Project description:The ‘Genetic Epidemiology of Asthma in Costa Rica’ is a family-based cross-sectional cohort ascertained between February 2001 and August 2008 on a Hispanic population isolate from the Central Valley of Costa Rica. The study recruited children between 6 to 14 years of age with moderate persistent asthma.
Project description:Data from multiple high throughput technologies such as RNA sequencing (RNA-Seq) and protein mass spectrometry (MS/MS) are often used to assist in predicting eukaryote genome features such as genes, splice variants, and single nucleotide variants (SNVs). The genomes of parasitic nematodes causing neglected tropical diseases are often poorly annotated. Angiostrongylus costaricensis, a nematode that causes an intestinal inflammatory disease known as abdominal angiostrongyliasis (AA), is one example. Currently, no drugs or treatments are available for AA, a public health problem in Latin America, especially in Costa Rica and Brazil. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction supplemented the reference annotation with a) novel coding and non-coding genes; b) pieces of evidence of alternative splicing generating new proteoforms; c) a list of SNVs specific to the Brazilian strain (Crissiumal). To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of a parasitic nematode. We hope this supplemented genome annotation can assist the future development of drugs to treat AA caused by either Brazil strain (Crissiumal) or Costa Rica strain.
Project description:Perennial ryegrass (Lolium perenne L.) is the most cultivated cool-season grass worldwide with crucial roles in carbon fixation and fodder for livestock. Protection of these grasses from biotic and abiotic factors are dictated through a mutually-beneficial relationship with endophytes that confer bioprotective properties. Common endophytes of the genus Epichloë promote the health and survival of cool-season forages greases and protect the plants from fluctuating environmental conditions. Climate change, and specifically, a steady increase in atmospheric CO2 levels, presents a dramatic and imminent threat faced by our ecosystem, which poses substantial pressures on plant health and survival. Defining the relationships between endophytes and the host plant may uncover mechanisms of bioprotection, which can be exploited to promote adaptable plant systems in rising CO2 conditions. In this study, we quantify changes in biomass and seed production of L. perenne L. at 400 and 800 ppm CO2 and identify endophyte-specific changes in metabolite production. Additionally, we discover protein-level changes from both the endophyte and plant perspectives, which underscore the compatible relationship between a common, natural endophyte and L. perenne L., compared to an incompatible and detrimental relationship the epichloid strain, AR1. Taken together, our data set provides new understanding into the intricacy of compatibility between endophyte and host from multiple molecular levels and suggests opportunity to promote plant robustness and survivability in rising CO2 environmental conditions through application of bioprotective epichloid strains.