The Biochemical Evolution Lab

ColeB Our laboratory studies the mechanisms by which fish and aquatic invertebrates cope with environmental stress, in particular salinity/ osmotic stress. We use targeted proteomics, Skyline, and PanoramaWeb as key tools for obtaining insight into the dynamic regulation of molecular phenotypes (proteomes) in cells and tissues exposed to environmental stress at physiological (acute) and evolutionary (long-term, chronic) time scales. To enable novel insight into these mechanisms much of our work focuses on molecular tool development. Some tools developed in our lab are now used for applied purposes, e.g. our immortalized tilapia cell lines are being used for development and production of viral vaccines to benefit aquaculture.
pATM What is the role of stress-induced evolution (SIE) for biodiversity? What are the underlying molecular mechanisms of SIE? The concept of SIE is based on the realization that macromolecular damage comprises the common denominator of cellular stress (Kültz, 2005). SIE has also been referred to as stress-induced evolutionary innovation (SIEI) (Wagner et al., 2019). It represents an exciting, novel mechanism of evolution that has the potential to mechanistically explain biological phenomena that reach beyond the theoretical framework underlying the Modern synthesis of Neo-Darwinism (Heng, 2019). We study mechanisms of SIE using experimental evolution of vertebrate cell lines and archaea (Halobacterium salinarium) in combination with genome topology analyses and proteomics. The image shows vertebrate cell nuclei stained with anti-phospho-Ser1981-ATM kinase antibody (green) and counterstained with propidium iodide (red) to visualize stress-induced genome rearrangements.
BML1 What are the mechanistic drivers for the evolution of high stress tolerance and what are the mechanistic constraints that render most species stenotopic (= having low stress tolerance)? Evolution has given rise to species that are uniquely adapted to a wide variety of extreme habitats. Our lab studies the biochemical and evolutionary mechanisms that facilitate such adaptation. We aim to better understand how the minimal stress proteome has evolved to facilitate high environmental stress tolerance (Kültz, 2003). The proteome represents the sum of expressed proteins in a given tissue at a particular time. It signifies the ultimate link connecting the genomic blueprint with environmental context-dependent structure and function of organisms.
How do organisms and their cells sense and memorize stressful environmental contexts during their life cycle, development, and aging?
BML1The dynamic proteome directly determines higher order phenotypes (complex morphology, physiology, behavior). Therefore, proteomics approaches allow studies of organisms and their tissues as integrated systems rather than a single or few molecules/ traits at a time. Integrated, systems-level proteomics approaches facilitate network analyses and network decomposition. The combination of quantitative proteomics with functional genomics permits causal linkages of genotypes to adaptive phenotypes. Our ultimate goal is to decipher the logic by which stress-responsive signaling networks control transcriptional and proteome regulatory networks. Comparative network analyses in euryhaline and stenohaline species reveal targets of evolution in stressful environments. To transform correlational networks into causality networks we combine molecular phenotyping (quantitative proteomics, DIA mass spectrometry ) with functional genomics (gene targeting, genome editing).

Event Date
Alexa is admitted to Medical School15-Oct-2020
John's PhD exit seminar scheduled for Nov. 17, 202014-Oct-2020
Dietmar receives ASUCD Academic Excellence in Education Award for the second consecutive year13-Oct-2020
Lizzy passes QE - Congrats!28-Sep-2020
Meranda has arrived in Davis - Welcome!20-Sep-2020
Book chapter on iono- and osmoregulation published in The physiology of fishes07-Sep-2020
Lizzy joins UC Davis Phi Kappa Phi Honor Society19-Aug-2020
Jens' manuscript published in bioRxiv05-Aug-2020
Chanhee's paper published in Scientific Reports22-Jul-2020
Special JEZ-A issue on Cellular Stress Responses of Animals published29-Jun-2020
Chanhee's paper accepted in Scientific Reports10-Jun-2020
Lizzy receives Jastro award from GGE04-Jun-2020
Chanhee, Jens and Larken awarded ABGG summer fellowship03-Jun-2020
John's paper published in Int.Comp.Biol.27-May-2020
Larken awarded Hart, Cole, Goss Fellowship21-May-2020