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

Scholarly Works (61 results)

  • Article
  • Peer Reviewed
UC Riverside Previously Published Works (2017)
Plant pathogens cause serious crop losses worldwide. Recent new studies demonstrate that spraying double-stranded RNAs (dsRNAs) and small RNAs (sRNAs) that target essential pathogen genes on plant surfaces confer efficient crop protection. This so-called spray-induced gene silencing (SIGS) strategy of disease control is potentially sustainable and environmentally friendly.
    Cover page: Spray-Induced Gene Silencing: a Powerful Innovative Strategy for Crop Protection
    • Thesis
    • Peer Reviewed
    UC Riverside Electronic Theses and Dissertations (2015)

    Botrytis cinerea is a necrotrophic fungal pathogen that causes gray mold disease on a broad range of plant species. Many pathogens secrete protein effectors into host cells to evade the host immune system; however, my dissertation project shows that B. cinerea small RNAs (Bc-sRNAs) act as a novel type of pathogen effector to silence host defense genes.

    Small RNAs (sRNAs) are short non-coding RNAs that normally associate with Argonaute (AGO) protein and suppress the genes with complementary sequences. The role of host sRNAs in plant-pathogens interactions has been well characterized, and recent studies also revealed the function of pathogen sRNAs in infection processes. In the first chapter of this thesis, I will review the current progress of the role of both host sRNAs and microbial pathogen sRNAs during host-pathogen interactions.

    Bc-sRNA effectors are induced during plant infection and trigger silencing of host plant genes. We identified and confirmed three Bc-sRNAs (Bc-siR3.1, Bc-siR3.2 and Bc-siR5) that can translocate into host cells and hijack host RNAi machinery to silence host immunity related target genes. The B. cinerea dcl1 dcl2 double mutant has lost Bc-siR3.1, Bc-siR3.2, and Bc-siR5, which significantly compromised its virulence. The second chapter will present these findings.

    Chapter 3 will cover the identification and characterization of a new Bc-sRNA effector, Bc-siR37, which has multiple predicted target genes in both Arabidopsis and tomato (Solanum lycopersicum), and most are putatively related to plant defense. We further characterize three of these candidate targets, At-WRKY7, At-PMR6, and At-FEI2, and confirm that they are negatively correlated with Bc-siR37 and positively regulate plant immunity against B. cinerea.

    Comparative analysis of Bc-sRNAs transcriptome in wild-type B. cinerea and the dcl1 dcl2 double mutant indicates that most retrotransposon region-derived Bc-sRNAs are DCL-dependent, and most predicted Bc-sRNA effectors are generated from retrotransposon regions. The compromised virulence of the B. cinerea dcl1 dcl2 double mutant is probably due to failure to produce many Bc-sRNA effectors. Finally, we successfully use host-induced gene silencing (HIGS) of B. cinerea DCL1 and DCL2 to enhance plant resistant against gray mold disease. The final chapter will focus on these results.

      Cover page: The Role of Fungal Pathogen Small RNAs in Host-Microbe Interactions
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2015)
      In this paper, we consider the use of H(div) elements in the velocity-pressure formulation to discretize Stokes equations in two dimensions. We address the error estimate of the element pair RT0-P0, which is known to be suboptimal, and render the error estimate optimal by the symmetry of the grids and by the superconvergence result of Lagrange inter-polant. By enlarging RT0 such that it becomes a modified BDM-type element, we develop a new discretization [Formula: see text]. We, therefore, generalize the classical MAC scheme on rectangular grids to triangular grids and retain all the desirable properties of the MAC scheme: exact divergence-free, solver-friendly, and local conservation of physical quantities. Further, we prove that the proposed discretization [Formula: see text] achieves the optimal convergence rate for both velocity and pressure on general quasi-uniform grids, and one and half order convergence rate for the vorticity and a recovered pressure. We demonstrate the validity of theories developed here by numerical experiments.
        Cover page: Convergence Analysis of Triangular MAC Schemes for Two Dimensional Stokes Equations
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2022)
        Tools for sequence-specific DNA binding have opened the door to new approaches in investigating fundamental questions in biology and crop development. While there are several platforms to choose from, many of the recent advances in sequence-specific targeting tools are focused on developing Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated (CRISPR-Cas)-based systems. Using a catalytically inactive Cas protein (dCas), this system can act as a vector for different modular catalytic domains (effector domains) to control a gene's expression or alter epigenetic marks such as DNA methylation. Recent trends in developing CRISPR-dCas systems include creating versions that can target multiple copies of effector domains to a single site, targeting epigenetic changes that, in some cases, can be inherited to the next generation in the absence of the targeting construct, and combining effector domains and targeting strategies to create synergies that increase the functionality or efficiency of the system. This review summarizes and compares DNA targeting technologies, the effector domains used to target transcriptional control and epi-mutagenesis, and the different CRISPR-dCas systems used in plants.
          Cover page: CRISPR-CAS mediated transcriptional control and epi-mutagenesis
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2020)

          Background

          5' methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing.

          Results

          Using an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole-genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions.

          Conclusion

          We suggest that EM-seq is a more accurate and reliable approach than WGBS to detect methylation. Compared to WGBS, the results of EM-seq are less affected by differences in library preparation conditions or by the skewed base composition in the converted DNA. It may therefore be more desirable to use EM-seq in methylation studies.
            Cover page: Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2018)
            Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. The exomes of more than 600 ESCCs have been sequenced in the past 4 years, and numerous key aberrations have been identified. Recently, researchers reported both inter- and intratumor heterogeneity. Although these are interesting observations, their clinical implications are unclear due to the limited number of samples profiled. Epigenomic alterations, such as changes in DNA methylation, histone acetylation, and RNA editing, also have been observed in ESCCs. However, it is not clear what proportion of ESCC cells carry these epigenomic aberrations or how they contribute to tumor development. We review the genomic and epigenomic characteristics of ESCCs, with a focus on emerging themes. We discuss their clinical implications and future research directions.
              Cover page: Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2014)
              Since climatic condition is the important foundation for human subsistence and development and the key factor in sustainable development of economy and society, climate change has been a global issue attracting great attentions of politicians, scientists, governments, and the public alike throughout the world. Existing climate regionalization in China aims to characterize the regional differences in climate based on years of the mean value of different climate indexes. However, with the accelerating climate change nowadays, existing climate regionalization cannot represent the regional difference of climate change, nor can it reflect the disasters and environmental risks incurred from climate changes. This paper utilizes the tendency value and fluctuation value of temperature and precipitation from 1961 to 2010 to identify the climate change quantitatively, and completes the climate change regionalization in China (1961–2010) with county administrative regionalization as the unit in combination with China’s terrain feature. Level-I regionalization divides China’s climate change (1961–2010) into five tendency zones based on the tendency of temperature and precipitation, which are respectively Northeast China-North China warm-dry trend zone, East China-Central China wet-warm trend zone, Southwest China-South China dry-warm trend zone, Southeast Tibet-Southwest China wet-warm trend zone, and Northwest China-Qinghai-Tibet Plateau warm-wet trend zone; level-II regionalization refers to fourteen fluctuation regions based on level-I regionalization according to the fluctuation of temperature and precipitation.
                Creative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC Santa Barbara Previously Published Works (2017)
                Intrinsically stretchable semiconductors will facilitate the realization of seamlessly integrated stretchable electronics. However, to date demonstrations of intrinsically stretchable semiconductors have been limited. In this study, a new approach to achieve intrinsically stretchable semiconductors is introduced by blending a rigid high-performance donor-acceptor polymer semiconductor poly[4(4,4dihexadecyl4Hcyclopenta [1,2b:5,4b' ] dithiopen2yl) alt [1,2,5] thiadiazolo [3,4c] pyridine] (PCDTPT) with a ductile polymer semiconductor poly(3hexylthiophene) (P3HT). Under large tensile strains of up to 75%, the polymers are shown to orient in the direction of strain, and when the strain is reduced, the polymers reversibly deform. During cyclic strain, the local packing order of the polymers is shown to be remarkably stable. The saturated field effect charge mobility is shown to be consistently above 0.04 cm2 V-1s-1 for up to 100 strain cycles with strain ranging from 10% to 75% when the film is printed onto a rigid test bed. At the 75% strain state, the charge mobility is consistently above 0.15 cm2 V-1s-1. Ultimately, the polymer blend process introduced here results in an excellent combination of device performance and stretchability providing an effective approach to achieve intrinsically stretchable semiconductors.
                  Cover page: Plastic Deformation of Polymer Blends as a Means to Achieve Stretchable Organic Transistors
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2017)
                  Students' motivational beliefs about learning physical science are critical for achieving positive educational outcomes. In this study, we incorporated expectancy-value theory to capture the heterogeneity of adolescents' motivational trajectories in physics and chemistry from seventh to twelfth grade and linked these trajectories to science-related outcomes. We used a cross-sequential design based on three different cohorts of adolescents (N = 699; 51.5 % female; 95 % European American; M ages for youngest, middle, and oldest cohorts at the first wave = 13.2, 14.1, and 15.3 years) coming from ten public secondary schools. Although many studies claim that physical science motivation declines on average over time, we identified seven differential motivational trajectories of ability self-concept and task values, and found associations of these trajectories with science achievement, advanced science course taking, and science career aspirations. Adolescents' ability self-concept and task values in physics and chemistry were also positively related and interlinked over time. Examining how students' motivational beliefs about physical science develop in secondary school offers insight into the capacity of different groups of students to successfully adapt to their changing educational environments.
                    Cover page: Does Everyone’s Motivational Beliefs about Physical Science Decline in Secondary School?: Heterogeneity of Adolescents’ Achievement Motivation Trajectories in Physics and Chemistry
                    • Article
                    • Peer Reviewed
                    UC Irvine Previously Published Works (2019)
                    Prior research suggests that stress plays role in the etiology and progression of hypertension. To lend a more accurate depiction of the underlying mechanisms between stress and hypertension, this study aims to assess the associations between perceived stress and hypertension across varying levels of social support and social network among Asian Americans. We conducted a cross-sectional study using data on 530 Chinese, Korean and Vietnamese Americans recruited from a liver cancer prevention program in the Washington D.C.-Baltimore metropolitan area. Hypertension prevalence was 29.1%. Individuals with high perceived stress were 61% more likely to have hypertension compared to those with low levels of perceived stress (odds ratio 1.61, 95% confidence interval 1.15, 2.46). There was no evidence that social support and social network acted as effect modifiers. Social support had a direct beneficial effect on hypertension, irrespective of whether individuals were under stress. The relationship between perceived stress and hypertension was modified by gender and ethnicity whereby a significant positive association was only observed among male or Chinese participants. Our study highlights the importance of understanding the associations between stress, social support, and hypertension among Asian American subgroups. Findings from the study can be used to develop future stress management interventions, and incorporate culturally and linguistically appropriate strategies into community outreach and education to decrease hypertension risk within the Asian population.
                      Cover page: The Association Between Perceived Stress and Hypertension Among Asian Americans: Does Social Support and Social Network Make a Difference?
                      Top