Scholars@Duke
L. Ryan Baugh

L. Ryan Baugh

Professor of Biology
Biology
ryan.baugh@duke.edu
Duke Box 90338, Durham, NC 27708-4129
4314 French Family Science Center, Duke Box 90338, Durham, NC 27708

Selected Publications

Early life starvation and Hedgehog-related signaling activate innate immunity downstream of daf-18/PTEN and lin-35/Rb causing developmental pathology in adult C. elegans.

Journal Article PLoS genetics · December 2025 Early life experiences such as malnutrition can affect development and adult disease risk, but the molecular basis of such protracted effects is poorly understood. In the nematode C. elegans, extended starvation during the first larval stage causes the dev ... Full text Cite

DAF-18/PTEN protects LIN-35/Rb from CLP-1/CAPN-mediated cleavage to promote starvation resistance.

Journal Article Life science alliance · June 2025 Starvation resistance is a fundamental trait with profound influence on fitness and disease risk. DAF-18, the Caenorhabditis elegans ortholog of the tumor suppressor PTEN, promotes starvation resistance. PTEN is a dual phosphatase, and DAF-18 promot ... Full text Cite

Structure-specific variation in per- and polyfluoroalkyl substances toxicity among genetically diverse Caenorhabditis elegans strains.

Journal Article Toxicological sciences : an official journal of the Society of Toxicology · May 2025 Per- and polyfluoroalkyl substances (PFAS) are in 99% of humans and are associated with a range of adverse health outcomes. It is impossible to test the >14,500 structurally diverse "forever chemicals" for safety, therefore improved assays to quantify stru ... Full text Cite

Developmental and conditional regulation of DAF-2/INSR ubiquitination in Caenorhabditis elegans.

Journal Article G3 (Bethesda, Md.) · March 2025 Insulin/IGF signaling (IIS) regulates developmental and metabolic plasticity. Conditional regulation of insulin-like peptide expression and secretion promotes different phenotypes in different environments. However, IIS can also be regulated by other, less ... Full text Cite

<i>ist-1/IRS1</i> affects L1 starvation resistance in <i>daf-16/FoxO-</i> dependent and independent fashion.

Journal Article microPublication biology · January 2025 The mammalian IRS1 gene is an important adaptor for the insulin and insulin-like growth factor receptors, but its sole homolog in the nematode C. elegans , ist-1 , has received relatively little attention. We show that ist-1 /IRS1 has ... Full text Open Access Cite

Structure-specific variation in per- and polyfluoroalkyl substances toxicity among genetically diverse Caenorhabditis elegans strains.

Journal Article bioRxiv · June 2, 2024 BACKGROUND: There are >14,500 structurally diverse per- and polyfluoroalkyl substances (PFAS). Despite knowledge that these "forever chemicals" are in 99% of humans, mechanisms of toxicity and adverse health effects are incompletely known. Furthermore, the ... Full text Link to item Cite

Insulin/IGF-dependent Wnt signaling promotes formation of germline tumors and other developmental abnormalities following early-life starvation in Caenorhabditis elegans.

Journal Article Genetics · February 2023 The Developmental Origins of Health and Disease hypothesis postulates that early-life stressors can predispose people to disease later in life. In the roundworm Caenorhabditis elegans, prolonged early-life starvation causes germline tumors, uterine masses, ... Full text Cite

Early-life starvation alters lipid metabolism in adults to cause developmental pathology in Caenorhabditis elegans.

Journal Article Genetics · February 2023 Early-life malnutrition increases adult disease risk in humans, but the causal changes in gene regulation, signaling, and metabolism are unclear. In the roundworm Caenorhabditis elegans, early-life starvation causes well-fed larvae to develop germline tumo ... Full text Cite

Alternative somatic and germline gene-regulatory strategies during starvation-induced developmental arrest.

Journal Article Cell reports · October 2022 Nutrient availability governs growth and quiescence, and many animals arrest development when starved. Using C. elegans L1 arrest as a model, we show that gene expression changes deep into starvation. Surprisingly, relative expression of germline-enriched ... Full text Cite

Using population selection and sequencing to characterize natural variation of starvation resistance in Caenorhabditis elegans.

Journal Article eLife · June 2022 Starvation resistance is important to disease and fitness, but the genetic basis of its natural variation is unknown. Uncovering the genetic basis of complex, quantitative traits such as starvation resistance is technically challenging. We developed a synt ... Full text Cite

Genetic analysis of daf-18/PTEN missense mutants for starvation resistance and developmental regulation during Caenorhabditis elegans L1 arrest.

Journal Article G3 (Bethesda, Md.) · May 2022 Mutations in the well-known tumor suppressor PTEN are observed in many cancers. PTEN is a dual-specificity phosphatase that harbors lipid and protein-phosphatase activities. The Caenorhabditis elegans PTEN ortholog is daf-18, which has pleiotropic effects ... Full text Cite

Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.

Journal Article Genome biology and evolution · April 2022 The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, ... Full text Cite

Rotenone Modulates Caenorhabditis elegans Immunometabolism and Pathogen Susceptibility.

Journal Article Frontiers in immunology · January 2022 Mitochondria are central players in host immunometabolism as they function not only as metabolic hubs but also as signaling platforms regulating innate immunity. Environmental exposures to mitochondrial toxicants occur widely and are increasingly frequent. ... Full text Cite

Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs.

Journal Article eLife · October 2021 Despite reports of parental exposure to stress promoting physiological adaptations in progeny in diverse organisms, there remains considerable debate over the significance and evolutionary conservation of such multigenerational effects. Here, we investigat ... Full text Cite

DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence.

Journal Article PLoS genetics · July 2021 Quiescence, an actively-maintained reversible state of cell cycle arrest, is not well understood. PTEN is one of the most frequently lost tumor suppressors in human cancers and regulates quiescence of stem cells and cancer cells. The sole PTEN ortholog in ... Full text Cite

Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans.

Journal Article Nature ecology & evolution · June 2021 Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing decreases the effective population size, effective recombination rate and heterozygosity within a specie ... Full text Cite

Liquid-culture protocols for synchronous starvation, growth, dauer formation, and dietary restriction of Caenorhabditis elegans.

Journal Article STAR protocols · March 2021 Featured Publication Standard laboratory culture of Caenorhabditis elegans utilizes solid growth media with a bacterial food source. However, this culture method limits control of food availability and worm population density, factors that impact many life-history trait ... Full text Open Access Cite

Selfing is the safest sex for Caenorhabditis tropicalis.

Journal Article eLife · January 2021 Featured Publication Mating systems have profound effects on genetic diversity and compatibility. The convergent evolution of self-fertilization in three Caenorhabditis species provides a powerful lens to examine causes and consequences of mating system transitions. Amo ... Full text Cite

Alternative somatic and germline gene-regulatory strategies during starvation-induced developmental arrest

Journal Article · 2021 SUMMARY Nutrient availability governs growth and quiescence, and many animals arrest development when starved. Somatic and germline cells have distinct functions and constraints, suggesting different regulatory mechanisms contribute to an integrat ... Full text Cite

Starvation Responses Throughout the Caenorhabditiselegans Life Cycle.

Journal Article Genetics · December 2020 Featured Publication Caenorhabditis elegans survives on ephemeral food sources in the wild, and the species has a variety of adaptive responses to starvation. These features of its life history make the worm a powerful model for studying developmental, behavioral, and m ... Full text Cite

Nongenetic inheritance and multigenerational plasticity in the nematode C. elegans.

Journal Article eLife · August 2020 A rapidly growing body of literature in several organisms suggests that environmentally-induced adaptive changes in phenotype can be transmitted across multiple generations. Although within-generation plasticity has been well documented, multigenerational ... Full text Cite

Balancing selection maintains hyper-divergent haplotypes inC. elegans

Journal Article · 2020 Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing significantly decreases the effective population size, effective recombination rate, and heterozygosity ... Full text Cite

Population Selection and Sequencing of Caenorhabditis elegans Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance.

Journal Article G3 (Bethesda, Md.) · October 2019 To understand the genetic basis of complex traits, it is important to be able to efficiently phenotype many genetically distinct individuals. In the nematode Caenorhabditis elegans, individuals have been isolated from diverse populations around the ... Full text Cite

Insulin/IGF Signaling and Vitellogenin Provisioning Mediate Intergenerational Adaptation to Nutrient Stress.

Journal Article Current biology : CB · July 2019 The roundworm C. elegans reversibly arrests larval development during starvation [1], but extended early-life starvation reduces reproductive success [2, 3]. Maternal dietary restriction (DR) buffers progeny from starvation as young larvae, preserving repr ... Full text Cite

Pervasive Positive and Negative Feedback Regulation of Insulin-Like Signaling in Caenorhabditis elegans.

Journal Article Genetics · January 2019 The Caenorhabditis elegans insulin-like signaling network supports homeostasis and developmental plasticity. The genome encodes 40 insulin-like peptides and one known receptor. Feedback regulation has been reported, but the extent of feedback and it ... Full text Cite

Nonselective autophagy reduces mitochondrial content during starvation in Caenorhabditis elegans.

Journal Article American journal of physiology. Cell physiology · December 2018 Starvation significantly alters cellular physiology, and signs of aging have been reported to occur during starvation. Mitochondria are essential to the regulation of cellular energetics and aging. We sought to determine whether mitochondria exhibit signs ... Full text Cite

Neurohormonal signaling via a sulfotransferase antagonizes insulin-like signaling to regulate a Caenorhabditis elegans stress response.

Journal Article Nature communications · December 2018 Insulin and insulin-like signaling regulates a broad spectrum of growth and metabolic responses to a variety of internal and environmental stimuli. For example, the inhibition of insulin-like signaling in C. elegans mediates its response to both osmotic st ... Full text Cite

Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans.

Journal Article BMC biology · October 2018 BackgroundDevelopmental physiology is very sensitive to nutrient availability. For instance, in the nematode Caenorhabditis elegans, newly hatched L1-stage larvae require food to initiate postembryonic development. In addition, larvae arrested in ... Full text Cite

Transgenerational Effects of Extended Dauer Diapause on Starvation Survival and Gene Expression Plasticity in Caenorhabditis elegans.

Journal Article Genetics · September 2018 Phenotypic plasticity is facilitated by epigenetic regulation, and remnants of such regulation may persist after plasticity-inducing cues are gone. However, the relationship between plasticity and transgenerational epigenetic memory is not understood. Daue ... Full text Cite

Correction: Maternal Diet and Insulin-Like Signaling Control Intergenerational Plasticity of Progeny Size and Starvation Resistance.

Journal Article PLoS genetics · August 2018 [This corrects the article DOI: 10.1371/journal.pgen.1006396.]. ... Full text Cite

Pervasive positive and negative feedback regulation of insulin-like signaling inCaenorhabditis elegans

Journal Article · 2018 The C. elegans insulin-like signaling network supports homeostasis and developmental plasticity. The genome encodes 40 insulin-like peptides and one receptor. Feedback regulation has been reported, but the extent of feedback and its effect on signaling dyn ... Full text Cite

Perception of environmental polypeptides inC. elegansactivates insulin/IGF signaling and alters lipid metabolism

Journal Article · 2018 Food perception affects animal physiology in complex ways. We uncoupled the effects of food perception and ingestion in the roundworm C. elegans . Perception was not sufficient to promote development, but larvae exposed to food without ingestion failed to ... Full text Cite

Dauer diapause has transgenerational effects on starvation survival and gene expression plasticity

Journal Article · 2018 ABSTRACT Phenotypic plasticity is facilitated by epigenetic regulation, and remnants of such regulation may persist after plasticity-inducing cues are gone. However, the relationship between plasticity and transgenerational epigenetic memory is no ... Full text Cite

daf-16/FoxO promotes gluconeogenesis and trehalose synthesis during starvation to support survival.

Journal Article Elife · October 24, 2017 daf-16/FoxO is required to survive starvation in Caenorhabditis elegans, but how daf-16IFoxO promotes starvation resistance is unclear. We show that daf-16/FoxO restructures carbohydrate metabolism by driving carbon flux through the glyoxylate shunt and gl ... Full text Link to item Cite

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode.

Journal Article Current biology : CB · October 2017 Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduc ... Full text Cite

Insulin-like signalling to the maternal germline controls progeny response to osmotic stress.

Journal Article Nature cell biology · March 2017 In 1893 August Weismann proposed that information about the environment could not pass from somatic cells to germ cells, a hypothesis now known as the Weismann barrier. However, recent studies have indicated that parental exposure to environmental stress c ... Full text Cite

Neurohormonal signalling controls insulin sensitivity and specificity in C. elegans

Journal Article · 2017 Insulin and insulin-like growth factor signalling regulates a broad spectrum of growth and metabolic responses to a variety of internal and environmental stimuli. Such responses can be tailored to the environment so that changes in insulin signalling resul ... Full text Cite

Maternal Diet and Insulin-Like Signaling Control Intergenerational Plasticity of Progeny Size and Starvation Resistance.

Journal Article PLoS genetics · October 2016 Maternal effects of environmental conditions produce intergenerational phenotypic plasticity. Adaptive value of these effects depends on appropriate anticipation of environmental conditions in the next generation, and mismatch between conditions may contri ... Full text Open Access Cite

L1 arrest, daf-16/FoxO and nonautonomous control of post-embryonic development.

Journal Article Worm · April 2016 Post-embryonic development is governed by nutrient availability. L1 arrest, dauer formation and aging illustrate how starvation, anticipation of starvation and caloric restriction have profound influence on C. elegans development, respectively. Insulin-lik ... Full text Open Access Cite

Transgenerational Effects of Early Life Starvation on Growth, Reproduction, and Stress Resistance in Caenorhabditis elegans.

Journal Article Genetics · September 2015 Starvation during early development can have lasting effects that influence organismal fitness and disease risk. We characterized the long-term phenotypic consequences of starvation during early larval development in Caenorhabditis elegans to determine pot ... Full text Open Access Link to item Cite

Ins-4 and daf-28 function redundantly to regulate C. elegans L1 arrest.

Journal Article Developmental biology · October 2014 Caenorhabditis elegans larvae reversibly arrest development in the first larval stage in response to starvation (L1 arrest or L1 diapause). Insulin-like signaling is a critical regulator of L1 arrest. However, the C. elegans genome encodes 40 insulin-like ... Full text Open Access Cite

Identification of late larval stage developmental checkpoints in Caenorhabditis elegans regulated by insulin/IGF and steroid hormone signaling pathways.

Journal Article PLoS genetics · June 2014 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 in response to poor nutritional conditions require ... Full text Open Access Cite

Pol II docking and pausing at growth and stress genes in C. elegans.

Journal Article Cell reports · February 2014 Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed postrecruitment regulation of RNA polymerase II (Pol II) during starvation and recovery in Caenorhabditis elegans, suggesting that promoter-proximal pausing pro ... Full text Open Access Cite

To grow or not to grow: nutritional control of development during Caenorhabditis elegans L1 arrest.

Journal Article Genetics · July 2013 It is widely appreciated that larvae of the nematode Caenorhabditis elegans arrest development by forming dauer larvae in response to multiple unfavorable environmental conditions. C. elegans larvae can also reversibly arrest development earlier, during th ... Full text Open Access Cite

Succinylated octopamine ascarosides and a new pathway of biogenic amine metabolism in Caenorhabditis elegans.

Journal Article The Journal of biological chemistry · June 2013 The ascarosides, small-molecule signals derived from combinatorial assembly of primary metabolism-derived building blocks, play a central role in Caenorhabditis elegans biology and regulate many aspects of development and behavior in this model organism as ... Full text Open Access Cite

WormSizer: high-throughput analysis of nematode size and shape.

Journal Article PloS one · January 2013 The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfi ... Full text Open Access Cite

Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans.

Journal Article Genome research · October 2012 Nutrient availability profoundly influences gene expression. Many animal genes encode multiple transcript isoforms, yet the effect of nutrient availability on transcript isoform expression has not been studied in genome-wide fashion. When Caenorhabditis el ... Full text Open Access Cite

Metazoan operons accelerate recovery from growth-arrested states.

Journal Article Cell · June 2011 Existing theories explain why operons are advantageous in prokaryotes, but their occurrence in metazoans is an enigma. Nematode operon genes, typically consisting of growth genes, are significantly upregulated during recovery from growth-arrested states. T ... Full text Open Access Cite

Sensitive and precise quantification of insulin-like mRNA expression in Caenorhabditis elegans.

Journal Article PloS one · March 2011 Insulin-like signaling regulates developmental arrest, stress resistance and lifespan in the nematode Caenorhabditis elegans. However, the genome encodes 40 insulin-like peptides, and the regulation and function of individual peptides is largely uncharacte ... Full text Open Access Cite

Staging worms for next-generation analysis.

Journal Article Nature methods · October 2009 Full text Cite

RNA Pol II accumulates at promoters of growth genes during developmental arrest.

Journal Article Science (New York, N.Y.) · April 2009 When Caenorhabditis elegans larvae hatch from the egg case in the absence of food, their development is arrested (L1 arrest), and they show increased stress resistance until food becomes available. To study nutritional control of larval development, we ana ... Full text Cite

Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.

Journal Article Molecular systems biology · January 2008 Biological networks are inherently modular, yet little is known about how modules are assembled to enable coordinated and complex functions. We used RNAi and time series, whole-genome microarray analyses to systematically perturb and characterize component ... Full text Open Access Cite

Optofluidic microscope: A novel high resolution microscope-on-a-chip system

Journal Article LEOS Summer Topical Meeting · December 1, 2006 Cite

A compact optofluidic microscope

Journal Article Proceedings of SPIE the International Society for Optical Engineering · December 1, 2006 We demonstrate a novel optical imaging device that can be directly integrated into a microfluidic network, and therefore enables on-chip imaging in a microfluidic system. This micro imaging device, termed optofluidic microscope (OFM) is free of bulk optics ... Full text Cite

Optofluidic microscopy--a method for implementing a high resolution optical microscope on a chip.

Journal Article Lab on a chip · October 2006 We report a novel microfluidics-based lensless imaging technique, termed optofluidic microscopy (OFM), and demonstrate Caenorhabditis elegans imaging with an OFM prototype that gives comparable resolution to a conventional microscope and a measured resolut ... Full text Cite

Caution, regulatory network assembly in progress

Conference Developmental Biology · July 2006 Full text Cite

DAF-16/FOXO regulates transcription of cki-1/Cip/Kip and repression of lin-4 during C. elegans L1 arrest.

Journal Article Current biology : CB · April 2006 Development is typically studied as a continuous process under laboratory conditions, but wild animals often develop in variable and stressful environments. C. elegans larvae hatch in a developmentally arrested state (L1 arrest) and initiate post-embryonic ... Full text Cite

Optofluidic microscope - A novel microscope-on-a-chip system

Journal Article Optics Infobase Conference Papers · January 1, 2006 We report the implementation of a novel microscope-on-a-chip system, termed the "Optofluidic Microscope (OFM)". The OFM prototype is high resolution, compact and capable of high-throughput sample imaging. In addition, it has the capability to achieve super ... Cite

The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo.

Journal Article Development (Cambridge, England) · April 2005 Maternal and zygotic activities of the homeodomain protein PAL-1 specify the identity and maintain the development of the multipotent C blastomere lineage in the C. elegans embryo. To identify PAL-1 regulatory target genes, we used microarrays to compare t ... Full text Cite

Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions.

Journal Article Genome biology · January 2005 Phenotypic robustness is evidenced when single-gene mutations do not result in an obvious phenotype. It has been suggested that such phenotypic stability results from 'buffering' activities of homologous genes as well as non-homologous genes acting in para ... Full text Open Access Cite

Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome.

Journal Article Development (Cambridge, England) · March 2003 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 m ... Full text Cite

A deletion-generator compound element allows deletion saturation analysis for genomewide phenotypic annotation.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · July 2002 With the available eukaryotic genome sequences, there are predictions of thousands of previously uncharacterized genes without known function or available mutational variant. Thus, there is an urgent need for efficient genetic tools for genomewide phenotyp ... Full text Cite

Expression of exogenous protein in the egg white of transgenic chickens.

Journal Article Nature biotechnology · April 2002 Using a replication-deficient retroviral vector based on the avian leukosis virus (ALV), we inserted into the chicken genome a transgene encoding a secreted protein, beta-lactamase, under the control of the ubiquitous cytomegalovirus (CMV) promoter. Biolog ... Full text Cite

Consistent production of transgenic chickens using replication-deficient retroviral vectors and high-throughput screening procedures.

Journal Article Poultry science · February 2002 We have developed a novel method of DNA extraction combined with a high-throughput method of gene detection allowing thousands of potentially transgenic chicks to be screened quickly and reliably. By using this method and a replication-deficient retroviral ... Full text Cite

Quantitative analysis of mRNA amplification by in vitro transcription.

Journal Article Nucleic acids research · March 2001 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 in vitro transcription is reported to maintain representation of mRN ... Full text Cite

Identification and characterization of Escherichia coli DNA helicase II mutants that exhibit increased unwinding efficiency.

Journal Article Journal of bacteriology · January 1998 Using a combination of both ethyl methanesulfonate and site-directed mutagenesis, we have identified a region in DNA helicase II (UvrD) from Escherichia coli that is required for biological function but lies outside of any of the seven conserved motifs (T. ... Full text Cite

Conserved motifs II to VI of DNA helicase II from Escherichia coli are all required for biological activity.

Journal Article Journal of bacteriology · December 1997 There are seven conserved motifs (IA, IB, and II to VI) in DNA helicase II of Escherichia coli that have high homology among a large family of proteins involved in DNA metabolism. To address the functional importance of motifs II to VI, we employed site-di ... Full text Cite