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Open Access Publications from the University of California

Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2021)

Experimental evolutionary studies are excellent approaches to study the coadaptation of the musculoskeletal with locomotor behavior in real time. My dissertation examines mice from 4 replicate High Runner (HR) lines bred for voluntary wheel running as young adults and their 4 non-selected Control (C) lines. Chapter 1 involved the analysis of skeletal data from generation 11 and found that HR mice have evolved larger hip and knee surface areas, which would lower stress (force per unit area), acting on the hindlimb during running. This chapter demonstrates that skeletal dimensions and muscle masses can evolve rapidly in response to directional selection on locomotor behavior. Chapter 2 examined the rapid and longer-term effects of selective breeding on the skeleton. HR mice reached an apparent selection limit between generations 16-28, running ~3-fold more than C mice. Analysis of bone data from generations 11, 16, 21, 37, 57, and 68 revealed unique results. I found few differences between HR and C mice for these later generations, and some of the differences in bone dimensions identified in earlier generations were no longer statistically significant. Chapter 3 highlighted aspects of phenotypic plasticity achieved through exercise. Muscle attachment site morphology reflects muscle mass and function and therefore, paleontologists have routinely used characteristics of muscle entheses to infer the past loading history of individual specimens. I used mice from generation 57 that were housed with or without wheels for throughout ontogeny to quantify the genetic differences in muscle attachment site morphology between HR and C mice, as well as plastic changes resulting from chronic exposure to exercise. My results demonstrate that muscle attachment site morphology can be (but is not always) affected by chronic exercise. Chapter 4 investigated a negative correlation between average running speed and time spent running on wheels that exists among the HR lines. I hypothesized that this trade-off may be related to evolved changes in muscle physiology and used in-situ preparations to quantify muscle contractile properties, including speed and endurance. I found that muscle-level speed and endurance do trade-off in these mice, but not in a way that maps to the observed organismal-level speed-endurance trade-off.

  • 7 supplemental ZIPs
Cover page: Skeletal Evolution and Muscle Physiology in House Mice Selectively Bred for High Levels of Voluntary Wheel-Running Behavior
  • Article
  • Peer Reviewed
UC Riverside Previously Published Works (2022)
The gut microbiome can affect various aspects of both behavior and physiology, including exercise ability, but effects on voluntary exercise have rarely been studied. We studied females from a selection experiment in which 4 replicate High Runner (HR) lines of mice are bred for voluntary exercise and compared with 4 non-selected control (C) lines. HR and C mice differ in several traits that likely interact with the gut microbiome, including higher daily running distance, body temperatures when running, spontaneous physical activity when housed without wheels, and food consumption. After two weeks of wheel access to reach a stable plateau in daily running, mice were administered broad-spectrum antibiotics for 10 days. Antibiotic treatment caused a significant reduction in daily wheel-running distance in the HR mice (-21%) but not in the C mice. Antibiotics did not affect body mass or food consumption in either HR or C mice, and we did not observe sickness behavior. Wheel running by HR mice did not recover during the 12 days following cessation of antibiotics. The decreased wheel-running in HR but not C mice, with no apparent negative side effects of antibiotics, suggests that the HR microbiome is an important component of their high-running phenotype.
    Cover page: Oral antibiotics reduce voluntary exercise behavior in athletic mice.
    • Article
    • Peer Reviewed
    UC Merced Previously Published Works (2015)
    Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.
      Cover page: Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems
      • Article
      • Peer Reviewed
      UC Merced Previously Published Works (2020)
      Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).
        Cover page: Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems
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