Timothy Butterfield

Plant structural traits can act as barriers for herbivore attachment, feeding, and oviposition. In particular, epicuticular waxes (EWs) on the aerial surfaces of many land plants offer protection from biotic and abiotic stresses. In rice (Oryza sativa L.), mutations that reduce EWs have been previously reported. However, whether such mutations affect rice water weevil (Lissorhoptrus oryzophilus Kuschel) and fall armyworm (Spodoptera frugiperda Smith) performance has not been investigated yet… Show more

Plant structural traits can act as barriers for herbivore attachment, feeding, and oviposition. In particular, epicuticular waxes (EWs) on the aerial surfaces of many land plants offer protection from biotic and abiotic stresses. In rice (Oryza sativa L.), mutations that reduce EWs have been previously reported. However, whether such mutations affect rice water weevil (Lissorhoptrus oryzophilus Kuschel) and fall armyworm (Spodoptera frugiperda Smith) performance has not been investigated yet. The aim of our study was to characterize the EWs of EW mutants and wild-type rice plants by gas chromatography-mass spectrometry and compare the resistance of mutant and wild-type plants against rice water weevil and fall armyworm.

We hypothesized that mutants with reduced EWs would have weaker resistance to pests than wild-type plants. Three mutant lines (6-1A, 7-17A, and 11-39A) and their wild-type parent (cv. 'Sabine') were used to test this hypothesis. Levels of EWs were significantly lower in mutant lines than in the wild-type, and qualitative differences in EW composition were also observed. Reduction in EWs significantly affected performance of insects in experiments conducted under greenhouse conditions. Experiments with rice water weevils were conducted in arenas in which females were given a choice of the mutants and the wild-type for oviposition. Number of first instars emerging from the three EW mutants (an indication of oviposition preference) was higher on the three EW mutants than on wild-type plants with normal wax levels. Similarly, in no-choice experiments using whole plants or detached leaves, weight gains of armyworms on leaves were higher on the mutant lines than on the wild-type. These results indicate that EW traits are involved in rice resistance to weevils and armyworms. Understanding the plant traits that contribute to resistance to rice pests will be helpful for the development of resistant varieties for reducing pest insect damage. Show less

We showed previously that gallic acid is produced in walnut from 3-dehydroshikimate by a shikimate dehydrogenase (JrSkDH). This study focuses on the next step in the hydrolysable tannin pathway, the formation of 1-O-galloyl-β-D-glucose from the phenolic gallic acid and UDP glucose by a glycosyltransferase. JrGGT1 (UGT84A73) and JrGGT2 (UGT84A74) are predicted to be two such glycosyltransferases, which we expressed in tobacco plants. GC-MS analysis of the transgenic tobacco revealed moderate… Show more

We showed previously that gallic acid is produced in walnut from 3-dehydroshikimate by a shikimate dehydrogenase (JrSkDH). This study focuses on the next step in the hydrolysable tannin pathway, the formation of 1-O-galloyl-β-D-glucose from the phenolic gallic acid and UDP glucose by a glycosyltransferase. JrGGT1 (UGT84A73) and JrGGT2 (UGT84A74) are predicted to be two such glycosyltransferases, which we expressed in tobacco plants. GC-MS analysis of the transgenic tobacco revealed moderate, yet significant alterations in plant secondary metabolism, such as depleted phenolic acids, including gallic acid. We postulate that these effects are due to JrGGT1 and JrGGT2 activity, as JrGGT orthologs glycosylate these phenolic compounds in vitro. Moreover, JrGGT expression in tobacco caused upregulation of shikimic acid pathway metabolites and differing responses in phenylpropanoids, such as phenolic acids and flavonoids. In transcriptome analysis of walnut pellicle tissues, both JrGGTs showed substantial and significant expression correlations with the gallic acid-producing JrSkDHs and were highly coexpressed with the genetic circuits constituting the shikimic acid and phenylpropanoid biosynthetic pathways. Verification of JrGGT gene expression by transcriptome analysis of 20 walnut tissues revealed striking similarities with that of the pellicle data, with the greatest expression in roots, wood, buds, and leaves of Juglans regia cv. Chandler: tissues that typically accumulate hydrolysable tannins. Like the transgenic tobacco, pellicle metabolomic analyses revealed that many phenylpropanoids correlated negatively with JrGGT expression, while shikimic acid pathway metabolites correlated positively with JrGGT expression. This research supports the hypothesis that JrGGT1 and JrGGT2 play non-trivial roles in metabolism of phenolic acids, flavonoids, and ostensibly, tannins. Show less

Walnut pellicle color is a key quality attribute that drives consumer preference and walnut sales. For the first time a high-throughput, computer vision-based phenotyping platform using a custom algorithm to quantitatively score each walnut pellicle in L* a* b* color space was deployed at large-scale. This was compared to traditional qualitative scoring by eye and was used to dissect the genetics of pellicle pigmentation. Progeny from both a bi-parental population of 168 trees ('Chandler' ×… Show more

Walnut pellicle color is a key quality attribute that drives consumer preference and walnut sales. For the first time a high-throughput, computer vision-based phenotyping platform using a custom algorithm to quantitatively score each walnut pellicle in L* a* b* color space was deployed at large-scale. This was compared to traditional qualitative scoring by eye and was used to dissect the genetics of pellicle pigmentation. Progeny from both a bi-parental population of 168 trees ('Chandler' × 'Idaho') and a genome-wide association (GWAS) with 528 trees of the UC Davis Walnut Improvement Program were analyzed. Color phenotypes were found to have overlapping regions in the 'Chandler' genetic map on Chr01 suggesting complex genetic control. In the GWAS population, multiple, small effect QTL across Chr01, Chr07, Chr08, Chr09, Chr10, Chr12 and Chr13 were discovered. Marker trait associations were co-localized with QTL mapping on Chr01, Chr10, Chr14, and Chr16. Putative candidate genes controlling walnut pellicle pigmentation were postulated. Show less

Natural pesticides have attracted substantial interest due to the increase in organic agriculture and enhanced attention to environmental pollution. Plant Growth Promoting Bacteria (PGPB) are applied for both disease control and growth enhancement; PGPBs are known to elicit Induced Systemic Response (ISR) in plants. However, less is known about the effect of botanical pesticides, such as the azadirachtin-containing neem extracts, on plant metabolism. This study aimed to investigate the effects… Show more

Natural pesticides have attracted substantial interest due to the increase in organic agriculture and enhanced attention to environmental pollution. Plant Growth Promoting Bacteria (PGPB) are applied for both disease control and growth enhancement; PGPBs are known to elicit Induced Systemic Response (ISR) in plants. However, less is known about the effect of botanical pesticides, such as the azadirachtin-containing neem extracts, on plant metabolism. This study aimed to investigate the effects of foliar application of the above-mentioned natural pesticides on the metabolic profiling of tomato. Leaf application of Bacillus subtilis fostered Induced Systemic Resistance (ISR) in treated plants via the Jasmonic acid pathway, and enhanced production of secondary metabolites such as flavonoids, phytoalexins and auxins. Changes in sterols and terpenes, as well as an increase in glucosinolates were also observed. Interestingly, azadirachtin-treated tomatoes also showed an increase in ISR and our results revealed that most of the enriched metabolites are shared with a B. subtilis treatment, suggesting conserved biochemical responses. These (un)expected findings indicate that plants are not insensitive to application of natural pesticide and while Azadirachtin is applied as a direct pesticide, it also stimulates a defense response in tomatoes very similar to B. subtilis induced ISR. Show less

The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional… Show more

The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits. Show less

Plants respond to pathogens with both active and passive defense mechanisms. These defense responses include the induction of defense or defense-related genes such as polyphenol oxidase (PPO) and pathogenesis-related (PR) proteins. The role of PPO in the interaction between bacterial blight [Xanthomonas arboricola pv. juglandis (Xaj)] and walnut (Juglans regia) was studied. JrPPO-1 and P14a genes were identified in two walnut cultivars, Chandler and Serr, using standard polymerase chain… Show more

Plants respond to pathogens with both active and passive defense mechanisms. These defense responses include the induction of defense or defense-related genes such as polyphenol oxidase (PPO) and pathogenesis-related (PR) proteins. The role of PPO in the interaction between bacterial blight [Xanthomonas arboricola pv. juglandis (Xaj)] and walnut (Juglans regia) was studied. JrPPO-1 and P14a genes were identified in two walnut cultivars, Chandler and Serr, using standard polymerase chain reaction (PCR) to understand their inducible ability in response to Xaj. ‘Serr’ and ‘Chandler’ were inoculated with Xaj strain 417. PPO activity in leaves was assayed at 0, 24, 72, 96, 120, and 144 hours after inoculation. Results showed a steady increase in activity commencing within 24 hours of inoculation. Increase in PPO activity was close to 2-fold greater in ‘Chandler’ than in ‘Serr’ at all time points examined. Real-time PCR analysis showed differences between cultivars in PPO gene expression. The JrPPO-1 gene was highly expressed in both cultivars 24 hours after inoculation but expression in ‘Serr’ was much greater than in ‘Chandler’. Significant expression of P14a gene was observed in both cultivars within 24 hours. Expression in ‘Serr’ was strong and maximized with a significant increase at 96 hours. Expression in ‘Chandler’ was far weaker than ‘Serr’ at 24 hours and did not increase further. Our results imply that the walnut–bacterial blight interaction induces the expression of JrPPO-1 and P14a as well as the activity of PPO. Show less

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS -… Show more

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software. Show less

Master's Thesis


Plants perceive and respond to a variety of stimuli from the external environment. These stimuli include, among others, light, mechanical force, gravity, volatile and nonvolatile chemicals—almost the entire suite of stimuli that higher animals perceive (Weiler, 2003). While both plants and animals must interact with their environment, they do so in different manners. Whereas an animal may temporarily or permanently relocate itself when local conditions are… Show more

Master's Thesis


Plants perceive and respond to a variety of stimuli from the external environment. These stimuli include, among others, light, mechanical force, gravity, volatile and nonvolatile chemicals—almost the entire suite of stimuli that higher animals perceive (Weiler, 2003). While both plants and animals must interact with their environment, they do so in different manners. Whereas an animal may temporarily or permanently relocate itself when local conditions are undesirable, a plant must adapt to those conditions or fail to thrive.
In both plants and animals, there has been extensive study of stimuli perception for over a century. In the plant literature, however, the last two decades have been replete with remarkable discoveries that have challenged canonical dogmas of cell signaling such as receptor localization and action, the critical role of calcium ions as signal mediators, as well as hormonal cross-talk—apparent interconnectedness between hormonal signals and commands. Amidst the exciting discoveries detailing the activities and mechanisms of calcium, auxin, cytokinins, gibberellins, and steroid signaling molecules, accumulating evidence implicates a signaling role for extracellular ATP (eATP) in plants. Show less

Expression of two Arabidopsis (Arabidopsis thaliana) apyrase (nucleoside triphosphate-diphosphohydrolase) genes with high similarity, APY1 and APY2, was analyzed during seedling development and under different light treatments using beta-glucuronidase fusion constructs with the promoters of both genes. As evaluated by beta-glucuronidase staining and independently confirmed by other methods, the highest expression of both apyrases was in rapidly growing tissues and/or tissues that accumulate… Show more

Expression of two Arabidopsis (Arabidopsis thaliana) apyrase (nucleoside triphosphate-diphosphohydrolase) genes with high similarity, APY1 and APY2, was analyzed during seedling development and under different light treatments using beta-glucuronidase fusion constructs with the promoters of both genes. As evaluated by beta-glucuronidase staining and independently confirmed by other methods, the highest expression of both apyrases was in rapidly growing tissues and/or tissues that accumulate high auxin levels. Red-light treatment of etiolated seedlings suppressed the protein and message level of both apyrases at least as rapidly as it inhibited hypocotyl growth. Adult apy1 and apy2 single mutants had near-normal growth, but apy1apy2 double-knockout plants were dwarf, due primarily to reduced cell elongation. Pollen tubes and etiolated hypocotyls overexpressing an apyrase had faster growth rates than wild-type plants. Growing pollen tubes released ATP into the growth medium and suppression of apyrase activity by antiapyrase antibodies or by inhibitors simultaneously increased medium ATP levels and inhibited pollen tube growth. These results imply that APY1 and APY2, like their homologs in animals, act to reduce the concentration of extracellular nucleotides, and that this function is important for the regulation of growth in Arabidopsis. Show less

Materials for cell wall growth are delivered to the wall by secretory vesicles, and recent studies have highlighted the role of secretion in plant growth generally and plant gravitropic growth specifically. Funke and Edelmann (2000) show that the growth of graviresponding nodes of Tradescantia is controlled by auxin-induced secretion and subsequent infiltration of wall materials that promotes wall extension. Similarly, Zhang and Hasenstein (2000) demonstrate that Brefeldin A, a potent inhibitor… Show more

Materials for cell wall growth are delivered to the wall by secretory vesicles, and recent studies have highlighted the role of secretion in plant growth generally and plant gravitropic growth specifically. Funke and Edelmann (2000) show that the growth of graviresponding nodes of Tradescantia is controlled by auxin-induced secretion and subsequent infiltration of wall materials that promotes wall extension. Similarly, Zhang and Hasenstein (2000) demonstrate that Brefeldin A, a potent inhibitor of the delivery of secretory vesicles from the trans-Golgi to the plasma membrane in plant cells (Driouich et al, 1993), blocks the asymmetric delivery of expansins to the cell wall of graviresponding maize roots. They further show that this effect is correlated with a delay in the graviresponse. The data of Morris and Robinson (1998) reveal that Brefeldin A also blocks actin-dependent cycling of PIN proteins, which serve as important auxin efflux facilitators, to the plasma membrane, and they strongly suggest that other auxin transport inhibitors may work by interfering with membrane-trafficking processes. Show less

Extracellular ATP is a known receptor agonist in animals and was previously shown to alter plant growth, and so we investigated whether ATP derivatives could function outside plant cells as signaling agents. Signaling responses induced by exogenous nucleotides in animal cells typically include increases in free cytoplasmic calcium concentration ([Ca(2+)](cyt)). We have evaluated the ability of exogenously applied adenosine 5'-[gamma-thio]triphosphate (ATPgammaS), adenosine… Show more

Extracellular ATP is a known receptor agonist in animals and was previously shown to alter plant growth, and so we investigated whether ATP derivatives could function outside plant cells as signaling agents. Signaling responses induced by exogenous nucleotides in animal cells typically include increases in free cytoplasmic calcium concentration ([Ca(2+)](cyt)). We have evaluated the ability of exogenously applied adenosine 5'-[gamma-thio]triphosphate (ATPgammaS), adenosine 5'-[beta-thio]diphosphate (ADPbetaS), and adenosine 5'-O-thiomonophosphate to alter [Ca(2+)](cyt) in intact apoaequorin transgenic Arabidopsis thaliana seedlings. ATPgammaS and ADPbetaS increase [Ca(2+)](cyt), and this increase is enhanced further when the nucleotides are added with the elicitor oligogalacturonic acid. Exogenous treatment with ATP also increases the level of transcripts encoding mitogen-activated protein kinases and proteins involved in ethylene biosynthesis and signal transduction. The increase in [Ca(2+)](cyt) induced by nucleotide derivatives can be ablated by Ca(2+)-channel blocking agents and by the calcium chelator 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), and the changes in gene expression can be partially blocked by these agents. These observations suggest that extracellular ATP can activate calcium-mediated cell-signaling pathways in plants, potentially playing a physiological role in transducing stress and wound responses. Show less

A volatile situation that erupted in the early 1990’s was at least four decades in the making. In order to better understand the circumstances that presently exist, it is necessary to trace the events that resulted in the tank farm facilities relocation. Although the outcome of the relocated tank farms was positive, it revealed many deep seeded issues that had been long suppressed, including growing resentment towards a government that had become deaf and blind to the needs of the residents in… Show more

A volatile situation that erupted in the early 1990’s was at least four decades in the making. In order to better understand the circumstances that presently exist, it is necessary to trace the events that resulted in the tank farm facilities relocation. Although the outcome of the relocated tank farms was positive, it revealed many deep seeded issues that had been long suppressed, including growing resentment towards a government that had become deaf and blind to the needs of the residents in East Austin. Tensions between governmental agencies at state, county and city levels over political power, at times, hindered progress at the tank farms. These issues were exacerbated because of seemingly limited inter-governmental communication and collaboration. But once the issues were publicly aired, it became a way towards resolution and relationship transformation. Overall this story is an example of community empowerment. This particular community made a positive change in their environment, using media coverage as a resource, and insisted that their voices be heard.

After the success of community involvement into relocating the tank farms, the neighborhood organizations, lead by PODER, continued their activism in shaping their urban environment by concentrating on issues like the Holly Power Plant, the Bergstrom Air Force Base conversion and solid waste trucking facility (Taylor 3/21/93, par 15-16). The community has had limited success these post-tank farm campaigns, but has set an example of how a community can become empowered to transform the environment in which they live. This document seeks to propose solutions and builds for this site. Show less