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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Article
  • Peer Reviewed
UC Berkeley Previously Published Works (2016)
The genetic transformation of monocot grasses is a resource intensive process, the quality and efficiency of which is dependent in part upon the method of DNA introduction, as well as the ability to effectively separate transformed from wildtype tissue. Agrobacterium-mediated transformation of Brachypodium has relied mainly on Agrobacterium tumefaciens strain AGL1. Currently the antibiotic hygromycin B has been the selective agent of choice for robust identification of transgenic calli in Brachypodium distachyon and Brachypodium sylvaticum but few other chemicals have been shown to work as well for selection of transgenic Brachypodium cells in tissue culture. This study demonstrates that Agrobacterium rhizogenes strain 18r12v and paromomycin selection can be successfully used for the efficient generation of transgenic B. distachyon and B. sylvaticum. Additionally we observed that the transformation rates were similar to or higher than those obtained with A. tumefaciens strain AGL1 and hygromycin selection. The A. rhizogenes strain 18r12v harboring the pARS1 binary vector and paromomycin selection is an effective means of generating transgenic Brachypodium plants. This novel approach will facilitate the transgenic complementation of T-DNA knockout mutants of B. distachyon which were created using hygromycin selection, as well as aid the implementation of more complex genome manipulation strategies which require multiple rounds of transformation.
    Cover page: Use of Agrobacterium rhizogenes Strain 18r12v and Paromomycin Selection for Transformation of Brachypodium distachyon and Brachypodium sylvaticum
    • Article
    • Peer Reviewed
    Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 18, Issue 4 (2017)

    Introduction: Estimates suggest that hundreds of thousands of sex trafficking victims live in theUnited States. Several screening tools for healthcare professionals to identify sex trafficking victimshave been proposed, but the effectiveness of these tools in the emergency department (ED) remainsunclear. Our primary objective in this study was to evaluate the feasibility of a screening survey toidentify adult victims of sex trafficking in the ED. We also compared the sensitivity of emergencyphysician concern and a screening survey for identifying sex trafficking victims in the ED anddetermined the most effective question(s) for identifying adult victims of sex trafficking.

    Methods: We enrolled a convenience sample of medically stable female ED patients, age 18-40 years.Patients completed a 14-question survey. Physician concern for sex trafficking was documented priorto informing the physician of the survey results. A “yes” answer to any question or physician concernwas considered a positive screen, and the patient was offered social work consultation. We defined a“true positive” as a patient admission for or social work documentation of sex trafficking. Demographicand clinical information were collected from the electronic medical record.

    Results: We enrolled 143 patients, and of those 39 (27%, 95% confidence interval [CI] [20%-35%])screened positive, including 10 (25%, 95% CI [13%-41%]) ultimately identified as victims of sextrafficking. Sensitivity of the screening survey (100%, 95% CI [74%-100%]) was better than physicianconcern (40%, 95% CI [12%-74%]) for identifying victims of sex trafficking, difference 60%, 95% CI[30%-90%]. Physician specificity (91%, 95% CI [85%-95%]), however, was slightly better than thescreening survey (78%, 95% CI [70%-85%]), difference 13%, 95% CI [4%-21%]. All 10 (100%, 95%CI[74%-100%]) “true positive” cases answered “yes” to the screening question regarding abuse.

    Conclusion: Identifying adult victims of sex trafficking in the ED is feasible. A screening survey appearsto have greater sensitivity than physician concern, and a single screening question may be sufficient toidentify all adult victims of sex trafficking in the ED

      Cover page: Screening for Victims of Sex Trafficking in the Emergency Department: A Pilot ProgramCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2023)
      Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.
        Cover page: The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2014)
        Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.
          Cover page: Comprehensive molecular profiling of lung adenocarcinoma
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2012)
          Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.
            Cover page: Comprehensive genomic characterization of squamous cell lung cancers
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2013)
            We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.
              Cover page: Integrated genomic characterization of endometrial carcinoma
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