Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (37 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2009)
Gap junctions are clusters of intercellular channels which enable direct cell-to cell cytoplasmic communication both electrically and chemically. Gap junctions play an important role in determining cell fate and function during development, underlining the functionality of their plasticity in developing systems. In the work presented here, Hirudo medicinalis, a European leech, was used to study gap junctional protein expression in both the whole embryonic and adult leech central nervous system (CNS) as well as in single neurons. First, quantitative studies revealed that Hm-inx1, a neural specific innexin, and Hm- inx2, a glial specific innexin, are both expressed at relatively higher levels in the embryo than in the adult. Aside from suggesting greater possible coupling among cells in the early leech CNS, this up-regulation may explain how glial cells regulate synapse numbers in neurons early in leech development. Second among 12 previously characterized innexins and two novel innexins, Hm-inxs 13 and 14, four (Hm-inxs 4, 11, 12, and 13) were found to be expressed in the adult CNS but not in the young embryo, while one (Hm-inx8) was found to be expressed in the young embryo but not in the adult. Finally, three specific types of neurons, Retzius (R) serotonergic neurons, anterior pagoda (AP) motor neurons, and pressure (P1) neurons, were found to express unique subsets of innexins. All three cells express Hm-inxs 1 and 6. In addition, R cells express Hm-inx2, AP cells express Hm-inx4, and P1 cells express Hm-inx3 and Hm-inx11.
    Cover page: Evaluating innexins quantitatively and qualitatively in the developing leech : identified neurons in Hirdudo medicinalis express unique subsets of the innexin genes / c Brandon Sarkis Kandarian
    • Thesis
    • Peer Reviewed
    UC Irvine Electronic Theses and Dissertations (2016)

    Microfluidic technology has important applications in Point-of-Care (POC) diagnostics, and in high throughput screening and sequencing through the introduction of small, automated and portable microfluidic devices commonly known as Lab-on-Chip (LOC) devices, and Micro Total Analysis System (µTAS). These devices can perform biochemical and fluidic assays in automated fashion, using smaller amounts of samples and in faster periods of time when compared to traditional methods. However, LOC devices require the integration of active fluidic components as well as a wide array of sensors and actuators on the chip, which has presented a significant challenge in the traditional methods of fabricating microfluidics. In this dissertation, the use of the Printed Circuit Board (PCB) is proposed as a heterogeneous integration platform for microfluidic LOC devices. A novel heterogeneous integration architecture is demonstrated that enables the integration of microfluidics, electronics and optics on PCBs, and promotes standardized, scaled and cost effective fabrication of LOC devices. The fabrication and integration processes are described by demonstrating several microfluidic LOC devices built on PCBs, and integrated with key LOC functions on the chip, such as sample preparation, analyte extraction, and optical detection.

      Cover page: Heterogeneous Integration of Microfluidics on Printed Circuit Boards for Lab-on-Chip ApplicationsCreative Commons 'BY-NC-ND' version 4.0 license
      • Thesis
      • Peer Reviewed
      UC Riverside Electronic Theses and Dissertations (2012)

      Aphids cause extensive economic losses to cultivated crops worldwide. Their success as pests is in part due to their complex life cycle, wide host range, and the ability of a female aphid to contain not only the developing embryos of her daughters, but also those of her grand-daughters which develop within her daughters. The latter results in build up of immense populations very quickly. Resistant plants represent an environmental friendly approach to combat aphid pests. Better understanding of plant-aphid interaction will contribute to engineering durable plant resistance. In tomato (Solanum lycopersicum), the Mi-1 gene confers resistance to potato aphid (Macrosiphum euphorbiae), root-knot nematode (RKN) (Meloidogyne sp.), whitefly (Bemisia tabaci), and tomato psyllid (Bactericera cockerelli). This incompatible tomato interaction with RKN is characterized by hypersensitive response and vast transcriptional reprogramming, including differential regulation of transcription factors (TFs). Using gene knock-down approach in Chapter one, a role for SlWRKY70 TF was identified in Mi-1-mediated tomato resistance against potato aphid and RKN. Gene expression analysis showed that the regulation of this TF by Salicylic acid and Jasmonic acid hormones is conserved between tomato and Arabidopsis thaliana. The study of SlWRKY70 revealed that there is no consistent nomenclature for plant WRKY TF family. For this reason a phylogenetic analysis was conducted using sequences from 15 plant species. Chapter two presents the analysis and the established orthologous relationship of WRKY TFs among these plant species. Consequently, this analysis allowed the design of a systemic nomenclature for the WRKY TF family to include the inferred orthology relationships. Chapters three and four pursued another approach to understand plant-aphid interactions. These chapters focused on identifying the aphid effectors and putative lineage-specific set of genes through sequencing the aphid and its salivary gland transcriptomes. In Chapter three sequencing and annotation of the potato aphid transcriptome enabled us to conduct comparative sequence analysis with three other aphid species, as well as seven additional species of insects from different clades and a planktonic crustacean. This analysis identified a set of aphid-specific genes, which may contribute to aphid's unconventional biology. The transcripts of a subset of these aphid-specific genes were expressed in the salivary glands suggesting that they are involved in aphid-host interactions. To study this interaction in more detail, the potato aphid salivary gland transcriptome was sequenced in Chapter four. This enabled identification of secreted proteins based on prediction of secretion signal peptides. In planta functional characterization of eight of these putative aphid secreted proteins identified roles for two, Me10 and Me23, in altering tomato responses to the aphid's advantage.

      • 12 supplemental files
      Cover page: Tomato-Potato Aphid Interactions: Insights into Plant Defense and the Aphid Pest
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2014)
      The unexpected diversity of the human microbiome and metabolome far exceeds the complexity of the human genome. Although we now understand microbial taxonomic and genetic repertoires in some populations, we are just beginning to assemble the necessary computational and experimental tools to understand the metabolome in comparable detail. However, even with the limited current state of knowledge, individual connections between microbes and metabolites, between microbes and immune function, and between metabolites and immune function are being established. Here, we provide our perspective on these connections and outline a systematic research program that could turn these individual links into a broader network that allows us to understand how these components interact. This program will enable us to exploit connections among the microbiome, metabolome, and host immune system to maintain health and perhaps help us understand how to reverse the processes that lead to a wide range of immune and other diseases.
        Cover page: Finding the Missing Links among Metabolites, Microbes, and the Host
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2016)
        Neurodevelopment is a complex process governed by both intrinsic and extrinsic signals. While historically studied by researching the brain, inputs from the periphery impact many neurological conditions. Indeed, emerging data suggest communication between the gut and the brain in anxiety, depression, cognition, and autism spectrum disorder (ASD). The development of a healthy, functional brain depends on key pre- and post-natal events that integrate environmental cues, such as molecular signals from the gut. These cues largely originate from the microbiome, the consortium of symbiotic bacteria that reside within all animals. Research over the past few years reveals that the gut microbiome plays a role in basic neurogenerative processes such as the formation of the blood-brain barrier, myelination, neurogenesis, and microglia maturation and also modulates many aspects of animal behavior. Herein, we discuss the biological intersection of neurodevelopment and the microbiome and explore the hypothesis that gut bacteria are integral contributors to development and function of the nervous system and to the balance between mental health and disease.
          Cover page: The Central Nervous System and the Gut Microbiome
          • Article
          • Peer Reviewed
          Clinical Practice and Cases in Emergency Medicine, Volume 3, Issue 3 (2019)
          We present a case of acute lower gastrointestinal (GI) bleeding in the emergency department, in which specialists were not emergently available to render their support. A quick intervention using balloon tamponade technique with a Minnesota tube helped stabilize the patient until intensive care, gastroenterology, and surgical specialists could intervene. We also review previous cases from the literature in which a balloon tamponade method was used to control GI hemorrhage. Our novel application of the Minnesota tube is important for emergency physicians to consider for cases of acute lower GI bleeding, particularly in emergent presentations when specialists are not readily available in-hospital.
            Cover page: Novel Application of Balloon Tamponade in Management of Acute Lower Gastrointestinal HemorrhageCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2016)
            In this work, we present hardware and software implementations of flexible polar systematic encoders and decoders. The proposed implementations operate on polar codes of any length less than a maximum and of any rate. We describe the low-complexity, highly parallel, and flexible systematic-encoding algorithm that we use and prove its correctness. Our hardware implementation results show that the overhead of adding code rate and length flexibility is little, and the impact on operation latency minor compared to code-specific versions. Finally, the flexible software encoder and decoder implementations are also shown to be able to maintain high throughput and low latency.
              Cover page: Flexible and Low-Complexity Encoding and Decoding of Systematic Polar Codes
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2019)
              Microglia, the resident immune cells in the brain, are essential for modulating neurogenesis, influencing synaptic remodeling, and regulating neuroinflammation by surveying the brain microenvironment. Microglial dysfunction has been implicated in the onset and progression of several neurodevelopmental and neurodegenerative diseases; however, the multitude of factors and signals influencing microglial activity have not been fully elucidated. Microglia not only respond to local signals within the brain but also receive input from the periphery, including the gastrointestinal (GI) tract. Recent preclinical findings suggest that the gut microbiome plays a pivotal role in regulating microglial maturation and function, and altered microbial community composition has been reported in neurological disorders with known microglial involvement in humans. Collectively, these findings suggest that bidirectional crosstalk between the gut and the brain may influence disease pathogenesis. Herein, we discuss recent studies showing a role for the gut microbiome in modulating microglial development and function in homeostatic and disease conditions and highlight possible future research to develop novel microbial treatments for disorders of the brain.
                Cover page: Microbiome–microglia connections via the gut–brain axis
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2014)
                The discovery of the size and complexity of the human microbiome has resulted in an ongoing reevaluation of many concepts of health and disease, including diseases affecting the CNS. A growing body of preclinical literature has demonstrated bidirectional signaling between the brain and the gut microbiome, involving multiple neurocrine and endocrine signaling mechanisms. While psychological and physical stressors can affect the composition and metabolic activity of the gut microbiota, experimental changes to the gut microbiome can affect emotional behavior and related brain systems. These findings have resulted in speculation that alterations in the gut microbiome may play a pathophysiological role in human brain diseases, including autism spectrum disorder, anxiety, depression, and chronic pain. Ongoing large-scale population-based studies of the gut microbiome and brain imaging studies looking at the effect of gut microbiome modulation on brain responses to emotion-related stimuli are seeking to validate these speculations. This article is a summary of emerging topics covered in a symposium and is not meant to be a comprehensive review of the subject.
                  Cover page: Gut microbes and the brain: paradigm shift in neuroscience.
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2014)
                  The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-microbe interactions affect immunity, metabolism, development, and behavior, and dysbiosis of gut bacteria contributes to disease. Despite advances in correlating changes in the microbiota with various conditions, specific mechanisms of host-microbiota signaling remain largely elusive. We discuss the synthesis of microbial metabolites, their absorption, and potential physiological effects on the host. We propose that the effects of specialized metabolites may explain present knowledge gaps in linking the gut microbiota to biological host mechanisms during initial colonization, and in health and disease.
                    Cover page: Specialized Metabolites from the Microbiome in Health and Disease
                    Top