First name,Last name,Preferred title,Overview,Position,Department,Individual
Bruce,Riley,Professor,"My lab studies inner ear development in zebrafish. A prominent feature of our research is to investigate how cell-cell signaling and downstream gene-interactions control development. One project in the lab focuses on how cell signaling regulates ectodermal patterning during gastrulation to establish the otic placode, the precursor of the inner ear. Our recent work shows that localized Fgf signaling is especially critical for inducing formation of the otic placode, and members of the Pax2/5/8 family of transcription factors are important mediators of Fgf signaling. During later stages of inner ear development, we are exploring how sensory hair cells and neurons are regulated. Our studies address how these cells initially form, how they are genetically maintained, and how they become specialized for hearing vs. balance. We are also investigating how zebrafish can replace dead and damaged hair cells, an ability that mammals have lost. The inability to regenerate hair cells explains why humans show progressive irreversible hearing loss as we age. It is hoped that activating or augmenting human homologs of genes shown to operate in zebrafish might help restore hearing and balance in humans.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n0dbb8253
Deborah,Bell-Pedersen,Professor,"Research in the Bell-Pedersen lab focuses on determining how the circadian clock functions in organisms to regulate daily rhythms in gene expression, behavior, and physiology. The molecular clock in higher eukaryotes involves a master clock in the brain regulating clocks in peripheral tissues, posing significant obstacles for understanding circadian output mechanisms. Thus, a major strength of our work is using a single-celled model eukaryote, Neurospora crassa, to elucidate the underlying mechanisms of rhythmic gene expression and protein synthesis. Clock dysfunction in humans is associated with a wide range of diseases, including cardiovascular disease, cancer, metabolic disorders, mental illness, sleep disorders, and aging. In addition, daily changes in metabolism and cell division rates influence the efficacy and toxicity of many pharmaceuticals, including cancer drugs. Therefore, knowing how clocks work to control rhythmic gene expression, and what they regulate, is critical for the development of therapeutics. Research to understand clock-controlled rhythmic gene expression has focused primarily on transcriptional mechanisms, and little was known about posttranscriptional control. We discovered that the clock regulates highly conserved translation initiation and elongation factors, tRNA synthetase levels, and ribosome heterogeneity. This regulation determines what mRNAs are rhythmically translated and the accuracy of the translation process (translation fidelity). We are capitalizing on these exciting discoveries to determine how the clock regulates translation fidelity. These studies will provide the foundation for understanding the impact of daily rhythms in translation fidelity on protein diversity beyond what is encoded for in the genome.",Professor and Associate Department Head,Biology,https://scholars.library.tamu.edu/vivo/display/n2a2bfb97
Joseph,Sorg,Professor,"My lab is focused on the mechanisms of spore germination and bile acid resistance in Clostridium difficile. C. difficile is a Gram-positive, spore forming, anaerobe that causes infections in people who have undergone antibiotic regimens. Previously, we had shown that certain bile acids promote C. difficile spore germination while others inhibit germination. Bile acids are small molecules made by the liver that help the absorption of fat and cholesterol in the GI tract while also serving as a protective barrier against invading pathogens. Because C. difficile spores use the ratios of bile acids as cues for germination, the actively growing bacteria must have adapted means to avoid their toxic properties. We are currently focused on identifying these factors and the mechanisms by which C. difficile spores germinate.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n2b4d6c14
Karl,Aufderheide,Emeritus Associate Professor,"Cell/Developmental Biology. Developmental Genetics. Intracellular differentiation of eukaryotes, especially ciliates. General interests in: intracellular pattern formation and morphogenesis; molecular aspects of gene expression in ciliate protozoa; development of organelles, including intracellular motility and organelle localization. Specific interests in: signal transduction, regulation of cytoskeletal organization, and motility in the social amoeba Dictyostelium; organization, patterning and morphogenesis of surface-related cytoskeletal and membranous structures of ciliates, especially Paramecium; applications of laser optical force trap technology to developmental problems in Paramecium tetraurelia and Tetrahymena thermophila; 2 molecular aspects of serotype gene expression in P. tetraurelia; development of exocytotic organelles (the trichocysts) in P. tetraurelia. General approach involves use of classical and modern light and electron microscopic techniques, integrated with genetic, molecular, mechanical or physiological manipulations of the cells.",Associate Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n3ed65e09
Beiyan,Nan,Assistant Professor,"I am interested in understanding the mechanisms of fundamental biological processes in bacteria. My lab uses soil bacterium Myxococcus xanthus as the model organism. Several aspects of M. xanthus make it an ideal model for understanding bacterial physiology. First, M. xanthus cells utilize sophisticated systems to move on solid surfaces, which involve cytoplasmic and periplasmic proteins, filamentous cytoskeletons, membrane channels, cell wall, and cell surface components. Second, cells constantly communicate with each other and with their environment. Cells usually move in coordinated groups but also as isolated ""adventurous"" individuals, which allows this bacterium to feed on soil detritus and prey on other microorganisms. Third, when the availability of nutrients or prey decrease in the environment, most cells exhibit behaviors that include aggregation into fruiting bodies and conversion of individual cells into spores.
I have been using the super resolution photo-activated localization microscopy (PALM) to track single molecule dynamics of proteins in live bacterial cells. With this technique, I have achieved 10 millisecond time resolution (100 frames per second) and 80 nm spatial resolution. These studies were initiated because the most widely used fluorescence microscopy techniques (including confocal, deconvolution, etc.) can only provide resolution to about 200 nm due to the diffraction of light, which is often insufficient for many studies because of the small size of bacterial cells (usually a few hundred nanometers in diameter).
Our research topics cover motility, development (fruiting body formation and biofilm formation), cytoskeleton, and cell wall assembly.",Assistant Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n3fe4c57e
Charles,Criscione,Professor,"I examine fundamental ecological and evolutionary questions in parasite systems and consider my research to be at the interface of ecology, evolution, and genetics. Parasitology provides a rich subject area for studies of ecology and evolutionary biology. Numerous topics such as ecosystem dynamics, mating systems, or coevolution can be addressed because parasites are extremely diverse. By diversity, I include not only the myriad of taxa that have independently evolved a parasitic lifestyle, but also the diversity in life cycles, modes of reproduction, host species, and ecosystems utilized by parasites. This diversity also allows for comparative studies to address theories or unifying principles that span ecosystems or taxonomic groups. Furthermore, there are many practical applications such as studying the evolution of drug resistance, or using parasite community structure to assess ""ecosystem health"". My research interests address both basic and applied questions, and span three overlapping subject areas: 1) Evolution: Population Genetics, Mating Systems, and Molecular Epidemiology, 2) Ecology: Biodiversity, Conservation, and Natural History, and 3) Genetics and Ecological Genomics.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n41a8b584
Luis,Garcia,Professor,"I am interested in understanding how behavioral states are regulated at the molecular and genetic level. My lab addresses this complex question in the well-studied nematode Caenorhabditis elegans. Several physical aspects of this worm make it convenient for integrating whole organism system biology studies with genetic/molecular analysis of neurobiology and behavior. C. elegans is an anatomically simple organism; it is 1mm in size, and it contains ~ 1000 somatic cells, a third of which are neurons. The worm is also transparent, and thus every cell can be visualized by light microscopy. Behavioral mutants can be efficiently generated through standard chemical mutagenesis. In addition, gene functions involved in motivational and behavioral regulation can be determined by transgenic techniques.
My lab investigates the interplay between feeding and sex-specific mating behavior to understand how chemo/mechano-sensory and motor outputs are controlled under various physiological conditions. We study male mating by using genetics to de-construct this behavior into its fundamental sensory-motor components. We then use a combination of transgenics, pharmacology, classical genetics and laser microsurgery to understand how individual motor sub-behaviors are coordinated to produce gross behaviors during periods when the animal is food deprived, and when it is food satiated.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n4cd2f794
Christine,Merlin,Associate Professor,"Our research broadly lies in understanding how organisms respond and adapt to changing environments, with an emphasis on circadian biology. Organisms from bacteria to humans use circadian clocks to control a plethora of biochemical, physiological and behavioral rhythms. These clocks are synchronized to daily and seasonal environmental changes to allow organisms to tune specific activities at the appropriate times of day or year.
In our laboratory, we use the eastern North American migratory monarch butterfly (Danaus plexippus) as a model system to study animal clock mechanisms and the role of circadian clocks and clock genes in a fascinating biological output, the animal long-distance migration. Every fall, like clockwork, millions of monarch butterflies start migrating thousands of miles from North America to reach their overwintering sites in central Mexico. During their journey south, migrating monarchs use a time-compensated sun compass orientation mechanism to maintain a constant flight bearing. Circadian clocks located in the antennae provide the critical internal timing device for compensation of the sun movement across the sky over the course of the day. The recent sequencing of the monarch genome and the establishment of genetic tools to knockout clock genes (and others) in vivo using nuclease-mediated gene targeting approaches provides us with a unique opportunity to uncover the molecular and cellular underpinnings of the butterfly clockwork, its migratory behavior and their interplay.",Assistant Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n5a23a5d7
Thomas,Mcknight,Professor and Head,"My lab is currently investigating mechanisms that regulate telomerase activity in plants. We previously showed that the pattern of telomerase expression in plants is remarkably similar to the pattern seen in humans, despite fundamental differences in development between plants and animals. Telomerase is abundantly expressed in reproductive organs but is undetectable in most vegetative organs (Fitzgerald et al., 1996). Additionally, telomerase can be induced in leaves and other vegetative organs by exposure to exogenous auxin.
To isolate genes that regulate telomerase, we screened a large population of activation tagged lines of Arabidopsis thaliana, and found that several lines that ectopically express telomerase in leaves. The first line we characterized over-expressed a gene encoding a small zinc finger transcription factor we designated TELOMERASE ACTIVATOR 1 (Ren et al., 2004). This factor does not bind to the promoter for TERT, which encodes the catalytically active subunit of telomerase. Instead, it binds to and activates transcription of BT2, a gene encoding a component of a ubiquitin ligase (Ren et al., 2007). Our working model is that the BT2 ubiquitin ligase marks a telomerase repressor for destruction, thereby allowing expression of telomerase. Efforts in the lab are currently focused on identifying the presumed telomerase repressor protein and other proteins that interact with BT2.",Professor and Head,Biology,https://scholars.library.tamu.edu/vivo/display/n5c3b294a
Terry,Thomas,Professor,"My interests are evolutionarily broad and include animals, plants and fungi. A major focus of the lab is the genomic analysis of gene expression programs during plant gene expression programs, particularly during embryogenesis and seed development, and the underlying regulatory mechanisms required for the initiation and maintenance of these programs. This work has illustrated the combinatorial interactions of cis and trans -acting factors that result in specific gene regulatory events. We are also using genomics tools to study the interaction of the rice blast fungus, Magnaporthe grisea , with plant hosts; the circadian control of gene expression; and the development of the vertebrate retina. An additional focal area is the utilization of molecular and cellular approaches for crop improvement. As part of these research activities, we have developed or adapted high throughput genomics approaches to accelerate the gene discovery process and subsequent analysis of gene expression and function.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n79201ac5
Lisa,Campbell,Emerita Professor,My research focuses on phytoplankton population dynamics; harmful algal blooms and mechanisms of bloom formation; transcriptomics and metabolomics of marine dinoflagellates; ocean observing systems; and flow cytometry and imaging-in-flow cytometry.,Professor||Professor,Oceanography||Biology,https://scholars.library.tamu.edu/vivo/display/n7a7d6659
Alex,Keene,Professor and Department Head,,Professor and Department Head,Biology,https://scholars.library.tamu.edu/vivo/display/n8650c3cf
Michael,Benedik,Regents Professor,My laboratory studies basic biological problems using molecular genetic methods with simple microbial systems. Additionally we are developing novel microbial approaches for biotechnological applications.,Regents Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nac9856e5
Mahul,Chakraborty,Assistant Professor,,Assistant Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nd1041b0d
Alan,Pepper,Associate Professor,"My laboratory uses genetic, molecular, and genomic tools to study how terrestrial plants adapt, both in a short-term sense (phenotypic plasticity) and in a long-term sense (adaptive evolution), to the vast diversity of environments found on our planet.
My laboratory is studying the molecular and physiological mechanisms of 'downstream' developmental responses to light using genetic and molecular tools available in the model plant Arabidopsis thaliana. In another project, we are using comparative genomics to investigate the genetic basis of the evolution-under-domestication of developmental processes in cultivated cottons (Gossypium spp.) and their wild relatives. Gossypium is in the Malvaceae family and, as such, shares a recent common ancestor with Arabidopsis and other plants in the Brassicaceae family.
We are also investigating the genetic mechanisms of plant adaptation to the stresses of extreme environments such as drought, low mineral nutrients (N,P,K) and heavy metals, in wild relatives of Arabidopsis, such as the rare endemic plant Caulanthus amplexicaulis (Brassicaceae.) This work has led us to become more broadly interested in the conservation and ecological genetics of rare plants, particularly geoendemics.",Associate Professor,Biology,https://scholars.library.tamu.edu/vivo/display/ndc106a4d
Michael,Manson,Professor,"Bacteria have a limited behavioral repertoire. Their most conspicuous behavior is chemotaxis - the pursuit of molecules that are favorable to acquire and the avoidance of chemicals that are best to avoid. The simplicity of bacterial motility and chemotaxis and the amenability of the model species Escherichia coli to genetic, biochemical and physiological manipulation have facilitated rapid advances in understanding the molecular mechanisms of biological energy conversion and signal transduction.
Our laboratory studies the inputs and outputs of chemotaxis. Ligands interact with the periplasmic receptor domain of a chemotactic signal transducer that spans the cell membrane. This interaction is converted into an intracellular signal that is communicated to the flagella. Molecules can be sensed either by binding directly to a receptor or by first interacting with a periplasmic binding protein, which then interacts with a receptor.",Professor||Professor,Biology||Biochemistry and Biophysics,https://scholars.library.tamu.edu/vivo/display/ne190242a
Deborah,Siegele,Associate Professor,"Phenotypes are observable characteristics of an organism that result from the expression of a particular genotype in a particular environment. Examples of phenotypic traits in microbes are motility, sporulation, ability to perform anaerobic respiration, and resistance/sensitivity to an antibiotic.
Until recently, phenotypic information has been captured as free text descriptions in research papers. Ambiguities in natural language confound attempts to retrieve information across sources. For example, ""serotype"" and ""serovar"" both refer to the same phenotype, but a simple text-based query with either word alone would miss the other. Or a single term, such as ""sporulation"" is used to refer to multiple, distinct processes in different organisms. Issues such as these hamper the ability to integrate different phenotypic data sets for the same organism or to use phenotypic information in one organism to predict possible phenotypes in another organism. Ideally, phenotype information should be stored in a consistent, computable format for ease of data integration and mining.
Controlled vocabularies are used to provide both consistent terminology and a structured data format for the capture of biological information. Ontologies are controlled vocabularies of defined terms with unique identifiers and precise relationships to each other. There are phenotype ontologies available for many eukaryotic organisms, including fungi. However, when the OMP project was initiated, none of the existing ontologies was appropriate to comprehensively capture phenotypes for Bacteria or Archaea or to enable comparisons across microbial taxa.
The Siegele lab and our collaborators at TAMU and the Univ. of Maryland (IGS) are developing a formal Ontology of Microbial Phenotypes (OMP). Our lab is focused on term development and annotating microbial phenotypes. OMP can be accessed at microbialphenotypes.org. Releases of OMP are available at github.com/microbialphenotypes.",Associate Professor,Biology,https://scholars.library.tamu.edu/vivo/display/ne333d587
Darrell,Pilling,Research Assistant Professor,,Research Assistant Professor,Biology,https://scholars.library.tamu.edu/vivo/display/ne8a9ecc1
Wayne,Versaw,Professor,"Compartmentalization of metabolic pathways and other cellular functions is a hallmark of eukaryotic cells. This feature is extreme in plants due to the presence of organelles not found in most other eukaryotes - plastids. Plastids are a diverse group of interrelated organelles that perform a wide range of metabolic functions including photosynthesis, nitrogen and sulfur assimilation and the synthesis of amino acids, starch and fatty acids. These functions are coordinated with metabolic processes in the cytosol through dynamic exchange of metabolites and ions across the plastid inner envelope membrane.
My lab is studying phosphate (Pi) transport processes that link the metabolic pathways in the plastid and cytosol. The concentrations of Pi in the cytosol and plastid stroma influence photosynthesis and the partitioning and storage of fixed carbon. Transporters involved in the movement of Pi across the plastid inner membrane include members of the pPT, PHT2 and PHT4 families. We are using genetics, cell biology, biochemistry and molecular physiology to investigate the function and physiological roles of these transporters. Recent findings suggest that some members of the PHT4 family are targeted to chloroplasts, whereas others function in heterotrophic plastids and one resides in the Golgi apparatus.
Other projects in the lab include the genetic and biochemical characterization of Pi transport processes in the filamentous fungus Neurospora crassa. Mutants with altered phosphate uptake properties have been isolated, and these have led to the identification of Pi transporter genes, as well as genes with putative regulatory functions.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nea6b0d01
Tapasree,Roy Sarkar,Assistant Professor,"The dynamic interaction of cancer cells with the tumor microenvironment (TME) is crucial to stimulate the heterogeneity of cancer cells, and to increase multidrug resistance ending in cancer cell progression and metastasis. Understanding the underlying molecular & cellular mechanisms governing these interactions can be used as a novel strategy to disrupt cancer cell-TME interaction and contribute to the development of efficient therapeutic strategies. By integrating cutting-edge cellular and molecular biology, bioinformatics, and bioengineering approaches, our lab is investigating the complexity of TME.",Assistant Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nf08a1119
Paul,Hardin,Distinguished Professor,"A diverse array of organisms including prokaryotic and eukaryotic microbes, plants, and animals display daily rhythms in physiology, metabolism and/or behavior. These rhythms are not passively driven by environmental cycles of light and temperature, but are actively controlled by endogenous circadian clocks that are set by environmental cycles, keep time in the absence of environmental cues, and activate overt physiological, metabolic and behavioral rhythms at the appropriate time of day. This remarkable conservation of circadian clock function through evolution suggests that maintaining synchrony with the environment is of fundamental importance. Our understanding of the circadian clock is particularly important for human health and well-being. The clearest examples of circadian clock dysfunction are those that result in abnormal sleep-wake cycles, but clock disturbances are also associated with other ailments including epilepsy, cerebrovascular disease, depression, and seasonal affective disorder. The realization that disorders of the sleep-wake cycle such as Familial Advanced Sleep Phase Syndrome can result from alterations in clock gene function underscores the clinical importance of understanding the molecular organization of the circadian system.
Work in my laboratory focuses on defining the molecular mechanisms that drive circadian clock function in the fruit fly, Drosophila melanogaster. We previously found that the core timekeeping mechanism is based on core and interlocked transcriptional feedback loops. Our studies currently focus on (1) defining post-translational regulatory mechanisms that operate in the core loop to set the 24 hour period, (2) determining whether interlocked loops are important for circadian timekeeping and/or output, (3) understanding how circadian oscillator cells are determined during development, and (4) defining mechanisms that control rhythms in olfactory and gustatory physiology and behavior.",Distinguished Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nf27056c4
Richard,Gomer,Distinguished Professor,"Our laboratory is working on three areas of biomedicine, trying to move observations from basic research into the clinic. First, we are studying how the sizes of tissues and tumors are regulated, and how this can be manipulated for therapeutic purposes. As a model system, we are using the simple eukaryote Dictyostelium discoideum, which allows us to combine techniques such as biochemistry, genetics, computer modeling, and cell biology to study tissue size regulation. We have found that a secreted protein as well as the unusual molecule polyphosphate are signals in negative feedback loops that inhibit Dictyostelium cell proliferation, and we are studying the signal transduction pathway to understand similar mechanisms in humans.
Second, we are studying how some secreted proteins can make cells move away from the source of the signal. We found such a signal (called a chemorepellent) in Dictyostelium, and then found a similar signal in humans. We are working to understand the signal transduction pathway for both. The human signal repels neutrophils, and we found that this can be used therapeutically in mouse models of neutrophil-driven diseases such as rheumatoid arthritis and acute respiratory distress syndrome.
Third, we have found that a human blood protein called Serum Amyloid P (SAP) regulates a key step in the formation of scar tissue as well as the formation of the scar-like lesions in fibrosing diseases such as congestive heart failure and pulmonary fibrosis. We are studying this mechanism, and a biotech company (Promedior, now sold to Roche) we co-founded is testing SAP as a therapy for fibrosis in patients in a Phase 3 trials.",Distinguished Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nf41f3898
Uel,Mcmahan,Professor,"McMahan and his research group provide one of the cornerstones for Texas A&M's new Interdisciplinary Life Sciences Building and its related teaching and research efforts. His work focuses on how the nervous system's synapses form in the embryo and function in the adult in various animal species. It relies on high-resolution imaging, chemical characterization and experimental manipulation of specific macromolecules and organelles, which altogether provide insights unobtainable via any other approach. The findings bear directly on the problems of understanding the molecular basis of human brain diseases and restoring brain function after trauma.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nfc3672e7
Matthew,Sachs,Professor,"Understanding the mechanisms by which upstream open reading frames (uORFs) in mRNA transcripts control gene expression is currently the major focus of my laboratory. A substantial component of this work is focused on the uORF-encoded fungal arginine attenuator peptide (AAP). The major goal of this work is to understand the mechanism by which a nascent peptide encoded by this uORF controls the movement of ribosomes on mRNA and regulates gene expression. Control mechanisms mediated by uORFs and nascent peptides exist in mammals, fungi, plants, viruses, and bacteria, but relatively little is known of the molecular details of such control. The AAP is encoded by a uORF in the 5?-leader regions of mRNAs specifying the first enzyme in fungal arginine (Arg) biosynthesis. Synthesis of the AAP rapidly reduces gene expression in response to Arg. AAP-mediated regulation is observed in vivo in both Neurospora crassa and Saccharomyces cerevisiae and in vitro, using fungal, plant and animal extracts. The nascent AAP causes the ribosome to stall when the concentration of Arg is high.",Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nfe74574c