BRAENDLE

Christian BRAENDLE

Gene-environment interactions in development and evolution

 

Main interests

  • Phenotypic plasticity, genotype-by-environment interactions and genetic assimilation
  • Genotype-phenotype map: from developmental variation to life history variation
  • Evolution and ecology of Caenorhabditis nematodes

Scientific Questions

Environmental variation is a key force shaping the function and evolution of developmental mechanisms. Therefore, it is essential to understand how environmental variation modulates developmental processes and resulting phenotypic variation. Much of our research therefore addresses the questions of how developmental systems respond to environmental variation and how such responses evolve. Using the nematode Caenorhabditis elegans and related species, we aim to answer four main questions: How does development integrate variable environmental information to alter phenotypic outcomes? How do developmental responses to environmental variation evolve? How do quantiative developmental traits evolve within species? What are developmental changes underlying adaptive evolution of life histories? We investigate these questions by focusing on molecularly well-characterized processes, such as vulval cell fate patterning, germline development and dauer formation.

Our Strategy

Although genotype-by-environment interactions are common and important determinants of phenotypic variation, the mechanisms by which genetic and environmental variation interact to generate trait variation remain poorly understood. Our projects thus aim to characterize the molecular and developmental basis of genotype-by-environment interactions, how such interactions evolve and how they in turn may impact the evolutionary process itself. In our research, we use the nematode Caenorhabditis elegans and related species as model organisms, and we integrate quantitative experimental approaches from developmental and evolutionary genetics.

Research Aims

Phenotypic plasticity, genotype-by-environment interactions and genetic assimilation

We focus on the environmental context-dependence of developmental processes (e.g. germ cell proliferation, gametogenesis, dauer formation) to characterize the molecular basis and evolution of phenotypic plasticity. Primarily, we aim to identify developmental and molecular determinants of natural variation in these phenotypes through a combination of quantitative and developmental genetic approaches.

Genotype-phenotype map: from developmental variation to life history variation

How complex traits, such as life history traits, emerge through developmental integration of numerous gene-environment, gene-gene interactions, and higher-order interactions among cells and tissues, remains largely unknown. We therefore study the nematode hermaphrodite germline to ask how variation in different parameters of this developmental system translates into variation in reproductive life histories.

Evolution and ecology of Caenorhabditis nematodes

Although C. elegans is increasingly being used in evolutionary studies, there is still very little information on its natural history, ecology, phylogenetic context, and the genetic structure of its natural populations. We therefore contribute to current community efforts to sample and characterize natural Caenorhabditis populations to generate a more comprehensive evolutionary ecological context for C. elegans and its close relatives.

Researchers

GIMOND Clotilde - +33 489150842
MIGNEROT-FUSTE Laure - +33 489150842

Engineers & Technicians

BOULEAU-MARNETTO Charlotte - +33 489150842
SANDJAK Asma - +33 489150842
BOLELLI Lucie - +33 489150842
BOUVET Orianne - +33 489150842

Students

LE PARC Amélie - +33 489150842

 

Recent publications

  1. Fausett, SR, Sandjak, A, Billard, B, Braendle, C. Higher-order epistasis shapes natural variation in germ stem cell niche activity. Nat Commun. 2023;14 (1):2824. doi: 10.1038/s41467-023-38527-0. PubMed PMID:37198172 PubMed Central PMC10192456.
  2. Huang, Y, Lo, YH, Hsu, JC, Le, TS, Yang, FJ, Chang, T et al.. Widespread sex ratio polymorphism in Caenorhabditis nematodes. R Soc Open Sci. 2023;10 (3):221636. doi: 10.1098/rsos.221636. PubMed PMID:36938539 PubMed Central PMC10014251.
  3. Gimond, C, Poullet, N, Braendle, C. Isolating Caenorhabditis elegans from the Natural Habitat. Methods Mol Biol. 2022;2468 :283-292. doi: 10.1007/978-1-0716-2181-3_15. PubMed PMID:35320571 .
  4. Fausett, S, Poullet, N, Gimond, C, Vielle, A, Bellone, M, Braendle, C et al.. Germ cell apoptosis is critical to maintain Caenorhabditis elegans offspring viability in stressful environments. PLoS One. 2021;16 (12):e0260573. doi: 10.1371/journal.pone.0260573. PubMed PMID:34879088 PubMed Central PMC8654231.
  5. Grover, M, Fasseas, MK, Essmann, C, Liu, K, Braendle, C, Félix, MA et al.. Infection of C. elegans by Haptoglossa Species Reveals Shared Features in the Host Response to Oomycete Detection. Front Cell Infect Microbiol. 2021;11 :733094. doi: 10.3389/fcimb.2021.733094. PubMed PMID:34722333 PubMed Central PMC8552708.
  6. Lee, D, Zdraljevic, S, Stevens, L, Wang, Y, Tanny, RE, Crombie, TA et al.. Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans. Nat Ecol Evol. 2021;5 (6):794-807. doi: 10.1038/s41559-021-01435-x. PubMed PMID:33820969 PubMed Central PMC8202730.
  7. Vigne, P, Gimond, C, Ferrari, C, Vielle, A, Hallin, J, Pino-Querido, A et al.. A single-nucleotide change underlies the genetic assimilation of a plastic trait. Sci Adv. 2021;7 (6):. doi: 10.1126/sciadv.abd9941. PubMed PMID:33536214 PubMed Central PMC7857674.
  8. Noble, LM, Yuen, J, Stevens, L, Moya, N, Persaud, R, Moscatelli, M et al.. Selfing is the safest sex for Caenorhabditis tropicalis. Elife. 2021;10 :. doi: 10.7554/eLife.62587. PubMed PMID:33427200 PubMed Central PMC7853720.
  9. Ben-David, E, Pliota, P, Widen, SA, Koreshova, A, Lemus-Vergara, T, Verpukhovskiy, P et al.. Ubiquitous Selfish Toxin-Antidote Elements in Caenorhabditis Species. Curr Biol. 2021;31 (5):990-1001.e5. doi: 10.1016/j.cub.2020.12.013. PubMed PMID:33417886 .
  10. Billard, B, Vigne, P, Braendle, C. A Natural Mutational Event Uncovers a Life History Trade-Off via Hormonal Pleiotropy. Curr Biol. 2020;30 (21):4142-4154.e9. doi: 10.1016/j.cub.2020.08.004. PubMed PMID:32888477 .
  11. Billard, B, Gimond, C, Braendle, C. [Genetics and evolution of developmental plasticity in the nematode C. elegans: Environmental induction of the dauer stage]. Biol Aujourdhui. 2020;214 (1-2):45-53. doi: 10.1051/jbio/2020006. PubMed PMID:32773029 .
  12. Lee, D, Zdraljevic, S, Cook, DE, Frézal, L, Hsu, JC, Sterken, MG et al.. Selection and gene flow shape niche-associated variation in pheromone response. Nat Ecol Evol. 2019;3 (10):1455-1463. doi: 10.1038/s41559-019-0982-3. PubMed PMID:31548647 PubMed Central PMC6764921.
  13. Gimond, C, Vielle, A, Silva-Soares, N, Zdraljevic, S, McGrath, PT, Andersen, EC et al.. Natural Variation and Genetic Determinants of Caenorhabditis elegans Sperm Size. Genetics. 2019;213 (2):615-632. doi: 10.1534/genetics.119.302462. PubMed PMID:31395653 PubMed Central PMC6781899.
  14. Shin, H, Braendle, C, Monahan, KB, Kaplan, REW, Zand, TP, Mote, FS et al.. Developmental fidelity is imposed by genetically separable RalGEF activities that mediate opposing signals. PLoS Genet. 2019;15 (5):e1008056. doi: 10.1371/journal.pgen.1008056. PubMed PMID:31086367 PubMed Central PMC6534338.
  15. Stevens, L, Félix, MA, Beltran, T, Braendle, C, Caurcel, C, Fausett, S et al.. Comparative genomics of 10 new Caenorhabditis species. Evol Lett. 2019;3 (2):217-236. doi: 10.1002/evl3.110. PubMed PMID:31007946 PubMed Central PMC6457397.
  16. Frézal, L, Demoinet, E, Braendle, C, Miska, E, Félix, MA. Natural Genetic Variation in a Multigenerational Phenotype in C. elegans. Curr Biol. 2018;28 (16):2588-2596.e8. doi: 10.1016/j.cub.2018.05.091. PubMed PMID:30078564 PubMed Central PMC6984962.
  17. Grimbert, S, Vargas Velazquez, AM, Braendle, C. Physiological Starvation Promotes Caenorhabditis elegans Vulval Induction. G3 (Bethesda). 2018;8 (9):3069-3081. doi: 10.1534/g3.118.200449. PubMed PMID:30037804 PubMed Central PMC6118308.
  18. Ferrari, C, Salle, R, Callemeyn-Torre, N, Jovelin, R, Cutter, AD, Braendle, C et al.. Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes. BMC Ecol. 2017;17 (1):43. doi: 10.1186/s12898-017-0150-z. PubMed PMID:29258487 PubMed Central PMC5738176.
  19. Ludewig, AH, Gimond, C, Judkins, JC, Thornton, S, Pulido, DC, Micikas, RJ et al.. Larval crowding accelerates C. elegans development and reduces lifespan. PLoS Genet. 2017;13 (4):e1006717. doi: 10.1371/journal.pgen.1006717. PubMed PMID:28394895 PubMed Central PMC5402976.
  20. Vielle, A, Callemeyn-Torre, N, Gimond, C, Poullet, N, Gray, JC, Cutter, AD et al.. Convergent evolution of sperm gigantism and the developmental origins of sperm size variability in Caenorhabditis nematodes. Evolution. 2016;70 (11):2485-2503. doi: 10.1111/evo.13043. PubMed PMID:27565121 .
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Open engineer position in biology (Ingénieur d’étude)

CDD 12-24 months in Nice, France

We are looking for a highly motivated research engineer  (Ingénieur d’étude) to join our research group “Gene-environment interactions in development and evolution” (http://www.braendlelab.net) at the Institute of Biology Valrose (CNRS – Inserm – University of Nice) (http://ibv.unice.fr).

Our team focuses on the molecular analysis of gene-environment interactions and the evolution of development using the nematode C. elegans. Our research combines approaches from developmental genetics, evolutionary biology and ecology.

Tasks

The successful candidate will primarily contribute to a large-scale phenotyping effort using microscopy quantification of diverse set of developmental and life history phenotypes (germline and reproductive system, vulval cell lineages, developmental timing and reproductive schedules).

Additional tasks will involve:
– microscopy sample preparation (immunohistochemistry, single-molecule FISH, etc).
– molecular biology (PCR, DNA/RNA purification, genotyping, CRISPR-Cas-9 gene editing).
C. elegans genetics, handling, maintenance.

Particularly encouraged are applicants with prior experience in C. elegans research and developmental or evolutionary genetics.

To apply, send a CV, a letter of motivation, and the contact information for two referees as a single PDF file to Christian Braendle (braendle@unice.fr). Informal inquiries are welcome.

Contract and starting: The contract is for an initial duration of 12 months, with a possible extension of up to 24 months. The starting date is flexible, at the earliest on November 1, 2018.

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Research technician in biology
(Assistant Ingénieur en biologie)

CDD 12-24 months in Nice, France

We are looking for a highly motivated research technician (Assistant Ingénieur) to join our research group “Gene-environment interactions in development and evolution” (http://www.braendlelab.net) at the Institute of Biology Valrose (CNRS – Inserm – University of Nice) (http://ibv.unice.fr).

Our team focuses on the molecular analysis of gene-environment interactions and the evolution of development using the nematode C. elegans. Our research combines approaches from developmental genetics, evolutionary biology and ecology.

Tasks

The technician will primarily contribute to a large-scale phenotyping effort using microscopy quantification of diverse set of developmental and life history phenotypes (germline and reproductive system, vulval cell lineages, developmental timing and reproductive schedules).

Additional tasks will involve:

– microscopy sample preparation (immunohistochemistry, single-molecule FISH, etc).
– molecular biology (PCR, DNA/RNA purification, genotyping, CRISPR-Cas-9 gene editing).
C. elegans genetics, handling, maintenance.

Particularly encouraged are applicants with prior experience in C. elegans research and developmental or evolutionary genetics.

 

To apply, send a CV, a letter of motivation, and the contact information for two referees as a single PDF file to Christian Braendle (braendle@unice.fr). Informal inquiries are welcome.

Contract and starting: The contract is for an initial duration of 12 months, with a possible extension of up to 24 months. The starting date is flexible, at the earliest on November 1, 2018.

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PhD position: Evolutionary Genetics of Development

A PhD position is available in the context of a research project between the laboratory of Christian Braendle (Institut de Biologie Valrose, Nice; http://www.braendlelab.net) and Henrique Teotonio (Institut de Biologie, Ecole Normale Superieure, Paris; http://www.ibens.ens.fr/spip.php?rubrique28&lang=en)

The project will characterize the effects of different breeding systems on the evolution of C. elegans hermaphrodite germline development. The key objectives are (1) to perform experimental evolution under different sex ratios of males, females and hermaphrodites; (2) to characterize the genetic basis of hermaphrodite germline traits through genetic transformation methods and a genome-wide association study; and (3) to determine how natural selection at candidate loci depends on hermaphrodite germline developmental evolution.

The candidate should have a Master’s degree in evolutionary biology and an understanding of the fundamental problems of quantitative genetics, population genetics and developmental genetics, including QTL and GWAS mapping. Candidates with experience in computer programming, experimental evolution, developmental phenotyping and statistical analysis of large data sets are preferred. The PhD student will be expected to conduct full-time independent research in the Braendle lab.

The PhD position is funded by the National Agency of French Research (ANR) for three years, subject to an initial evaluation after 6 months, with a potential one-year extension.
The starting date is flexible.

To apply, send a CV, a letter of motivation, and the contact information for two referees as a single PDF file to Christian Braendle (braendle@unice.fr). Informal inquiries are welcome.

For relevant background information see:
Carvalho et al. 2014. http://doi.org/10.1186/1471-2148-14-117
Poullet et al. 2016. http://doi.org/10.1111/evo.13032
Noble et al. 2017. http://doi.org/10.1534/genetics.117.300406
Teotonio et al. 2017. http://doi.org/10.1534/genetics.115.186288

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PhD position: The role of developmental genetic architecture in shaping evolutionary trends

A PhD position is available in the context of a research project between the laboratory of Christian Braendle (Institut de Biologie Valrose, Nice; http://www.braendlelab.net) and Marie-Anne Félix (Institut de Biologie, Ecole Normale Superieure, Paris; http://www.ibens.ens.fr/spip.php?rubrique29&lang=en).

Project description
Mutation is the ultimate source that generates phenotypic variation. Random mutation, however, does not translate into random phenotypic variation because development limits or biases the mutationally inducible phenotypic spectrum. Hence, the mutationally inducible phenotypic spectrum is fundamental in determining the potential phenotypic trajectories that can be explored by evolution. Whether and how such biases in the introduction of phenotypic variation may influence evolutionary trends – particular directions of evolutionary variation in the phenotypic space – remains extremely poorly understood. In the proposed project, we aim to generate comprehensive empirical insights into the nature and evolution of mutational variance of a developmental system.
This project will therefore investigate how developmental architecture may limit or bias the phenotypic spectrum obtained after random mutation. Whether such biases in the production of phenotypic variation may influence evolutionary trends is poorly understood. Here we address this problem using random mutation lines to explore whether differential mutational sensitivity of developmental cell fates can explain divergent evolutionary patterns in the fates of different homologous vulval precursor cells in two clades of nematodes. This project will (1) quantify mutability of these cell fates in wild isolates of Caenorhabditis and Oscheius, (2) connect these experimental data with patterns of evolutionary variation in these traits in the two genera, and (3) characterize the developmental genetic basis for this differential mutability. The results will be among the first to causally connect mutability, developmental biology and evolutionary trends. This approach is unique as it integrates molecular and evolutionary genetic analysis at the single-cell level.

The candidate should have a Master’s degree in evolutionary or developmental biology and an understanding of the fundamental problems of quantitative and developmental genetics. The PhD student will be expected to conduct full-time independent research in the Braendle lab.

The PhD position is funded by the National Agency of French Research (ANR) for three years, subject to an initial evaluation after 6 months, with a potential one-year extension. The starting date is flexible.

To apply, send a CV, a letter of motivation, and the contact information for two referees as a single PDF file to Christian Braendle (braendle@unice.fr). Informal inquiries are welcome.

For relevant background information see:
Braendle et al. 2010. https://doi.org/10.1371/journal.pgen.1000877
Grimbert & Braendle 2014. https://doi.org/10.1111/ede.12091
Félix & Barkoulas 2015. https://doi.org/10.1038/nrg3949
Besnard et al. 2017. https://doi.org/10.1534/genetics.117.203521

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Two PhD positions: Evolutionary Genetics of Development

Second call: April 6, 2018

Two PhO positions are available in the context of a research project between the laboratories of Henrique Teotonio (Institut de Biologie, Ecole Normale Superieure, Paris; http://www.ibens.ens.fr/spip.php?rubrique28&lang=en) and Christian Braendle (Institut de Biologie Valrose, Nice; http://www.braendlelab.net).

The project will characterize the effects of different breeding systems on the evolution of C. elegans hermaphrodite germline development. The key objectives are (1) to perform experimental evolution under different sex ratios of males, females and hermaphrodites; (2) to characterize the genetic basis of hermaphrodite germline traits through genetic transformation methods and a
genome-wide association study; and (3) to determine how natural selection at candidate loci depends on hermaphrodite germline developmental evolution.

Candidates are expected to have a master’s degree in evotutionary biology and an understanding of the fundamental problems of quantitative genetics, population genetics and developmental genetics, including QTL and GWAS mapping. Candidates with experience in computer programming, experimental evolution, developmental phenotyping and statistical analysis of large data sets are preferred. The PhD students will be expected to conduct full-time independent research in both the Teotonio and Braendle labs.

The PhO positions are funded by the National Agency of French Research (ANR) for three years, subject to an initial evaluation after 6 months, with a potential one-year extension. Successful applicants can start their PhD in summer-fall 2018.

To apply, send a CV, a letter of motivation, and the contact information for two referees as a single PDF file to Henrique Teotonio (teotonio@biologie.ens.fr) and Christian Braendle (braendle@unice.fr), with subject PhD_ANR. Informal inquiries are welcome.

For relevant background information see:
Carvalho et al. 2014. http://doi.org/10.1186/1471-2148-14-117
Poullet et al. 2016. http://doi.org/10.1111/evo.13032
Noble et al. 2017. http://doi.org/10.1534/genetics.117.300406
Teolonio et al. 2017. http://doi.org/10.1534/genetics.115.186288

2012 - Fellow at the Institute for Advanced Study, Berlin

2010 - Schlumberger Award

2008 - ATIP, CNRS

1995 - Fund for Young Talented People, Swiss Study Foundation

1994 - Winner of highest award in the Swiss science contest for young people “Schweizer Jugend Forscht”

Maternal self-sacrifice in C. elegans: an example of genetic assimilation

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Evolution of a trade-off between two life history traits in the nematode C. elegans.

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Genetic basis of sperm size in C. elegans: a role for the chromatin remodeling complex NURF-1

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iBV - Institut de Biologie Valrose

"Sciences Naturelles"

Université Nice Sophia Antipolis
Faculté des Sciences
Parc Valrose
06108 Nice cedex 2