First name,Last name,Preferred title,Overview,Position,Department,Individual
Rodolfo,Aramayo,Associate Professor,"My current research primarily focuses on understanding the organization, distribution, and comparison of information in Biological Systems. Our work encompasses two key levels of investigation:
Molecular Genetics: We employ the filamentous fungus Neurospora crassa as a model organism to uncover and comprehend the intricate molecular components responsible for sequence-based comparisons between homologous chromosomes, leading to the initiation of Meiotic Silencing, a phenomenon driven by RNA-mediated processes. Currently, our primary focus centers on the exploration of whether genes recognized for their significance in Meiotic Transvection/Silencing also contribute to the occurrence of Repeat Induced Point Mutation (RIP) phenomena.
Computational Analysis: We are developing novel computational pipelines dedicated to detecting sequence variations within related genomes. We are particularly intrigued by the prospect of simplifying (i.e., digitizing) the information present in DNA, RNA, and Proteins so as to simplify its manipulation and analysis. We think that digitizing emerging genomic data will not only enable us to use this data effectively but also to integrate it into Artificial Intelligence, Data Clustering, and Image Recognition Algorithms, in ways not done before. We posit that this process of converting biological features into digital equivalents has the potential to simplify genomic information, making it easier to uncover previously unnoticed patterns through complex computational comparisons. This approach has already yielded promising results by revealing unexpected informational patterns across various organisms' chromosomes. We believe that it will streamline and enhance our ability to comprehend different cellular and organismal states. Moreover, it holds significant promise in revolutionizing our understanding of diseases, particularly Cancer and Metagenomics. This informational perspective also contributes to our comprehension of genome evolution, especially in the field of comparative genomics and microbial metagenomics.",Associate Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n14287b36
Benjamin,Neuman,Professor,,Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n193ea580
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
Duncan,Mackenzie,Associate Professor,"Hormones secreted by the thyroid gland are of primary importance in the regulation of such fundamental physiological processes as growth, nutrient utilization, and reproduction. In my laboratory we examine the regulation of the secretion of thyroid hormones and their actions in poikilothermic vertebrates in order to understand the evolution of thyroid function. We are presently focusing on the regulation on thyroid hormone secretion and the mechanisms of iodine transport in commercially-important fish species such as the red drum (Sciaenops ocellatus), the channel catfish (Ictalurus punctatus), and even the zebrafish (Danio rerio).
This research is aimed at providing new insights into the potentially ancient role of thyroid hormones in nutrient assimilation, as well as elucidating evolutionary trends in the regulation of thyroid function. These studies may serve identify ways in which the pituitary-thyroid axis may be manipulated to enhance aquaculture production or endangered species conservation.",Associate Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n33bd0e42
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
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
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
Jolene,Ramsey,Visiting Assistant Professor,,Visiting Assistant Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n6b53d6ec
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
Andrew,Tag,Instructional Assistant Professor,,"Director, Introductory Biology Program||Instructional Associate Professor",Biology||Biology,https://scholars.library.tamu.edu/vivo/display/n8989ea81
William,Cohn,Instructional Assistant Professor,,Instructional Assistant Professor,Biology,https://scholars.library.tamu.edu/vivo/display/n952f03c2
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
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
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
James,Erickson,Associate Professor,"Alternative developmental fates are often determined by small differences in the concentrations of signaling molecules. In many cases, cells respond to these signals within narrowly defined temporal windows and are unresponsive to the same signal molecules at other times in development. A number of aspects of Drosophila sex determination make it an ideal experimental system to study how strict temporal controls and small quantitative differences in protein concentration can elicit different developmental fates.",Associate Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nf4575bc8
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