Associate Professor. Studies the relationship between microbiota and behavior, particularly circadian rhythms. Uses Drosophila to take advantage of the large repertoire of molecular genetic tools available, the simpler microbiome, and the deep level of neurobiological understanding. Specifically, they chose the circadian network to study its interaction with gut microbes because its behavioral outputs and molecular components are well characterized and because there is evidence suggesting that gut microbes are communicating with this network. To explore this relationship, flies are treated with wide spectrum antibiotics and found that sleep behavior and the homeostatic response to sleep deprivation are altered. They are currently manipulating gene expression to determine the gene and signaling pathways involved.

Professor. Focused on pests and diseases of coffee and their biological control. Organisms of interest include the coffee berry borer (CBB, a beetle, the most destructive pest of coffee worldwide), the coffee leaf rust fungus (CLR, the most destructive pathogen of coffee), fungi with potential for biological control of CBB and CRR, and the microbiome of coffee plant roots. Current projects include: (1) metatranscriptome studies, to study the role of gene expression in virulence in the pathogen and resistance in the host, (2) population genetics and phylogeography of the coffee leaf rust pathogen, and (3) functional and phylogenetic diversity of fungal hyperparasites of the CLR pathogen. These projects combine field and lab experiments with ‘omics methods such as RNAseq and genome sequencing. 

Professor. Dr. García-Arrarás has pioneered the use of the echinoderm Holothuria glaberrima to study organ regeneration. His research focuses on the molecular aspects of regeneration of the radial nerve cord and the digestive tract, specifically on the identification of genes and gene pathways that underlie the regeneration process. His lab has generated an expressed sequence tag (EST) database for H. glaberrima sequences obtained from multiple DNA libraries, of normal and regenerating organs. The lab just published a genome draft of the model animal and is finalizing a complete genome that will provide the base for future genomic experiments and analyses. This, combined with a recently NSF-funded project to determine the role of the microbiota during intestinal regeneration, provides a new area of research in gene expression for incoming students.

Associate Professor. Focuses on the molecular basis of neural adaptation. Through the integration of molecular genomics, behavioral analyses, and neurophysiology, his lab strives to resolve how the nervous system utilizes a finite number of genes to carefully modulate neural activity and adapt to an ever-changing environment. A central component of this effort is directed to understanding the mechanisms of transcriptional memory that perpetuate drug-induced adaptations and promote addiction. Students in the lab combine the powerful Drosophila genetic model and a range of genomic and neurophysiological techniques to identify and categorize epigenetic regulatory mechanisms.

Professor. Dr. Giray’s lab combines genomics, including WGA and transcriptomics approaches, with classic and new behavioral assays to study honeybee social behavior, both in the field and in the laboratory. They probe the neural and molecular bases of plasticity in a mini brain. Simple questions, such as if colony conditions influence expression of defensive response of individuals, have been answered by undergraduate research students. In a recent study, the lab demonstrated that the level of aggressive response to threats, depended on frequency of certain genotypes in a colony. No particular genotype makes a single bee more likely to sting, instead it is a group phenotype. The combination of experimentally accessible social behavior and techniques to probe underlying neurogenomics mechanisms make this research program especially suitable for undergraduate research.

Professor. Utilizes powerful high-end approaches in genomics and functional genetics to address fundamental questions in evolutionary and developmental biology. His work aims to better understand the interplay between molecules and gene networks underlying the evolution of novel phenotypes and finally how to protect and conserve the diversity of animal forms with specific focus on the one in the tropics. His current research is at the forefront of the evolutionary genomic and developmental fields, which focuses on a simple but extremely complex fundamental question in biology: How do changes in DNA result in changes in phenotype? Leveraging phenotypic diversity in butterfly populations with cutting-edge DNA sequencing methods and functional validation, his lab explores how genetic changes impact the evolution and diversification of adaptive traits.

Assistant Professor. The goal of the laboratory is to characterize the transcriptional and non-transcriptional effects of estrogen receptors and the gene expression network involved in their cellular function. Particular interest focuses on rapid non-genomic receptor signaling. Students are involved in the generation and bioinformatic analyses of large datasets including but not limited to RNAseq, ChiPseq, large scale analysis of proteins and phospho-arrays using in vitro cell models. The fellows will also gather experience in working with cell culture, molecular subcloning, gene expression, Western blot and DNA/RNA molecular techniques.

Professor. The acquisition of remotely sensed data at a variety of spatial and times scales, is providing unprecedented opportunities for evaluating the impacts of global and regional changes, as well as the consequences of these changes for couple natural-human systems. A second project in the lab focuses on the plantmicrobiota-soil associations in landslides and landslide-prone environments. Students in the Restrepo lab will acquire skills in remote sensing, big data, and geographical information systems tools to test hypotheses and perform data analysis.

Assistant Professor. Aims at understanding interactions between the gut microbiome and the intestinal epithelium. Lactobacillus species are commensal bacteria commonly found in the fly and mammalian small intestines and are generally considered probiotic agents. Studies using flies mono-associated with Lactobacillus plantarum (L. plantarum) have uncovered significant insights into host-microbial interactions. Recent findings have shed light onto how L.plantarum interact with the gut epithelium without resulting in an activation of the immune response. Students will work towards identifying genes in L.plantarum that are needed for the activation of the genes in the fly intestinal cells. These students will gather experience in working with the fruit fly Drosophila melanogaster, performing bacterial mutagenesis, and designing and performing genetic screenings in Drosophila and L.plantarum.

Assistant Professor. Determining a transcription factor’s intrinsic DNA-binding preferences is a critical step for decoding gene regulatory networks that control cell function. Students in the lab will engage in multiple aspects of the characterization of transcription factors, including the generation of large datasets of transcription factor binding preferences. They will learn molecular cloning methods, protein expression/purification, DNA-binding assays, and the use of bioinformatics tools to integrate “big data” to identify putative binding sites across genomes. The lab mission is to uncover the molecular mechanisms by which proteins and small molecules bind to DNA and RNA to interpret genetic information.

The ongoing work in the lab has three goals. The first goal is aimed at characterizing the behavioral and molecular effects of spatial novelty on the acquisition of intravenous cocaine self-administration (SA). The second goal of the present proposal is to focus on the functional role of CREB phosphorylation within the NAc and limbic-related structures in novelty-elicited acquisition of cocaine SA. This aim includes using antisense oligonucleotide technology to examine the role of newly synthesized CREB in recognition of spatial novelty prior to cocaine SA. Findings from these proposed experiments will provide new data on the involvement of CREB regulation within Nac in eliciting novelty-induced behaviors related to cocaine reward. Finally, the last goal of the present proposal is to characterize the role of the protein kinase C (PKC) within the Nac in the phosphorylation of CREB elicited by spatial novelty effects on cocaine SA in rats. Experimental results from this goal will also contribute to establishing the specific role of protein kinase C (PKC) within the NAc in regulating CREB phosphorylation in novelty-elicited acquisition of cocaine SA. To accomplish these goals, direct brain drug microinfusions will be used in conjunction with cocaine intravenous SA and novelty protocols in rats. Protein analysis of CREB phosphorylation will be conducted in all studies.

We utilize ecological monitoring tools and advanced genetic techniques to explore the ecology and evolution of marine organisms across the Caribbean. One aspect of our research centers on the hypothesis that environmental changes, alongside species interactions, contribute to phenotypic plasticity and invasive traits in an invasive seagrass, Halophila stipulacea. To test this hypothesis, we conducted a reciprocal transplant experiment involving H. stipulacea and native seagrass Syringodium filiforme to assess how species interactions influence their acclimation and adaptation. Preliminary results have unveiled that the invasive seagrass demonstrated comparable growth in both reciprocal transplant sites while displaying altered vegetative traits suggestive of a distinct growth strategy. We aim to dive deeper into these findings to investigate if these changes in vegetative traits are linked to epigenetic modifications underlying the plant’s invasiveness. Project participants will leverage bioinformatics tools to assemble the current Halophila genome from raw sequencing data, predict potential genes within this assembly, and create a gene transfer file (GTF) by annotating these genes with their genomic coordinates and functional elements. While the genome has been sequenced, the assembly process from raw reads remains to be conducted. Additionally, they will align methylome sequences to identify specific methylated genes associated with invasive characteristics. This project offers a unique opportunity to gain invaluable skills in genome assembly, GTF annotation, and methylome alignment, crucial for unraveling the mysteries behind invasive seagrass dynamics. 

Understanding fundamental dynamics that shape the geographic distribution of species is critical for predicting responses to global change and in disentangling the factors that generate and maintain global biodiversity patterns. Our lab works in diverse systems, from plants through birds and mammals to humans, to reveal how species persist and coexist across diverse and dynamic environments to understand the distribution of life on Earth. Our work is macroecological in scope and bridges scales of biological organization – from physiology, traits, and behavior of individuals to spatiotemporal dynamics of populations to the distributions of species and assembly of communities across and among continents. We address questions by leveraging large ecological, environmental, geographic, and phylogenetic datasets unified across disparate sources and through the creative application of computational and statistical techniques. Within these themes, research participants will choose between projects that provide opportunities to learn skills such as the management, statistical analysis, and visualization of big data in ecology, phylogenetic comparative methods, geographic analyses (GIS), or simulation approaches.