Project description:RNA-Sequencing performed on 177 honey bee whole-brains, divided into "soldier" and "forager" groups from Puerto Rican honey bee colonies.
Project description:A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large sequencing centers.
Project description:The Puerto Rican parrot (Amazona vittata), endemic to Puerto Rico, is the only native parrot in the United States and is classified as a critically endangered species. There are two captive populations of A. vittata in Puerto Rico located in the Iguaca Aviary in El Yunque National Rainforest and the José L. Vivaldi Aviary in the Río Abajo Forest. To characterize the microbial communities of A. vittata's stool, 21 stool samples from captive birds were collected, DNA extracted and sequenced using Illumina MiSeq. Sequences were processed by removing host sequences (A. vittata genome) and low-quality reads. Taxonomic and functional profiles were generated using MG-RAST. The most abundant domain was Bacteria (96%), followed by Virus (3%), and Eukaryota (0.6%). Among the functions in the microbiome, the most abundant was related to carbohydrates (14%), followed by clustering-based subsystems (12%), protein metabolism (8%), and amino acids and derivatives (7%). This dataset describes the stool microbiome of A. vittata using a metagenomics approach. Data can be used to develop holistic conservation strategies for A. vittata and other endangered birds, as well as to search for bioprospects with potential biomedical and biotechnological applications.
Project description:Viral strains, age, and host factors including genetics and proteins are associated with variable immune responses against SARS-CoV-2 and disease severity. We hypothesized that unique proteins/pathways are associated with COVID-19 disease severity in Puerto Rican Hispanics. A total of 121 men and women aged 21-80 years-old were recruited in Puerto Rico. Plasma samples were collected from unvaccinated COVID-19 infected subjects during acute disease (n=39) and compared to COVID-19 negative individuals (n=56) during acute disease using proteomics and cytokine expression. Infected individuals were stratified based on symptomatology as follows: mild (n=18), moderate (n=13), and severe (n=8). Quantitative proteomics was performed in plasma samples using Tandem Mass Tag (TMT) labeling. Cytokines in plasma were quantified using a human cytokine array. Proteomics analyses revealed 56 differentially regulated proteins and the top 3 pathways that were predicted to be inhibited in severe patients including LXR/RXR signaling, Production of NO and ROS in macrophages, and Synaptogenesis signaling. Decreased cadherin-13 validated by ELISA, which participates in synaptogenesis, is a novel protein is a novel protein not previously reported in other studies of COVID-19 severity and validated by ELISA. Cytokine analyses showed that TNF⍺ levels decreased with disease severity. This study uncovers potential host predictors of COVID-19 severity and new avenues for treatment in Puerto Rican Hispanics.