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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2024)

This dissertation advances our knowledge of allopolyploidy, genomic adaptations, and heat stress responses in plants, focusing on Nicotiana section Repandae and two Boechera species, Boechera arcuata and Boechera perennans. Through comparative genomic and transcriptomic analyses, it elucidates the genetic mechanisms underlying these processes and their evolutionary implications. In Nicotiana section Repandae, I investigate global gene expression and subgenome dominance among three allotetraploid species derived from hybridization between N. sylvestris and N. obtusifolia about 4.5 million years ago. My findings reveal consistent subgenome dominance of N. obtusifolia across various developmental stages, impacting flower size and morphology. This dominance plays a significant role in shaping the genetic architecture and evolutionary trajectory of these species. In Boechera, I examine genomic adaptations to extreme environments, focusing on B. arcuata and B. perennans, which inhabit distinct climatic regions. Through comparative genomics and functional analysis, I identify unique and expanded gene families associated with environmental resilience. Gene Ontology enrichment reveals significant terms related to photosynthesis and stress response, particularly in B. perennans. The results highlight the evolutionary processes enabling these species to thrive in diverse habitats. I further investigate gene expression profiles and evolutionary patterns of heat stress responses in B. arcuata and B. perennans. Using RNA sequencing data, I identify differentially expressed genes under control and basal heat stress conditions, with the top 50 upregulated genes predominantly being heat shock proteins. GO enrichment analysis reveals distinct metabolic and enzyme activity responses, indicating species-specific adaptations. Positive selection tests identify amino acid sites under evolutionary pressure, suggesting adaptive changes contributing to thermotolerance. By integrating comparative genomic and transcriptomic analyses, here I provide insights into the genetic and evolutionary mechanisms driving these processes in Nicotiana and Boechera species, offering valuable information for future research and potential applications in improving crop resilience.

    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2019)
    Age and estrogens may impact the mobility of N-methyl-D-aspartate receptors (NMDARs) in hippocampal synapses. Here, we used serial section immunogold electron microscopy to examine whether phosphorylated tyrosine 1472 NR2B (pY1472), which is involved in the surface expression of NMDARs, is altered in the dorsal hippocampus of young (3-4 months old) and aged (∼24 months old) ovariectomized rats treated with 17β-estradiol or vehicle for 2 days. The number of gold particles labeling pY1472 was higher in presynaptic and postsynaptic compartments of aged rats with low estradiol (vehicle-treated) compared to other groups. In terminals, pY1472 levels were elevated in aged rats but reduced by estradiol treatment to levels seen in young rats. Conversely, the mitochondria number was lower in aged females but was restored to young levels by estradiol. In the postsynaptic density and dendritic spines, estradiol reduced pY1472 in young and aged rats. As phosphorylation at Y1472 blocks NR2B endocytosis, reduction of pY1472 by estradiol suggests another mechanism through which estrogen enhances synaptic plasticity by altering localization of NMDAR subunits within synapses.
      Cover page: Effects of estrogen and aging on synaptic morphology and distribution of phosphorylated Tyr1472 NR2B in the female rat hippocampus.
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2023)
      Estrogens via estrogen receptor alpha (ERα) genomic and nongenomic signaling can influence plasticity processes in numerous brain regions. Using mice that express nuclear only ERα (NOER) or membrane only ERα (MOER), this study examined the effect of receptor compartmentalization on the paraventricular nucleus of the hypothalamus (PVN) and the hippocampus. The absence of nuclear and membrane ERα expression impacted females but not males in these two brain areas. In the PVN, quantitative immunohistochemistry showed that the absence of nuclear ERα increased nuclear ERβ. Moreover, in the hippocampus CA1, immuno-electron microscopy revealed that the absence of either nuclear or membrane ERα decreased extranuclear ERα and pTrkB in synapses. In contrast, in the dentate gyrus, the absence of nuclear ERα increased pTrkB in synapses, whereas the absence of membrane ERα decreased pTrkB in axons. However, the absence of membrane only ERα decreased the sprouting of mossy fibers in CA3 as reflected by changes in zinc transporter immunolabeling. Altogether these findings support the idea that both membrane and nuclear ERα contribute overlapping and unique actions of estrogen that are tissue- and cellular-specific.
        Cover page: Both Nuclear and Membrane Estrogen Receptor Alpha Impact the Expression of Estrogen Receptors and Plasticity Markers in the Mouse Hypothalamus and Hippocampus
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2016)
        Non-randomised studies of the effects of interventions are critical to many areas of healthcare evaluation, but their results may be biased. It is therefore important to understand and appraise their strengths and weaknesses. We developed ROBINS-I (“Risk Of Bias In Non-randomised Studies - of Interventions”), a new tool for evaluating risk of bias in estimates of the comparative effectiveness (harm or benefit) of interventions from studies that did not use randomisation to allocate units (individuals or clusters of individuals) to comparison groups. The tool will be particularly useful to those undertaking systematic reviews that include non-randomised studies.
          Cover page: ROBINS-I: a tool for assessing risk of bias in non-randomised studies of interventionsCreative Commons 'BY' version 4.0 license
          • Article
          LBL Publications (2007)
          We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
            Cover page: The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
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