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The presence of human pharmaceuticals in the environment has raised concerns regarding their potential adverse effects on non-target aquatic organisms. Pharmaceuticals are designed to target specific molecular pathways in humans in order to produce known pharmacological and physiological responses, before toxicological effects are seen. The “Read-Across Hypothesis” stipulates that pharmaceuticals can produce similar biological effects in fish, as in humans, if the molecular target is conserved, and the internal (blood plasma) concentrations are similar. The read-across hypothesis was tested using ibuprofen, a non-steroidal anti-inflammatory drug, and the model fish test species, the fathead minnow (Pimephales promelas), to determine if ibuprofen can cause similar target-mediated effects in teleost fish and humans, at comparable blood plasma concentrations. Fathead minnows were exposed, using continuous flow-through systems, for ≤96 hours to a range of ibuprofen water concentrations (100, 270, 370 and 500 µg/L) to determine if plasma concentrations similar to human therapeutic plasma concentrations (HTPCs, or Cmax) could be established in fish blood plasma. The mode of action of ibuprofen was used to identify relevant endpoints (i.e. cyclooxygenase (COX) enzyme) in order to examine target-mediated effects following drug exposure. The water and plasma ibuprofen concentrations were determined using LC-MS/MS. The measured ibuprofen plasma concentrations in individual fish were linked to target-mediated effects on COX gene expression, COX enzyme activity and prostaglandin E2 (PGE2) synthesis (products of COX activity), which were quantified using molecular (QPCR) and biochemical (colourimetric and enzyme immunoassay) assays, and linked with the Cmax of ibuprofen. It was demonstrated that in fish with a mean ibuprofen plasma concentration 1.8-fold below the Cmax, PGE2 concentrations (the most robust endpoint) was significantly inhibited following ibuprofen exposure. However, in fish exposed to an ibuprofen concentration closer to (2 to 3-fold above) environmentally relevant water concentrations (i.e. 9 µg/L), when the mean plasma concentration was 224-fold below the Cmax, fish did not respond to ibuprofen exposure. This study provides qualitative and quantitative evidence for the applicability of the “read-across hypothesis”, and highlights its potential utility for prioritising pharmaceuticals for environmental risk assessment.

The studies in this dissertation research were conducted to investigate the possible mode of action by which a brominated flame retardant, 2, 2-Bis (bromomethyl)-1, 3-propanediol (BMP) causes genotoxicity. Binding of BMP to DNA and BMP induced DNA strand breaks were investigated in SV-40 immortalized human uroepithelial cells (UROtsa) as an in vitro model for the bladder (a tissue that developed cancer after two year exposure to BMP in rodents). Results showed binding of [¹⁴C]-BMP equivalents to DNA increased with increased exposure time and concentration of [¹⁴C]-BMP. Comet analysis indicated BMP significantly increased the extent of DNA strand breaks at 1 and 3 h of incubation. However, strand breaks were repaired by 6 h of incubation. The DNA damaging effects of BMP at 1 h was concentration dependent. Compared with the parent compound, BMP-glucuronide (the predominant metabolite of BMP) bound less to DNA and produced less DNA strand breaks in UROtsa cells. Evidences that the BMP induced strand breaks were the result of an oxidative stress include: a concentration and time dependent increase in ROS generation; increased expression of Nrf2 and HSP70; complete attenuation of BMP induced DNA strand breaks by the antioxidant, NAC; and the presence of the oxidized base 8-OHguanine. UROtsa cells appear to be target cells for BMP because, as compared to rat hepatocytes (non-target cells), these cells lack the ability to detoxify BMP via glucuronidation and also because they are deficient in glutathione, a major intracellular antioxidant molecule. Both of these genotoxic events, DNA binding and oxidative DNA damage may, in part, contribute to BMP carcinogenicity observed in rodents. The relevance of current results to humans is remained to be established.

Doctor of Philosophy / Biochemistry and Molecular Biophysics Interdepartmental Program / Subbaratnam Muthukrishnan / In this study, I have used dsRNA-mediated down-regulation of transcripts/proteins of several potential targets in the model beetle, Tribolium castaneum to identify a molecular target of the “chitin inhibitor”, diflubenzuron (DFB). The elytron of the red flour beetle, T. castaneum, was chosen as the model tissue for studying the mode of action of DFB and its molecular target(s). We have standardized the protocol for topical administration of DFB on precisely aged prepupae to achieve the desired level of mortality (90-95%) on day 5 of the pharate adult stage. Exposure of prepupae to DFB at 1000 ppm results in a near complete loss of chitin in the newly forming adult procuticle of the elytron and the body wall. Global analysis of transcripts by RNA Seq was carried out to look for differential expression of several critical genes of cuticle assembly in these insects compared to mock-treated controls. Interestingly, genes directly involved in the biosynthetic pathway of chitin were not among those affected by DFB. However, immunolocalization studies have shown that several proteins of chitin metabolism including chitin synthase A, which is involved in the synthesis of cuticular chitin, are present in near normal amounts but are mislocalized in DFB-treated insects. Assays for chitin synthase using elytral extracts have indicated that the enzyme preparations from DFB-treated insects are catalytically inactive. By using RNA interference and competition studies with fluorescently-tagged glibenclamide (a sulfonylurea compound) or DFB, we have identified a long-sought molecular receptor of DFB as an ABCC class transporter. DFB-treatment and RNAi of a specific ABCC-type transporter gene lead to identical phenotypes including loss of chitin, loss of laminar architecture of the cuticle, and mislocalization of CHS from its normal plasma membrane location to intracellular locations presumably by affecting vesicular transport. Further, using an in vitro chitin synthesizing system consisting of microsomes prepared from elytral tissue, which exhibits all of the hallmarks of cuticular chitin-synthesizing epidermal cells including sensitivity to DFB, further insights into the mechanistic details of how this class of insecticides inhibits chitin synthesis have been obtained.

Unlike their bacterial counterparts, diseases caused by fungal pathogens are harder to treat due to a lack of discrete targets. Current antifungals are very broad spectrum and fall into three major classes: polyenes which target the cell membrane, azoles which target sterol biosynthesis and the echinocandins which target the cell wall. Recently a novel macrolide antibiotic produced by WAC 2288 was discovered in a co-culturing screen between various actinomycetes and pathogenic fungi. The active compound, a large type I polyketide compound called ibomycin, was specifically able to inhibit the growth of Cryptococcus neoformans but not Candida albicans. A combination of traditional and genetic approaches were used to identify the mode of action of ibomycin. Despite having characteristics associated with membrane perturbing agents such as fungicidal activity, causing hemolysis and even membrane localization in vivo, it does not seem that ibomycin disrupts the membrane in a sterol-dependent manner. We found evidence to suggest that ibomycin is not involved in disruption of cell wall biosynthesis based on localization in vivo and absence of viability rescue in presence of sorbitol. The results of haploinsufficiency and homozygous profiling of yeast deletion strains suggest that is no single protein target for ibomycin, but rather that membrane perturbation of ibomycin leads to downstream effects that impair vesicular trafficking and protein transport. Based on preliminary evidence, it is predicted that C. albicans is able to bind ibomycin but evades the induced toxic effects by barring access to its cell membrane. / Thesis / Master of Science (MSc)

Annual bluegrass is a winter annual grass that is problematic on golf putting greens due to its light green color, prolific seedhead production and intolerance to stress. On creeping bentgrass putting greens, herbicides for annual bluegrass control are limited. A new herbicide, methiozolin, developed by Moghu Research Center, LLC, in Daejeon, South Korea, safely and selectively controls annual bluegrass in creeping bentgrass and several other turfgrass species. Methiozolin typically controls annual bluegrass over several weeks, allowing desirable turfgrass time to grow into areas previously infested by annual bluegrass with little surface disruption. The mode of action of methiozolin is unknown, but has been proposed to act as either a cell wall biosynthesis inhibitor (CBI) or an inhibitor of tyrosine aminotransferase (TAT). Field studies were conducted at Virginia Tech to investigate strategies promoting surface recovery on putting greens following atypically rapid annual bluegrass loss resulting from methiozolin application, intensive core-cultivation as well as potential interactions with plant growth regulators (PGR's), like ethephon. In the rapid annual bluegrass removal study, all treatments receiving additional fertility via synthetic fertilizer with or without trinexapac-ethyl or biostimulant recovered 1 to 3 weeks more quickly than treatments that did not include additional fertility. Addition of the PGR trinexapac-ethyl inconsistently regulated speed of canopy recovery, both increasing and decreasing recovery speed. Under normal maintenance conditions, methiozolin does not negatively influence putting green recovery, however, if the putting green is exposed to droughty conditions, methiozolin can reduce recovery time by several weeks. Core-cultivation should be avoided in conjunction with methiozolin and ethephon applications because when this procedure was conducted on the same day as herbicide application it significantly damaged creeping bentgrass, reducing cover to 19% at 2000 g ai ha⁻¹, compared to the non-treated at 62%. Regarding the question of methiozoling mode of action, laboratory studies supported the claim that addition of exogenous 4-hydroxyphenylpyruvate (4-HPP) alleviates symptoms of methiozolin exposure in lesser duckweed, a model monocot species, but feeding various turfgrass species and annual bluegrass exogenous 4-HPP did not alleviate symptoms. Creeping bentgrass secondary root length and density was not affected by methiozolin, although annual bluegrass, Kentucky bluegrass and perennial ryegrass secondary root lengths were reduced. Based on these data, it does not appear that TAT inhibition is a primary mode of action of methiozolin in turfgrass. Studies were conducted to determine if methiozolin inhibited cell wall biosynthesis in desirable turfgrass species and annual bluegrass. All species exhibited decreased enrichment of ¹³C in cell-wall sugars form ¹³C-glucose in response to methiozolin and a known cell wall biosynthesis inhibitor, indaziflam. Indaziflam and methiozolin at 0.01 µM inhibited ¹³C enrichment of all sugars less than methiozolin at 1.0 µM, for xylose, arabinose and glucose, but not galactose. Addition of 4-HPP increased incorporation of ¹³C into xylose, but had no other influence on ¹³C incorporation into other cell wall sugars. Lack of species specific response indicates that cell wall biosynthesis inhibition is probably not the source of interspecific species responses observed in the field. / Ph. D.

A citricultura brasileira ocupa lugar de destaque no agronegócio nacional, sendo o país o maior produtor de laranja e suco de laranja do mundo. A faia (Fagus sylvatica) é uma das principais espécies das florestas na Europa, sendo usada como ornamental e por possui alto valor econômico devido à produção de madeira. Um dos principais entraves no cultivo dessas espécies é a ocorrência de doenças principalmente as causadas por espécies de Phytophthora que além de causar grandes prejuízos, os métodos de controle são difíceis e onerosos. Existem trabalhos na literatura que apontam os fosfitos como alternativa sustentável, eficaz e economicamente viável para o controle de doenças causadas por oomicetos. Entretanto, o Comitê de Ação a Resistência à Fungicidas (FRAC) classifica os fosfitos, como produtos com ingrediente ativo sem mecanismo de ação definido. Neste contexto, este trabalho teve como objetivo avaliar o produto comercial à base de fosfito de potássio, Phytogard® no controle das doenças causadas por Phytophthora nicotianae em citros e Phytophthora plurivora em faia, bem como avaliar através de análises bioquímicas se esse produto induz resistência em plântulas de citros. Além disso, foram realizados estudos in vitro para avaliar o efeito direto do Phytogard® sobre o desenvolvimento de P. nicotianae e P. plurivora e verificar os possíveis mecanismos de ação desse produto sobre esses patógenos. Foram utilizadas plântulas de citros e faia que foram aspergidas com diferentes concentrações de Phytogard® e, posteriormente, inoculadas com os patógenos. Foram avaliadas a incidência das doenças, o consumo de água e a quantidade de DNA dos patógenos nos tecidos das raízes dos hospedeiros. Ao final do experimento, foram realizadas análises bioquímicas dos tecidos das plântulas de citros. Nos experimentos in vitro, o micélio dos patógenos foi exposto a concentrações crescentes de Phytogard® sendo determinado o crescimento micelial, produção de massa fresca de micélio e de zoósporos. Avaliou-se a perda de eletrólitos, peroxidação de lipídios e a atividade da enzima β-1,3 glucanase do micélio exposto ao produto. Foi avaliada também a morfologia das hifas tratadas ou não com o Phytogard® através da técnica de Microscopia Eletrônica de Varredura (MEV). Os resultados mostraram que o Phytogard®, em todas as concentrações aplicadas controla de maneira preventiva as doenças causadas por P. nicotianae e P. plurivora em citros e faia, respectivamente. Em citros, o produto altera a atividade de algumas proteínas relacionadas à patogênese, mas não é possível concluir que o controle seja mediado por indução de resistência. O Phytogard® inibe o crescimento micelial e a produção de zoósporos de P. nicotianae e P. plurivora. Além disso, o produto modifica a morfologia das hifas, atua na permeabilidade de membrana e na síntese de parede celular do micélio dos patógenos. / The Brazilian citrus production is important to national agribusiness, and the country is the largest orange and orange juice world producer. Beech (Fagus sylvatica) is one of the main forest species in Europe and is used as ornamental and also it has a high economic value due to the production of wood. One of the main problems in the cultivation of these species is the occurrence of diseases, mainly caused by Phytophthora species. Besides causing extensive damage control methods are difficult and costly. There are studies in the literature that show phosphites as a sustainable alternative, effective and economically viable for the control of diseases caused by oomycetes. However, the Fungicide Resistance Action Committee (FRAC), classifies the phosphites as products with the active ingredient with no defined mode of action. In this context, this work aimed to evaluate the commercial product based on potassium phosphite Phytogard® on the control of diseases caused by Phytophthora nicotianae in citrus plants and Phytophthora plurivora in beech plants and evaluate through biochemical assays whether this product induces resistance in citrus seedlings. In addition, in vitro studies were carried out to evaluate the direct effect of Phytogard® on the development of P. nicotianae and P. plurivora and to understand the possible mode of action of the product on these pathogens. Citrus seedlings were sprayed with different concentrations of Phytogard® and then inoculated with the pathogen. We evaluated the diseases incidence, water uptake and the amount of pathogens DNA in the host roots. At the end of the experiment, biochemical assays with citrus seedlings were made. In in vitro experiments, the pathogen mycelium was exposed to increasing concentrations of Phytogard® and mycelial growth, production of fresh mycelium and zoospores by these pathogens were determined. We also evaluated the electrolyte leakage, lipid peroxidation and the β-1,3 glucanase activity in the mycelium exposed to the product. It was also evaluated the hyphae morphology from mycelium treated or not with Phytogard® by using scanning electron microscopy. The results showed that in all concentrations of Phytogard® preventively controled diseases caused by P. nicotianae and P. plurivora in citrus and beech plants, respectively. In citrus, the product changed the activities of some pathogenesis-related proteins, but it is not possible to conclude that the control was mediated by resistance induction. The Phytogard® inhibited mycelial growth and zoospore production by P. nicotianae and P. plurivora. Furthermore, the product modified the hyphae morphology, changed membrane permeability and mycelium cell wall synthesis in the pathogens.

N-Methylthio beta-lactams represent a promising new family of antibacterial agents whose in vitro activity is confined largely to Staphylococcus species, including multidrug-resistant forms of S. aureus. Originally developed in the 1980's for use as synthetic intermediates, N-methylthio beta-lactams have recently been shown in these laboratories to possess intriguing biological properties which are addressed in Chapters I-IV. In terms of the antibacterial activities, the structural features and species specificities exhibited by these compounds are unlike those of any existing family of beta-lactam drugs. The lactams seem to exert their effects intracellularly, requiring passage of the bioactive species through the cellular membrane, rather than acting extracellularly on cell wall components in the manner of penicillin and related antibiotics. The lipophilic nature of these molecules, which lack the polar side chain functionality of all other microbially-active Beta-lactams, suggests the compounds do not target the penicillin binding proteins within bacterial membranes. The most active members of this Beta-lactam class appear to be those bearing an aryl (Ar) substituent at C4 of the ring. The synthesis and structure-activity relationship of these analogues is discussed in Chapter III. Moreover, microscopy and 3H pulse-labeling studies, which are described in Chapter IV, demonstrate that N-methylthio beta-lactams appear to be inhibitors of protein biosynthesis.

Includes vita. / Title from PDF of title page. / Document formatted into pages; contains 173 pages. / Thesis (Ph.D.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: N-Methylthio beta-lactams represent a promising new family of antibacterial agents whose in vitro activity is confined largely to Staphylococcus species, including multidrug-resistant forms of S. aureus. Originally developed in the 1980's for use as synthetic intermediates, N-methylthio beta-lactams have recently been shown in these laboratories to possess intriguing biological properties which are addressed in Chapters I-IV. In terms of the antibacterial activities, the structural features and species specificities exhibited by these compounds are unlike those of any existing family of beta-lactam drugs. The lactams seem to exert their effects intracellularly, requiring passage of the bioactive species through the cellular membrane, rather than acting extracellularly on cell wall components in the manner of penicillin and related antibiotics. / ABSTRACT: The lipophilic nature of these molecules, which lack the polar side chain functionality of all other microbially-active Beta-lactams, suggests the compounds do not target the penicillin binding proteins within bacterial membranes. The most active members of this Beta-lactam class appear to be those bearing an aryl (Ar) substituent at C4 of the ring. The synthesis and structure-activity relationship of these analogues is discussed in Chapter III. Moreover, microscopy and 3H pulse-labeling studies, which are described in Chapter IV, demonstrate that N-methylthio beta-lactams appear to be inhibitors of protein biosynthesis. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

<p>While a number of different proteomic, genomic, and computational approaches exist for the characterization of drug action, each of the experimental approaches developed to date has both strengths and weaknesses. Currently, there is no one "perfect" assay for drug mode-of-action studies. A protocol that could assay all the proteins in the proteome for both direct and indirect binding interactions of drugs would greatly facilitate studies of drug action. Recently, the SPROX (stability of proteins from rates of oxidation) technique was developed as a chemical modification- and mass spectrometry-based strategy for detecting protein-ligand interactions by monitoring the change in thermodynamic stability of proteins upon ligand binding. This is accomplished by monitoring the denaturant dependent oxidation of globally protected methionine residues. The SPROX technique has been interfaced with bottom-up proteomics methods to allow for the proteome-wide analysis of protein-ligand interactions. However, the strategy has been limited by the need to detect and quantify methionine containing peptides in the bottom-up proteomics experiment. </p><p>The work in this dissertation is focused on evaluating the current SPROX protocol, developing modifications to improve proteome coverage, and applying the SPROX platform to two different drug mode-of-action studies. Three main strategies were employed to improve protein coverage. First, a chemo-selective isolation of un-oxidized methionine containing peptides was employed to enrich for methionine containing peptides, and it was found to produce a ~2-fold improvement in proteomic coverage. Second, a pre-fractionation strategy involving the use of isoelectric focusing was employed to decrease sample complexity prior to LC-MS/MS analysis and it was found to generate a ~2-3 fold improvement in proteomic coverage, however when combined with the methionine enrichment strategy the improvement was ~6-fold as the benefits of both were additive. Third, a tryptophan modification strategy was developed that could ultimately expand the number of useful peptides in proteome-wide SPROX experiments to include those that contain tryptophan. Also, investigated was the use of several different mass spectrometer systems (including a bench-top quadrupole and orbitrap system and two different quadrupole time-of-flight systems) in the SPROX protocol. The results of these studies indicate that there is a significant advantage in proteome coverage when faster mass spectrometers are used. The use of high energy collision dissociation (HCD) in the orbitrap system was also more advantageous than the use of collision induced dissociation (CID) in the Q-ToF systems. Regardless of the mass spectrometer used, the major source of error in the SPROX experiment was found to be the random error associated with the LC-MS/MS analysis of isobaric mass tagged peptides. This random error was found to yield a false discovery rate of between 3 and 10% for "hit" peptides in the SPROX experiment. </p><p>The above improvements in the SPROX protocol were used in two protein-ligand binding experiments. One set of experiments involved studies on two small molecules with a specific anti-cancer phenotype in human colon cancer cells. These studies identified 17 proteins as potential "hits" of these two small molecules. After preliminary validation of these proteins, approximately 50% were eliminated as false positives and one protein, p80/nucleophosim, showed consistent data indicating a destabilizing interaction with both small molecules. The destabilization is indicative of an indirect interaction with the small molecules that would be mediated through a protein-protein interaction network. In another set of experiments the breast cancer drug, tamoxifen, and its main, active metabolite, 4-hydroxy tamoxifen, were assayed for binding to the proteins in a yeast cell lysate to better understand its adverse effects on yeast cells. The results of these studies identified ~80 proteins as potential "hits" of these two drugs. After preliminary validation of these proteins, approximately 30% were eliminated as false positives and one protein, SIS1, type II Hsp40, showed consistent data indicative of a direct binding interaction.</p> / Dissertation