College of Agriculture & Natural Resources

Permanent URI for this communityhttp://hdl.handle.net/1903/1598

The collections in this community comprise faculty research works, as well as graduate theses and dissertations.

Browse

Subject: search.filters.subject.CRISPR

Search Results

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    INVESTIGATION INTO THE ROLE OF UVR8 IN BALANCING GROWTH AND ACCLIMATION TO UV-B RADIATION IN NATURAL AND TRANSGENIC POPULUS VARIANTS
    (2021) Wong, Tiffany Marie; Eisenstein, Edward; Sullivan, Joseph; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Research on woody plants offers promise for the development of next-generation biofuel feedstocks with reduced lignin recalcitrance and enhanced saccharification for ethanol production. Natural variants of Populus trichocarpa with diverse lignin content and saccharification differences, and transgenic Populus deltoides constructed for reduced lignin levels for improved cellulose extraction, offer clues to enhance biofuel production but with a tradeoff to overall fitness and biomass. One concern of engineering lignin relates to the protection of plants against environmental stress such as UV-B radiation. Secondary metabolite biosynthesis initiated by UV-B, particularly phenylpropanoids (lignin precursors) and flavonoids, plays an important role in managing and protection of UV stress. Genetic modifications affecting the production of these compounds may have significant physiological consequences. Thus, the goal of this research was to develop a model for biosynthetic compensation of low-lignin Populus to UV-B stress. The effect of UV-B on Populus was evaluated by spectroscopic and metabolomic measurements on leaves. UV-B promoted shifts in physiological and metabolomic responses of natural and transgenic Populus with varying levels of lignin were complex, reflecting compensation from variety of biosynthetic alterations. Therefore, the impact of modulating the expression of the photoreceptor, UVR8, in regulating the response of Populus to UV-B was pursued. Modulation of UVR8 expression in Populus hybrid was achieved by constructing transgenic plants using CRISPR and RNAi, in wild-type, and an RNAi-constructed cinnamyl alcohol dehydrogenase knockdown line. UV-B response of UVR8 modulated Populus indicated that flavonoids were upregulated in UVR8 overexpression lines, and that in a CAD knockdown background, these effects were slightly enhanced. Salicylates were upregulated in UVR8 knockout poplars, suggesting metabolic flux in the pathway, but little difference was seen relative to wild-type plants in CAD lines, and UV-B treatment had little effect. An interesting and unexpected finding was that UVR8 modulated Populus exhibited more rapid growth than wild-type plants. The findings underscore the key role of UVR8 in synchronizing protective metabolic responses to UV-B and suggest an additional function of the photoreceptor in regulating growth and development of Populus through shifts in the chemical equilibria of UVR8 monomers and dimers and interactions with other regulatory factors.
  • Thumbnail Image
    Item
    Plant genome editing with TALEN and CRISPR
    (Springer Nature, 2017-04-24) Malzahn, Aimee; Lowder, Levi; Qi, Yiping
    Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. The process relies on the use of sequence specific nucleases (SSNs) to make DNA double stranded breaks at user defined genomic loci, which are subsequently repaired by two main DNA repair pathways: non-homologous end joining (NHEJ) and homology directed repair (HDR). NHEJ can result in frameshift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. In recent years, transcription activator-like effector nucleases and clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR associated protein 9 or CRISPR from Prevotella and Francisella 1 have emerged as the preferred SSNs for research purposes. Here, we review their applications in plant research, discuss current limitations, and predict future research directions in plant genome editing.
  • Thumbnail Image
    Item
    ALTERNATIVE APPROACHES IN MOLECULAR CHARACTERIZATION OF FOODBORNE PATHOGENS: SHIGA TOXIN-PRODUCING Escherichia coli AND Salmonella SEROTYPES
    (2014) Toro Ibaceta, Magaly Alejandra; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Shiga toxin-producing E. coli (STEC) and Salmonella enterica subspecies enterica (S. enterica) are two major foodborne pathogens. They cause almost 1.5 million of cases of disease each year in the US. Due to their public health impact, development of new methods for their detection and identification are top priority. This research focused on identifying alternative molecular methods and markers for the identification of STEC and Salmonella. First, a suspension array was developed to simultaneously identify the seven most prevalent STEC (O26, O45, O103, O111, O121, O145, and O157) in the US. The panel targeted genes wzx or wzy and Shigatoxin genes. Testing and optimization employed four to eleven isolates of each serotype in the panel. STEC fluorescence values were 30 to >270 times greater than those of negative controls, demonstrating the method's effectiveness for the molecular serotyping of STEC. STEC strains (n=194) of 43 serotypes were examined for clustered regularly interspaced short palindromic repeats (CRISPR) arrays to study relatedness among serotypes. A subset of strains (n=81) was analyzed for cas and virulence genes to determine a possible relationship. CRISPR spacer content correlated well with serotypes, although some strains with different serogroup but the same H type shared identical arrays (O26:H11, O103:H11, and O111:H11). cas and virulence genes were not associated, but strains with greater probability of causing outbreaks and disease showed fewer spacers than those less likely to cause them (p<0.05). Therefore, CRISPR array content correlated well with STEC serotype, and CRISPR-cas systems were inversely related to strain virulence potential. Finally, the CRISPR arrays of 221 S. enterica of 53 serotypes were analyzed to define their relationship. CRISPR-cas systems of 50 S. enterica serotype Bareilly (S. Bareilly) were analyzed to resolve intra-serotype variations. CRISPR arrays correlated well with serotypes, although some serotypes displayed more than one type of array (e.g. S. Bareilly). Additionally, CRISPR-cas system elements reflected S. Bareilly phylogeny, but the array content was not linked to food vehicle or isolate's geographical origin. In conclusion, CRISPR array are useful for designing molecular serotyping assays, but a range of strains should be included to account for variation in S. enterica.