Bio

Professional Education


  • Bachelor of Science, University of Arkansas Fayetteville (2008)
  • Doctor of Philosophy, University of California Berkeley (2015)

Stanford Advisors


Publications

All Publications


  • Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor. Proceedings of the National Academy of Sciences of the United States of America Cleves, P. A., Tinoco, A. I., Bradford, J., Perrin, D., Bay, L. K., Pringle, J. R. 2020

    Abstract

    Reef-building corals are keystone species that are threatened by anthropogenic stresses including climate change. To investigate corals' responses to stress and other aspects of their biology, numerous genomic and transcriptomic studies have been performed, generating many hypotheses about the roles of particular genes and molecular pathways. However, it has not generally been possible to test these hypotheses rigorously because of the lack of genetic tools for corals or closely related cnidarians. CRISPR technology seems likely to alleviate this problem. Indeed, we show here that microinjection of single-guide RNA/Cas9 ribonucleoprotein complexes into fertilized eggs of the coral Acropora millepora can produce a sufficiently high frequency of mutations to detect a clear phenotype in the injected generation. Based in part on experiments in a sea-anemone model system, we targeted the gene encoding Heat Shock Transcription Factor 1 (HSF1) and obtained larvae in which >90% of the gene copies were mutant. The mutant larvae survived well at 27 C but died rapidly at 34 C, a temperature that did not produce detectable mortality over the duration of the experiment in wild-type (WT) larvae or larvae injected with Cas9 alone. We conclude that HSF1 function (presumably its induction of genes in response to heat stress) plays an important protective role in corals. More broadly, we conclude that CRISPR mutagenesis in corals should allow wide-ranging and rigorous tests of gene function in both larval and adult corals.

    View details for DOI 10.1073/pnas.1920779117

    View details for PubMedID 33168726

  • Insights into coral bleaching under heat stress from analysis of gene expression in a sea anemone model system. Proceedings of the National Academy of Sciences of the United States of America Cleves, P. A., Krediet, C. J., Lehnert, E. M., Onishi, M., Pringle, J. R. 2020

    Abstract

    Loss of endosymbiotic algae ("bleaching") under heat stress has become a major problem for reef-building corals worldwide. To identify genes that might be involved in triggering or executing bleaching, or in protecting corals from it, we used RNAseq to analyze gene-expression changes during heat stress in a coral relative, the sea anemone Aiptasia. We identified >500 genes that showed rapid and extensive up-regulation upon temperature increase. These genes fell into two clusters. In both clusters, most genes showed similar expression patterns in symbiotic and aposymbiotic anemones, suggesting that this early stress response is largely independent of the symbiosis. Cluster I was highly enriched for genes involved in innate immunity and apoptosis, and most transcript levels returned to baseline many hours before bleaching was first detected, raising doubts about their possible roles in this process. Cluster II was highly enriched for genes involved in protein folding, and most transcript levels returned more slowly to baseline, so that roles in either promoting or preventing bleaching seem plausible. Many of the genes in clusters I and II appear to be targets of the transcription factors NFkappaB and HSF1, respectively. We also examined the behavior of 337 genes whose much higher levels of expression in symbiotic than aposymbiotic anemones in the absence of stress suggest that they are important for the symbiosis. Unexpectedly, in many cases, these expression levels declined precipitously long before bleaching itself was evident, suggesting that loss of expression of symbiosis-supporting genes may be involved in triggering bleaching.

    View details for DOI 10.1073/pnas.2015737117

    View details for PubMedID 33168733

  • Unknown to Known: Advancing Knowledge of Coral Gene Function. Trends in genetics : TIG Cleves, P. A., Shumaker, A., Lee, J., Putnam, H. M., Bhattacharya, D. 2019

    Abstract

    Given the catastrophic changes befalling coral reefs, understanding coral gene function is essential to advance reef conservation. This has proved challenging due to the paucity of genomic data and genetic tools available for corals. Recently, CRISPR/Cas9 gene editing was applied to these species; however, a major bottleneck is the identification and prioritization of candidate genes for manipulation. This issue is exacerbated by the many unknown ('dark') coral genes that may play key roles in the stress response. We review the use of gene coexpression networks that incorporate both known and unknown genes to identify targets for reverse genetic analysis. This approach also provides a framework for the annotation of dark genes in established interaction networks to improve our fundamental knowledge of coral gene function.

    View details for DOI 10.1016/j.tig.2019.11.001

    View details for PubMedID 31882190

  • Strength in numbers: Collaborative science for new experimental model systems PLOS BIOLOGY Waller, R. F., Cleves, P. A., Rubio-Brotons, M., Woods, A., Bender, S. J., Edgcomb, V., Gann, E. R., Jones, A. C., Teytelman, L., von Dassow, P., Wilhelm, S. W., Collier, J. L. 2018; 16 (7): e2006333

    Abstract

    Our current understanding of biology is heavily based on a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster the development of ecologically and taxonomically diverse marine protist genetic models. The development of new models faces many barriers, some technical and others institutional, and this often discourages the risky, long-term effort that may be required. To lower these barriers and tackle the complexity of this effort, a highly collaborative community-based approach was taken. Herein, we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research.

    View details for PubMedID 29965960

  • CRISPR/Cas9-mediated genome editing in a reef-building coral PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Clevesa, P. A., Strader, M. E., Bay, L. K., Pringle, J. R., Matz, M. V. 2018; 115 (20): 5235?40

    Abstract

    Reef-building corals are critically important species that are threatened by anthropogenic stresses including climate change. In attempts to understand corals' responses to stress and other aspects of their biology, numerous genomic and transcriptomic studies have been performed, generating a variety of hypotheses about the roles of particular genes and molecular pathways. However, it has not generally been possible to test these hypotheses rigorously because of the lack of genetic tools for corals. Here, we demonstrate efficient genome editing using the CRISPR/Cas9 system in the coral Acropora millepora We targeted the genes encoding fibroblast growth factor 1a (FGF1a), green fluorescent protein (GFP), and red fluorescent protein (RFP). After microinjecting CRISPR/Cas9 ribonucleoprotein complexes into fertilized eggs, we detected induced mutations in the targeted genes using changes in restriction-fragment length, Sanger sequencing, and high-throughput Illumina sequencing. We observed mutations in ?50% of individuals screened, and the proportions of wild-type and various mutant gene copies in these individuals indicated that mutation induction continued for at least several cell cycles after injection. Although multiple paralogous genes encoding green fluorescent proteins are present in A. millepora, appropriate design of the guide RNA allowed us to induce mutations simultaneously in more than one paralog. Because A. millepora larvae can be induced to settle and begin colony formation in the laboratory, CRISPR/Cas9-based gene editing should allow rigorous tests of gene function in both larval and adult corals.

    View details for PubMedID 29695630

  • Glucose-Induced Trophic Shift in an Endosymbiont Dinoflagellate with Physiological and Molecular Consequences PLANT PHYSIOLOGY Xiang, T., Jinkerson, R. E., Clowez, S., Tran, C., Krediet, C. J., Onishi, M., Cleves, P. A., Pringle, J. R., Grossman, A. R. 2018; 176 (2): 1793?1807

    Abstract

    Interactions between the dinoflagellate endosymbiont Symbiodinium and its cnidarian hosts (e.g. corals, sea anemones) are the foundation of coral-reef ecosystems. Carbon flow between the partners is a hallmark of this mutualism, but the mechanisms governing this flow and its impact on symbiosis remain poorly understood. We showed previously that although Symbiodinium strain SSB01 can grow photoautotrophically, it can grow mixotrophically or heterotrophically when supplied with Glc, a metabolite normally transferred from the alga to its host. Here we show that Glc supplementation of SSB01 cultures causes a loss of pigmentation and photosynthetic activity, disorganization of thylakoid membranes, accumulation of lipid bodies, and alterations of cell-surface morphology. We used global transcriptome analyses to determine if these physiological changes were correlated with changes in gene expression. Glc-supplemented cells exhibited a marked reduction in levels of plastid transcripts encoding photosynthetic proteins, although most nuclear-encoded transcripts (including those for proteins involved in lipid synthesis and formation of the extracellular matrix) exhibited little change in their abundances. However, the altered carbon metabolism in Glc-supplemented cells was correlated with modest alterations (approximately 2x) in the levels of some nuclear-encoded transcripts for sugar transporters. Finally, Glc-bleached SSB01 cells appeared unable to efficiently populate anemone larvae. Together, these results suggest links between energy metabolism and cellular physiology, morphology, and symbiotic interactions. However, the results also show that in contrast to many other organisms, Symbiodinium can undergo dramatic physiological changes that are not reflected by major changes in the abundances of nuclear-encoded transcripts and thus presumably reflect posttranscriptional regulatory processes.

    View details for PubMedID 29217594

    View details for PubMedCentralID PMC5813547

  • Transcription factor NF-kappa B is modulated by symbiotic status in a sea anemone model of cnidarian bleaching SCIENTIFIC REPORTS Mansfield, K. M., Carter, N. M., Nguyen, L., Cleves, P. A., Alshanbayeva, A., Williams, L. M., Crowder, C., Penvose, A. R., Finnerty, J. R., Weis, V. M., Siggers, T. W., Gilmore, T. D. 2017; 7: 16025

    Abstract

    Transcription factor NF-?B plays a central role in immunity from fruit flies to humans, and NF-?B activity is altered in many human diseases. To investigate a role for NF-?B in immunity and disease on a broader evolutionary scale we have characterized NF-?B in a sea anemone (Exaiptasia pallida; called Aiptasia herein) model for cnidarian symbiosis and dysbiosis (i.e., "bleaching"). We show that the DNA-binding site specificity of Aiptasia NF-?B is similar to NF-?B proteins from a broad expanse of organisms. Analyses of NF-?B and I?B kinase proteins from Aiptasia suggest that non-canonical NF-?B processing is an evolutionarily ancient pathway, which can be reconstituted in human cells. In Aiptasia, NF-?B protein levels, DNA-binding activity, and tissue expression increase when loss of the algal symbiont Symbiodinium is induced by heat or chemical treatment. Kinetic analysis of NF-?B levels following loss of symbiosis show that NF-?B levels increase only after Symbiodinium is cleared. Moreover, introduction of Symbiodinium into nave Aiptasia larvae results in a decrease in NF-?B expression. Our results suggest that Symbiodinium suppresses NF-?B in order to enable establishment of symbiosis in Aiptasia. These results are the first to demonstrate a link between changes in the conserved immune regulatory protein NF-?B and cnidarian symbiotic status.

    View details for PubMedID 29167511

  • Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Cleves, P. A., Ellis, N. A., Jimenez, M. T., Nunez, S. M., Schluter, D., Kingsley, D. M., Miller, C. T. 2014; 111 (38): 13912-13917
  • Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6. Proceedings of the National Academy of Sciences of the United States of America Cleves, P. A., Ellis, N. A., Jimenez, M. T., Nunez, S. M., Schluter, D., Kingsley, D. M., Miller, C. T. 2014; 111 (38): 13912-13917

    Abstract

    Developmental genetic studies of evolved differences in morphology have led to the hypothesis that cis-regulatory changes often underlie morphological evolution. However, because most of these studies focus on evolved loss of traits, the genetic architecture and possible association with cis-regulatory changes of gain traits are less understood. Here we show that a derived benthic freshwater stickleback population has evolved an approximate twofold gain in ventral pharyngeal tooth number compared with their ancestral marine counterparts. Comparing laboratory-reared developmental time courses of a low-toothed marine population and this high-toothed benthic population reveals that increases in tooth number and tooth plate area and decreases in tooth spacing arise at late juvenile stages. Genome-wide linkage mapping identifies largely separate sets of quantitative trait loci affecting different aspects of dental patterning. One large-effect quantitative trait locus controlling tooth number fine-maps to a genomic region containing an excellent candidate gene, Bone morphogenetic protein 6 (Bmp6). Stickleback Bmp6 is expressed in developing teeth, and no coding changes are found between the high- and low-toothed populations. However, quantitative allele-specific expression assays of Bmp6 in developing teeth in F1 hybrids show that cis-regulatory changes have elevated the relative expression level of the freshwater benthic Bmp6 allele at late, but not early, stages of stickleback development. Collectively, our data support a model where a late-acting cis-regulatory up-regulation of Bmp6 expression underlies a significant increase in tooth number in derived benthic sticklebacks.

    View details for DOI 10.1073/pnas.1407567111

    View details for PubMedID 25205810

    View details for PubMedCentralID PMC4183278

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