A5034205126- Genetics, Aging, and Longevity in Model Organisms
- Circadian rhythm and melatonin
- Bioinformatics and Genomic Networks
- Spaceflight effects on biology
- Heat shock proteins research
- CRISPR and Genetic Engineering
- Gene Regulatory Network Analysis
- CNS Lymphoma Diagnosis and Treatment
- Microbial Metabolic Engineering and Bioproduction
- Vascular Tumors and Angiosarcomas
- Protein Structure and Dynamics
- Gut microbiota and health
- Mitochondrial Function and Pathology
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Marine Biology and Ecology Research
- Xenotransplantation and immune response
- Cutaneous lymphoproliferative disorders research
- Neuroendocrine regulation and behavior
- Evolution and Genetic Dynamics
- Pancreatic and Hepatic Oncology Research
- Agriculture Sustainability and Environmental Impact
- Protist diversity and phylogeny
- Single-cell and spatial transcriptomics
- Microbial Community Ecology and Physiology
- Bacterial Genetics and Biotechnology
Massachusetts Institute of Technology
2024
Genesis Foundation
2023
Northwestern University
2022-2023
Bay Institute
2023
California Institute of Technology
2016-2020
Howard Hughes Medical Institute
2016-2018
Hospital Médica Sur
2011
Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán
2010
Over the last ten years, there has been explosive development in methods for measuring gene expression. These can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze is associate ontologies (hierarchical, descriptive vocabularies with controlled relations terms) look enrichment specific terms. Although Gene Ontology (GO) available Caenorhabditis elegans, it does not include...
Abstract Recent human decedent model studies 1,2 and compassionate xenograft use 3 have explored the promise of porcine organs for transplantation. To proceed to studies, a clinically ready donor must be engineered its successfully tested in nonhuman primates. Here we describe design, creation long-term life-supporting function kidney grafts from genetically transplanted into cynomolgus monkey model. The was carry 69 genomic edits, eliminating glycan antigens, overexpressing transgenes...
Genome-wide experiments routinely generate large amounts of data that can be hard to interpret biologically. A common approach interpreting these results is employ enrichment analyses controlled languages, known as ontologies, describe various biological parameters such gene molecular or function. In C. elegans, three distinct the Gene Ontology (GO), Anatomy (AO), and Worm Phenotype (WPO) are used annotate function, expression phenotype, respectively (Ashburner et al. 2000; Lee Sternberg,...
Abstract Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, bacteria by partitioning low-concentration substrates though they compete for one simple, dominant substrate. We allowed ocean self-assemble leachates the brown seaweed Fucus vesiculosus and...
When nutrients in their environment are exhausted, bacterial cells become arrested for growth. During these periods, a primary challenge is maintaining cellular integrity with reduced capacity renewal or repair. Here, we show that the heat-shock protease FtsH generally required growth arrest survival of Pseudomonas aeruginosa, and this requirement independent role regulating lipopolysaccharide synthesis, as has been suggested Escherichia coli We find ftsH interacts diverse genes during...
Pheromones exchanged by conspecifics are a major class of chemical signals that can alter behavior, physiology, and development. In particular, males females communicate with potential mating partners via sex pheromones to promote reproductive success. Physiological developmental mechanisms which facilitate progeny production remain largely enigmatic. Here, we describe how Caenorhabditis elegans male pheromone, ascr#10, improves the oogenic germline. Before most signs aging become evident,...
Significance Transcriptome profiling quantitatively measures gene expression genome-wide. There is widespread interest in using transcriptomic profiles as phenotypes for epistasis analysis. Though measurements can be performed individual transcripts, this results many scores that must interpreted independently. We developed a statistic summarizes these measurements, simplifying Moreover, analysis has previously only been on cDNA extracted from single cells. show whole-organism RNA-sequencing...
Abstract Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle physiology of question. Caenorhabditis elegans XX animals are hermaphrodites that exhaust their sperm after 3 d egg-laying. Even though C. can live for many days cessation egg-laying, molecular this state has not been as intensely studied other parts cycle, despite documented changes behavior metabolism. To study effects depletion aging during first 6 adulthood, we measured...
Abstract Sex pheromones not only improve the reproductive success of recipients, but also impose costs, such as a reduced life span. The underlying mechanisms largely remain to be elucidated. Here, we show that even brief exposure physiological amounts dominant Caenorhabditis elegans male pheromone, ascr#10, alters expression thousands genes in hermaphrodites. most dramatic effect on transcriptome is upregulation expressed during oogenesis and downregulation associated with gametogenesis....
We report the clinicopathologic features of 13 cases intramucosal carcinoma (IMC) gallbladder. All IMCs were incidental findings in cholecystectomy specimens for cholelithiasis. However, one patients had a pancreas, and gallbladder incidentally removed during Whipple procedure showed an IMC. Another patient small cell gallbladder, sections Of IMCs, 10 well-differentiated adenocarcinomas, 1 was moderately differentiated adenocarcinoma, undifferentiated carcinoma, squamous carcinoma. patients,...
Abstract Genome-wide experiments have the capacity to generate massive amounts of unbiased data about an organism. In order interpret this data, dimensionality reduction techniques are required. One approach is annotate genes using controlled languages and test experimental datasets for term enrichment probabilistic methods. Although gene, phenotype anatomy ontologies exist C. elegans , no unified software offers analyses all same methodology. Here, we present WormBase Enrichment Suite,...
Although transcriptomes have recently been used as phenotypes with which to perform epistasis analyses, they are not yet study intragenic function/structure relationships. We developed a theoretical framework allelic series using transcriptomic phenotypes. As proof-of-concept, we apply our methods an of
Sex pheromones improve reproductive success, but also impose costs. Here we show that even brief exposure to physiological amounts of the dominant C. elegans male pheromone, ascr#10, alters expression thousands genes in hermaphrodites. The most dramatic effect on transcriptome was upregulation expressed during oogenesis and downregulation associated with gametogenesis. Among detrimental effects ascr#10 hermaphrodites is increased risk persistent infections caused by pathological pharyngeal...
Abstract Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle physiology of question. Although C. elegans is traditionally thought as hermaphrodite, XX animals exhaust their sperm become endogenous females after 3days egg-laying. Themolecular this state has not been intensely studied other parts cycle, despite documented changes behavior metabolism that occur at stage. To study female , we measured transcriptomes 1st day adult...
Although transcriptomes have recently been used to perform epistasis analyses, they are not yet study intragenic function/structure relationships. We developed a theoretical framework allelic series using transcriptomic phenotypes. As proof-of-concept, we apply our methods an of dpy-22 , highly pleiotropic Caenorhabditis elegans gene orthologous the human MED12 which is subunit Mediator complex. Our identify functional regions within that modulate activity upon various genetic modules.