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Open Access Publications from the University of California

Scholarly Works (9 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2015)
Skeletal muscle fibrosis is a condition that is characterized by an increase in extracellular matrix proteins, particularly collagen, in muscle. Fibrosis is a defining characteristic of muscle pathologies, where fibrotic scars decrease muscle strength and range of motion in patients suffering from various diseases. Given that fibrosis is present in a diverse range of pathologies, understanding how fibrosis affects muscle structure and the mechanisms behind its development are critical to finding treatments. Thus, this dissertation investigates muscle fibrosis from a biochemical, biomechanical and cellular perspective to gain a thorough understanding of this devastating condition. The work in this dissertation begins with the development and characterization of a genetic knockout animal, the nesprin 1 -- desmin double knockout mouse. This mouse was created to investigate the importance of myonuclear anchorage for skeletal muscle health. Nuclear anchorage was found to be dramatically decreased in double knockout animals, suggesting that nesprin 1 and desmin play overlapping roles. Interestingly, the loss of nuclear anchorage in these mice corresponded with dramatic muscle fibrosis as marked by increases in both collagen content and passive mechanical properties. However, a causal relationship between collagen content and tissue modulus was not found. Given this, Chapter 3 examines collagen crosslinking as a potential source of tissue stiffness. Surprisingly, the amount of collagen crosslinking did not dictate tissue mechanical properties. These findings suggest other parameters, such as ECM organization or glycosaminoglycan content, or a combination of these factors could be driving muscle mechanical properties. Chapter 4 then builds on the studies in chapters 2 and 3 by examining the cells responsible for ECM production, particularly collagen type I, in fibrotic DKO skeletal muscle. Since it has been shown that various cell types produce collagen I, to indiscriminately label all cells contributing to fibrosis, collagen I reporter mice were bred with DKO mice. With the creation of this mouse, it was discovered that collagen I producing cells are a heterogeneous population composed of fibro/adipogenic progenitor cells, skeletal muscle progenitor cells and a third population that are hypothesized to be fibroblasts. Furthermore, these cell populations were dramatically increased in fibrotic skeletal muscle, and the percentage of collagen producing cells in each cell population also increased. This study increases our knowledge of the cellular mechanisms behind muscle fibrosis, and can potentially contribute to the creation of anti-fibrotic therapies
    Cover page: Biochemical, Biomechanical and Cellular Investigation of Skeletal Muscle Fibrosis
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2019)
    Rising atmospheric CO2 concentration is a key driver of enhanced global greening, thought to account for up to 70% of increased global vegetation in recent decades. CO2 fertilization effects have further profound implications for ecosystems, food security and biosphere-atmosphere feedbacks. However, it is also possible that current trends will not continue, due to ecosystem level constraints and as plants acclimate to future CO2 concentrations. Future predictions of plant response to rising [CO2 ] are often validated using single-generation short-term FACE (Free Air CO2 Enrichment) experiments but whether this accurately represents vegetation response over decades is unclear. The role of transgenerational plasticity and adaptation in the multigenerational response has yet to be elucidated. Here, we propose that naturally occurring high CO2 springs provide a proxy to quantify the multigenerational and long-term impacts of rising [CO2 ] in herbaceous and woody species respectively, such that plasticity, transgenerational effects and genetic adaptation can be quantified together in these systems. In this first meta-analysis of responses to elevated [CO2 ] at natural CO2 springs, we show that the magnitude and direction of change in eight of nine functional plant traits are consistent between spring and FACE experiments. We found increased photosynthesis (49.8% in spring experiments, comparable to 32.1% in FACE experiments) and leaf starch (58.6% spring, 84.3% FACE), decreased stomatal conductance (gs , 27.2% spring, 21.1% FACE), leaf nitrogen content (6.3% spring, 13.3% FACE) and Specific Leaf Area (SLA, 9.7% spring, 6.0% FACE). These findings not only validate the use of these sites for studying multigenerational plant response to elevated [CO2 ], but additionally suggest that long-term positive photosynthetic response to rising [CO2 ] are likely to continue as predicted by single-generation exposure FACE experiments.
      Cover page: FACE facts hold for multiple generations; Evidence from natural CO2 springs
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2016)

      Background

      Consuming watercress is thought to provide health benefits as a consequence of its phytonutrient composition. However, for watercress there are currently limited genetic resources underpinning breeding efforts for either yield or phytonutritional traits. In this paper, we use RNASeq data from twelve watercress accessions to characterize the transcriptome, perform candidate gene mining and conduct differential expression analysis for two key phytonutritional traits: antioxidant (AO) capacity and glucosinolate (GLS) content.

      Results

      The watercress transcriptome was assembled to 80,800 transcripts (48,732 unigenes); 71 % of which were annotated based on orthology to Arabidopsis. Differential expression analysis comparing watercress accessions with 'high' and 'low' AO and GLS resulted in 145 and 94 differentially expressed loci for AO capacity and GLS respectively. Differentially expressed loci between high and low AO watercress were significantly enriched for genes involved in plant defence and response to stimuli, in line with the observation that AO are involved in plant stress-response. Differential expression between the high and low GLS watercress identified links to GLS regulation and also novel transcripts warranting further investigation. Additionally, we successfully identified watercress orthologs for Arabidopsis phenylpropanoid, GLS and shikimate biosynthesis pathway genes, and compiled a catalogue of polymorphic markers for future applications.

      Conclusions

      Our work describes the first transcriptome of watercress and establishes the foundation for further molecular study by providing valuable resources, including sequence data, annotated transcripts, candidate genes and markers.
        Cover page: Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
        • Article
        • Peer Reviewed
        Publications (2022)
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2022)
          Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.
            Cover page: Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2014)
            Proper localization and anchorage of nuclei within skeletal muscle is critical for cellular function. Alterations in nuclear anchoring proteins modify a number of cellular functions including mechanotransduction, nuclear localization, chromatin positioning/compaction and overall organ function. In skeletal muscle, nesprin 1 and desmin are thought to link the nucleus to the cytoskeletal network. Thus, we hypothesize that both of these factors play a key role in skeletal muscle function. To examine this question, we utilized global ablation murine models of nesprin 1, desmin or both nesprin 1 and desmin. Herein, we have created the nesprin-desmin double-knockout (DKO) mouse, eliminating a major fraction of nuclear-cytoskeletal connections and enabling understanding of the importance of nuclear anchorage in skeletal muscle. Globally, DKO mice are marked by decreased lifespan, body weight and muscle strength. With regard to skeletal muscle, DKO myonuclear anchorage was dramatically decreased compared with wild-type, nesprin 1(-/-) and desmin(-/-) mice. Additionally, nuclear-cytoskeletal strain transmission was decreased in DKO skeletal muscle. Finally, loss of nuclear anchorage in DKO mice coincided with a fibrotic response as indicated by increased collagen and extracellular matrix deposition and increased passive mechanical properties of muscle bundles. Overall, our data demonstrate that nesprin 1 and desmin serve redundant roles in nuclear anchorage and that the loss of nuclear anchorage in skeletal muscle results in a pathological response characterized by increased tissue fibrosis and mechanical stiffness.
              Cover page: Disruption of both nesprin 1 and desmin results in nuclear anchorage defects and fibrosis in skeletal muscle
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2012)

              Unlabelled

              BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.

              Results

              BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.

              Availability

              BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.
                Cover page: BioJava: an open-source framework for bioinformatics in 2012
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2015)
                A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases, but many of the most popular vegetables are low in phytonutrients. Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients, and therefore understanding the genetic basis of this variation is important for breeding efforts to enhance nutritional quality. In this study, lettuce recombinant inbred lines, generated from a cross between wild and cultivated lettuce (Lactuca serriola and Lactuca sativa, respectively), were analysed for antioxidant (AO) potential and important phytonutrients including carotenoids, chlorophyll and phenolic compounds. When grown in two environments, 96 quantitative trait loci (QTL) were identified for these nutritional traits: 4 for AO potential, 2 for carotenoid content, 3 for total chlorophyll content and 87 for individual phenolic compounds (two per compound on average). Most often, the L. serriola alleles conferred an increase in total AOs and metabolites. Candidate genes underlying these QTL were identified by BLASTn searches; in several cases, these had functions suggesting involvement in phytonutrient biosynthetic pathways. Analysis of a QTL on linkage group 3, which accounted for >30% of the variation in AO potential, revealed several candidate genes encoding multiple MYB transcription factors which regulate flavonoid biosynthesis and flavanone 3-hydroxylase, an enzyme involved in the biosynthesis of the flavonoids quercetin and kaempferol, which are known to have powerful AO activity. Follow-up quantitative RT-PCR of these candidates revealed that 5 out of 10 genes investigated were significantly differentially expressed between the wild and cultivated parents, providing further evidence of their potential involvement in determining the contrasting phenotypes. These results offer exciting opportunities to improve the nutritional content and health benefits of lettuce through marker-assisted breeding.
                  Cover page: Elucidating the genetic basis of antioxidant status in lettuce (Lactuca sativa)
                  • Article
                  LBL Publications (2004)

                  A four year (2000-2004) comprehensive joint industry, University and National Lab project was carried out in a 20 square mile area in a producing gas field in the Northwest part of the San Juan Basin in New Mexico to develop and apply multi-scale seismic methods for detecting and quantifying fractures in a naturally fractured gas reservoirs. 3-D surface seismic, multi-offset 9-C VSP, 3-C single well seismic, and well logging data were complemented by geologic/core studies to model, process and interpret the data. The overall objective was to determine the seismic methods most useful in mapping productive gas zones. Data from nearby outcrops, cores, and well bore image logs suggest that natural fractures are probably numerous in the subsurface reservoirs at the site selected and trend north-northeast/south-southwest despite the apparent dearth of fracturing observed in the wells logged at the site (Newberry and Moore wells). Estimated fracture spacing is on the order of one to five meters in Mesaverde sandstones, less in Dakota sandstones. Fractures are also more frequent along fault zones, which in nearby areas trend between north-northeast/south-southwest and northeast-southwest and are probably spaced a mile or two apart. The maximum, in situ, horizontal, compressive stress in the vicinity of the seismic test site trends approximately north-northeast/south-southwest. The data are few but they are consistent. The seismic data present a muc h more complicated picture of the subsurface structure. Faulting inferred from surface seismic had a general trend of SW - NE but with varying dip, strike and spacing. Studies of P-wave anisotropy from surface seismic showed some evidence that the data did have indications of anisotropy in time and amplitude, however, compared to the production patterns there is little correlation with P-wave anisotropy. One conclusion is that the surface seismic reflection data are not detecting the complexity of fracturing controlling the production. Conclusions from the P-wave VSP studies showed a definite 3-D heterogeneity in both P- and S-wave characteristics. The analysis of shear-wave splitting from 3D VSP data gave insight into the anisotropy structure with depth around the borehole. In the reservoir, the VSP shear-wave splitting data do not provide sufficient constraints against a model of lower symmetry than orthorhombic, so that the existence of more than one fracture set must be considered. It was also demonstrated that a VTI and orthorhombic symmetry could be well defined from the field data by analyzing shear-wave splitting patterns. The detection of shear-wave singularities provides clear constraints to distinguish between different symmetry systems. The P-wave VSP CDP data showed evidence of fault detection at a smaller scale than the surface seismic showed, and in directions consistent with a complicated stress and fracture pattern. The single well data indicated zones of anomalous wave amplitude that correlated well with high gas shows. The high amplitude single well seismic data could not be explained by well bore artifacts, nor could it be explained by known seismic behavior in fractured zones. Geomechanical and full wave elastic modeling in 2- and 3-D provided results consistent with a complicated stress distribution induced by the interaction of the known regional stress and faults mapped with seismic methods. Sophisticated modeling capability was found to be a critical component in quantifying fractures through seismic data. Combining the results with the historical production data showed that the surface seismic provided a broad picture consistent with production, but not detailed enough to consistently map complex structuring which would allow accurate well placement. VSP and borehole methods show considerable promise in mapping the scale of fracturing necessary for more successful well placement. Specific recommendations are given at which scale each method and fracture complexity is appropriate.

                    Cover page: A Handbook for the Application of Seismic Methods for Quantifying Naturally Fractured Gas Reservoirs in the San Juan Basin, New Mexico
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