systems to advance our understanding of how our eye work and to detect abnormalities in the cornea early on in the disease process. One aspect of my group focuses on animal research to understand the basics of our visual system. The second aspect is a patient-based research to facilitate the diagnosis and management of corneal disease.
Through this program, students will have the opportunity to develop a multidisciplinary skills-set that will help them offset challenges on the job-market and develop a successful career. I was trained myself as a mathematician and engineer and later on developed a passion for vision science. This multidisciplinary mindset has served me in a very positive way. My research interests include corneal imaging, corneal disease and mechanism, light interaction with biological tissue, interferometry, optical metrology, optical coherence tomography, fluorescence microscopy, optical design and image processing.
John Beggs
Research combining biological experiments and computer simulations directed toward understanding fundamental emergent properties of living neural networks and how these properties may contribute to neural function.
Micheal Berger
Our current understanding of elementary particle physics is dominated by the "standard model" of strong, weak and electromagnetic interactions: all predictions of the model agree well with the experimental data. However this model is almost certainly not the final story, because many puzzling questions remain to be answered: Why are there three generations of elementary particles with such a wide range in masses? What is the origin of mass? Why did nature choose the forces that we observe? These issues will be addressed in the near future at existing and planned collider facilities, so research at the microscopic frontier should be as exciting as it has been in the past. Most of my research is dedicated to exploring the possibility of physics beyond the Standard Model. We know that there must exist new forces that have remained hidden from us that will provide the answers to the above questions. My research is directed toward discovering and understanding these new interactions. Recently my research has included work on supersymmetry (an extension of the familiar spacetime symmetries) and its phenomenology, grand unified theories, particle astrophysics and cosmology, and the search for the mechanism that breaks the weak interaction symmetry. I have also been looking recently at the possibility of extending our ability to probe short distance scales with a high energy collider employing muon beams.
John Carini
Experimental condensed matter physics; quantum mechanical properties of electrons in nanostructures and disordered materials; superconductivity in nanostructures and disordered materials.
Harold Evans
I am intrigued by questions such as: "Why is there mass?" and "Why do the four fundamental forces in nature appear to be different?" Finding answers to these questions will certainly involve a deeper understanding of the phenomenon of electro-weak symmetry breaking. So it is in this area that my research interests lie. I have probed this phenomenon using a variety of tools - the tau-lepton, the b-quark, searches for new physics - and at a variety of particle accelerators - LEP, the Tevatron, LHC. I am currently a member of the large, international collaborations D0 at Fermilab outside of Chicago and Atlas at CERN near Geneva. We keenly anticipate making breakthroughs in our knowledge of electro-weak symmetry breaking in the years to come using these energy-frontier accelerators.
As an experimentalist, I am also fascinated by the devices we build to make our measurements. In particular, I am involved in several projects developing high-speed electronics to aid in the collection of the unprecedented amounts of data we will accumulate in the near future.
Charles Horowitz
Theoretical nuclear physics. Physics of neutrinos and supernovae; physics and the question of extraterrestrial life.
Alan Kostelecky
Theoretical physics
Chen-Yu Liu
My research group focuses primarily on experimental tests of fundamental symmetries. Other than using high energy colliders to directly create new particles, we search for the footprints of exotic particles in low temperature, low energy systems. These searches look for the parity violating, CP violating, or time reverseal violating features in the systems of interest.
Currently, we concentrate on two areas of low-energy particle physics. The first is the development of ultra-cold neutron (UCN) sources for fundamental physics experiments, the other is a search for the electric dipole moment (EDM) of the electron in solid state system and EDM of the neutron.
Joshua Long
Josh Long's research concentrates on experimental tests of particle physics at low energies. One experiment, under construction at the Oak Ridge National Laboratory, is a new search for a permanent electric dipole moment of the neutron (nEDM). An nEDM signal would be an example of time reversal symmetry violation and a key to understanding the matter-antimatter asymmetry in the universe. Another experiment, based at the Indiana University Cyclotron Facility, is a test of the Newtonian inverse square law (ISL) at distance ranges less than 100 microns. Modifications to the ISL at short range, arising from new elementary particles or even extra spacetime dimensions, are predicted from many models that attempt to describe gravity and the other fundamental interactions in the same theoretical framework.
Jim Musser
MINOS is an experiment based at Fermilab which is designed to search for oscillations between neutrino species. Recent results from a number of recent experiments have suggested that muon neutrinos are mixing (oscillating) with a second neutrinos species, most probably with the tau neutrino. Mixing between neutrino species is possible only if neutrinos are massive, contrary to present assumptions. MINOS promises to provide an exceptionally important result in one of the most exciting and active areas of particle physics research at this time.
NOVA is a planned experiment at Fermilab that uses the same neutrino beam employed by MINOS, with a new far detector that is optimized to observe the sub-dominant oscillations that are the key to understanding CP violation in the lepton sector.
CREST promises to provide the first measurements of the cosmic electron flux at energies greater then 10 TeV. I am the Spokesman for this multi-institutional project (which involves U. Michigan, U. Chicago, Penn State University, and Northern Kentucky University).
Phil Richerme
My research interests lie at the intersection of atomic physics and quantum information, where collections of cold, trapped ions can serve as well-isolated systems for studying quantum many-body physics or as a new computational resource for solving classically intractable problems. Each trapped ion encodes a quantum spin, and lasers provide the "connections" to couple the spins together. I am particularly interested to investigate new ion trap geometries and methods to realize 2D and 3D spin lattices, which can exhibit important physics that is inaccessible to the current 1D systems. Scaling these systems to hundreds of coupled spins (and beyond) will likely require construction of cryogenic traps, which will provide the ions exquisite isolation from their background environments.
Babak Seradjeh
The biggest mysteries of the world are not hiding only in faraway galaxies or among subatomic particles. Instead, they may be in your hand, literally, as you hold a pencil. When you use that pencil to draw a line on a sheet of paper, you are creating your own sample of "graphene," which has been hailed as a wonder material and garnered its discoverers the 2010 Nobel Prize in physics. In recent years, graphene and many other materials have been shown to host exotic physics previously thought to only exist either in the large-scale fabric of cosmos or in the subatomic space between elementary particles. This is an exciting era in the science that studies such physics in everyday materials, known as condensed matter physics. My research is focused on the theoretical study and understanding of stable exotic particles that are realized in such materials as topological insulators and superconductors. I am also interested in demonstrating novel uses of these materials that could lead to breakthrough technologies and solve substantial computational, economic, or social problems.
Sima Setayeshgar
I am a physicist with interests at the interface between physics and biology on scales ranging from the molecular and cellular to the macroscopic. Powerful experimental methods, such as genetic tools, microfluidics, two-photon and fluorescence microscopy and single molecule techniques have made biological systems an exciting area for quantitative research. In approaching such problems, a physicist must contend with the sheer complexity of biological systems and the limitations arising from the difficulties in carrying out reproducible experiments. The fact that problems and their methods of solution are common across different biological systems - for example, phototransduction in the retina and chemotactic signal transduction in E. coli - points to the existence of organizing principles, making this quest especially rewarding
Matthew Shepherd
Our group has focused on studying the spectrum of light quark mesons using data that are being collected at the BESIII experiment in at the Institute for High Energy Physics in Beijing. We are also building the GlueX experiment at Jefferson Lab, which will search for exotic hybrid mesons.
It is through the study of the spectrum and properties of light quark hadrons we hope to understand the strong interactions that are described by Quantum Chromodynamics (QCD). QCD in the low-energy, non-perturbative regime is fascinating because it explains the confinement of quarks within hadrons. It also predicts the existence of exotic forms of matter such as hybrids, where the gluons binding the quarks in a meson carry additional degrees of freedom, and glueballs, matter composed entirely of gluons. Experimental confirmation of these predicted forms of matter and subsequent measurement of their properties would provide validation of and valuable input to the quantitative understanding of QCD.
W. Michael Snow
Neutron physics. Weak interactions of the neutron: neutron decay and Standard Model tests of the electrweak theory, nucleon-nucleon weak interaction studies as probes of quark-quark correlations in the QCD ground state. Precision measurements of coherent scattering lengths in few body systems using neutron interferometry. Development of polarized 3He-based neutron polarizers and analyzers. Searches for neutron interactions beyond the Standard Model. Search for Chameleon dark energy using neutron interferometry.
Richard Van Kooten
My primary research interests concentrate on the study of particles containing b quarks and searches for new particles not described by our current Standard Model, such as those predicted by Supersymmetry and the "missing link" of the Standard Model: the Higgs boson. I have pursued these studies at the highest energy electron-positron colliders in the world, and am now continuing these studies at the energy frontier of hadronic colliders. I am also participating in planning for experimentation at the next generation of linear electron-positron colliders.
I am currently working on the D0 Collaboration, a large international group of physicists collecting data from proton-antiproton collisions at center-of-mass energies of 2 TeV, for a while longer, highest collision energy in the world, with the D0 Upgrade Detector at the Fermi National Laboratory outside of Chicago. Specifically, my group is involved in the scintillating fiber tracker and studies of b hadron physics such as B_s oscillations, B_s CP-violating phase, and new b baryons.
I have now begun work on the ATLAS Collaboration collecting data from proton-proton collisions at center-of-mass energies of up to 14 TeV. The ATLAS detector is located on the Large Hadron Collider at the European Laboratory for Particle Physics (CERN) in Geneva, Switzerland. My group is involved in the barrel transition radiation tracker, the high-level trigger, high-luminosity LHC upgrades (Level 1 trigger), and vector boson scattering, particularly concerning the high-energy behavior of the Higgs in the restoration of unitarity
Shixiong Zhang
My research is focused on the controlled synthesis and nano-scale measurement of novel nanostructured materials. The material systems that I am currently interested in include correlated oxides and topological insulators. I use pulsed laser deposition to fabricate thin films and planar heterostructures, and chemical vapor deposition to grow 1D nanowires and 2D nanoplatelets. I am particularly interested in exploring their emergent physical (structural, electrical, magnetic and thermoelectric) properties that arise from unique aspects associated with the nanoscale geometry, and aim to understand the underlying physical origins via correlated nano-scale measurements using multi-functional scanning probe microscopy and low temperature magnetization and transport techniques.
John Bates
My main research goal is to learn how children's behavior problems and social competencies develop. I am especially interested in family interaction processes and child temperament, but also consider child social cognitive and affective characteristics and broader socioeconomic variables. A recent interest concerns the role of children's sleep in their daily adjustment. We have studied these issues mostly through longitudinal research. We have learned, for example, that early child temperament and mother-child interaction characteristics are somewhat predictive of children's later adjustment, as measured especially by the parents' report of child behavior problems, and also by teachers and peers at school and by laboratory observers. We have been considering the effects of mother-child relationship and temperament as interacting predictors of later adjustment. We have found that in dyads where mothers are low in restrictive control, temperament is more predictive of late
Bennett Bertenthal
My research focuses on the origins, development, and basic processing mechanisms involved in the perception and representation of actions by social and non-social stimuli. Recent neuroimaging, electrophysiological, and behavioral findings reveal that planning, observation, and imaging of actions share a common neural substrate. Our investigations incorporate behavioral, electrophysiological, and eye movement methods for studying the functional implications of this common substrate in infants, children and adults. Experimental tasks involving imitation, response priming, search for hidden objects, predictive tracking and reaching, gaze cueing and pointing, and the effects of authorship and expertise, are used for investigating the links between the observation and execution of actions. We are especially interested in the interplay between automatic and intentional processes in performing these tasks, and whether the perception of social stimuli requires knowledge of goals and intentions.
Heather Bradshaw
Two fields that I have a passion for are neuroscience and the biochemistry of lipid signaling. My group combines these fields to understand how lipid signaling drives changes in all aspects of neurophysiology through a systems neuroscience approach. One lipid signaling system currently being investigated centers on endogenous cannabinoids. Cannabinoids are lipids from the plant Cannabis, also known as marijuana.
Cannabinoid compounds activate receptors throughout the body and the nervous system and regulate a myriad of neurophysiological pathways. These receptors did not evolve to prepare for the likelihood that an organism would someday ingest compounds from a cannabis plant. They evolved in concert with endogenous signaling molecules that are collectively called endocannabinoids. The most studied of these are the lipid signaling molecules, Anandamide and 2-arachidonoyl glycerol. However, there is growing evidence that these two lipids are not alone in exerting cannabimimetic (cannabinoid-like) effects in the body. Many of these novel endocannabinoid analogs are produced throughout the nervous system.
Interestingly, Anandamide is arguably the world’s most famous molecule in a very specific class of molecules structurally referred to as N-acyl amides. While it is true that N-acyl amides are not yet particularly well known throughout scientific communities, we will argue that they are quite well known throughout all of the plant and animal kingdoms in that they are ubiquitous molecules that are formed from simple fatty acids and amines and are likely present in most-if not all-forms of life. This presence provides an opportunistic situation for them to be used as signaling molecules and as metabolic precursors to additional signaling molecules. How they are synthesized, metabolized, and what they do in each of these systems is largely unknown.
What are they doing in the brain and body?! Well… that’s what we are in the process of finding out. One of our primary techniques we use in order to study these endogenous lipids is through mass spectrometry. The picture at the top of the page shows a partial view of the internal core of one of the tandem mass spectrometers we have used in our studies over the years. Combining an expertise in lipid mass spectrometry and neuroscience is a powerful combination that allows us to work with collaborators from around the world and to ultimately come to new and exciting
Joshua Brown
My interests are wide-ranging but focus on the frontal lobes. How do people and animals learn, optimize, and control goal-directed behavior in complex and changing environments? These abilities entail reinforcement learning, planning, prediction, expectation, evaluation, and sequential ordering of movements, in addition to complex sensory processing. Currently I have three main research thrusts:
1) Develop computational models of brain circuitry involved in cognitive control. My earlier model of the Anterior Cingulate Cortex, or ACC (Alexander & Brown, 2011, Nature Neuroscience), suggests that ACC is critically involved in predicting and evaluating outcomes. We are currently developing computational neural models of goal-directed planning and decision-making, involving the interaction of the hippocampus, ventral prefrontal cortex, parietal cortex, and visual cortex.
2) Test computational model predictions with fMRI. Computational modeling often provides counter-intuitive, non-trivial predictions that strongly guide empirical investigations. We are exploring the neural mechanisms of planning and decision-making across the brain, using newer fMRI methods such as quantitative computational neural model regressors for fMRI analysis.
3) Investigate the neural bases of cognitive impairment in clinical populations using fMRI and computational modeling, especially addiction. We are interested in how impairments in decision making play out in addiction, and how methods such as neurostimulation can be used to treat clinical disorders. We have developed novel methods for administering operant drug reward such as nicotine from an e-cigarette to humans in the fMRI scanner, to understand real-time addiction processes. Computational modeling provides a framework for understanding the nature of information processing in both normal and pathological human brains.
Thomas Busey
My research consists of three topic areas that are highly inter-related. In collaboration with Geoff Loftus, I have addressed the temporal aspects of information processing tasks such as character identification and binocular information acquisition. This work has produced 6 peer-reviewed articles in major journals. More recently I have expanded my research focus to look at how the information that is acquired by these early perceptual mechanisms is processed in memory tasks. Several research projects have addressed the nature of the representation of perceptual information, and the use of this information in recognition and metacognitive tasks. This research line has produced 4 articles and book chapters, with several other articles under review.
Mathematical Modeling of Visual Information Processing
The processing of a perceptual stimulus is not instantaneous. The sensory response tends to be extended in time, and the nature of this temporal delay affects how the stimulus is processed. This research line uses quantitative models to address the interactions between lower-level sensory processes and higher-level perceptual and information processing mechanisms. We measure the temporal properties of the sensory response, which are signatures of the underlying neural pathways that subserve the processing of a particular task. In this research line I have addressed the processes that underlie character recognition, binocular summation, localization and identification, and temporal inhibition.
Articles based on this research appear in The Psychological Review, Journal of Experimental Psychology: Human Perception and Performance, Perception & Psychophysics, and Vision Research. A seventh article is accepted pending revision at The Journal of Mathematical Psychology.
Visual Mechanisms Associated with Face Perception
Information that is acquired by the early sensory and perceptual mechanisms studied in the previous research area must be stored and later matched with other stimuli to enable recognition. Vision researchers attempting to understand how the visual system encodes visual information have typically used relatively simple stimuli such as sine-wave gratings or gaussian patches. These findings may not reveal how those initial representations are combined by higher-order visual processing mechanism that are responsible for more complex stimuli such as faces. My research investigates the visual mechanisms that are involved in complex pattern perception. We have been most interested in how faces are represented in memory, and what features are included in this representation. In conjunction with my graduate student Anne Arici, we have developed quantitative models that account for different aspects of face recognition data.
Articles describing this research are published in Psychological Science and Journal of Experimental Psychology: Learning Memory & Cognition.
Confidence and Accuracy in Eyewitness Testimony
Jurors often believe, and are often explicitly told by judges, that confident eyewitnesses are more accurate than unconfident eyewitnesses. However, a very small to nil correlation between an eyewitness' confidence and accuracy is often reported in the literature. Motivated by this applied area, I am conducting a series of experiments looking at the basic calibration issues underlying memory performance and a subject's ability to monitor and report their confidence in the accuracy of their memory reports.
We find that confidence is not just important for eyewitness identification; other aspects of confidence can affect the recognition response. As a result, this topic area is intrinsically tied to the previous area.
Jonathon Crystal
Research in my lab is focused on developing new animal models of cognition. One benefit of studying cognition in animals is that it may provide insight into impairments in cognition observed in people. Cognitive impairments in people are debilitating, and developing insight into the origins of such impairments offers a tool to improve the effectiveness of treatments. Significant obstacles nonetheless impede the development of animal models of disordered cognition. Although there is a long history of studying learning and memory in animals, these types of cognitive processes may not match those observed clinically (e.g., Alzheimer's disease features severe impairments in episodic memory). Thus, it is possible that drug-development programs may identify agents effective at the pre-clinical level that subsequently fail when translated to a clinical trial in people. Ultimately, the expansion of the suite of cognitive processes that may be modeled in animals may translate to improved therapies for debilitating memory impairments observed in humans. The long-range goal is to understand how animals process and remember events in time and provide a neuroanatomically guided theoretical framework for understanding memory disorders.
Current projects in the lab focus on: Animal models of episodic memory. Animal models of prospective memory. Animal models of retrieval practice.
Brian D’Onofrio
My research, rooted in the field of developmental psychopathology, explores the causes and treatments of child and adolescent psychopathology through three main approaches: (1) family-based designs, (2) longitudinal analyses, and (3) intervention studies.
First, we use several advanced designs that rigorously test alternative hypotheses when we examine how specific environmental risk and protective factors influence the psychopathology. In particular, we use within-individual comparisons (e.g., we examine the risks of ADHD medication use when the same individual is on and off their medication), sibling-comparisons (e.g., we compare siblings who are differentially exposed to maternal smoking during pregnancy or maternal psychotropic use during pregnancy), cousin-comparisons (e.g., we study cousins who are differentially exposed to parental suicide), and offspring of twins (e.g., we study the offspring of identical twins who differed in their age at first childbearing).
Longitudinal analyses constitute the second major research program that we are using to study causal mechanisms. One of the main limitations of cross-sectional research is the inability to account for reciprocal influences. We, therefore, analyze longitudinal studies to examine the development of children's adjustment over time and how environmental factors influence and are influenced by individuals. Longitudinal analyses also provide the opportunity to whether there are sensitive periods of development. Furthermore, longitudinal studies enable us to explore how early risk factors influence outcomes across the lifespan.
Joseph Farley
Dr. Farley studies the cellular and molecular bases of behavioral and neural plasticity, particularly those which involve changes in the biophysical properties of excitable membranes. Using voltage- and patch-clamp recording techniques with native neuronal membranes and artificial bilayers, as well as site-directed mutagenesis studies of cloned ion channel subunits in heterologous expression systems (e.g., Xenopus oocytes), he studies the cellular and molecular bases of associative learning in invertebrates and cellular models of memory (e.g., LTP) in the mammalian brain. Changes in potassium and calcium ion channels, their contributions to cellular mechanisms of coincidence- and non-coincidence detection, and the molecular mechanisms underlying those changes, such as protein kinase C-, PKA, tyrosine kinase-, and phosphatase-dependent (PP1, PP2B) changes in channel activities are of current interest.
Emily Fyfe
My research focuses on cognitive development with an emphasis on early mathematics knowledge. More specifically, I run the Learning, Education, and Development lab. The LEAD Lab is dedicated to exploring the cognitive processes involved in how people learn – and particularly how children think, learn, and solve problems in mathematics. Our research is motivated by a key question: How can we support children’s learning so that it leads to the creation of robust and meaningful knowledge? To address this question, we typically conduct behavioral experiments in which we manipulate aspects of the learning environment and examine its impact on target learning outcomes. We combine high-density trial-by-trial data with global measures of knowledge to reveal learning processes and key mechanisms of change. Importantly, this work bridges psychology and education. The results inform theories of learning and have implications for designing effective learning environments.
William P. Hetrick
Dr. Hetrick is a clinical and cognitive neuroscientist whose research interests focus on the behavioral, cognitive, and biological bases of severe psychological disorders, such as schizophrenia, substance abuse, and autism. His laboratory uses behavioral, cognitive, and electrophysiological methods, including EEG, EMG, MRI, and brain stimulation techniques. In collaboration with Dr. Ken Mackie’s group, he also conducts non-human animal research utilizing translational methods that can be applied across species. In recent years, a specific focus of his research team has been the study of the role of the cerebellum in psychological conditions, especially psychotic disorders, autism, and heavy cannabis use.
Ed Hirt
My research focuses primarily on human motivation and its consequences for performance. Much of my work looks at situations in which people must engage in self-regulation and self-control to balance their individual goal pursuit against temptations and obstacles. We explore the contributions of both personality factors such as self-esteem and self-beliefs as well as environmental constraints such as depletion or competing demands on one's goal setting as well as one's ability to sustain motivation and achieve success at goal pursuit.
Andrea Hohmann
Functional roles of the brain's own cannabis-like (endocannabinoid) system in the nervous system; mechanisms of pain and analgesia; mechanisms of action of drugs of abuse; novel therapeutics
Amy Holtzworth-Munroe
studies marital or intimate partner violence, with a focus on male batterers. Research examines the social skills deficits of violent husbands and subtypes of violent men. Some research on battered women, marital distress, and marital therapy, but primary focus is marital violence.
Karin James
Action and perception interactions during learning; development of object recognition; neural correlates of music processing; reading acquisition
Thomas James
Visual and haptic perception; object recognition; cross-sensory integration; priming and adaptation; functional neuroimaging
Dan Kennedy
My research focuses on the neural and cognitive mechanisms underlying human social behavior, and how these mechanisms break down in individuals with autism -- a neurodevelopmental disorder that features impaired social functioning. Research methods include eye tracking, functional neuroimaging, and behavioral and cognitive testing, and study populations include healthy children and adults, individuals with autism and other neurodevelopmental disorders, and patients with localized brain lesions.
Anne Krendl
Our research uses social neuroscience and behavioral approaches to understand social cognition (the manner in which people process, store, and apply information about others) and how it changes over the lifespan. Our research uses behavioral and social neuroscience approaches to understand social cognition , and how it changes over the lifespan. We are interested in questions related to social stigma (e.g., race, age, gender, mental/physical illness), and how being stigmatized affects its targets (e.g., decisions to seek mental health treatment). We are also interested in how healthy aging affects social cognition (e.g., how older adults understand what other people are thinking and interact with them).
Mis-wiring of neuronal circuits during early life is likely to be a major cause of neurological disorders, including autism and schizophrenia. The Lu lab is interested in how activity-dependent processes during brain development fine-tune the establishment of neural circuits and how sensory experiences affect neural circuit wiring and cognitive behaviors. Specifically, we are interested in exploring the role of the metabotropic glutamate receptor 5 (mGluR5), a group 1 metabotropic glutamate receptor. mGluR5 mutations have been identified in some ADHD and schizophrenic patients. We employ mouse genetic tools to understand the contribution of mGluR5 signaling in specific neuronal populations to sensory circuit formation, synaptic function/plasticity, and behavior. We are also exploring the role of the endogenous cannabinoid (endocannabinoid) system in fetal brain development and investigating how prenatal cannabis exposure affects brain development and later behaviors. Understanding the effects of endocannabinoids during neural circuit formation will not only shed light on normal brain development and function but will also allow us to assess endocannabinoid-based therapies and the effects of cannabis use on the developing fetus.
Proper brain function requires an active maintenance program to sustain neuronal health. Environmental stressors detrimentally impact the nervous system, predisposing it to neuronal dysfunction and degeneration if neuroprotective mechanisms are weakened. Recent studies by others and us revealed that NMNAT2 (nicotinamide mononucleotide adenylyl transferase 2) is a neuroprotective protein that is central to maintain neuronal integrity and facilitate proper neural function throughout life. NMNAT2 abundance is significantly reduced in Alzheimer’s Disease (AD) brains. Increasing Nmnat2 expression in neurodegenerative animal models reduced neurodegeneration. We hope to elucidate the mechanisms underlying NMNAT2’s neuroprotection and how NMNAT2 expression is down-regulated in pathological conditions. In addition, we hope to develop NMNAT2-specific therapies to prevent or reduce neurodegeneration.
Ken Mackie
Regulation of CB1 cannabinoid receptor signaling; regulation of endocannabinoid production; Role of endocannabinoids in synaptic plasticity; novel cannabinoid receptors
Ehren Newman
We study how neural circuits generate memory using methods from systems-, behavioral-, and computational- neuroscience. We use electrophysiology, optical recording and circuit manipulation techniques, and computer simulations to study how memories are formed and retrieved in freely behaving rats.
Franco Pestilli
The Cognitive and Computational Neuroscience lab lead by Dr. Pestilli works at the interface between computational neuroimaging, data science and neuroinformatics. Primary goal is to understand how human perception and cognition is implemented in the biological tissues properties and activity of the brain cells. Projects in the lab span among different topics such as perception, attention, and motivation as well as, Vision, clinical neuroscience, aging. Major effort in the lab is the development of the new generation cloud computing platform for neuroscience research: brainlife.io
Anne Prieto
The research in my laboratory focuses on understanding the signaling mechanisms that underlie the establishment and maintenance of mature neuronal phenotypes in the developing brain. In particular, we investigate the potential functional roles of receptor protein tyrosine kinases (RPTKs) and their ligands in the central nervous system. Currently, we study a novel RPTK family, the Axl subfamily, which includes at least 4 members, Tyro-3, Axl, Mer and Rek. They share a common ligand, the molecule Gas6 (for growth-arrest specific gene-6) capable of inducing receptor phosphorylation and thus initiating intracellular signaling events upon binding. Our current efforts are focused on possible roles for these receptors and their cognate ligand in promoting the survival or growth of subsets of neural cells, in mediating cell adhesion, and in modifying synaptic function and plasticity
Aina Puce
My research program focuses on the neural basis of social cognition - the ability to interpret the actions, intentions and emotions of others. Non-verbal communication is a main theme in the laboratory, as is the context in which the action is presented in. We are developing activation tasks that attempt to mimic real-life situations as closely as possible. Our experiments use combinations of different techniques including behavior, functional MRI, event-related potentials, eye tracking and transcranial magnetic stimulation. The final technique or techniques used are determined by the particular scientific question being asked. The laboratory has multimodal integration capability.
Linda B. Smith
Psychology and cognitive science—word learning by children and neural nets.
Olaf Sporns
Cara Wellman
My research focuses on the neurobiology of aging and stress, two critical variables in the development and expression of the psychopathology. By using simple animal models that permit the manipulation and control of these variables, I hope to understand the neural causes and consequences of abnormal behavior. I am using two such models to characterize age and stress induced changes in the structure and neurochemistry of neurons in frontal cortex.
Chen Yu
Research Area: Cognitive Science, Developmental Psychology
Research Interests: Cognitive development; language acquisition; perceptual intelligence; machine learning
NOTE: Many of these faculty members are also listed under Cognitive Science and Neuroscience.
Raquel Anderson
Raquel Anderson is a professor in the Department of Speech, Language and Hearing Sciences. She is also adjunct/affiliate faculty in Cognitive Sciences and the Latino Studies Program, and currently directs the graduate level bilingual track program in Speech-Language Pathology (STEPS) in the department. At her lab, research focuses on studying the language learning abilities of children with typical language skills and children with atypical language skills. In particular, she studies children who are learning two languages, with a special emphasis on Spanish-English speaking children. Her main focus is in the area of grammatical skill, but research in other areas, such as phonology, is also conducted via her lab. The age ranges studied include preschool through early elementary school. At present, research projects include: (1) first language loss in Spanish-English speaking children; (2) longitudinal study of grammatical skill in child dual language learners (Spanish & English); (3) verb phrase use in Spanish-speaking children with language impairment; and (4) phonological development in Spanish-English speaking preschoolers.
Tessa Bent
Research in the Speech Perception Laboratory focuses on the perceptual consequences of phonetic variability in speech. The main topics under investigation are how listeners adapt to the variability present in the speech signal, how this learning can best be facilitated, and how children develop the ability to accurately and effortlessly perceive highly variable speech signals, including foreign-accented speech.
Lisa Gershkoff
Dr. Lisa Gershkoff-Stowe is an associate professor in the Speech, Language and Hearing Sciences Department and Cognitive Science Program, and director of the Baby Language Lab. The focus of her research is children's language learning. Studies carried out in her laboratory are designed to explore the changing relation between language comprehension and production and, in particular, why there are gaps between what children understand and say. Dr. Gershkoff-Stowe is trained as a developmental psychologist; she teaches courses on childhood language, infant communication, and experimental research methods.
Larry Humes
Currently Professor and Director of the Audiology Research Laboratory. He received his Bachelor's degree from Purdue University, his Master's degree from Central Michigan University, and his Ph.D. from Northwestern University. He has been at Indiana University since 1986 and the research in his laboratory has been supported by NIH throughout this time. He has over 130 scholarly publications and more than 200 presentations on a variety of topics in audiology and hearing science. His most recent research activities have been focused on age-related changes in auditory perception, including speech perception, and on outcome measures for hearing aids.
Steven Lulich
My laboratory is involved in a variety of projects concerning control of the vocal tract during sound production - both speech and music. Using state-of-the-science equipment and software that we have developed, two specific projects are 1) a longitudinal study of elementary school children's normal and disordered speech development, and 2) a study of how vocal tract manipulations enable advanced techniques in clarinet performance. We are also involved in studies of speech articulation in several foreign languages and in Parkinson's Disease.
Robert Withnell
The auditory system is capable of detecting signals embedded in thermal (kT) noise (see Hudspeth, 1997). The relative contribution of the outer and middle ear in setting this auditory sensitivity remains unclear, while it seems that the cochlea acts to enhance signal detection by an internal amplification process that is frequency-specific but, as yet, not well understood (see Dallos et al. 2006, Chan & Hudspeth, 2005). Concomitant with this internal amplification process in the cochlea is sound radiating out of the ear, or otoacoustic emissions, that provide a non-invasive window into cochlear mechanical function (e.g., Shera & Guinan, 2007). My research focuses on the biophysics of the mammalian ear, the goal being a better understanding of how the mechanics of the ear set auditory sensitivity. My current investigations include:
