Matching Items (33)
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- All Subjects: Linguistics
- All Subjects: Synthetic Biology
- Creators: Pruitt, Kathryn
- Status: Published
Description
Arabic is widely known for the lack of copulas in nominal sentences in the present tense. Arabic employs a copula ‘kana’ in the past and future tenses. However, in some constructions the presence of a third person pronoun is necessary for the purpose of emphasis or ambiguity reduction. The data investigated in this thesis was from Classical Arabic, Standard Arabic, and the Western Saudi ‘Hijazi’ dialect. The thesis briefly discussed the grammaticalization of a transitive verb to a non-present tense copula in Classical Arabic. In addition, the thesis discussed the process of copularization that was a result of grammaticalization of the demonstrative third person pronoun ‘huwa’ to a present tense copula in Standard Arabic. It was shown that the pronoun went through a process of reanalysis from the specifier to the head position of PredP driven by Feature Economy and the Head Preference Principle. The result was the loss of the person feature. The new copula developed and attached to the negative particle ‘ma’ in the Hijazi dialect losing all its phi-features. These phenomena are known as the copula and negative cycles, respectively. The analysis was based on the Generative Grammar framework and the Minimalist program. This study attempted to shed light on Arabic copulas and contribute to more understanding of the use of these copulas in question and negative constructions. It may also help in typological studies, which may lead to a better understanding of the linguistic theory and the language faculty.
ContributorsAlsaeedi, Mekhlid Owaidh M (Author) / Gelderen, Elly van (Thesis advisor) / Pruitt, Kathryn (Committee member) / Adams, Karen (Committee member) / Arizona State University (Publisher)
Created2015
Description
ABSTRACT
The absence of the consonant sound /p/ in Libyan Arabic leads Libyan speakers of English to pronounce /p/ as /b/. This study examines how Libyan Arabic speakers distinguish the English /p/ and /b/ in their production of L2 English. The study also examines the effect of the production contexts and the learning environment on two groups of Libyan Arabic speakers' attainment of the English /p/ in the USA and Libya. The study collected voice recordings of word-initial /p/ and /b/ in isolated-words, minimal pairs, and sentences in English from both Libyan Arabic speakers and American English speakers. The study also collected Libyan Arabic stop consonants /b/, /t/, /d/, /k/, and /g/ from the Libyan participants. The voice recording data were collected using the WhatsApp mobile application from all participants and the Libyan Arabic participants were also asked to fill an online survey. Using voice onset time (VOT) as a measurement tool, this study measured the English and Libyan Arabic data through Praat software. The findings show that most Libyan Arabic participants distinguish between /p/ and /b/, but they did not have as high VOT averages as the American participants' /p/. It also reveals that the production context, especially in minimal pairs and sentence contexts, has an effect on their participants' production. However, the learning environment does not have an effect on the Libyan participants' pronunciation of /p/ in this study.
The absence of the consonant sound /p/ in Libyan Arabic leads Libyan speakers of English to pronounce /p/ as /b/. This study examines how Libyan Arabic speakers distinguish the English /p/ and /b/ in their production of L2 English. The study also examines the effect of the production contexts and the learning environment on two groups of Libyan Arabic speakers' attainment of the English /p/ in the USA and Libya. The study collected voice recordings of word-initial /p/ and /b/ in isolated-words, minimal pairs, and sentences in English from both Libyan Arabic speakers and American English speakers. The study also collected Libyan Arabic stop consonants /b/, /t/, /d/, /k/, and /g/ from the Libyan participants. The voice recording data were collected using the WhatsApp mobile application from all participants and the Libyan Arabic participants were also asked to fill an online survey. Using voice onset time (VOT) as a measurement tool, this study measured the English and Libyan Arabic data through Praat software. The findings show that most Libyan Arabic participants distinguish between /p/ and /b/, but they did not have as high VOT averages as the American participants' /p/. It also reveals that the production context, especially in minimal pairs and sentence contexts, has an effect on their participants' production. However, the learning environment does not have an effect on the Libyan participants' pronunciation of /p/ in this study.
ContributorsGarib, Ali A. A (Author) / Pruitt, Kathryn (Thesis advisor) / Renaud, Claire (Committee member) / González López, Verónica (Committee member) / Arizona State University (Publisher)
Created2014
Description
The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli.
1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin.
2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists.
ContributorsDaer, René (Author) / Haynes, Karmella (Thesis advisor) / Brafman, David (Committee member) / Nielsen, David (Committee member) / Kiani, Samira (Committee member) / Arizona State University (Publisher)
Created2017
Description
This dissertation investigates the precise degree to which prosody and syntax are related. One possibility is that the syntax-prosody mapping is one-to-one (“isomorphic”) at an underlying level (Chomsky & Halle 1968, Selkirk 1996, 2011, Ito & Mester 2009). This predicts that prosodic units should preferably match up with syntactic units. It is also possible that the mapping between these systems is entirely non-isomorphic, with prosody being influenced by factors from language perception and production (Wheeldon & Lahiri 1997, Lahiri & Plank 2010). In this work, I argue that both perspectives are needed in order to address the full range of phonological phenomena that have been identified in English and related languages, including word-initial lenition/flapping, word-initial segment-deletion, and vowel reduction in function words, as well as patterns of pitch accent assignment, final-pronoun constructions, and the distribution of null complementizer allomorphs. In the process, I develop models for both isomorphic and non-isomorphic phrasing. The former is cast within a Minimalist syntactic framework of Merge/Label and Bare Phrase Structure (Chomsky 2013, 2015), while the latter is characterized by a stress-based algorithm for the formation of phonological domains, following Lahiri & Plank (2010).
ContributorsKruger, William Wriley (Author) / Gelderen, Elly van (Thesis advisor) / Carnie, Andrew (Committee member) / Pruitt, Kathryn (Committee member) / Arizona State University (Publisher)
Created2019
Description
Synthetic manipulation of chromatin dynamics has applications for medicine, agriculture, and biotechnology. However, progress in this area requires the identification of design rules for engineering chromatin systems. In this thesis, I discuss research that has elucidated the intrinsic properties of histone binding proteins (HBP), and apply this knowledge to engineer novel chromatin binding effectors. Results from the experiments described herein demonstrate that the histone binding domain from chromobox protein homolog 8 (CBX8) is portable and can be customized to alter its endogenous function. First, I developed an assay to identify engineered fusion proteins that bind histone post translational modifications (PTMs) in vitro and regulate genes near the same histone PTMs in living cells. This assay will be useful for assaying the function of synthetic histone PTM-binding actuators and probes. Next, I investigated the activity of a novel, dual histone PTM binding domain regulator called Pc2TF. I characterized Pc2TF in vitro and in cells and show it has enhanced binding and transcriptional activation compared to a single binding domain fusion called Polycomb Transcription Factor (PcTF). These results indicate that valency can be used to tune the activity of synthetic histone-binding transcriptional regulators. Then, I report the delivery of PcTF fused to a cell penetrating peptide (CPP) TAT, called CP-PcTF. I treated 2D U-2 OS bone cancer cells with CP-PcTF, followed by RNA sequencing to identify genes regulated by CP-PcTF. I also showed that 3D spheroids treated with CP-PcTF show delayed growth. This preliminary work demonstrated that an epigenetic effector fused to a CPP can enable entry and regulation of genes in U-2 OS cells through DNA independent interactions. Finally, I described and validated a new screening method that combines the versatility of in vitro transcription and translation (IVTT) expressed protein coupled with the histone tail microarrays. Using Pc2TF as an example, I demonstrated that this assay is capable of determining binding and specificity of a synthetic HBP. I conclude by outlining future work toward engineering HBPs using techniques such as directed evolution and rational design. In conclusion, this work outlines a foundation to engineer and deliver synthetic chromatin effectors.
ContributorsTekel, Stefan (Author) / Haynes, Karmella (Thesis advisor) / Mills, Jeremy (Committee member) / Caplan, Michael (Committee member) / Brafman, David (Committee member) / Arizona State University (Publisher)
Created2019
Description
ABSTRACT
This dissertation investigates the copular/locative and existential predications in Arabic. The main focus is on the typology and syntax of the existential predications. The negation of such predications reveals interesting results. The Negative Existential Cycle (Croft, 1991) is a model that describes the process by which verbal negators arise from existential negators. I discuss data of existentials and negative existentials from Standard Arabic, Saudi Arabic dialect, and Gulf Pidgin Arabic.
I argue for canonical vs. non-canonical word orders in copular/locative and existential sentences, respectively. I examine the grammaticalization path of the existentials from their locative content in each language form. Then, I investigate the syntactic word order of the copular/locative and existential constructions in each variety.
I investigate the negation of the existential construction in each variety. First, Standard Arabic is shown to be at stage A in the Negative Existential Cycle. The Hijazi and Najdi Arabic spoken by elders show further developments. Hijazi Arabic appears to be at stage B, while Najdi Arabic appears to be at stage B and an intermediate stage B ~ C. Second, I show that in Saudi Arabic the negative existential has been extended to the verbal domain. Saudi Arabic is at stages A, B, and B ~ C, while Qassimi Arabic is at stages A and B. Third, I show that the existential construction in Gulf Pidgin Arabic is only negated by the negative existential predicate, while the verbal sentences are negated by the negative existential and the verbal negator. Therefore, Gulf Pidgin Arabic is at stages B and C in the Negative Existential Cycle.
Finally, I discuss the syntax of copular/locative and existential predications in each variety. I propose a unified syntactic structure. Existential and possessive predications are analyzed as inverse copular sentences (Moro, 1997) as opposed to the canonical copular/locative sentences. The unified structure accounts for the agreement facts, such as partial vs. full agreement in existential and copular/locative predications, respectively.
The data investigated here will contribute to Arabic comparative and historical linguistics. More Arabic dialects’ data is needed to determine their stages in the Negative Existential Cycle.
This dissertation investigates the copular/locative and existential predications in Arabic. The main focus is on the typology and syntax of the existential predications. The negation of such predications reveals interesting results. The Negative Existential Cycle (Croft, 1991) is a model that describes the process by which verbal negators arise from existential negators. I discuss data of existentials and negative existentials from Standard Arabic, Saudi Arabic dialect, and Gulf Pidgin Arabic.
I argue for canonical vs. non-canonical word orders in copular/locative and existential sentences, respectively. I examine the grammaticalization path of the existentials from their locative content in each language form. Then, I investigate the syntactic word order of the copular/locative and existential constructions in each variety.
I investigate the negation of the existential construction in each variety. First, Standard Arabic is shown to be at stage A in the Negative Existential Cycle. The Hijazi and Najdi Arabic spoken by elders show further developments. Hijazi Arabic appears to be at stage B, while Najdi Arabic appears to be at stage B and an intermediate stage B ~ C. Second, I show that in Saudi Arabic the negative existential has been extended to the verbal domain. Saudi Arabic is at stages A, B, and B ~ C, while Qassimi Arabic is at stages A and B. Third, I show that the existential construction in Gulf Pidgin Arabic is only negated by the negative existential predicate, while the verbal sentences are negated by the negative existential and the verbal negator. Therefore, Gulf Pidgin Arabic is at stages B and C in the Negative Existential Cycle.
Finally, I discuss the syntax of copular/locative and existential predications in each variety. I propose a unified syntactic structure. Existential and possessive predications are analyzed as inverse copular sentences (Moro, 1997) as opposed to the canonical copular/locative sentences. The unified structure accounts for the agreement facts, such as partial vs. full agreement in existential and copular/locative predications, respectively.
The data investigated here will contribute to Arabic comparative and historical linguistics. More Arabic dialects’ data is needed to determine their stages in the Negative Existential Cycle.
ContributorsAlsaeedi, Mekhlid (Author) / Gelderen, Elly van (Thesis advisor) / Adams, Karen (Committee member) / Pruitt, Kathryn (Committee member) / Veselinova, Ljuba (Committee member) / Arizona State University (Publisher)
Created2019
Description
Transgene expression in mammalian cells has been shown to meet resistance in the form of silencing due to chromatin buildup within the cell. Interactions of proteins with chromatin modulate gene expression profiles. Synthetic Polycomb transcription factor (PcTF) variants have the potential to reactivate these silence transgenes as shown in Haynes & Silver 2011. PcTF variants have been constructed via TypeIIS assembly to further investigate this ability to reactive transgenes. Expression in mammalian cells was confirmed via fluorescence microscopy and red fluorescent protein (RFP) expression in cell lysate. Examination of any variation in conferment of binding strength of homologous Polycomb chromodomains (PCDs) to its trimethylated lysine residue target on histone three (H3K27me3) was investigated using a thermal shift assay. Results indicate that PcTF may not be a suitable protein for surveying with SYPRO Orange, a dye that produces a detectable signal when exposed to the hydrophobic domains of the melting protein. A cell line with inducible silencing of a chemiluminescent protein was used to determine the effects PcTF variants had on gene reactivation. Results show down-regulation of the target reporter gene. We propose this may be due to PcTF not binding to its target; this would cause PcTF to deplete transcriptional machinery in the nucleus. Alternatively, the CMV promoter could be sequestering transcriptional machinery in its hyperactive transcription of PcTF leading to widespread down-regulation. Finally, the activation domain used may not be appropriate for this cell type. Future PcTF variants will address these hypotheses by including multiple Polycomb chromodomains (PCDs) to alter the binding dynamics of PcTF to its target, and by incorporating alternative promoters and activation domains.
ContributorsGardner, Cameron Lee (Author) / Haynes, Karmella (Thesis director) / Stabenfeldt, Sarah (Committee member) / Barrett, The Honors College (Contributor) / Department of Finance (Contributor) / Harrington Bioengineering Program (Contributor)
Created2015-05
Description
Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Synthetic biology is an emerging engineering disciple, which designs and controls biological systems for creation of materials, biosensors, biocomputing, and much more. To better control and engineer these systems, modular genetic components which allow for highly specific and high dynamic range genetic regulation are necessary. Currently the field struggles to demonstrate reliable regulators which are programmable and specific, yet also allow for a high dynamic range of control. Inspired by the characteristics of the RNA toehold switch in E. coli, this project attempts utilize artificial introns and complementary trans-acting RNAs for gene regulation in a eukaryote host, S. cerevisiae. Following modification to an artificial intron, splicing control with RNA hairpins was demonstrated. Temperature shifts led to increased protein production likely due to increased splicing due to hairpin loosening. Progress is underway to demonstrate trans-acting RNA interaction to control splicing. With continued development, we hope to provide a programmable, specific, and effective means for translational gene regulation in S. cerevisae.
ContributorsDorr, Brandon Arthur (Author) / Wang, Xiao (Thesis director) / Green, Alexander (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This thesis investigates similarities in the diachronic sound changes found in Eastern Old Japanese dialects and in Ryukyuan languages and tests a hypothesis of language contact. I examine three sound changes attested in the Eastern Old Japanese corpus of Kupchik (2011). These three are denasalization of prenasalized obstruents, the fortition of the labial glide [w] and prenasalized / simple voiced fricative [(n)z], and the irregular raising of Eastern Old Japanese mid vowels. Extralinguistic and linguistic evidence is presented in support of a hypothesis for language contact between 8th century Ryukyuan speakers and Eastern Old Japanese speakers. At present, many assumptions bog down any potential evidence of contact. However, cases where reconstructed Ryukyuan could have donated a form into EOJ do exist. With future research into early Ryukyuan development and the lexicons, phonologies, and syntactic patterns of Ryukyuan languages, more can be said about this hypothesis. Alongside testing a hypothesis of language contact, this thesis can also be viewed as an analysis of Eastern Old Japanese spelling variation of the three changes mentioned above.
ContributorsMakiyama, Alexander Koji (Author) / Pruitt, Kathryn (Thesis advisor) / Adams, Karen (Committee member) / Gelderen, Elly van (Committee member) / Arizona State University (Publisher)
Created2015