Project description:Transcriptomic profiling of T. chinensis and T. ramosissima shows responses due to water deficit that are common between the two species and differences that shows their invasiveness originating from southern and northern united states. Several drought related genes that were up-regulated common in both species and transcription factors unique to T.chinensis and T. ramosissima were also found. Gene Ontology classification shows similar functional categories in both the species. Differences in two species due to water deficit were also illustrated in networks constructed from genes enriched in biological processes and molecular functions.
Project description:Understanding the genomic toolkit that enabled animal terrestrialization, the shift from aquatic to terrestrial habitats, is key to uncovering the evolutionary origins of land biodiversity. Yet, the genomic basis of the physiological and metabolic adaptations required for life on land remains poorly understood across most terrestrial animal phyla. Planarians (Platyhelminthes) offer a powerful model, as only one terrestrial lineage, the Geoplanidae (order Tricladida), is known. Here, we integrated genomics, transcriptomics, and proteomics to explore the genetic changes potentially supporting terrestrial adaptation. We identified a major burst of gene gain in the lineage leading to Tricladida, preceding the radiation of terrestrial planarians. Upon abiotic stress exposure, terrestrial and freshwater species exhibited distinct responses: most differentially expressed genes belonged to orthogroups gained in Tricladida, with over half under strong directional selection in terrestrial flatworms, suggesting their adaptive relevance. Transcriptomic profiles revealed divergent strategies: terrestrial species upregulated ancient genes, while freshwater species downregulated a separate set of ancestral genes. Across all datasets, the abiotic stress response toolkit in terrestrial planarians was markedly different from freshwater relatives, with significant regulatory divergence. Our results highlight gene gain and co-option, rather than lineage-specific innovations, as key drivers of terrestrial flatworm evolution, emphasizing genomic exaptation and regulatory shifts as central to terrestrialization in Platyhelminthes. This study provides the first genome-wide view of the genetic basis of flatworm terrestrialization and sheds light on broader patterns of animal terrestrial adaptation.
Project description:Sex specificity of the C. elegans metabolome
Russell N. Burkhardt1, Alexander B. Artyukhin1,3, Erin Z. Aprison2, Brian J. Curtis1, Bennett W. Fox1, Andreas H. Ludewig1, Amaresh Chaturbedi4, Oishika Panda1, Chester J. J. Wrobel1, Siu S. Lee4, Ilya Ruvinsky2, and Frank C. Schroeder1,
1Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
2Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, United States
3Current address: Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, United States
4Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
Correspondence to fs31@cornell.edu
Project description:Sex specificity of the C. elegans metabolome
Russell N. Burkhardt1, Alexander B. Artyukhin1,3, Erin Z. Aprison2, Brian J. Curtis1, Bennett W. Fox1, Andreas H. Ludewig1, Amaresh Chaturbedi4, Oishika Panda1, Chester J. J. Wrobel1, Siu S. Lee4, Ilya Ruvinsky2, and Frank C. Schroeder1,
1Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
2Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, United States
3Current address: Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, United States
4Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
Correspondence to fs31@cornell.edu
Project description:White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially successful hybrid striped bass (M. chrysops x M. saxatilis). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision). Significant differential expressed genes and gene ontology of pairwise comparisons between control diet and each test diet are presented and discussed.
Project description:Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationships within the species of this genus are unclear, which makes difficult the authentication of the species used for the medicinal industry. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences.
Project description:Here we developed a new high-throughput polymorphism detection and genotyping method based on identifying restriction cut site polymorphisms using a microarray platform. We compared the genomes of 20 individual urchins; 10 from the northern part of the species range (Boiler Bay, OR) and 10 from the southern part of the range (San Diego, CA).
Project description:Channel catfish and blue catfish represent two economically important freshwater aquaculture species in the United States. Our study aims to investigate the gene expression differences between these two catfish species by high-throughput RNA sequencing to understand their associated phenotypic differences in growth and disease resistant. Our transcriptomic analyses provide some insights into gene function differences between the two species and the molecular basis of channel catfish growth advantage in the tank culture environment.
Project description:The mechanisms underlying exercise-induced effects in the skeletal muscle during cancer cachexia progression have not been fully described. Here, we tested the hypothesis that different exercise training protocols could attenuate metabolic impairment in a severe model of cancer cachexia. Moderate-intensity training (MIT) and high-intensity interval training (HIIT) improved running capacity and prolonged lifespan in tumor-bearing rats. HIIT also reduced oxidative stress and reestablished muscle contractile function. An unbiased proteomics screening revealed that COP9 signalosome complex subunit 2 (COPS2), also known as thyroid receptor interacting protein 15 (TRIP15) or ALIEN, is one of the most downregulated proteins at the early stage of cancer cachexia progression. HIIT restored COPS2/TRIP15/ALIEN protein expression to the control levels. Moreover, lung cancer patients with low endurance capacity had lower muscle COPS2/TRIP15/ALIEN protein content compared to age- and sex-matched control subjects. We further established an in vitro model of cancer-induced muscle wasting using tumor cells-conditioned media to explore the potential protective role of COPS2/TRIP15/ALIEN for myotubes homeostasis. This in vitro model indicate that tumor cells produce factors that directly affect myotube metabolism, but COPS2/TRIP15/ALIEN overexpression is not able to fully reestablish metabolic homeostasis and protein content in myotubes incubated with tumor cells-conditioned media. The current study provides new insight into the role of exercise training as a co-therapy for cancer cachexia and uncovers COPS2/TRIP15/ALIEN as a novel potential target for cancer cachexia.