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Browsing by Subject "Department of Plant Biology"

Now showing 1 - 7 of 7
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    Comparative Population Genetics of Poplars to Examine Causes of Differing Levels of Nucleotide Diversity
    (2010-04-21) Ditah, Callistus
    Species can differ dramatically in the amount of DNA variation contained within the genomes of different individuals. Generally, the magnitude of nucleotide diversity for a species is described by the equation: θ = 4Nem where θ is the amount of diversity in DNA sequence among individuals of a species, Ne is the population size, and m is the baseline mutation rate. Different types of genomes or taxonomic groups often show orders of magnitude variation in mutation rate. However, when closely related species differ in θ, it is generally assumed this reflects differences in population size (Ne), since mutation rates tend to be evolutionarily conserved over shorter time scales. This assumption is almost never empirically tested. Poplar trees (genus Populus) are an ecologically and genetically diverse group that provides an ideal system to study this issue. According to previous work, nucleotide diversity differs remarkably among poplar species in North America and Europe. This could reflect a difference in average Ne among species, perhaps because past glacial histories impacted species’ population sizes differently on each continent. However, most European and North American species are not closely related; thus the difference in diversity could also reflect an inherited difference in mutation rate between divergent sections of the genus.
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    Does Gene Expression Pattern Predict Pathogen Growth? Testing Inferences from a Proposed Model of the Arabidopsis thaliana Defense Signaling Network
    (2010-04-21) Longlet, Michael J.
    Agriculture is a globally significant and influential component of local economies as a fundamental principle of functional community is a reliable source of food. A primary challenge for plants in survival is the recognition and suppression of pathogen infection. Studies using the model organism, Arabidopsis thaliana indicate recognition of non-self, complex signal transduction and effector expression exist as primary defense mechanisms to ultimately suppress pathogen proliferation, (Jones and Dangl, 2006). Microarray experiments have provided quantitative gene expression profiles of plant defense responses and indicated rapid transcriptional activation of thousands of genes upon pathogen infection, (Katagiri, 2004). Furthermore, gene expression profiling of pathogen induced genes combined with reverse genetics have been used as high-dimensional data to construct a model of the Arabidopsis defense signaling network, (Sato et. al., unpublished). The network model successfully predicted known defense-gene interactions. Thus, we assume the network model provides a means to efficiently predict uncharacterized mutant phenotypes. Currently, it is not clear which transcriptionally induced genes actually contribute to defense against the pathogen. This project focused on evaluating whether or not eight transcriptionally induced genes in microarray studies actually contribute to the defense response against the pathogen Pseudomnas syringae p.v. maculicola.
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    Growth studies of a New Species of Xanthophyta: The Significance of Renewable Source of an Essential Lipid
    (2012-04-18) Mengistu, Sinafik
    Production of eicosapentaenoic acid (EPA) from a new species of Xanthophyceae, Heterococcus coloradii nelson, was discovered among snow fields in the Rocky Mountains and may have beneficial health products without the serious environmental costs of fishing or the negative consequences of fish farming. Algae, which can be produced easily in large quantities with limited environmental cost, can provide this new source of essential nutrients. Growing algae may provide a much more cost effective and simpler production means of producing lipids. Furthermore, the maintenance of adequate levels of docosahexaenoic acid (DHA), which is poorly made in the human body from α-linolenic acid, is an important concern for human health. The metabolite of EPA, DHA, has been implicated in promoting healthy development of newborns, reduces the risk of heart disease, and decreases inflammatory factors.
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    Post-Mating Reproductive Isolation and Hybrid Pollen Inviability Between Two Subspecies of Clarkia xantiana (Onagraceae)
    (2011-04-13) Kopp, Jason
    The origin of new species of organisms (speciation) is a source of continual debate in the realm of evolutionary biology. When two diverging populations of the same species become reproductively isolated from each other speciation can occur because of phenotypic or genetic changes. Phenotypic changes prevent mating from happening (pre-mating changes) and genetic changes render hybrids, or the product of the two populations, sterile (post-mating changes). For my study, I examined the post-mating isolation between two subspecies of Clarkia xantiana, an endemic, native herb of California. The species is currently divided into two subspecies Clarkia xantiana ssp. xantiana and Clarkia xantiana ssp. parviflora. These two subspecies overlap in distribution in a narrow contact zone (sympatric zone). In sympatry, these subspecies rarely form hybrids in nature but can be forced to produce hybrids in the lab. My study focused on the fertility of pollen grains (male fertility) in the parents and hybrids of these two subspecies to assess post-mating isolation. Answering these questions provides insight into the mechanisms behind speciation due to post-mating changes, an understudied but fundamental process of evolutionary biology.
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    Reverse Genetics Approach to Identify Genes Required for Glandular Trichome Development in Medicago truncatula
    (2009-04-08) York, Sam
    Trichome development has been used as an important model system to study plant development. The traditional method for doing this has involved inducing mutations in simple plants such as Arabidopsis thaliana and screening for mutant phenotypes. Once these phenotypes are identified several laboratory techniques can be used to determine in which genes the mutations occurred. We used a reverse approach to identifying these genes by starting with a list of the genes most commonly expressed only in the glandular trichomes of Medicago truncatula. We used PCR amplification to isolate these DNA fragments. We then cloned the fragments into the pCR8 and then pHG8 vectors. When agrobacteria are transformed with the pHG8 vector and grown on a Medicago truncatula tissue culture a double-stranded RNA copy of the vector becomes present in the plant cell. The machinery of the cell recognizes the double-stranded RNA construct and inhibits the expression of any regions of the genome that have the same nucleotide sequence. This effectively knocks out the gene we inserted into the plasmid. The tissue cultures can then be screened for a mutant phenotype in their trichome development. If a mutant phenotype is observed it suggests that the gene we started with has a role in the development of glandular trichomes in Medicago truncatula. By finding these genes we can then compare them to the many known genes that are responsible for trichome development in Arabidopsis thaliana; we can address the question of whether trichome development is controlled by the same genetic pathways throughout the plant kingdom.
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    Sucrose Transporters in Selaginella moellendorffi
    (2010-04-21) Baker, Rebecca
    Vascular tissue in plants functions in long distance transport of water, nutrients and metabolites. The evolution of vascular tissue is thought to be important for the development of large land plants. Phloem is one type of vascular tissue, it mainly transports sugars from photosynthetic leaves to the rest of the plant. Selaginella (a Lycophyte) is one of the earliest vascular plants and the Selaginella moellendorffi genome has been recently sequenced by the Department of Energy Joint Genome Institute (JGI). Selaginella has phloem tissue and now we know that it also has five sucrose transporter (SUT) genes. SUTs transport sucrose into the phloem in higher plants and we are interested to know if SUTs have the same function in Selaginella. By phylogenetic analysis, 4 of the Selaginella SUTs are type III and 1 is type II. This is interesting because type I SUTs are present and essential for dicot plants but also are not present in monocots. To study the function of Selaginella SUTs we attempted to clone cDNAs for all five genes. This was done by reverse transcription PCR and TA cloning into Gateway vector pCR8. PCR products of the right length were obtained for 4 of the SUT genes. After TA cloning, plasmids from E. coli 74 transformants were checked by restriction digest, and 11 clones were sequenced. However, only one correct cDNA was obtained (SmSUT4.3). This represents the first cloning of a sucrose transporter from a Lycophyte. Interestingly, the predicted SmSUT4.3 cDNA sequence incorrectly predicted the presence of one intron. Now that we have cloned SmSUT4.3, it will be subcloned into oocyte and yeast expression vectors to test the function of the protein.
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    Yeast-2-Hybrid Protein Analysis of Arabidopsis Thaliana Trichomes
    (2009-04-08) Saathoff, Katie
    Arabidopsis thaliana trichomes are specialized single-cellular structures on the surface of leaves. They have a unique, three dimensional, branching structure and can become morphologically mutated as the results of many genetic changes. One gene known to function in trichome development is At1g64690, also known as AtBLT. AtBLT contains a region of DNA that could form a coiled coil with a region that should also form a coiled coil in another gene. To identify genes that may interact with this region of AtBLT that also act in trichome development, yeast two hybrid analysis will be used. BLT will be expressed in a vector containing a DNA binding domain; and the gene of interest, in this case STIIA, will be expressed in a vector containing a DNA activation domain. The two constructs, acting as bait and prey, are expressed in yeast with a Gal reporter that will cause the yeast to metabolize beta-galactosidase and turn a blue color if the two proteins interact by forming a coiled coil and bringing the binding domain and activation domain together.