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Development of an artificial genetic system capable of Darwinian evolution

Description

The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules…

The principle of Darwinian evolution has been applied in the laboratory to nucleic acid molecules since 1990, and led to the emergence of in vitro evolution technique. The methodology of in vitro evolution surveys a large number of different molecules simultaneously for a pre-defined chemical property, and enrich for molecules with the particular property. DNA and RNA sequences with versatile functions have been identified by in vitro selection experiments, but many basic questions remain to be answered about how these molecules achieve their functions. This dissertation first focuses on addressing a fundamental question regarding the molecular recognition properties of in vitro selected DNA sequences, namely whether negatively charged DNA sequences can be evolved to bind alkaline proteins with high specificity. We showed that DNA binders could be made, through carefully designed stringent in vitro selection, to discriminate different alkaline proteins. The focus of this dissertation is then shifted to in vitro evolution of an artificial genetic polymer called threose nucleic acid (TNA). TNA has been considered a potential RNA progenitor during early evolution of life on Earth. However, further experimental evidence to support TNA as a primordial genetic material is lacking. In this dissertation we demonstrated the capacity of TNA to form stable tertiary structure with specific ligand binding property, which suggests a possible role of TNA as a pre-RNA genetic polymer. Additionally, we discussed the challenges in in vitro evolution for TNA enzymes and developed the necessary methodology for future TNA enzyme evolution.

ContributorsYu, Hanyang (Author) / Chaput, John C (Thesis advisor) / Chen, Julian (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)

Created2013

Ruihong Chang, violin

ContributorsChang, Ruihong (Performer) / ASU Library. Music Library (Publisher)

Created2018-03-29

Paul Schoenfeld and h\s Four souvenirs for violin and piano (1990)

Description

Four Souvenirs for Violin and Piano was composed by Paul Schoenfeld (b.1947) in 1990 as a showpiece, spotlighting the virtuosity of both the violin and piano in equal measure. Each movement is a modern interpretation of a folk or popular genre, re- envisioned over intricate jazz harmonies and rhythms. The…

Four Souvenirs for Violin and Piano was composed by Paul Schoenfeld (b.1947) in 1990 as a showpiece, spotlighting the virtuosity of both the violin and piano in equal measure. Each movement is a modern interpretation of a folk or popular genre, re- envisioned over intricate jazz harmonies and rhythms. The work was commissioned by violinist Lev Polyakin, who specifically requested some short pieces that could be performed in a local jazz establishment named Night Town in Cleveland, Ohio. The result is a work that is approximately fifteen minutes in length. Schoenfeld is a respected composer in the contemporary classical music community, whose Café Music (1986) for piano trio has recently become a staple of the standard chamber music repertoire. Many of his other works, however, remain in relative obscurity. It is the focus of this document to shed light on at least one other notable composition; Four Souvenirs for Violin and Piano. Among the topics to be discussed regarding this piece are a brief history behind the genesis of this composition, a structural summary of the entire work and each of its movements, and an appended practice guide based on interview and coaching sessions with the composer himself. With this project, I hope to provide a better understanding and appreciation of this work.

ContributorsJanczyk, Kristie Annette (Author) / Ryan, Russell (Thesis advisor) / Campbell, Andrew (Committee member) / Norton, Kay (Committee member) / Arizona State University (Publisher)

Created2015

On the origin of the living state

Description

The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a…

The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life.

ContributorsMathis, Cole (Nicholas) (Author) / Walker, Sara I (Thesis advisor) / Davies, Paul CW (Committee member) / Chamberlin, Ralph V (Committee member) / Lachmann, Michael (Committee member) / Arizona State University (Publisher)

Created2018