Browsing by Author "Winkel, Brenda S. J."
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- Adeno-associated virus rep78 expression in Arabidopsis thalianaSisco, Daniel (Virginia Tech, 2002-09-06)Adeno-associated virus type 2 (AAV-2) integrates preferentially into a defined site on human chromosome 19, and has been developed as a gene therapy vector. We propose to use this unique recombination event for site-specific integration of transgenes in plants. This strategy would alleviate problems associated with current plant transformation methods that integrate transgenes randomly. The AAV-2 gene encoding the enzyme that catalyzes the insertion (rep78) was introduced into Arabidopsis thaliana via Agrobacterium-mediated transformation. PCR and sequence analysis confirmed the presence of rep78 in two plant lines. RT-PCR demonstrated rep78 transcription in one plant line, but protein could not be detected in either line.
- Analysis of T-DNA alleles of flavonoid biosynthesis genes in Arabidopsis ecotype ColumbiaBowerman, Peter A.; Ramirez, Melissa V.; Price, Michelle B.; Helm, Richard F.; Winkel, Brenda S. J. (2012-09-04)BACKGROUND: The flavonoid pathway is a long-standing and important tool for plant genetics, biochemistry, and molecular biology. Numerous flavonoid mutants have been identified in Arabidopsis over the past several decades in a variety of ecotypes. Here we present an analysis of Arabidopsis lines of ecotype Columbia carrying T-DNA insertions in genes encoding enzymes of the central flavonoid pathway. We also provide a comprehensive summary of various mutant alleles for these structural genes that have been described in the literature to date in a wide variety of ecotypes. FINDINGS: The confirmed knockout lines present easily-scorable phenotypes due to altered pigmentation of the seed coat (or testa). Knockouts for seven alleles for six flavonoid biosynthetic genes were confirmed by PCR and characterized by UPLC for altered flavonol content. CONCLUSION: Seven mutant lines for six genes of the central flavonoid pathway were characterized in ecotype, Columbia. These lines represent a useful resource for integrating biochemical and physiological studies with genomic, transcriptomic, and proteomic data, much of which has been, and continues to be, generated in the Columbia background.
- Biochemical, Molecular and Functional Analysis of Volatile Terpene Formation in Arabidopsis RootsHuh, Jung-Hyun (Virginia Tech, 2011-07-20)Plants produce secondary (or specialized) metabolites to respond to a variety of environmental changes and threats. Especially, volatile compounds released by plants facilitate short and long distance interaction with both beneficial and harmful organisms. Comparatively little is known about the organization and role of specialized metabolism in root tissues. In this study, we have investigated the root-specific formation and function of volatile terpenes in the model plant Arabidopsis. As one objective, we have characterized the two root-specific terpene synthases, TPS22 and TPS25. Both enzymes catalyze the formation of several volatile sesquiterpenes with (E)-β-farnesene as the major product. TPS22 and TPS25 are expressed in the root in distinct different cell type-specific patterns and both genes are induced by jasmonic acid. Unexpectedly, both TPS proteins are localized to mitochondria, demonstrating a subcellular localization of terpene specialized metabolism in compartments other than the cytosol and plastids. (E)-β-Farnesene is produced at low concentrations suggesting posttranslational modifications of the TPS proteins and/or limited substrate availability in mitochondria. We hypothesize that the mitochondrial localization of TPS22 and TPS25 reflects evolutionary plasticity in subcellular compartmentation of TPS proteins with emerging or declining activity. Since (E)-β-farnesene inhibits Arabidopsis root growth in vitro, mitochondrial targeting of both proteins may fine tune (E)-β-farnesene concentrations to prevent possible autotoxic or inhibitory effects of this terpene in vivo. We further investigated the role of volatile terpenes in Arabidopsis roots in interaction with the soil-borne oomycete, Pythium irregulare. Infection of roots with P. irregulare causes emission of the C11-homoterpene (or better called C4-norterpene) 4,8-dimethylnona-1,3,7-triene (DMNT), which is a common volatile induced by biotic stress in aerial parts of plants but was not previously known to be produced in plant roots. We demonstrate that DMNT is synthesized by a novel, root-specific pathway via oxidative degradation of the C30-triterpene, arabidiol. DMNT exhibits inhibitory effects on P. irregulare mycelium growth and oospore germination in vitro. Moreover, arabidiol and DMNT biosynthetic mutants were found to be more susceptible to P. irregulare infection and showed higher rates of Pythium colonization in comparison to wild type plants. Together, our studies demonstrate differences and plasticity in the metabolic organization and function of terpenes in roots in comparison to aboveground plant tissues.
- A biosystematic study of the rare plant Paronychia virginica Sprengel (Caryophyllaceae) employing morphometric and allozyme analysesRohrer, Wendy L. (Virginia Tech, 1997-09-18)Paronychia virginica Spreng. (Caryophyllaceae) is a perennial evergreen herb of exposed, relatively xeric habitats. Approximately 10 mid-Appalachian populations remain in Virginia, West Virginia, and Maryland and are disjunct from populations located primarily in Texas, Oklahoma, and Arkansas. A study was conducted to test the hypothesis that eastern and western populations differ significantly and, therefore, represent at least two distinct taxa. Statistical analyses of 8 qualitative and 24 quantitative morphological characters indicated very highly significant (P < 0.001) variation between eastern and western populations of P. virginica. Characters differing most significantly included sepal pubescence, awn length, awn pubescence, awn curvature, length-width ratio of leaves, and shape of leaf apices. Starch gel electrophoresis was performed and six enzyme systems/nine loci (EST-2, EST-3, LAP, MDH-1, MDH-2, PGI, PGM-1, PGM-2, and SKDH) were identified as being consistently scorable and informative. Although gene flow between populations of P. virginica was shown to be restricted (mean FST = 0.353), populations are maintaining relatively high levels of genetic diversity. Genetic variability was quantified for each population and mean values for number of alleles per locus (A), percent loci polymorphic (P), and expected heterozygosity (HEXP) were found to be 1.95, 47.22%, and 0.204, respectively, exceeding those values reported for seed plants, widespread species, and endemic species. Hierarchical F statistics suggest higher levels of genetic variability within individual populations than among populations, regardless of geographic location. All statistically significant (P < 0.05) deviations from Hardy-Weinberg equilibrium indicated a deficiency in heterozygotes at the respective loci. Considering results from both the morphometric and allozyme analyses, the current author suggests recognizing two distinct subspecies, P. virginica subsp. virginica in the eastern U.S. and P. virginica subsp. scoparia in the south-central U.S. Conservation efforts should be focused on the maintenance of existing populations in both eastern and western regions of the U.S. in order to preserve the genetic and evolutionary potential of these taxa.
- Cell-Free Biosystems Comprised of Synthetic Enzymatic Pathways: Development of Building Blocks, Immobilization of Enzymes, Stabilization of Cascade Enzymes, and Generation of HydrogenMyung, Suwan (Virginia Tech, 2013-05-08)The production of hydrogen from low-cost abundant renewable biomass would be vital to sustainable development. Cell-free (in vitro) biosystems comprised of synthetic enzymatic pathways would be a promising biomanufacturing platform due to several advantages, such as high product yield, fast reaction rate, easy control and access, and so on. However, it is essential to produce (purified) enzymes at low costs and stabilize them for long periods to decrease biocatalyst costs. Thermophilic recombinant enzymes as building blocks were discovered and developed: fructose 1,6-bisphosphatase (FBP) from Thermotoga maritime, phosphoglucose isomerase (PGI) from Clostridium thermocellum, triose phosphate isomerase (TIM) from Thermus thermophiles and fructose bisphosphate aldolase (ALD) from T. maritima and T. thermophilus. The recombinant proteins were over-expressed in E. coli, purified and characterized. For purification and stabilization of enzymes, one-step, simple, low-cost purification and immobilization methods were developed based on simple adsorption of cellulose-binding module (CBM)-tagged protein on the external surface of high-capacity regenerated amorphous cellulose. Also, a simple, low-cost purification method of thermophilic enzymes was developed utilizing a combination of heat and ammonium sulfate precipitation. For development of cascade enzymes as building modules (biocatalyst modules), it was discovered that the presence of other enzymes/proteins had a strong synergetic effect on the stabilization of the thermolabile enzyme (e.g., PGI) due to the in vitro macromolecular crowding effect. And substrate channeling among CBM-tagged self-assembled three-enzyme complex (synthetic matabolon) immobilized on the easily-recycled cellulose-containing magnetic nanoparticles can not only increase cascade reaction rates greatly, but also decrease enzyme cost in cell-free biosystems. The high product yield and fast reaction rate of dihydrogen from sucrose was validated in a batch reaction containing fifteen enzymes comprising a non-natural synthetic pathway. The yield of dihydrogen production from 2 mM of sucrose was 96.7 % compared to theoretical yield at 37 °C. The maximum rate was increased 3.1 fold when the substrate concentration was increased from 2 to 50 mM in a fed-batch reaction. The research and development of cell-free biosystems for biomanufacturing require more efforts, especially in low-cost recombinant thermostable enzymes as building blocks, efficient cofactor recycling, enzyme and cofactor stabilization, and fast reaction rates.
- Cell-surface Tumoricidal Molecules and NF-kB in the Tumor-burdened HostMcConnell, Michael James (Virginia Tech, 2002-06-24)Tumor-distal immune suppression promotes tumor growth by preventing the recruitment of leukocytes to the tumor-proximal microenvironment. Tumor necrosis factor (TNF)-a is both secreted by and expressed on the cell-surface (mTNF-a) of macrophages. When stimulated with LPS, tumor-burdened host (TBH) macrophages secrete more TNF-a than normal host (NH) macrophages. In this study, I showed that mTNF-a is elevated both in freshly isolated and stimulated TBH macrophages. Additionally, I analyzed the expression of Fas and FasL on freshly isolated and LPS-stimulated macrophages and found no differences between TBH and NH macrophages. Fas and Fas ligand (FasL) cell-surface expression was analyzed on NH and TBH T-cells. While no difference was observed in freshly isolated cells, cell-surface expression of both proteins remained higher in TBH T-cells than NH T-cells after mitogenic stimulation. Fas and FasL analysis was also extended to the MethKDE fibrosarcoma and I found that these tumor cells express high levels of FasL. Because past observations show increased TNF-a mRNA expression in TBH macrophages relative to NH macrophages, I hypothesized that NF-kB activation may be increased as well. NF-kB is a transcription factor whose activation is required for TNF-a transcription. I observed increased NF-kB activation in both splenic and peritoneal TBH macrophages. Interestingly, electrophoretic mobility shift analysis (EMSA) suggests that different species of NF-kB were found in each distinct population of macrophages. Together, these data demonstrate that cell-surface tumoricidal molecules and NF-kB are dysregulated in the tumor-burdened host.
- Characterization of cytoplasmic diversity in soybean (Glycine max L. Merr) using mitochondrial markersHanlon, Regina (Virginia Tech, 1994-12-05)Soybean, Glycine max L. Merr, is used worldwide as an important source of protein and oil for a wide spectrum of edible feed and industrial purposes. Modem cultivars are derived from relatively few plant introductions (PIs) which severely limits diversity in soybean germplasm. The United States Department of Agriculture (USDA) maintains the soybean germplasm collection. Mitochondrial DNA sequences have been used as markers of diversity at the cytoplasmic level. This project included three objectives. The first was a classification of the 208 varieties of the USDA's 'old domestic collection' of soybean varieties with two mitochondrial restriction fragment length polymorphisms (RFLP) markers. Molecular techniques were used to search for additional sources of cytoplasmic diversity available to soybean breeders. The two polymorphic markers were, a 2.3 kb HindIII fragment isolated from 'Williams 82' mitochondrial DNA, and a portion of the mitochondrial atp6 gene. These markers were used to distinguish cytoplasmic groups based on hybridization analysis of HindIII-digested soybean DNA Four major groups were observed with the 2.3 kb marker in the old domestic collection, and several minor subgroups were also detected. The second objective included subcloning and sequencing the 0.9 kb and 1.7 kb HindIII-PstI clones flanking the 2.3 kb HindIII fragment from 'Williams 82' DNA The total 4.9 kb PstI sequence from 'Williams 82' mitochondrial DNA was used to search a sequence database for any homology to known mitochondrial sequences. The third objective compared restriction maps of the four cytoplasmic types in the regions containing homology to the 4.9 kb PstI fragment. DNAs from the four cytoplasmic types were digested with five enzymes and four specific clones (0.9 kb PstI-HindIII, 0.8 kb HindIII-XbaI, 1.5 kb Xbal-HindIII, 1.7 kb HindIII-PstI) were used as hybridization probes in Southern analysis to examine RFLP patterns and construct comparative restriction maps of the four cytoplasmic types of DNA.
- Characterization of IphP from Nostoc commune UTEX 584 and a Dual Specificity Protein Phosphatase from Anabaena PCC 7120Howell, Larry Daniel II (Virginia Tech, 1997-09-17)Protein phosphorylation is utilized universally as a mechanism of signal transduction. However, the use of tyrosine phosphorylation by bacteria has been a matter of dispute. Conventional wisdom dictated that "prokaryotic phosphorylation" was typified by phosphorylation of histidine and aspartate residues of proteins, while "eukaryotic phosphorylation" was characterized by modification of serine, threonine, or tyrosine residues. Increasing numbers of reports have emerged challenging the traditional view of "prokaryotic" and "eukaryotic" phosphorlyation. One of the strongest links unifying prokaryotic and eukaryotic protein phosphorylation to date is IphP, a genomically-encoded dual-specificity protein phosphatase from the cyanobacterium Nostoc commune UTEX 584 bearing the active-site signature sequence of eukaryotic tyrosine-specific and dual-specificity protein phosphatases. The catalytic properties and substrate specificity of IphP were examined in detail. The enzyme was able to discriminate among a variety of exogenous peptides and proteins. Kinetic studies revealed that IphP favors protein / peptide substrates over low molecular weight compounds. Heparin effected IphP activity in a substrate-dependent manner. Enzyme activity toward casein (P-Ser) and MAP kinase (P-Thr/P-Tyr) was stimulated in the presence of the polyanion, whereas activity was inhibited by heparin toward other protein substrates. Both stimulation and inhibition by heparin were dose-dependent. The ability to stimulate IphP activity toward select substrates was attributed to the ability of heparin to recruit the enzyme and substrate to the same microenvironment. To facilitate future genetic studies examining the role of tyrosine phosphorylation in cyanobacteria, we searched for evidence of protein tyrosine phosphorylation in Anabaena PCC 7120. In a collaborative effort with the laboratory of Dr. Potts, tyrosine phosphorylated proteins were identified in Anabaena utilizing several approaches, including comparative labelling with alpha- vs gamma-32P-ATP, phosphoamino acid analysis, and selective hydrolysis with a tyrosine specific protein phosphatase. Together, these data unequivocally demonstrate the presence of tyrosine-phosphorylated proteins in Anabaena PCC 7120. Extracts of Anabaena PCC 7120 were examined for protein tyrosine phosphatase activity. An apparent PTP activity was detected, partially purified, and characterized. The protein phosphatase was ~38kDa by SDS-PAGE and sucrose density gradient centrifugation and displayed dual-specificity protein phosphatase (DSP) activity in vitro. The enzyme was localized to the periplasm and was thus assigned the title PAD, for Periplasmic Anabaena DSP. Periplasmic phosphoproteins of ~120 and 55 kDa that had been radiolabelled in vitro were dephosphorylated by partially purified PAD. PAD activity varied in vivo ~5-fold in a rhthymic, seemingly diurnal manner. Periplasmic proteins, including the 55kDa protein, were labelled in vivo and the degree of radiolabel incorporated into these proteins varied inversely with PAD activity.
- Characterization of the thermostable nature of the alpha and beta tubulin proteins in Cyanidium caldarium and Cyanidioschyzon merolaeArnold, Matthew Scott (Virginia Tech, 2004-02-12)Microtubules are critically important cytoskeletal elements. Together with microtubule associated proteins (MAPs), they form the latticework on which eukaryotic life exists. Simply put, microtubules are polymers of tubulin heterodimers, which are composed of the globular proteins alpha and beta tubulin. In vivo, these monomers associate with one another to form heterodimers, which then polymerize to form microtubules. In mammals, microtubule polymerization is a temperature-dependent process with an optimum of 37°C (Detrich et al., 2000). If temperatures exceed this optimal temperature by even a few degrees, the microtubule will begin to dissemble due to denaturation of the tubulin subunit and permanent loss of both shape and function will occur. This thermal barrier seems to be consistent in most eukaryotic organisms. Two exceptions are the thermophilic red algae, Cyanidium caldarium and Cyanidioschyzon merolae. These thermophilic acidophiles have been discovered in volcanic vents around the globe from Yellow Stone Park to Italy and grow at optimal temperatures of around 55°C. These organisms have been primarily studied in the context of evolutionary biology because of their primitive characteristics. Very little is known about the molecular biology of these organisms, and certainly nothing is known about how the biochemistry of these organisms brings about the ability to survive the harsh conditions of their environment. Currently, my hypothesis concerning the thermostable tubulin expressed within these organisms is that there may be key amino acid differences in the tubulin's primary structure that confer enhanced thermostability. I am testing this hypothesis by sequencing the alpha and beta tubulin genes of Cyanidium caldarium and Cyanidioschyzon merolae, generating homology models of the tubulin dimers, and comparing these models to a known mesophilic tubulin heterodimer structure in order to identify potential structural differences.
- Characterizing the role in amino acid sensing and signaling of Amino Acid Permease 1 in ArabidopsisShelley, Brett A. (Virginia Tech, 2021-07-28)Amino acids are necessary for protein synthesis and specialized metabolism in plants. Yet very little is known about how plants sense and regulate when and where to allocate amino acids to meet the demand for nitrogen in growing tissues. In particular, while characterized in yeast and mammals, no amino acid sensor has been identified in plants. Amino Acid Permease 1 (AAP1) has been previously characterized and was shown to mediate amino acid uptake from the soil. aap1 knockout plants and several EMS mutants affected in AAP1 sequence display enhanced tolerance to toxic concentrations of amino acids. Yet, two of the corresponding variant proteins appear to be functional transporters, effectively dissociating amino acid transport and phenotype. To understand this apparent discrepancy, I precisely studied AAP1 localization of expression at the plant and cellular level, and in specific tissue types of the root where AAP1 function is required for the tolerance phenotype and the amino acid uptake activity. I showed that AAP1 protein is present in the endoplasmic reticulum of the cortex in wild type plants Yet, its ectopic expression in root tip and phloem increased amino acid uptake, while expression in cortex could not. This and other of my results do not support the current model of AAP1 functioning in amino acid uptake by the root. I propose that the main effect of mutations in AAP1 is a disturbance in amino acid metabolism, possibly triggered by altered amino acid sensing. In this new model, AAP1 would be necessary for sensing amino acid status of cortex cells, possibly in the endoplasmic reticulum, and adjust amino acid metabolic activity and uptake to current availability. In effect, disruption of the sensing function, either by complete loss of AAP1 function (knockout) or by uncoupling the transport and sensing function (EMS mutants), would lead to the various characteristics of the phenotype of the aap1 mutants I observed. My main hypothesis is that AAP1 is a transporter endowed with sensing function, i.e., an amino acid transceptor.
- Cloning and Characterization of a Gene Involved in Lipooligosaccharide Biosynthesis in Haemophilus somnusHensley, Jennifer A. (Virginia Tech, 1998-05-06)Repetitive tetramers of the DNA sequence 5'-CAAT-3' are present in several loci associated with lipooligosaccharide (LOS) phase variation in Haemophilus influenzae type b (Hib). In an attempt to identify H. somnus phase-variable LOS genes, the presence of CAAT repeats within the H. somnus 738 genome was confirmed using a (CAAT)7 probe. A 3.9 kb EcoRI fragment that reacted with the probe was cloned and sequenced. Sequence analysis confirmed the presence of 31 CAAT repeats downstream of two potential start codons, and indicated that small or large proteins would be encoded depending on the number of CAAT repeats. The larger gene products showed 46% amino acid homology to Lex2b from Hib, which influences LOS phase variation in that species. In H. somnus, this gene was named lob1 (lipooligosaccharide biosynthesis gene). Sequence analysis showed that randomly selected colonies most frequently contained 33 CAAT repeats in lob1, corresponding to a 294 amino acid product. Colonies selected for negative reactivity to mAb 5F5 were significantly more likely to have different numbers of CAAT repeats in lob1 than randomly selected colonies. The presence of lob1 in trans altered the LOS profile of a non-phase variable strain of H. somnus, and caused increased levels of reactivity to polyclonal antisera made to purified LOS from strain 738. Based on the ability of this gene to alter the LOS profile of a non-phase varying strain and the correlation of changes in CAAT repeats with mAb 5F5 reactivity, lob1 appears to be involved in LOS biosynthesis and phase variation.
- Cloning and sequencing of a β-glucosidase of cDNA from Sorghum bicolor (L.) Moench and analysis of expression in seedlingsCicek, Muzaffer (Virginia Tech, 1996-02-04)A full-length β-glucosidase encoding cDNA is isolated and sequenced from Sorghum bicolor (L) Moench. Using 5’- and 3’- end specific probes derived from the cDNA clone, the multiplicity of β-glucosidase genes and their expression in different tissues were studied. Southern blotting data showed that β-glucosidase is encoded by a small multigene family. Northern analysis data indicated that mRNA corresponding to the cloned gene is present at high levels in the node and mesocotyl 2 regions of the seedling and at low levels only in the zone of elongation region in roots. Other seedling parts such as mesocotyl 1, root sections adjacent to the seed and coleoptile sections do not have any detectable expression. The amino acid sequence data show 72% sequence identity between maize and sorghum β-glucosidase precursor proteins. In view of high sequence similarity between maize and sorghum β-glucosidase, immunoblotting analysis was performed with maize-anti-β-glucosidase serum. The immunoblotting results supported the results of Hosel et al., (1987) with respect to the occurrence of two distinct β-glucosidases being present in sorghum.
- Common Signaling Elements in Response Pathways Activated by the Endothelial Survival Factors VEGF and InsulinWang, Amanda Cyphers (Virginia Tech, 2008-12-02)Damage to the vasculature is a common occurrence in diabetes mellitus. At the cellular level, dysfunction of vascular endothelial cells is often associated with diabetic conditions. Multiple agents maintain the endothelium, including vascular endothelial growth factor (VEGF), an endothelial cell mitogen/survival factor, and insulin, which has anti-apoptotic effects on endothelial cells in addition to regulating glucose homeostasis. Insulin and VEGF, upon activating their respective tyrosine kinase receptors, can engage the PI3-kinase/Akt, MAPK, and PLC-γ/PKC pathways. Thus, crosstalk between VEGF and insulin signaling may occur at numerous points. Our objectives were twofold: 1) to characterize the combined effects of insulin and VEGF on downstream elements, and 2) to determine the ability of signaling intermediates principally associated with either insulin or VEGF signaling to interact directly. After treatment with VEGF, insulin, or both, cells expressing both VEGF receptor-2 (KDR) and the insulin receptor were immunoprecipitated for total Akt and PLC-γ. Isolates from cells stimulated with both ligands demonstrated activation of PLC-γ and Akt that was less than additive over fifteen minutes. Conversely, cells pretreated with advanced glycation end products showed increased Akt phosphorylation. The effect of insulin on VEGF bioactivity was also measured by PLC-γ-mediated hydrolysis of phosphatidylinositol. These studies suggested suppressed VEGF activity in the presence of insulin. To examine direct signaling interactions, recombinant reagents capable of selective binding (via SH2 domains) to phosphorylated receptors were generated. Overall results showed relatively unaffected VEGF activity in the presence of insulin; however, this relationship is likely altered within the diabetic state.
- Comparative characterization of Arabidopsis Subfamily III beta-galactosidasesGantulga, Dashzeveg (Virginia Tech, 2008-12-05)The Arabidopsis genome encodes 17 putative beta-galactosidases belonging to Glycosyl Hydrolase (GH) family 35, which have been classified into seven subfamilies based on sequence homology. The largest of these, Subfamily III, consists of six genes, Gal-1 (At3g13750), Gal-2 (At3g52840), Gal-3 (At4g36360), Gal-4 (At5g56870), Gal-5 (At1g45130), and Gal-12 (At4g26140) that share 60-81% sequence identity at the amino acid level. All six proteins have a signal peptide that may target them to the cell exterior. We report purification and biochemical characterization of all six members of Subfamily III, each expressed as a recombinant protein in Pichia pastoris and one also in native form, purified from Arabidopsis leaves, with a special emphasis on substrate specificities. Organ specific expression of the six Gal genes was examined by analysis of the microarray databases and by semi-quantitative RT-PCR. The relative abundance and size of the Gal-1, Gal-2, Gal-5, and Gal-12 proteins was studied by immunoblotting using isoform-specific anti-peptide antibodies. The protein expression patterns of the Gal genes were generally consistent with microarray and RT-PCR data, though some discrepancies were observed suggesting distinct mechanisms of regulation for transcription and translation. Localization of total beta-galactosidase activity was visualized using the substrate, 5-bromo-4-chloro-3-indolyl-beta-D-galatopyranoside (X-Gal), to stain whole plants. Subcellular localization of the four isoforms examined by immuno-dotblotting and western blotting showed that Gal-1, Gal-2, Gal-5 and Gal-12 are present in apoplastic and cell wall bound protein extracts. Immuno-EM analysis of Gal-1 and Gal-12 showed that these proteins are localized in the cell walls of vascular and epidermal tissues in mature root. Taken together, the biochemical properties, expression patterns, and subcellular localization of these isozymes indicate that the Subfamily III beta-galactosidases all have potential functions in restructuring the cell wall during plant growth and development.
- Controlled Expression and Functional Analysis of the Iron-Sulfur Cluster Biosynthetic Machinery in Azotobacter vinelandiiJohnson, Deborah Cumaraswamy (Virginia Tech, 2006-05-05)A system was developed for the controlled expression of genes in Azotobacter vinelandii by using genomic fusions to the sucrose catabolic regulon. This system was used for the functional analysis of the A. vinelandii isc genes, whose products are involved in the maturation of [Fe-S] proteins. For this analysis the scrX gene, contained within the sucrose catabolic regulon, was replaced by the A. vinelandii iscS, iscU, iscA, hscB, hscA, fdx, iscX gene cluster, resulting in duplicate genomic copies of these genes, one whose expression is directed by the normal isc regulatory elements (Pisc) and the other whose expression is directed by the scrX promoter (PscrX). Functional analysis of [Fe-S] protein maturation components was achieved by placing a mutation within a particular Pisc-controlled gene with subsequent repression of the corresponding PscrX-controlled component by growth on glucose as the carbon source. This experimental strategy was used to show that IscS, IscU, HscBA and Fdx are essential in A. vinelandii and that their depletion results in a deficiency in the maturation of aconitase, an enzyme that requires a [4Fe-4S] cluster for its catalytic activity. Depletion of IscA results in null growth only when cells are cultured under conditions of elevated oxygen, marking the first null phenotype associated with the loss of a bacterial IscA-type protein. Furthermore, the null growth phenotype of cells depleted for HscBA could be partially reversed by culturing cells under conditions of low oxygen. These results are interpreted to indicate that HscBA and IscA could have functions related to the protection or repair of the primary IscS/IscU machinery when grown under aerobic conditions. Conserved amino acid residues within IscS, IscU, and IscA that are essential for their respective functions and/or display a partial or complete dominant-negative growth phenotype were also identified using this system. Inactivation of the IscR repressor protein resulted in a slow growth phenotype that could be specifically attributed to the elevated expression of an intact [Fe-S] cluster biosynthetic system. This system was also used to investigate the extent to which the two [Fe-S] biosynthetic systems in A. vinelandii, Nif and Isc, can perform overlapping functions. Under normal laboratory growth conditions, no cross-talk between the two systems could be detected. However, elevated expression of Isc components as a consequence of inactivation of the IscR repressor protein results in a modest ability of the Isc [Fe-S] protein maturation components to replace the function of Nif-specific [Fe-S] protein maturation components. Similarly, when expressed at very high levels the Nif-specific [Fe-S] protein maturation components could functionally replace the Isc components. Oxygen levels were also found to affect the ability of the Nif and Isc systems to perform common functions. Nevertheless, the lack of significant reciprocal cross-talk between the Nif and Isc systems when they are produced only at levels necessary to satisfy their respective physiological functions, indicates a high level of target specificity with respect to [Fe-S] protein maturation.
- CRISPR3 Regulates Exopolysaccharide Production in Myxococcus xanthusWallace, Regina A. (Virginia Tech, 2013-10-10)Myxococcus xanthus, a model organism for studying development and Type IV pili (T4P), harbors three Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) on its chromosome. CRISPR systems, which function as an adaptive immune system in prokaryotes, are classified into three types based on CRISPR-associated genes. Evidence suggests that these three types mediate immunity slightly differently. M. xanthus CRISPR1 and CRISPR2 are Type I systems while CRISPR3 is a Type III-B system. In a genetic screen, a mariner transposon insertion in the 13th spacer of CRISPR3 (3SP13) was found to restore exopolysaccharide (EPS) production to a pilA mutant. Since the deletion of CRISPR3 failed to suppress a pilA mutation and expression of CRISPR3 from a heterologous promoter led to pilA suppression, it was concluded that the 3SP13 transposon insertion is a gain-of-function mutation. Deletion of the adjacent Repeat Associated Mysterious Proteins (RAMP) genes indicated that they are essential for the 3SP13 transposon insertion to suppress pilA, providing evidence that Type III-B systems may be involved in the regulation of chromosomal genes. We suggest that one of the spacers, once expressed and processed, may inhibit the expression of a negative regulator of EPS production in M. xanthus.
- The Design, Synthesis and Study of Mixed-Metal Ru,Rh and Os, Rh Complexes with Biologically Relevant ReactivityWang, Jing (Virginia Tech, 2013-01-23)A series of mixed-metal bimetallic complexes [(TL)2M(dpp)RhCl2(TL)]3 (M = Ru and Os, terminal ligands (TL) = phen, Ph2phen, Me2phen and bpy, terminal ligands (TL) = phen, bpy and Me2bpy ), which couple one Ru or Os polyazine light absorber (LA) to a cis-RhIIICl2 center through a dpp bridging ligand (BL), were synthesized using a building block method. These are related to previously studied trimetallic systems [{(TL)2M(dpp)2RhCl2]5+, but the bimetallics are synthetically more complex to prepare due to the tendency of RhIII halide starting materials to react with diimine ligands to form cis-[Rh(NN)2Cl2]+ motifs. The bimetallic complexes, [(phen)2Ru(dpp)RhCl2(bpy)]3+, [(phen)2Ru(dpp)RhCl2(phen)]3+, [(Ph2phen)2Ru(dpp)RhCl2(phen)]3+, [(Me2phen)2Ru(dpp)RhCl2(phen)]3+, [(bpy)2Ru(dpp)RhCl2(bpy)]3+, [(bpy)2Ru(dpp)RhCl2(Me2bpy)]3+ and [(bpy)2Os(dpp)RhCl2(phen)]3+, were characterized and studied by electrochemistry, electronic absorption spectroscopy, ESI-mass spectrometry, steady-state and time-resolved emission spectroscopy. Ï¿" ï¿" The electrochemical properties of bimetallic complexes with polyazine ligands exhibit a reversible one-electron metal-based oxidation, a quasi-reversible RhIII/IICl2 overlapped with a small amount of RhII/ICl and an irreversible RhII/ICl2 �reductions prior to the reversible bridging ligand dpp0/- �reduction. ï¿" ï¿" The title bimetallic complexes are efficient light absorbers due to the [(TL)2MII(dpp)] light absorber subunit. The bimetallics display ligand-based ï¿"'ï¿"* transitions in the UV region and metal-to-ligand charge transfer (MLCT) transitions in the visible region of the spectrum with approximately half the absorption extinction coefficient values relative to the trimetallics in the spectrum. The Os,Rh bimetallic complex, [(bpy)2Os(dpp)RhCl2(phen)]3+, displays Os(dï¿")'dpp(ï¿"*) CT transition at 521 nm and a low energy absorption band at 750 nm in the near-infrared region representing direct 1GS'3MLCT excitation due to the high degree of spin orbital coupling in Os complexes. The bimetallic complexes [(phen)2Ru(dpp)RhCl2(bpy)]3+, [(phen)2Ru(dpp)RhCl2(phen)]3+, [(Ph2phen)2Ru(dpp)RhCl2(phen)]3+, [(Me2phen)2Ru(dpp)RhCl2(phen)]3+, [(bpy)2Ru(dpp)RhCl2(bpy)]3+ and [(bpy)2Ru(dpp)RhCl2(Me2bpy)]3+ display Ru(dï¿")'dpp(ï¿"*) MLCT transitions centered at 505, 508, 515, 516, 510 and 506 nm, respectively. The bimetallic complex [(Ph2phen)2Ru(dpp)RhCl2(phen)]3+ displays enhanced absorption. Ï¿" ï¿" The photophysical properties of Ru,Rh bimetallic complexes are close to those of trimetallic analogues. In room temperature acetonitrile, both bimetallic and trimetallic complexes display a weak and short-lived emission from the Ru(dï¿")'dpp(ï¿"*) 3MLCT excited state. For example, the bimetallic complex [(phen)2Ru(dpp)RhCl2(bpy)]3+ emits at 766 nm and the trimetallic complex [{(phen)2Ru(dpp)}2RhCl2]5+ emits at 760 nm. At 77 K in 4:1 ethanol/methanol glass, the bimetallics, as well as trimetallics, exhibit a more intense blue-shifted emission with a longer lifetime, which is from the same 3MLCT excited state. At 77 K, the low temperature emission from the same 3MLCT state of [{(phen)2Ru(dpp)}2RhCl2]5+ blue-shifts to 706 nm with the emission lifetime of 1.8 ms and the bimetallic [(phen)2Ru(dpp)RhCl2(bpy)]3+ emits at 706 nm (t = 1.8 ms). The Ru,Rh complexes 3MLCT excited states can populate Ru(dï¿")'Rh(ds*) triplet metal-to-metal charge transfer (3MMCT) excited states through intramolecular electron transfer at room temperature, which is impeded in the rigid matrice at 77 K due to the large reorganizational energy and restricted molecular motion. The emission of Os,Rh bimetallic complex [(bpy)2Os(dpp)RhCl2(phen)]3+ could not be detected by our instruments likely due to its expected red-shifted emission which lies outside our detector window. ï¿" ï¿" �The Ru,Rh bimetallics display interesting and efficient photo-reactivity with DNA activated by visible light. The DNA gel shift assay, selective precipitation, ESI-mass spectrometry and polymerase chain reaction (PCR) studies suggest that Ru,Rh bimetallic complexes photobind to DNA following visible light excitation. This reactivity is not observed for analogous Ru,Rh,Ru trimetallics due to the steric protection of the Rh site in that motif. The bimetallic [(TL)2Ru(dpp)RhCl2(TL)]3+ systems can photobind and photocleave DNA through low-lying 3MMCT excited states when excited by the low energy visible light, with or without molecular oxygen. This is unusual but desirable reactivity for photodynamic therapy (PDT) drug development. The Os,Rh bimetallic complex [(bpy)2Os(dpp)RhCl2(phen)]3+ photobinds and photocleaves DNA under red therapeutic light excitation without molecular oxygen, an unprecedented result. Polymerase chain reaction experiments were used to evaluate the impact on DNA amplification of the DNA photo-modification and photo-damage induced by [(bpy)2Os(dpp)RhCl2(phen)]3+ under red light irradiation. Either photobinding or photocleavage induced by red light excitation of [(bpy)2Os(dpp)RhCl2(phen)]3+ on DNA inhibits amplification via PCR methods, a model for in vivo replication. Moreover, significant thermal stability of DNA photo-modification over 90 "C is required for PCR. A red light-activated drug that acts in an oxygen-independent mechanism to impede DNA amplification is unique in this field and desirable for study as a new class of PDT drugs.
- Development of antibodies for characterizing the Arabidopsis flavonoid biosynthetic pathwayCain, Cody Christopher (Virginia Tech, 1995-12-09)Polyclonal antibodies against the first two enzymes of the Arabidopsis thaliana flavonoid biosynthetic pathway were developed using conventional and phage antibody technology. cDNAs from Arabidopsis coding regions of chalcone synthase (CHS) and chalcone isomerase (CHI) were sub-cloned in frame into a bacterial expression vector as fusions with glutathione Stransferase (GST) using standard directional cloning techniques. Analysis of crude extracts of Escherichia coli containing GST .. CHS or GST .. CHI fusion protein indicated that the cells expressed equivalent amounts per volume of culture. CHS and CHI were purified to near homogeneity, yielding approximately 100 micrograms of GST .. CHS and 1 milligram of GST-CHI per liter of culture. The purified fusion proteins were injected into chickens and polyclonal lgY·s were purified from egg yolk Accumulation of CHS and CHI, as well as products of the pathway, were compared during the first eight days of Arabidopsis development. CHS and CHI are sequentially induced and reach maximal accumulation levels by day 5. Anthocyanidin levels are offset by one reaching maximal levels at day 6. The fusion proteins were also used to screen a phage-display library for Fabl fragments that recognize CHS and CHI epitopes. Preliminary data indicated that enrichment of phage displaying antibodies against CHS and CHI was successful. Phage-derived antibodies against CHS and CHI provide valuable tools for future experiments addressing Western blot analysis, immunolocalization experiments, and disruption of the flavonoid biosynthetic pathway by introduction of the corresponding genes into transgenic Arabidopsis plants.
- Development of intermonoploid somatic hybrids of potato and their molecular analysis based on polymorphism for retroelement Tst1Lightbourn, Gordon James (Virginia Tech, 2004-08-12)Inbred lines for hybrid crop production have been a mainstay of plant breeding. Biotechnological approaches to hasten the process are available including anther culture to halve the genome and protoplast fusion to create hybrids between incompatible partners. We applied these techniques to potato to evaluate their potential for breeding highly heterozygous, cross-pollinating species. Four families of monoploids (2n=1x=12), developed from diploid hybrids with diverse genomic constitutions but heavily favoring Solanum phureja, a primitive cultivated potato, were used in electrofusion experiments to create intermonoploid somatic hybrids (SH). The "monoploid sieve" results in the survival of only those gametes free of lethal and deleterious genes but generates sterile sporophytes, necessitating protoplast fusion for SH development. From six intermonoploid electrofusion combinations, 276 plants were regenerated over 6-9 months. Fusion conditions were optimized. Ploidy was determined by flow-cytometry and SH confirmed by microsatellite analysis. Field evaluations over three years revealed that intermonoploid SH were inferior to cultivars. Dihaploids derived by anther culture of a tetraploid intermonoploid SH were reduced in vigor with an increase in homozygosity, while 2x X 2x sexually derived populations had better yield than the SH, suggesting that producing SH introduced or eliminated factors required for productivity. Molecular analysis of the SH was conducted to examine genomic stability through protoplast isolation and plant regeneration. Sequence specific amplified polymorphism (S-SAP) represents a hybrid system incorporating amplified fragment length polymorphism (AFLP) technology in conjunction with the use of a defined genomic sequence, e.g., retrotransposon display (RD) when the defined sequence is anchored into a consensus sequence of a retrotransposon such as the long terminal repeat (LTR) sequence of Tst1. Parental monoploids, SH and various Solanaceae were evaluated by RD. Fluorescently-labeled retrotransposon-based primers were used in the ALFexpress automated fragment analyzer system. Eleven probes from RD were created for Southern blot analysis and used to verify taxonomic relationships between selected Solanaceae. Blots of intermonoploid somatic hybrids confirmed hybridity and occasional loss of genomic fragments. No activation or replication of retrotransposons was detected. Sequencing of inter-retrotransposon amplified polymorphism (IRAP) and S-SAP fragments revealed that all fragments had the expected Tst1 retroelement and/or the AFLP adaptor sequence. BLAST analysis identified 4 of the 17 fragments sequenced as part of the chloroplast genome, a tobacco anther-specific gene, repetitive DNA, and the phytochrome F gene.
- Discovering the Potential of Photoluminescent Ruthenium(II) Complexes as Photodynamic Therapy AgentsPadilla, Roberto (Virginia Tech, 2016-03-02)Anthracene was attached to light activated, ruthenium-based DNA disruptors to probe their distribution in cancer cells. The objective of this research is to understand the photophysical properties (Chapter 2), photoreactivity toward DNA and proteins (Chapter 3), and localization within cancer cells (Chapter 4) of ruthenium complexes that demonstrate promise as photodynamic therapy (PDT) agents. [(AnthbpyMe)(bpy)Ru(dpp)]2+ (1) and [(AnthbpyMe)2Ru(dpp)]2+ (2) absorb visible light with metal-to-ligand charge transfer (MLCT) transitions at 459 nm (16,000 M-1 cm-1 ) and 461 nm (21,000 M-1 cm-1 ), respectively. These species exhibit 3 MLCT emissions at λem = 661 nm and λem = 663 nm for 1 and 2, respectively, while the anthracene show emissions at 450 – 560 nm. The anthracene unit(s) quench the 3 MLCT to give quantum yields (lifetime) of Φem = 0.0059 [398(1) ns] and Φem = 0.0011 [414(1) ns] for 1 and 2, respectively. Voltammetry shows an irreversible anthracene oxidation at 1.23 – 1.28 V, RuIII/II oxidation at 1.53 – 1.55 V, and quasi-reversible reduction couples attributed to dpp0/-1 at 0.98 V. DNA gel shift assays demonstrate that complexes 1 and 2 modify DNA in the presence and absence of 3 O2 upon light activation to convert supercoiled DNA to a mixture of open circular (OC) DNA and a species that exhibit sa distinctly different migration rate than either OC and linear DNA. Binding constants, Kb, for complexes 1 and 2, toward DNA are 3.50 × 105 (3.50 × 104 ) and 4.50 × 103 (4.50 × 102 ) respectively. SDS-PAGE assays show that the complexes 1 and 2 modify bovine serum albumin (BSA) through an 3 O2-dependent mechanism upon light iii activation. The localization and PDT potency of the anthracene-Ru-dpp complexes are tested against F98 cells, which are rat glioma cells that simulate the infiltrative patterns of growth in cancer. Confocal microscopy demonstrates that complexes 1 and 2 internalize and localize primarily along the cell membrane and associate with dot-like vesicles within the cytoplasm. Complexes 1 and 2 show IC50 values of 107 µM and 85 µM, respectively, after 15 min of drug exposure and 1 h of PDT-treatment (λPDT = 455 nm).