Hypoallergenic legume crops and food allergy: factors affecting feasibility and risk.

Currently, the sole strategy for managing food hypersensitivity involves strict avoidance of the trigger. Several alternate strategies for the treatment of food allergies are currently under study. Also being explored is the process of eliminating allergenic proteins from crop plants. Legumes are a rich source of protein and are an essential component of the human diet. Unfortunately, legumes, including soybean and peanut, are also common sources of food allergens. Four protein families and superfamilies account for the majority of legume allergens, which include storage proteins of seeds (cupins and prolamins), profilins, and the larger group of pathogenesis-related proteins. Two strategies have been used to produce hypoallergenic legume crops: (1) germplasm lines are screened for the absence or reduced content of specific allergenic proteins and (2) genetic transformation is used to silence native genes encoding allergenic proteins. Both approaches have been successful in producing cultivars of soybeans and peanuts with reduced allergenic proteins. However, it is unknown whether the cultivars are actually hypoallergenic to those with sensitivity. This review describes efforts to produce hypoallergenic cultivars of soybean and peanut and discusses the challenges that need to be overcome before such products could be available in the marketplace.

Antisense Gene Silencing and Bacteriophages as Novel Disinfection Processes for Engineered Systems

The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.

Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.

In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.


For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 + 13.2 and 38.2 + 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.

Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of E. coli K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h-1, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 108 PFU/mL and 108 CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.

In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.

Finally, for an industrial application, the use of phages to inhibit invasive Lactobacilli in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of Lactobacillus plantarum during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.

In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.

Nowhere Landscape, for Clarinets, Trombones, Percussion, Violins, and Electronics and “The Map and the Territory: Documenting David Dunn’s Sky Drift”

1. nowhere landscape, for clarinets, trombones, percussion, violins, and electronics

nowhere landscape is an eighty-minute work for nine performers, composed of acoustic and electronic sounds. Its fifteen movements invoke a variety of listening strategies, using slow change, stasis, layering, coincidence, and silence to draw attention to the sonic effects of the environment—inside the concert hall as well as the world outside of it. The work incorporates a unique stage set-up: the audience sits in close proximity to the instruments, facing in one of four different directions, while the musicians play from a number of constantly-shifting locations, including in front of, next to, and behind the audience.

Much of nowhere landscape’s material is derived from a collection of field recordings

made by the composer during a road trip from Springfield, MA to Douglas, WY along US- 20, a cross-country route made effectively obsolete by the completion of I-90 in the mid- 20th century. In an homage to artist Ed Ruscha’s 1963 book Twentysix Gasoline Stations, the composer made twenty-six recordings at gas stations along US-20. Many of the movements of nowhere landscape examine the musical potential of these captured soundscapes: familiar and anonymous, yet filled with poignancy and poetic possibility.

2. “The Map and the Territory: Documenting David Dunn’s Sky Drift”

In 1977, David Dunn recruited twenty-six musicians to play his work Sky Drift in the

Anza-Borrego Desert in Southern California. This outdoor performance was documented with photos and recorded with four stationary microphones to tape. A year later, Dunn presented the work in New York City as a “performance/documentation,” playing back the audio recording and projecting slides. In this paper I examine the consequences of this kind of act: what does it mean for a recording of an outdoor work to be shared at an indoor concert event? Can such a complex and interactive experience be successfully flattened into some kind of re-playable documentation? What can a recording capture and what must it exclude?

This paper engages with these questions as they relate to David Dunn’s Sky Drift and to similar works by Karlheinz Stockhausen and John Luther Adams. These case-studies demonstrate different solutions to the difficulty of documenting outdoor performances. Because this music is often heard from a variety of equally-valid perspectives—and because any single microphone only captures sound from one of these perspectives—the physical set-up of these kind of pieces complicate what it means to even “hear the music” at all. To this end, I discuss issues around the “work itself” and “aura” as well as “transparency” and “liveness” in recorded sound, bringing in thoughts and ideas from Walter Benjamin, Howard Becker, Joshua Glasgow, and others. In addition, the artist Robert Irwin and the composer Barry Truax have written about the conceptual distinctions between “the work” and “not- the-work”; these distinctions are complicated by documentation and recording. Without the context, the being-there, the music is stripped of much of its ability to communicate meaning.

“Newter”-ing the Nicodemite: Reception of John Calvin’s Quatre sermons (1552) in Sixteenth-Century England

This dissertation examines the publication history of a single work: John Calvin’s 1552 Quatre sermons de M. Jehan Calvin traictans des matières fort utiles pour nostre temps, avec briefve exposition du Pseaume lxxxvii. Overlooked for both its contribution to Calvin’s wider corpus and its surprising popularity in English translation, successive editions of Quatre sermons display how Calvin’s argument against the behavior of so-called “Nicodemites” was adapted to various purposes unrelated to refuting religious dissimulation. The present study contributes to research in Calvin’s anti-Nicodemism by highlighting the fruitfulness of focusing on a discrete work and its reception. Borrowing a term (“Newter”) from John Field’s 1579 translation of Quatre sermons, this study’s title adumbrates its argument. English translators capitalized on the intrinsic malleability of a nameless and faceless opponent, the Nicodemite, and the adaptability of Quatre sermons’ genre as a collection of sermons to reshape—or, if you will, disfigure—both Calvin’s original foes and his case against them to advance various new agenda. Yet they were not the first to use the reformer’s sermons this way. They could have learned this from Calvin himself.

My examination of Quatre sermons opens by setting the work in the context of Calvin’s other writings and his political situation (Introduction, chapters one and two). Calvin’s unrelenting literary assault on French Nicodemism over three decades has long been recognized for its consistency and negativity. Yet scholars have tended to neglect how Calvin’s polemic against religious dissimulation could exhibit significant flexibility according to the needs of his context. Whereas Calvin’s preface promises simply to revisit his previous argument against participation in the Mass, his approach to Nicodemism in Quatre sermons seems adapted to accomplish goals beyond decrying false worship, offering a carefully-crafted apology for Calvin’s pastoral authority directed at his political situation. Repeatedly emphasizing God’s purpose to bless his children through the ministry of a rightly-ordered church, Quatre sermons marks a shift in Calvin’s anti-Nicodemite rhetoric away from purely negative critique, stressing instead God’s provision of spiritual nurture via political exile. Read in light of Calvin’s 1552 context, two audiences emerge: sermons ostensibly targeting believers in France who hid their faith also appear especially designed to silence Calvin’s foes in Geneva.

The remainder of the study examines the reception of Quatre sermons in the rapidly shifting religious and social contexts of Marian and Elizabethan England, where it appeared in more unique editions than any of Calvin’s writings besides the Institutio and the reformer’s 1542/45 Genevan Catechism. Calvin’s anti-Nicodemism has not been examined for its distinct contribution to the overall English reception of his thought. Five English versions of Quatre sermons appeared between 1553 and 1584—four of these under a Protestant queen, a situation quite different from the French context Calvin addressed. After situating Calvin’s position within the currents of Tudor Protestant anti-Nicodemism (chapter three), I place each of the five translations in its particular context, investigating prefaces, appendices, marginalia, and translation methods to discover how and why individuals used Quatre sermons (chapters four to six). Like Calvin in 1552, those who brought Quatre sermons to English readers were not primarily concerned with Nicodemism. Rather, the malleability of Calvin’s Nicodemite as polemical opponent and the flexibility of Quatre sermons as a sequence of discrete, interrelated parts made it popular with those eager to press Calvin into the service of a variety of diverse goals he could not have imagined, including turning his anti-Nicodemism against fellow members of the English church.