Dr. Agosto is an Associate Professor in the Department of Biology who works in genetics. In the last few years he has been studying the effect the microbiota on behavior, particularly on circadian rhythms. His lab uses Drosophila to attack this question 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 have found that knockdown of a cellular homeostasis gene called pumilio within the circadian network prevent the effects of sleep deprivation on gut microbes. They are currently manipulating this gene on neural and immune tissues to map the cellular loci of pumilio actions and further characterize the signaling pathways involved.

Dr. Bayman is a Professor in the Department of Biology. Bayman’s lab is crently 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. One current project is a metatranscriptome study of CBBs infected with biological control fungi, to study the role of gene expression in virulence in the pathogen and resistance in the host. Another looks at population genetics and phylogeography of the coffee leaf rust pathogen. Another focuses on functional and phylogenetic diversity of fungal hyperparasites of the CLR pathogen, which include several undescribed species. A recently published study looked at the role of Wolbachia in the microbiota of the CBB. These projects combine field experiments, lab experiments and genetics and ‘omics methods such as RNAseq, amplicon metagenomics, and genome sequencing.

Mechanisms of Transcription Factors Binding. Dr. Cadilla is a professor in the Department of Biochemistry. Craniofacial abnormalities are among the most common findings in birth defects. Transcription factors (TFs) of the helix-loop-helix (HLH) family have important roles during human development. Mutations in the Twist subfamily of bHLH TFs result in genetic disorders that impact the formation of mesodermal derivatives during vertebrate embryogenesis. The basic HLH (bHLH) subfamily members can act as repressors or activators, depending on their dimerization partner. The long-term goal of our laboratory is to determine the molecular mechanisms by which TWIST bHLH proteins decode genomic information, and how genetic variation modulates TWIST1/2-genome interactions that impact craniofacial development. Mutations in. TWIST1 and TWIST2 have been found to cause genetic disorders that impact the development of the head and facial structures. We aim to determine the binding affinities of TWIST1/2 and selected mutant proteins found in patients by EMSAs, biolayer interferometry and structural studies via methods such as circular dichroism, X-ray Crystallography, etc. To determine the DNA-sequence specificity of TWIST1 and TWIST2 complexes (as homodimers or heterodimers with E12 as partner) we use in vivo (ChIP) and in vitro (SELEX) DNA binding assays combined with DNA sequencing to determine the DNA binding specificity of these complexes and the role that specific histone modifications (both activating and inactivating marks) and chromatin structure (using ATAC-Seq). Bioinformatic analyses are performed to (1) interpret changes in gene targets between wild-type and mutant proteins and determine the TWIST binding site sequences used to regulate gene expression of target genes and (2) predict changes in gene targets between wild-type and mutant proteins.

Dr. Garcia-Arraras is a Professor in the Department of Biology and one of the P.I.s of the present proposal. Dr. García-Arrarás has pioneered the use of the echinoderm Holothuria glaberrima to study the process of regeneration and organogenesis. 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. 

Moreover, 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. Students will be involved in bioinformatics analyses to determine gene sequences, structural domains and gene characterization. In addition, transcriptome analyses are performed regularly to determine patterns of gene expression and the outcome of gene knockdown procedures. Finally, an NSF-funded project is aimed at determining the role of the microbiota during the regeneration of the intestine, Thus, 16S analyses are currently performed to identify the associated microbiota. 

Dr. Ghezzi is an Associate Professor in the Biology Dept. at UPR-RP. Dr. Ghezzi’s research revolves around 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. Drug addiction is a complex neurobiological condition characterized by compulsive and escalating drug use and is believed to arise in part from drug-induced neural adaptations that counteract the drug effects and contribute to the uncontrolled urge to consume the drug. Students in the Ghezzi Lab will combine the powerful Drosophila genetic model and a range of genomic and neurophysiological techniques to identify and categorize the epigenetic regulatory mechanisms that reprogram neural circuits and orchestrate the response to different drugs of abuse and other environmental insults.

Dr. Giray is a Professor in the Biology Dept. at UPR-RP. Honeybees live in a society composed of tens of thousands of almost sterile workers, a reproductive female, the queen, and hundreds of males. Studies on behavioral development of honeybee workers, queens, and males have revealed a rich and expanding repertoire under neuroendocrine regulation with evolutionary roots in the solitary reproductive cycle of insects. In addition to developmental plasticity, there also is a shortterm plasticity in behavior of honeybee workers under regulation of biogenic amines, under natural conditions. 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. Combining genomics and neural-behavioral approaches, 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, as measured by direct observations, genome level association studies, and gene expression are important within this research program and have been answered by undergraduate research students. In a recent study, the lab has demonstrated in colonies that the level of aggressive response to threats, depends 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. Examining genes involved in individual and colony phenotypes of bees benefits from combining behavioral, bioinformatics, and genomics techniques. This combination of experimentally accessible social behavior and techniques to probe underlying neurogenomics mechanisms make this research program especially suitable for undergraduate research experience

Dr. Godoy is a Microbial Ecologist who has investigated an eclectic collection of topics including evolution, community dynamics, and biofilm succession. She developed her career studying biodiversity associated with animal and human microbiomes using and developing metagenomic techniques. Her laboratory investigates microbiomes in a variety of disease contexts using various Omics techniques to understand the co-evolution, transmission, and functions of microbial-host symbioses. She has pioneered studies of microbiome-drive malignancies in Hispanics namely those associated with Human Papilloma virus. Indeed, her lab demonstrated that critical dysbiosis associated to cervical and oropharyngeal precancerous lesions indicate that microbial translocation of pro-inflammatory bacteria could be triggering carcinogenic events. She holds the largest biorepositories for studies of human microbiome in the island, with tens of thousands of biological samples from Hispanic participants and its corresponding metadata from study questionnaires. She has hundreds of 16S rRNA, ITS and shotgun sequenced datasets for the study of microbiome and HPV induced carcinogenesis. Students will be involved in data generation and bioinformatics analyses pertaining microbiome profiles, community sequence type definitions, and composition and function analyses combining multi-omics approaches. They will also be exposed to data curation, annotation, assembly, and characterization of genome bins from metagenomes. Her group’s mission is to translate microbial ecology to improve human health and empower education in the microbial sciences.

Dr. Janwa is a Professor in the Department of Mathematics and foremost expert in Information Theory of Communication Systems, with specialization in Data Integrity and Data Security, where he has made seminal contributions. His pathbreaking research on algebraic geometric methods in information theory. Several influential theorems bear his name (Janwa bounds on the covering radius of algebraic and algebraic geometric codes, Janwa-Wilson-McGuire theorems on singularity analysis of APN functions, Janwa-Moreno constructions of Ramanujan Cayley graphs, Hoeholdt-Janwa characterization of networks with few eigenvalues). More recently, NASA (in three different grants) has funded his research on Novel Network graph techniques to study the effects of microgravity on plants, mice and humans in the International Space Station. During the past two decades he has expanded his research in interdisciplinary direction: involving network sciences, information theory, neural networks, and quantum computing. He has mentored scores of undergraduate students several of whom have gone on to do graduate work and are now faculty members.

Dr. Louime is an Assistant Professor in the Department of environmental Sciences. Dr. Louime’s lab studies the ecology of marine microbial communities as an essential way for understanding ecosystem functions. The focus is to determine the dynamics of marine bacterial community diversity of the coastal waters around the island of Puerto Rico. Collected samples are characterized to determine temporal and seasonal variations in microbial communities, bacterioplanktons within several seashore marine samples. Using culture-independent, high-throughput pyrosequencing of the 16S rRNA V4 region, a snapshot of the longitudinal taxonomic profile of marine microbes around the island is obtained. Their studies highlight the importance of microbes’ biological activities in determining basic earth’s chemistry as well as potential diseases for humans and other species. This continuous monitoring is for a better understanding of global change in the quest of finding solutions for unprecedented and undesirable changes. The lab provides hands-on experiences to students in the area of environmental sample collection and processing, which include environmental metadata, genomic DNA extraction and characterization followed by bioinformatics analyses.

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.

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.