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
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
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
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
Jerome,Menet,Associate Professor,"Most organisms from bacteria to humans exhibit 24-hours rhythms in their biochemistry, physiology and behavior. Best exemplified by the sleep/wake cycle, these rhythms are remarkably widespread and include in humans hormonal (e.g., melatonin, insulin, cortisol), metabolic (e.g., glucose, cholesterol), physiological and behavioral oscillations. In fact, most biological functions are rhythmic and are set to perform optimally at the most appropriate time of the day. For example, the human digestion process performs better during the day when we are supposed to eat.
These circadian rhythms are generated by ""molecular clocks"", which consist of a few ""clock genes"" interacting in feedback loops, and which drive the rhythmic expression of a large number of genes, i.e. ~10% of the transcriptome in any tissues. This wide impact of clock genes in regulating gene expression is underscored by the surprisingly large number of pathologies developed by clock-deficient mice. In addition to being arrhythmic, these mice indeed develop pathologies as diverse as mania-like behaviors, learning and memory defects, depression, drug addiction, insomnia, metabolic diseases, arthropathy, hematopoiesis defects and cancers.
Research in our lab aims at characterizing how circadian clocks and clock genes regulate gene expression to provide insights into how and why clock dysfuntion leads to a wide spectra of pathologies. To this end, we are using a wide-range of molecular and biochemical techniques to investigate the circadian clock function at the genome-wide level (e.g., next-generation sequencing). We are currently extending some of our recent results and focus on 1) how clock genes rhythmically regulate chromatin environment and 2) the mechanisms involved in rhythmic post-transcriptional regulation of gene expression.",Associate Professor,Biology,https://scholars.library.tamu.edu/vivo/display/nf680fb91