Thesis (doctoral)--Lund University, 1997. / Added t.p. with thesis statement inserted.

Thesis (Ph. D.)--Illinois State University, 1999. / Title from title page screen, viewed July 20, 2006. Dissertation Committee: Brian J. Wilkinson (chair), Radheshyam K. Jayaswal, Alan J. Katz, Anthony J. Otsuka, David L. Williams. Includes bibliographical references and abstract. Also available in print.

This dissertation documents the development of an environmental framework for monitoring antimicrobial resistance gene (ARG) dissemination in the aquatic environment. The work opens with a review of the relevant literature and outlines the importance of an environmental framework for monitoring ARG dissemination as part of antimicrobial resistance risk assessments. The ability to interrogate sequencing data quickly and easily for the presence of ARGs is crucial in order to facilitate their monitoring in the environment. As current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria in the environment were limited in their effectiveness and scope, the dissertation begins by describing the design and implementation of a Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally-acquired ARGs in raw sequencing data. The suitability of metagenomic methods for monitoring the ARG content of effluents from faecal sources was then assessed via a pilot study of a river catchment. Novel metagenomes generated from effluents entering the catchment were interrogated for ARGs. The relative abundance of ARGs in effluents were determined to be higher relative to the background environment, as were sequences relating to human and animal pathogens and mobile genetic elements. Thus, effluents were implicated in the dissemination of ARGs throughout the aquatic environment. To determine if ARGs were potentially in use in the environment, the expression of ARGs within effluents was then evaluated across a series of longitudinal samples through the use of metatranscriptomics, and the presence of potential environmental antimicrobial selection pressures was examined. This demonstrated that the abundance of ARGs, as well as antimicrobial usage at the effluent source, was correlated with the transcription of ARGs in aquatic environments. The work described in this dissertation has also found that horizontally transmitted ARGs were present in pathogenic endospore-forming bacteria commonly found across the aquatic environment, potentially providing a mechanism for ARG persistence in the environment. Finally, these findings were integrated into a universal framework for monitoring ARG dissemination in aquatic environments and used to highlight the developments required to incorporate this framework into future environmental ARG research and to facilitate antimicrobial resistance risk assessments.

The introduction of glyphosate-resistant (GR) crops in the late 1990s changed the way producers used herbicides to control weeds. Since the introduction of GR crops producers have relied on glyphosate alone for weed control instead of utilizing multiple modes of action for weed control. This over-reliance resulted in several weed species developing resistance to glyphosate. This has resulted in organizations from the public and private sector questioning the sustainability of GR cropping systems. Researchers from Illinois, Indiana, Iowa, Mississippi, Nebraska, and North Carolina established 156 onarm trials to determine the sustainability of GR cropping systems. The objectives of this study were: to determine the economics of a university weed resistance best management practice (BMP) versus a producers’ normal production practice; to evaluate when a producer that is risk neutral (profit maximizing) or risk averse should adopt a weed resistance BMP; and to compare the influences of using a university weed resistance BMP to a producer’s normal production practice on the 27 most common weed species in Mississippi. In all instances, the university weed resistance BMP utilized multiple modes of action in conjunction with glyphosate. A university weed resistance BMP can provide the same level of control on 27 of the most common weeds in Mississippi that a producer has become accustomed to with a glyphosate alone system, while delaying or controlling GR weeds. A university weed resistance BMP resulted in an increase in weed control cost, but similar yields and economic returns when compared to a producer’s normal production practice. Rotating a GR crop with a different GR crop resulted in higher economic returns when compared to a continuous GR cropping system or a GR crop followed by a non-GR crop rotation. Producers are often reluctant to adopt a weed resistance BMP because of the perceived increased cost for weed control. A risk neutral or risk averse producer should adopt a weed resistance BMP and feel confident that their decision will provide weed control equivalent to a glyphosate alone weed control program before resistance developed, delay or control GR weeds and be economically sound.

A survey was conducted by phone to nearly 1,200 growers in six states (Illinois, Indiana, Iowa, Mississippi, Nebraska, and North Carolina) in 2005. The survey measured producers’ cropping history, perception of glyphosate-resistant (GR) weeds, past and present weed pressure, tillage practices, and herbicide use as affected by the adoption of GR crops. The objectives of this study were to determine the effect of GR crop use on producers’ tillage practices; changes in herbicide use patterns after adoption of a GR crop; effect of grower awareness of GR weeds on sources of information growers’ use; and growers’ perceptions on resistance management based on knowledge of GR weeds in their farming operation. The adoption of GR cropping systems contributed to large increases in the percentage of growers using no-till and reduced-till systems. Tillage intensity declined more in continuous GR cotton and GR soybean (45 and 23%, respectively) than in rotations that included GR corn or non-GR crops. Tillage intensity declined more in the states of Mississippi and North Carolina than in the other states, with 33% of the growers in these states shifting to more conservative tillage practices after the adoption of a GR crop. This was in part due to the lower amount of conservation tillage adoption in these states prior to GR crop availability. With respect to herbicide use patterns, frequently used herbicides for fall applications were 2,4-D and glyphosate; these herbicides were often used for preplant, burndown weed control in the spring. As expected, crop rotations using GR crops had a high percentage of respondents that made one to three POST applications of glyphosate per year. Overall, glyphosate use has continued to increase, with concomitant decreases in utilization of other herbicides. Concerning grower awareness of GR weeds and perceptions of resistance management in 2005, the majority of the growers (88%) were aware of a weed’s potential to develop resistance to glyphosate, while 44% were aware of state-specific, documented cases of glyphosate weed resistance. Growers that have had experience with GR weeds were more knowledgeable about resistance management practices that could be used to mitigate them.

Anthracnose, incited by Colletotrichum cereale, is a destructive disease of physiologically stressed creeping bentgrass putting greens in Mississippi and Alabama. Anthracnose severity and frequency of occurrence have increased over the past 15 years, and fungicide resistance may have had a role in the increase. In vitro bioassays were performed to evaluate thiophanate methyl and azoxystrobin against C. cereale isolates exposed to the fungicides and baseline isolates that had not been exposed to either fungicide. All isolates collected from creeping bentgrass were uninhibited by both fungicides at discriminatory doses. Partial nucleotide sequences of the â-tubulin 2 (thiophanate methyl) or cytochrome b (azoxystrobin) gene was compared to confirm fungicide resistance. Thiophanate methyl resistance was conferred by either a point mutation from glutamic acid to alanine at position 198, or phenylalanine to tyrosine at position 200. Azoxystrobin resistance was conferred by an amino acid point mutation from glycine to alanine at position 143.

In this paper, I will argue against the position of Carol Hay, who asserts that the oppressed have an obligation against oppression and that the bare minimum of this obligation is to resist internally. I will demonstrate that resisting internally leaves space for the oppressed to affirm the oppressors' false beliefs. Affirming the oppressor's false belief causes the oppressed person to disrespect themself. In order to understand why we must first understand what things contribute to our self-respect. Our ability to respect ourselves depends on many factors, but I will focus on two specifically. The first is our internal/self-image; this is how we see ourselves. The second is our external image; this is how we think people see us. One way we can disrespect ourselves is by causing conflict between these two elements, which undermines our self-respect. Hay's account is grounded on the oppressed person respecting themself. Therefore, if an oppressed person can disrespect themself while meeting the bare requirements of the duty to resist oppression, then we need to reconsider the bare minimum of the obligation to resist oppression. / Master of Arts / In this paper, I will argue against the position of Carol Hay, who asserts that the oppressed have an obligation against oppression and that the bare minimum of this obligation is to resist internally. I will demonstrate that resisting internally leaves space for the oppressed to affirm the oppressors' false beliefs. Affirming the oppressor's false belief causes the oppressed person to disrespect themself. In order to understand why we must first understand what things contribute to our self-respect. Our ability to respect ourselves depends on many factors, but I will focus on two specifically. The first is our internal/self-image; this is how we see ourselves. The second is our external image; this is how we think people see us. One way we can disrespect ourselves is by causing conflict between these two elements, which undermines our self-respect. Hay's account is grounded on the oppressed person respecting themself. Therefore, if an oppressed person can disrespect themself while meeting the bare requirements of the duty to resist oppression, then we need to reconsider the bare minimum of the obligation to resist oppression.

Proteus mirabilis PM13 is a well characterized chloramphenicol-sensitive isolate which spontaneously gives rise to resistant colonies on solid media containing chloramphenicol (50ug/ml) at a plating efficiency of between 10-4 and 10-5 per cell per generation. When a chloramphenicol resistant colony is grown in liquid medium in the absence of the antibiotic for I50 generations a population of predominantly sensitive cells arises. The cat gene responsible for the phenomenon is chromosomal, and has been cloned from P.mirabilis PMI3 with DNA prepared from cells grown in the absence or the presence of chloramphenicol. Recombinant plasmids which confer resistance to chloramphenicol carry an 8.5-kb PstI fragment irrespective of the source of host DNA. The location of The cat gene within the PstI fragment was determined by Southern blotting with a cat consensus 'active - site' oligonucleotide (5'-CCATCACAGACGGCATGATG-3') corresponding to the expected amino acid sequence of the active site region of chloramphenicol acetyltransferase. DNA sequence analysis has revealed a high degree of homology between the P. mirabllls cat -gene and the type I ca-t variant (Tn9), 76% at the amino acid level and 73% when nucleotides in the coding sequence are compared. The mechanism for the appearance and disappearance of chloramphenicol resistance in P. mirabilis appears to be associated with a host-specific trans-acting element which controls cat gene expression. A precedent for such a control network is given by phase variation in Salmonella typhimurium, where an invertible DNA segment controls the transcription of a trans-acting regulatory element. A comparison of the 5' regions of the S.typhimurium flagellin genes in and H2, which are alternately expressed by a flip-flop control mechanism with the 5' region of P.mirabilis cat show blocks of homology. Whether or not this homology is significant in the regulation of cat gene expression has not been determined.

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