A5027310847- Genetics, Aging, and Longevity in Model Organisms
- Circadian rhythm and melatonin
- Birth, Development, and Health
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Mitochondrial Function and Pathology
- Physiological and biochemical adaptations
- RNA Research and Splicing
- Reproductive Biology and Fertility
- Spaceflight effects on biology
- Genetic Mapping and Diversity in Plants and Animals
- Light effects on plants
- Animal Genetics and Reproduction
- Microfluidic and Bio-sensing Technologies
- FOXO transcription factor regulation
- Agriculture Sustainability and Environmental Impact
- Dietary Effects on Health
- Adipose Tissue and Metabolism
- Per- and polyfluoroalkyl substances research
- Photosynthetic Processes and Mechanisms
- Virus-based gene therapy research
- Digital Holography and Microscopy
- Protein Tyrosine Phosphatases
- Bacterial Genetics and Biotechnology
- DNA Repair Mechanisms
Duke University
2015-2025
Center for Genomic Science
2021-2022
Institut thématique Génétique, génomique et bioinformatique
2017
Center for Systems Biology
2009-2014
California Institute of Technology
2006-2009
Howard Hughes Medical Institute
2006-2009
Harvard University
2001-2008
University of Georgia
1997-2002
Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and vitro transcription is reported to maintain representation levels, however, quantitative data demonstrating this as well a description inherent limitations lacking. We show that published protocols produce template-independent product addition amplifying real target thus reducing the specific activity final...
We report a novel microfluidics-based lensless imaging technique, termed optofluidic microscopy (OFM), and demonstrate Caenorhabditis elegans with an OFM prototype that gives comparable resolution to conventional microscope measured limit of 490 ± 40 nm.
Temporal profiles of transcript abundance during embryonic development were obtained by whole-genome expression analysis from precisely staged C. elegans embryos. The result is a highly resolved time course that commences with the zygote and extends into mid-gastrulation, spanning transition maternal to control including presumptive specification most major cell fates. Transcripts for nearly half (8890) predicted open reading frames are detected levels majority them (>70%) change over time....
When Caenorhabditis elegans larvae hatch from the egg case in absence of food, their development is arrested (L1 arrest), and they show increased stress resistance until food becomes available. To study nutritional control larval development, we analyzed growth gene expression profiles during L1 arrest recovery. Larvae that were fed responded relatively slowly to starvation compared with rapid response feeding. Chromatin immunoprecipitation RNA polymerase II (Pol II) followed by deep...
Abstract Starvation during early development can have lasting effects that influence organismal fitness and disease risk. We characterized the long-term phenotypic consequences of starvation larval in Caenorhabditis elegans to determine potential develop it as a model for mechanistic studies. varied amount time larvae were developmentally arrested by after hatching (“L1 arrest”). Worms recovering from extended grew slowly, taking longer become reproductive, smaller adults. Fecundity was also...
The fundamental phenotypes of growth rate, size and morphology are the result complex interactions between genotype environment. We developed a high-throughput software application, WormSizer, which computes shape nematodes from brightfield images. Existing methods for estimating volume either coarsely model nematode as cylinder or assume worm opacity is invariant. Our estimate more robust to changes in optical density it only assumes radial symmetry. This open source written plugin...
Organisms in the wild develop with varying food availability. During periods of nutritional scarcity, development may slow or arrest until conditions improve. The ability to modulate developmental programs response poor requires a means sensing changing environment and limiting tissue growth. mechanisms by which organisms accomplish this adaptation are not well understood. We sought study question examining effects nutrient deprivation on Caenorhabditis elegans during late larval stages, L3...
Maternal and zygotic activities of the homeodomain protein PAL-1 specify identity maintain development multipotent C blastomere lineage in C. elegans embryo. To identify regulatory target genes, we used microarrays to compare transcript abundance wild-type embryos with mutant lacking a extra blastomeres. pal-1-dependent C-lineage expression was verified for select candidate genes by reporter gene analysis, though many are expressed additional lineages as well. The set validated includes 12...
daf-16/FoxO is required to survive starvation in Caenorhabditis elegans, but how daf-16IFoxO promotes resistance unclear. We show that restructures carbohydrate metabolism by driving carbon flux through the glyoxylate shunt and gluconeogenesis into synthesis of trehalose, a disaccharide glucose. Trehalose well-known stress protectant, capable preserving membrane organization protein structure during abiotic stress. Metabolomic, genetic, pharmacological analyses confirm increased trehalose...
Maternal effects of environmental conditions produce intergenerational phenotypic plasticity. Adaptive value these depends on appropriate anticipation in the next generation, and mismatch between may contribute to disease. However, regulation plasticity is poorly understood. Dietary restriction (DR) delays aging but maternal have not been investigated. We demonstrate DR roundworm C. elegans. Worms cultured fewer larger progeny. Nutrient availability assessed late larvae young adults, rather...
Phenotypic plasticity is facilitated by epigenetic regulation, and remnants of such regulation may persist after plasticity-inducing cues are gone. However, the relationship between transgenerational memory not understood. Dauer diapause in Caenorhabditis elegans provides an opportunity to determine how a plastic response early-life environment affects traits later life subsequent generations. We report that, extended diapause, postdauer worms initially exhibit reduced reproductive success...
The publication of the Caenorhabditis briggsae reference genome in 2003 enabled first comparative genomics studies between C. elegans and briggsae, shedding light on evolution content structure genus. However, despite being widely used, currently available is substantially less complete structurally accurate than genome. Here, we used high-coverage Oxford Nanopore long-read chromosome-conformation capture data to generate chromosome-level genomes for two strains: QX1410, a new strain closely...
Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed postrecruitment regulation of RNA polymerase II (Pol II) during starvation and recovery Caenorhabditis elegans, suggesting that promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol elongation genome wide by two complementary approaches analyzed conjunction with binding We confirmed bona fide also discovered docking. Pausing occurs at active...
Nutrient availability has profound influence on development. In the nematode C. elegans, nutrient governs post-embryonic L1-stage larvae remain in a state of developmental arrest after hatching until they feed. This “L1 arrest” (or "L1 diapause") is associated with increased stress resistance, supporting starvation survival. Loss transcription factor daf-16/FOXO, an effector insulin/IGF signaling, results arrest-defective and starvation-sensitive phenotypes. We show that daf-16/FOXO...
Caenorhabditis elegans larvae reversibly arrest development in the first larval stage response to starvation (L1 or L1 diapause). Insulin-like signaling is a critical regulator of arrest. However, C. genome encodes 40 insulin-like peptides, and it unknown which peptides participate nutritional control development. Work other contexts has revealed that genes can promote ("agonists") developmental ("antagonists"), suggesting such agonists feeding. We measured mRNA expression dynamics with high...