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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2018)

Students often fail to develop a sophisticated understanding of scientific topics despite years of formal education designed to help them do so. Through studying how students learn the physical sciences, conceptual change researchers have amassed a large body of evidence that people, rather than being empty vessels who passively accept scientific theories, already possess rich intuitive theories about the world. More recently, researchers have argued that these intuitive theories shape how people understand the social world as well. In this project, we explored these intuitive theories about people and how these intuitive theories differ from how experts in the social sciences think about people. To do this, we used the Delphi method, a method of surveying experts that uses iterative rounds of quantitative judgments and comments. We created seven Delphi panels, each comprised of professors from a specific field of the social sciences (Anthropology, Economics, Geography, History, Political Science, Psychology, and Sociology) and asked them to explain the most consequential ways that studying their field changes how one understands and explains the human world. Three of the panels were highly successful, one was moderately successful, and three were largely unsuccessful due to low participation. Findings indicate that social scientists can describe several consequential ways they think about the human world differently from those who have not studied the social sciences. Similarities and differences across fields of the social sciences are discussed, as well as differences within the fields as described by panelists. However, these disagreements within and across fields, and especially disagreements over the correct way to interpret terms, make it difficult to generalize across the social sciences as a whole.

    Cover page: Conceptual Change About People
    • Article
    • Peer Reviewed
    LBL Publications (2016)
    The vacancy ordering behavior of an A-site deficient perovskite system, Ca1-xLa2x/3TiO3, was studied using atomic resolution scanning transmission electron microscopy (STEM) in conjunction with electron energy-loss spectroscopy (EELS), with the aim of determining the role of A-site composition changes. At low La content (x = 0.2), adopting Pbnm symmetry, there was no indication of long-range ordering. Domains, with clear boundaries, were observed in bright-field (BF) imaging, but were not immediately visible in the corresponding high-angle annular dark-field (HAADF) image. These boundaries, with the aid of displacement maps from A-site cations in the HAADF signal, are shown to be tilt boundaries. At the La-rich end of the composition (x = 0.9), adopting Cmmm symmetry, long-range ordering of vacancies and La3+ ions was observed, with alternating La-rich and La-poor layers on (001)p planes, creating a double perovskite lattice along the c axis. These highly ordered domains can be found isolated within a random distribution of vacancies/La3+, or within a large population, encompassing a large volume. In regions with a high number density of double perovskite domains, these highly ordered domains were separated by twin boundaries, with 90° or 180° lattice rotations across boundaries. The occurrence and characteristics of these ordered structures are discussed and compared with similar perovskite systems.
      Cover page: Characterization of Ordering in A‑Site Deficient Perovskite Ca1–x La2x/3TiO3 Using STEM/EELS
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2013)

      Background

      The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites.

      Results

      The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules.

      Conclusions

      The draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders.
        Cover page: The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2020)

        Background

        Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.

        Results

        Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception.

        Conclusions

        These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
          Cover page: Gene content evolution in the arthropods
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2021)
          We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
            Cover page: 3D genomics across the tree of life reveals condensin II as a determinant of architecture type
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