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Open Access Publications from the University of California

Scholarly Works (14 results)

  • Article
UC Merced Undergraduate Research Journal, Volume 7, Issue 1 (2014)
Neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, and Huntington’s disease,affect up to 40 million people worldwide. These diseases in humans work by slowly degradingneural structures, but some species, such as planarians, can combat such afflictions by theirrobust regenerative properties. While it is known that the progressive loss of neural structures arecommon in these diseases, it is not known whether regeneration of neural structures can restorethe brain as it was. Our objective is to inhibit nou-darake (ndk), a gene associated withectopic brain formation, in genetically modified Schmidtea mediterranea planarians andanalyze both partial and full neural regeneration. Our general strategy starts by thedevelopment of three different planarian models utilizing RNA interference (RNAi): (1) SmedTOR(RNAi)planarians which exhibit only wound-healing abilities similar to humans, (2) Smedapc(RNAi)planarians which have disrupted anterior-posterior (A-P) polarity regenerating onlyposterior ends after amputation, and (3) Smed-βcatenin-B(RNAi) planarians which have disruptedA-P polarity regenerating only anterior ends after amputation. Afterwards, each planarian modelwill be given Smed-ndk(RNAi) and observed intact and after amputation. The proposed study willnot only present detailed spatiotemporal images of neural regeneration in multiple planarianmodels, but propose the planarian as a model organism for future neurodegenerative research. Our goal is to further the understanding of both partial and full neural regeneration in order tobring forth new treatments for neurodegenerative diseases.
    Cover page: Regeneration of lost brain tissues by genetic manipulation of nou-darake in Schmidtea mediterranea planarians
    • Thesis
    • Peer Reviewed
    UC Santa Barbara Electronic Theses and Dissertations (2023)

    Whether it is a single cell organism or a multicellular system, both need to undergo changes in mechanics in order to grow and shape themselves. In this thesis, we will look at the interplay between growth and mechanics, both at the unicellular and multicellular levels. For the single cell organism, we will look at how the mechanics of the cell wall are maintained during the process of tip growth in S. cerevisiae and explore the interplay of cell wall assembly and mechanics during the process of mating projection growth. For the multicellular system, we will characterize how the forces change during the process of growth and invasion in 4T1 breast cancer spheroids.Single celled organisms have various forms of growth, but a common type is called tip growth. In yeast, this mode of growth occurs during mating whereby two cells of different mating types grow towards each other. While the molecular pathways of this process have been documented, it is unclear how the mechanical integrity of the cell wall is maintained under the high internal turgor pressure of the organism during cell wall assembly and expansion. By combining theoretical and experimental approaches, we show that mechanical feedback is necessary to allow mating projection growth to occur in S. cerevisiae. We found that the mechanical feedback is provided by the Cell Wall Integrity pathway, which modulates cell wall assembly depending on mechanical changes in the cell wall and stabilizes mating projection growth. By experimentally perturbing key players of this pathway through genetic deletions of cell wall stress sensors, we were able to test the predictions provided by our theoretical description. Our results show that cell wall assembly and the mechanics of the cell wall must be tightly coordinated via a genetically-encoded mechanical feedback to ensure cell viability during morphogenesis. Multicellular cancer aggregates have been used as model systems to study different aspects of tumorigenesis. Here we will investigate the mechanical aspects of the process of invasion, which is one of the initial steps of metastatic growth. Multicellular aggregates, also called spheroids, have been used extensively as they are more representative of the physiology of a tumor and can be embedded in controlled microenvironments. While the forces that a tumor generates on the surrounding environment have been investigated, the forces within the tumor during invasion have never been explored, mainly due to a lack in technologies enabling direct mechanical measurements in 3D multicellular environments. By utilizing fluorescent cell-sized bioinert droplets as force transducers, we quantify how the mechanics within the tumor change as it begins to invade into a collagen type I matrix. Through the use of this technique and in-house developed software, we were able to show that while supracellular stresses remain low and constant during invasion, cell-scale stresses increase in invading spheroids while stresses in the non-invading spheroids stay relatively constant.

      Cover page: The Interplay Between Growth and Mechanics at the Unicellular and Multicellular Levels
      • Thesis
      • Peer Reviewed
      UCLA Electronic Theses and Dissertations (2020)

      Reinforced concrete (RC) moment frames and shear walls are amongst the most widely used lateral force resisting systems in regions of high seismicity in the US and around the world. Hence, understanding and accurately capturing the behavior of buildings with these lateral systems via nonlinear computer modeling is of great importance for design engineers. In 2018, a 10-story, full-scale, RC building utilizing these lateral systems was tested on the E-Defense shake table. This test provides a unique opportunity to analyze the response of a thoroughly instrumented building with special moment frames and special structural walls that are generally compliant with ASCE 7-16 and ACI 318-19 design requirements. Furthermore, it allows for the experimental verification of common nonlinear computer modeling techniques for these lateral systems. The direction of this research is to accurately capture the nonlinear global and local behavior of the 10-story test specimen subjected to ground shaking using a sophisticated non-linear computer model. Although this experimental test does present some difficulties, specifically the effect of the sliding-base foundation, validation studies demonstrate that the nonlinear model can accurately predict overall building behavior when subjected to ground excitation. This thesis outlines the experimental program of the shake table test and the nonlinear modeling approach used to best capture the response of the building.

        Cover page: Nonlinear Dynamic Analysis of a Ten-Story Reinforced Concrete Building
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2021)

        Background

        Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact as used in routine practice.

        Methods

        We performed a retrospective cohort study of all patients for whom plasma mNGS (Karius test) was performed for all indications at 5 United States institutions over 1.5 years. Comprehensive records review was performed, and standardized assessment of clinical impact of the mNGS based on the treating team's interpretation of Karius results and patient management was established.

        Results

        A total of 82 Karius tests were evaluated from 39 (47.6%) adults and 43 (52.4%) children and a total of 53 (64.6%) immunocompromised patients. Karius positivity rate was 50 of 82 (61.0%), with 25 (50.0%) showing 2 or more organisms (range, 2-8). The Karius test results led to positive impact in 6 (7.3%), negative impact in 3 (3.7%), and no impact in 71 (86.6%), and was indeterminate in 2 (2.4%). Cases with positive Karius result and clinical impact involved bacteria and/or fungi but not DNA viruses or parasites. In 10 patients who underwent 16 additional repeated tests, only 1 was associated with clinical impact.

        Conclusions

        The real-world impact of the Karius test as currently used in routine clinical practice is limited. Further studies are needed to identify high-yield patient populations, define the complementary role of mNGS to conventional microbiological methods, and discern how best to integrate mNGS into current testing algorithms.
          Cover page: Clinical Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-Free DNA for the Diagnosis of Infectious Diseases: A Multicenter Retrospective Cohort Study.
          • Article
          • Peer Reviewed
          UC Santa Barbara Previously Published Works (2018)
          The shaping of individual cells requires a tight coordination of cell mechanics and growth. However, it is unclear how information about the mechanical state of the wall is relayed to the molecular processes building it, thereby enabling the coordination of cell wall expansion and assembly during morphogenesis. Combining theoretical and experimental approaches, we show that a mechanical feedback coordinating cell wall assembly and expansion is essential to sustain mating projection growth in budding yeast (Saccharomyces cerevisiae). Our theoretical results indicate that the mechanical feedback provided by the Cell Wall Integrity pathway, with cell wall stress sensors Wsc1 and Mid2 increasingly activating membrane-localized cell wall synthases Fks1/2 upon faster cell wall expansion, stabilizes mating projection growth without affecting cell shape. Experimental perturbation of the osmotic pressure and cell wall mechanics, as well as compromising the mechanical feedback through genetic deletion of the stress sensors, leads to cellular phenotypes that support the theoretical predictions. Our results indicate that while the existence of mechanical feedback is essential to stabilize mating projection growth, the shape and size of the cell are insensitive to the feedback.
            • Article
            • Peer Reviewed
            UC Santa Barbara Previously Published Works (2018)
            The localization (or polarization) of proteins on the membrane during the mating of budding yeast (Saccharomyces cerevisiae) is an important model system for understanding simple pattern formation within cells. While there are many existing mathematical models of polarization, for both budding and mating, there are still many aspects of this process that are not well understood. In this paper we set out to elucidate the effect that the geometry of the cell can have on the dynamics of certain models of polarization. Specifically, we look at several spatial stochastic models of Cdc42 polarization that have been adapted from published models, on a variety of tip-shaped geometries, to replicate the shape change that occurs during the growth of the mating projection. We show here that there is a complex interplay between the dynamics of polarization and the shape of the cell. Our results show that while models of polarization can generate a stable polarization cap, its localization at the tip of mating projections is unstable, with the polarization cap drifting away from the tip of the projection in a geometry dependent manner. We also compare predictions from our computational results to experiments that observe cells with projections of varying lengths, and track the stability of the polarization cap. Lastly, we examine one model of actin polarization and show that it is unlikely, at least for the models studied here, that actin dynamics and vesicle traffic are able to overcome this effect of geometry.
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2024)
              Localized sources of morphogens, called signalling centres, play a fundamental role in coordinating tissue growth and cell fate specification during organogenesis. However, how these signalling centres are established in tissues during embryonic development is still unclear. Here we show that the main signalling centre orchestrating development of rodent incisors, the enamel knot (EK), is specified by a cell proliferation-driven buildup in compressive stresses (mechanical pressure) in the tissue. Direct mechanical measurements indicate that the stresses generated by cell proliferation are resisted by the surrounding tissue, creating a circular pattern of mechanical anisotropy with a region of high compressive stress at its centre that becomes the EK. Pharmacological inhibition of proliferation reduces stresses and suppresses EK formation, and application of external pressure in proliferation-inhibited conditions rescues the formation of the EK. Mechanical information is relayed intracellularly through YAP protein localization, which is cytoplasmic in the region of compressive stress that establishes the EK and nuclear in the stretched anisotropic cells that resist the pressure buildup around the EK. Together, our data identify a new role for proliferation-driven mechanical compression in the specification of a model signalling centre during mammalian organ development.
                Cover page: Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2022)

                Background

                Standard testing fails to identify a pathogen in most patients with febrile neutropenia (FN). We evaluated the ability of the Karius microbial cell-free DNA sequencing test (KT) to identify infectious etiologies of FN and its impact on antimicrobial management.

                Methods

                This prospective study (ClinicalTrials.gov; NCT02912117) enrolled and analyzed 55 patients with FN. Up to 5 blood samples were collected per subject within 24 hours of fever onset (T1) and every 2 to 3 days. KT results were compared with blood culture (BC) and standard microbiological testing (SMT) results.

                Results

                Positive agreement was defined as KT identification of ≥1 isolate also detected by BC. At T1, positive and negative agreement were 90% (9/10) and 31% (14/45), respectively; 61% of KT detections were polymicrobial. Clinical adjudication by 3 independent infectious diseases specialists categorized Karius results as: unlikely to cause FN (N = 0); definite (N = 12): KT identified ≥1 organism also found by SMT within 7 days; probable (N = 19): KT result was compatible with a clinical diagnosis; possible (N = 10): KT result was consistent with infection but not considered a common cause of FN. Definite, probable, and possible cases were deemed true positives. Following adjudication, KT sensitivity and specificity were 85% (41/48) and 100% (14/14), respectively. Calculated time to diagnosis was generally shorter with KT (87%). Adjudicators determined real-time KT results could have allowed early optimization of antimicrobials in 47% of patients, by addition of antibacterials (20%) (mostly against anaerobes [12.7%]), antivirals (14.5%), and/or antifungals (3.6%); and antimicrobial narrowing in 27.3% of cases.

                Clinical trials registration

                NCT02912117.

                Conclusion

                KT shows promise in the diagnosis and treatment optimization of FN.
                  Cover page: Plasma Microbial Cell-free DNA Next-generation Sequencing in the Diagnosis and Management of Febrile Neutropenia
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2022)

                  Objective

                  Chikungunya virus (CHIKV) causes persistent arthritis, and our prior study showed that approximately one third of CHIKV arthritis patients had exacerbated arthritis associated with exercise. The underlying mechanism of exercise-associated chikungunya arthritis flare (EACAF) is unknown, and this analysis aimed to examine the regulatory T-cell immune response related to CHIKV arthritis flares.

                  Methods

                  In our study, 124 Colombian patients with a history of CHIKV infection four years prior were enrolled and 113 cases with serologically confirmed CHIKV IgG were used in this analysis. Patient information was gathered via questionnaires, and blood samples were taken to identify total live peripheral blood mononuclear cells, CD4+ cells, T regulatory cells, and their immune markers. We compared outcomes in CHIKV patients with (n = 38) vs. without (n = 75) EACAF using t-tests to assess means and the Fisher's exact test, chi-squared to evaluate categorical variables, and Kruskal-Wallis tests in the setting of skewed distributions (SAS 9.3).

                  Results

                  33.6% of CHIKV cases reported worsening arthritis with exercise. EACAF patients reported higher global assessments of arthritis disease ranging from 0-100 (71.2 ± 19.7 vs. 59.9 ± 28.0, p=0.03). EACAF patients had lower ratios of T regulatory (Treg)/CD4+ T-cells (1.95 ± 0.73 vs. 2.4 ± 1.29, p = 0.04) and lower percentage of GARP (glycoprotein-A repetitions predominant) expression per Treg (0.13 ± 0.0.33 vs. 0.16 ± 0.24 p= 0.020).

                  Conclusion

                  These findings suggest relative decreases in GARP expression may indicate a decreased level of immune suppression. Treg populations in patients with CHIKV arthritis may contribute to arthritis flares during exercise, though current research is conflicting.
                    Cover page: Regulatory T-cells and GARP expression are decreased in exercise-associated chikungunya viral arthritis flares.
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2023)

                    Background

                    Clinical trials initiated during emerging infectious disease outbreaks must quickly enroll participants to identify treatments to reduce morbidity and mortality. This may be at odds with enrolling a representative study population, especially when the population affected is undefined.

                    Methods

                    We evaluated the utility of the Centers for Disease Control and Prevention's COVID-19-Associated Hospitalization Surveillance Network (COVID-NET), the COVID-19 Case Surveillance System (CCSS), and 2020 United States (US) Census data to determine demographic representation in the 4 stages of the Adaptive COVID-19 Treatment Trial (ACTT). We compared the cumulative proportion of participants by sex, race, ethnicity, and age enrolled at US ACTT sites, with respective 95% confidence intervals, to the reference data in forest plots.

                    Results

                    US ACTT sites enrolled 3509 adults hospitalized with COVID-19. When compared with COVID-NET, ACTT enrolled a similar or higher proportion of Hispanic/Latino and White participants depending on the stage, and a similar proportion of African American participants in all stages. In contrast, ACTT enrolled a higher proportion of these groups when compared with US Census and CCSS. The proportion of participants aged ≥65 years was either similar or lower than COVID-NET and higher than CCSS and the US Census. The proportion of females enrolled in ACTT was lower than the proportion of females in the reference datasets.

                    Conclusions

                    Although surveillance data of hospitalized cases may not be available early in an outbreak, they are a better comparator than US Census data and surveillance of all cases, which may not reflect the population affected and at higher risk of severe disease.
                      Cover page: Evaluating Demographic Representation in Clinical Trials: Use of the Adaptive Coronavirus Disease 2019 Treatment Trial (ACTT) as a Test Case.
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