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Title: Revisiting methylotrophy : the impact of lanthanides and lanthanide-dependent enzymes on the methylotrophic metabolic network
Creator: Huff, Anna Frances
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "The recent discovery of lanthanide (Ln3+)-dependent enzymes renewed interest in methylotrophs, although the impact of these enzymes is not understood. In Methylobacterium extorquens AM1, the Ca2+ -dependent MxaFI canonically oxidizes methanol to formaldehyde. The tetrahydromethanopterin (H4MPT) pathway oxidizes formaldehyde to formate. Formate is oxidized to CO2 by formate dehydrogenases (FDH) or partially reduced and assimilated. The genome of M. extorquens AM1 codes for three known Ln3+ ...
Show more"The recent discovery of lanthanide (Ln3+)-dependent enzymes renewed interest in methylotrophs, although the impact of these enzymes is not understood. In Methylobacterium extorquens AM1, the Ca2+ -dependent MxaFI canonically oxidizes methanol to formaldehyde. The tetrahydromethanopterin (H4MPT) pathway oxidizes formaldehyde to formate. Formate is oxidized to CO2 by formate dehydrogenases (FDH) or partially reduced and assimilated. The genome of M. extorquens AM1 codes for three known Ln3+ -dependent genes: xoxF, xoxF2, and exaF. XoxF may oxidize both methanol and formaldehyde in some organisms while ExaF demonstrated efficient activity with formaldehyde in the presence of La3+ providing a potential alternative to the H4MPT pathway. RNAseq data provided by Dr. Nathan Good found downregulation of mxa genes and the first gene of the H4MPT pathway, fae, and upregulation of xoxF, xoxF2, and exaF in the presence of La3+ suggesting changes to carbon distribution. I found a sharp decrease in accumulation formaldehyde and fourfold increase in accumulation of formate in the presence of La3+ and hypothesized this was due to the activity of Ln3+ enzymes. I measured the minimum inhibitory concentration (MIC) to methanol metabolism and found decreased sensitivity of a 2206fae mutant from 10 mM to more than 125 mM in the presence of La3+. RNAseq suggested changes to the production of CO2 which I corroborated finding an increased CO2 production of 1.8-fold in the presence of La3+. Together, these data provide the first profile of Ln3+ -dependent methylotrophic metabolism and provides new avenues for research."--Page ii.
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Title: Factors that influence an intern's learning about and enactment of discussion-based teaching
Creator: Meier, Jessica
Date: 2017
Collection: Electronic Theses & Dissertations
Description: This multi-case qualitative study examined the factors that influenced an intern's learning about and implementation of a core practice, discussion-based teaching (DBT) during her two semesters of student teaching. Influenced by theories of how teachers learn about and enact core practices, comparative case studies were conducted involving two cases: (1) an intern and her first mentor teacher and (2) the same intern and her second mentor teacher. Specifically, the purpose of studying each...
Show moreThis multi-case qualitative study examined the factors that influenced an intern's learning about and implementation of a core practice, discussion-based teaching (DBT) during her two semesters of student teaching. Influenced by theories of how teachers learn about and enact core practices, comparative case studies were conducted involving two cases: (1) an intern and her first mentor teacher and (2) the same intern and her second mentor teacher. Specifically, the purpose of studying each case was to understand (a) how the mentor and intern worked together to promote the intern's vision of DBT, (b) the ways in which opportunities for practice influenced the intern's enactment of DBT and (c) how the contextual and biographical factors influenced the intern's implementation and learning about DBT. Data sources included direct observations, semi-structured interviews, and audio-recorded conversations. Cross-case analysis suggested contextual factors were most influential in the intern's enactment of DBT, namely the opportunities for practice and learning community provided by her second mentor teacher. Evidence from the study shows interns can learn core practices such as DBT, but autonomy and exposure are not enough to build complex learning. Interns need to be placed with mentors who provide modeling, targeted feedback and collaboration, and regular opportunities for guided reflection around the core practice. Findings from the study have implications for teacher education programs as they prepare new teachers to enact core practices.
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Title: Incremental processing effects in nominal compounds
Creator: Parrish, Alicia
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Sentence processing shows the effects of a series of continual building, repairing, predicting, accessing, and remembering operations that may be the output of one underlying process or many. Within even smaller phrases such as nominal compounds, we see all of these operations having an effect. What is relatively unknown, though, is how these processes interact with each other in real time as the phrase is build up incrementally. This ERP study, through the use of an Icelandic triple noun...
Show more"Sentence processing shows the effects of a series of continual building, repairing, predicting, accessing, and remembering operations that may be the output of one underlying process or many. Within even smaller phrases such as nominal compounds, we see all of these operations having an effect. What is relatively unknown, though, is how these processes interact with each other in real time as the phrase is build up incrementally. This ERP study, through the use of an Icelandic triple noun compound paradigm that manipulates agreement features on the first and second constituents of the compound, investigates the nature of commitments to a structure and the processes that predict more structure or revise an interpreted structure. The findings are generally in line with models that have a parser make commitments to a structure as soon as possible, and the findings expand on that to say that syntactic mismatch is sufficient to trigger a structural prediction and that a revision of that prediction is identical to the revision of a structure built from incoming lexical items. This study further uses the paradigm to assess the predictions of Gibson's (1998) model of sentence processing that makes use of working memory costs. The study finds that, when incremental commitments are taken into account, we see the effects of syntactic agreement cues modulating working memory effects."--Page ii.
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Title: The Leber Congenital Amaurosis CEP290 cat model : working towards a cure
Creator: Minella, Andrea Louise
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Leber Congenital Amaurosis (LCA) is an early-onset and severe inherited retinaldystrophy. The most commonly implicated gene is the centrosomal 290kDa (CEP290)gene. There are currently no treatments for LCACEP290. Animal models are integral fortreatment safety and efficacy testing, with a feline model for CEP290 retinopathiesshowing promise for this purpose. This model has a spontaneous mutation in CEP290resulting in a progressive retinal degeneration and vision loss. This mutation...
Show moreLeber Congenital Amaurosis (LCA) is an early-onset and severe inherited retinaldystrophy. The most commonly implicated gene is the centrosomal 290kDa (CEP290)gene. There are currently no treatments for LCACEP290. Animal models are integral fortreatment safety and efficacy testing, with a feline model for CEP290 retinopathiesshowing promise for this purpose. This model has a spontaneous mutation in CEP290resulting in a progressive retinal degeneration and vision loss. This mutation alterssplicing and is predicted to result in a truncated protein. CEP290 is integrally involved inthe transport within photoreceptor cells, localizing to the interconnecting cilium.The CEP290 mutant cat ("rdAc") has a milder phenotype than the phenotypemost commonly associated with CEP290 mutations in people. Understanding thereason for this milder phenotype was an important aim of this dissertation. We analyzedthe wild-type and truncated mutant transcript levels and total CEP290 protein levels incat retinal tissue across genotypes (wild-type, heterozygous, homozygous mutant). Ourfindings show that the milder phenotype in mutant cats is likely the result of low-levelproduction of wild-type transcript and protein combined with production of truncatedprotein that we suspect retains some function. These measures can also serve asobjective markers of disease progression or treatment success in future studies.Further objective markers were investigated utilizing spectral-domain opticalcoherence tomography. By analyzing photoreceptor layer thickness (receptor plus/REC+) and the ellipsoid zone (EZ), a zone noted to change with disease in people, weshowed that REC+ thickness and EZ integrity can be used as markers of diseaseprogression. These findings support the cat as a CEP290 model, and show the affectedcats have a degeneration with central retinal sparing as described in human patients.We also developed an in vitro tool by developing primary fibroblast cell culturesfrom skin samples of CEP290 cats. We showed that cilia formation, which involvesCEP290, can be induced, opening the door for future cilia studies. We assessed cilialength as an objective marker of disease, however, no difference was found in cilialength across genotypes. Utilizing this new tool, we tested a CRISPR/Cas-9 genomeediting treatment in an attempt to replace the mutated region with a sequence thatwould direct splicing to the correct location. We achieved high efficiency transduction ofCRISPR components, however, we failed to detect insertion of our chosen sequence.As we work towards a treatment, it is imperative to develop an optimized methodto deliver the treatment to feline photoreceptors. To achieve this aim we tested hybridadeno-associated viral (AAV) vectors, the retinal viral vector of choice, in the wild-typefeline retina. We showed that all serotypes studied, AAV2/2, 2/5, 2/8, and 2/9, transducephotoreceptor cells with AAV2/8 and 2/9 showing higher transduction and faster onset.Interestingly, we found more efficient transduction of cones than rods, an unusualfinding that speaks to the need to use caution when extrapolating across species.It is our hope that these data will help the scientific community move closer totreatments for CEP290 retinopathies. We have added to the understanding of the rdAccat model and determined objective markers, supported the cat as a model, and havemade progress towards a treatment.
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Title: Prevention of environmental-toxicant triggered autoimmunity by consumption of the omega-3 polyunsaturated fatty acid, Docosahexaenoic acid
Creator: Bates, Melissa A.
Date: 2017
Collection: Electronic Theses & Dissertations
Description: While heredity is a primary predisposing factor for autoimmunity, cumulative exposures to environmental factors such as toxic stressors and diet greatly impact the latency and severity of autoimmune diseases such as lupus. The chapters within this dissertation test the hypothesis that dietary DHA prevents activation of autoreactive lymphocytes that establish the lung as a platform to exacerbate systemic autoimmunity after cSiO2 exposure in lupus-prone NZBWF1 mice. Herein, it is demonstrated...
Show moreWhile heredity is a primary predisposing factor for autoimmunity, cumulative exposures to environmental factors such as toxic stressors and diet greatly impact the latency and severity of autoimmune diseases such as lupus. The chapters within this dissertation test the hypothesis that dietary DHA prevents activation of autoreactive lymphocytes that establish the lung as a platform to exacerbate systemic autoimmunity after cSiO2 exposure in lupus-prone NZBWF1 mice. Herein, it is demonstrated that airway exposure to crystalline silica (cSiO2) triggers early loss of self-tolerance in the lung characterized by prolonged elevations in pro-inflammatory cytokines, and strikingly, early infiltration of autoreactive B and T cells into the lung which collectively drive production of autoantibodies that exacerbate systemic autoimmunity and glomerulonephritis in the lupus-prone female NZBWF1 mouse. Supplementing NZBWF1 mouse diets with docosahexaenoic acid (DHA), an ω-3 polyunsaturated fatty acid (PUFA), dose-dependently blocks this triggering in the lung, kidney, and systemic circulation. The anti-inflammatory effects of DHA were evident through ablation of lymphocytic infiltration and reduction of pro-inflammatory cytokines in the lungs that corresponded to reduced serum autoantibodies and cytokine concentrations and accordingly, reduced severity of cSiO2-triggered glomerulonephritis in the kidneys of NZBWF1 mice. To elaborate on these findings, we utilized an integrative approach with quantitative immunohistochemistry, transcriptomics, and targeted proteomics to identify relevant cell populations and putative molecular pathways responsible for cSiO2-driven autoimmunity and targets for the ameliorative effects of DHA. Taken together, the findings in this dissertation establish a model that permits dissection of the countervailing roles of cSiO2 (potentiation) and DHA (attenuation) in initiation and progression of autoimmunity. The results from these studies demonstrate how modification of cellular lipids with the ω-3 fatty acid, DHA, could be harnessed to attenuate lupus and related autoimmune diseases triggered by toxic environmental stressors.
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Title: Characterization of Nannochloropsis Oceanica CCMP1779 grown in light
Creator: Poliner, Eric
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Nannochloropsis is a genus of fast-growing microalgae that have a high lipid content. Nannochloropsis species have a high triacylglycerol (TAG) content and contain a large amount of the omega-3 long-chain polyunsaturated fatty acid, eicosapentaenoic acid (EPA). There is a growing interest in Nannochloropsis species as models for the study of microalga lipid metabolism and as a platform for synthetic biology. Genome sequences are available for several species, and genetic engineering...
Show moreNannochloropsis is a genus of fast-growing microalgae that have a high lipid content. Nannochloropsis species have a high triacylglycerol (TAG) content and contain a large amount of the omega-3 long-chain polyunsaturated fatty acid, eicosapentaenoic acid (EPA). There is a growing interest in Nannochloropsis species as models for the study of microalga lipid metabolism and as a platform for synthetic biology. Genome sequences are available for several species, and genetic engineering techniques are being introduced. In this study, I developed a new generation of transgenic vectors for gene stacking and marker-free gene disruption in Nannochloropsis oceanica CCMP1779. These tools enable gene specific studies and were applied to investigate a lipid biosynthetic pathway that is co-expressed under different light conditions. As for all photosynthetic organisms, light plays an important role in driving metabolism and regulation by photosensing in Nannochloropsis species. Each day photosynthetic organisms must maximize their energy capture during the day and be able to sustain themselves during the night. Nannochloropsis cultures synchronize cell division during a light:dark cycle, with cell division occurring at night, along with the usage of stored metabolites that are accumulated during the day. RNA-sequencing measures global transcript abundance, that ultimately might lead to changes in enzymatic activity, metabolism and physiology. I investigated the role of transcriptional regulation on metabolite levels and cell physiology using RNA-sequencing. In the study I found coordination between cell growth, triacylglycerol and hexose content, and transcript abundance of the genes in relevant pathways. Briefly anabolic processes were phased to the light period and catabolic processes phased to the dark period. Furthermore, promoters for transgenic expression were chosen based on transcriptomic measurements gathered in this study. Eicosapentaenoic acid is a high-value fatty acid that is a necessary nutrient for humans, with a biosynthetic pathway consisting of 5 fatty acids desaturases (FADs) and a fatty acid elongase (FAE). Interestingly, the genes of this biosynthetic pathway were strongly co-expressed during light:dark cycles, and I set out to characterize the pathway. Expression of isolated cDNAs in S. cerevisiae resulted in the production of the expected long-chain polyunsaturated fatty acids (LC-PUFAs), and ultimately EPA when all 4 LC-PUFA FADs and an FAE were co-expressed. Selected FADs were overexpressed in N. oceanica and resulted in increased LC-PUFA and EPA content. CRISPR/Cas9 is a potent tool for gene editing. The RNA-guided nuclease, Cas9, was tested as a fusion with green fluorescent protein (GFP) and NanoLuciferase (Nlux) reporters, and the Cas9-Nlux fusion was readily detectable for efficient screening of transformants for recombinant protein production. Single-guide RNAs (sgRNAs) when fused to 5’ and 3’ self-cleaving ribozymes efficiently targeted genes. The two components of the system were expressed from a bidirectional promoter. N. oceanica is capable of expressing transgenes from circular episomal DNA, and an episomal CRISPR construct was generated. The nitrate reductase gene was targeted and the mutants generated with frame-shifts in the coding sequence were unable to grow on nitrate. When antibiotic selection was removed, the episome was lost, and a mutant line that was “cured” of the episome was isolated. These tools are being utilized for gene specific studies in N. oceanica.
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Title: Preservice teachers' self-efficacy, intent to use, and technology integration descriptions : a study of technology learning experiences and their effects
Creator: Amalfitano, Tracy Ellen Russo
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Today’s teachers are charged with transforming education through technology, providing all learners with access and meaningful experiences across content areas in ways of teaching and learning they may never have experienced themselves. This dissertation examines the effect of increasing preservice teachers’ prior personal learning experiences using digital instructional tools has on their self-efficacy, intent to use, levels of technology integration, and instructional features described in...
Show moreToday’s teachers are charged with transforming education through technology, providing all learners with access and meaningful experiences across content areas in ways of teaching and learning they may never have experienced themselves. This dissertation examines the effect of increasing preservice teachers’ prior personal learning experiences using digital instructional tools has on their self-efficacy, intent to use, levels of technology integration, and instructional features described in context of their future teaching using similar digital tools. Set within an educational technology teacher preparation course, the aim of this quasi-experimental study was to describe the effects resulting from intentional pedagogical changes using existing course content and assessments for teacher technology preparation improvement. Interventions to increase personal learning experiences using three focal tools (Interactive PowerPoint, Webquests, and Digital Storytelling) were administered in three of six course sections prior to participants completing course activities using these tools to create teaching materials. Surveys were administered in all sections to investigate changes in participants’ overall digital self-efficacy and their stated intent to use the focal tools. Written reflections about possible future focal tool uses in teaching and technology integrated lesson plans written at the end of the course were analyzed to examine differences in technology integration levels using the Replacement, Amplification, and Transformation framework (Hughes, Thomas, & Scharber, 2006). Additionally, key instructional features in the written descriptions (student learning, instructional methods, curriculum/content, and structural factors) were investigated. Students in both the control and treatment sections showed significant growth in computer self-efficacy during the course. The intervention changes to increase prior personal learning experiences did not result in a significant difference between groups in self-efficacy growth or stated intent-to-use. A significant difference between treatment and control groups was found in the described integration levels for Webquest as well as the number of instructional features described related to structural factors for Interactive PowerPoint. No significant differences between groups were found in the descriptions of future use for Digital Storytelling or the final Technology Integrated Lesson Plan.
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Title: Examining organizational supports within domestic violence programs that support or hinder responses to reproductive coercion
Creator: McGirr, Sara
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Reproductive coercion (RC) is a newly identified but commonly experienced form of domestic violence (DV) with serious potential consequences for women's health and well-being. Despite the high prevalence of RC against DV survivors, initial reports suggest that few DV advocates regularly engage in RC-related practices with their clients. In order to better understand the factors that may be impeding advocates' RC-responsiveness, the study examined data collected via a brief online survey of...
Show moreReproductive coercion (RC) is a newly identified but commonly experienced form of domestic violence (DV) with serious potential consequences for women's health and well-being. Despite the high prevalence of RC against DV survivors, initial reports suggest that few DV advocates regularly engage in RC-related practices with their clients. In order to better understand the factors that may be impeding advocates' RC-responsiveness, the study examined data collected via a brief online survey of more than 300 domestic violence advocates across the U.S. and its territories. Results identified critical barriers and facilitators to RC-responsive practice in DV organizations on the intrapersonal and organizational ecological levels. While intrapersonal factors (levels of comfort discussing sexuality and comfort discussing reproductive health) influenced advocates' frequency of universal and targeted RC practice, the level of RC-responsive supports provided by advocates' organizations was much more impactful. In addition to supporting the assertion that intervention on multiple ecological levels has the greatest potential for successful change in professionals' behavior, the study's results also provide initial insight into a minimum level of organizational supports that may be necessary to promote more frequent RC-responsive practice in DV organizations. This guidance may prove useful for agencies aiming to improve their RC-responsiveness; by focusing on those factors, DV programs and their staff will ultimately be better prepared and better able to support survivors of RC in regaining their reproductive control.
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Title: Two sides on "normal" : a comparison of eight views on U.S. rapprochement with Vietnam, 1989-1995
Creator: Clason, Nathan Robert
Date: 2017
Collection: Electronic Theses & Dissertations
Description: ABSTRACTTWO SIDES ON "NORMAL:" A COMPARISON OF EIGHT VIEWS ON U.S. RAPPROCHEMENT WITH VIETNAM, 1989-1995ByNathan Robert Clason This thesis is a comparative study of the views of eight entities regarding the prospect of normalization of diplomatic relations between the United States and the Socialist Republic of Vietnam from 1989-1995. It first describes the views and actions of five entities in favor of normalization. These include the four US presidential administrations from Carter to...
Show moreABSTRACTTWO SIDES ON "NORMAL:" A COMPARISON OF EIGHT VIEWS ON U.S. RAPPROCHEMENT WITH VIETNAM, 1989-1995ByNathan Robert Clason This thesis is a comparative study of the views of eight entities regarding the prospect of normalization of diplomatic relations between the United States and the Socialist Republic of Vietnam from 1989-1995. It first describes the views and actions of five entities in favor of normalization. These include the four US presidential administrations from Carter to Clinton, the Vietnamese Communist Party, the Senate Select Committee on POW/MIA Affairs (1991-1993), US Senators John McCain and John Kerry, and US businesses. It then examines the views and actions of three entities opposed to normalization. These include Ann Mills Griffiths, the Executive Director of the National League of POW/MIA Families; Texas billionaire Ross Perot; and politicians such as Robert Dornan and Vietnamese Americans from Orange County, California. By using a comparative approach, this thesis identifies several strange political alliances and enmities that would not have been clear in a more linear history. It includes a review of Vietnamese Communist Party documents that challenges some of the conclusions of the earliest diplomatic histories about normalization. It uses primary sources from key Senate Hearings to challenge elements of cultural histories about the myth of live US prisoners of war abandoned in Southeast Asia, and it personalizes the views of Ann Mills Griffiths and some Vietnamese Americans to give better context to their ardent opposition to normalization.
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Title: Holding hands with death : ethical promises and political failures of our humanitarian present
Creator: Ivanovic, Mlado
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Taking the point of departure in the urgent social challenges tied with current failures of humanitarian management and inclusion of Non-Western others in "developed" Western societies, this dissertation explores the ways in which representation and knowledge about human suffering guides our (un)willingness to act ethically with respect to vulnerable strangers and the difficult conditions they endure." -- Abstract.

Title: Blurring boundaries within mathematics education : prospective K-8 teachers interrogating intersectional identities, narratives, and positionings in out-of-school contexts
Creator: Guzmán, Lynette DeAun
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Mathematics teacher noticing as a pedagogical practice--attending to, interpreting, and responding to children's mathematical thinking--is growing within mathematics education communities. Much of the research literature primarily focuses on supporting teacher noticing of children's mathematical thinking within classroom contexts, such as analyzing classroom artifacts and video recordings. Recent efforts to support teachers make connections between mathematics and children's funds of...
Show more"Mathematics teacher noticing as a pedagogical practice--attending to, interpreting, and responding to children's mathematical thinking--is growing within mathematics education communities. Much of the research literature primarily focuses on supporting teacher noticing of children's mathematical thinking within classroom contexts, such as analyzing classroom artifacts and video recordings. Recent efforts to support teachers make connections between mathematics and children's funds of knowledge, however, often involve professional work outside of classrooms where teachers learn about children's lived experiences and communities. While there is a growing expectation that teachers draw on children's funds of knowledge to support mathematics learning, this kind of professional work requires an ability to notice mathematics in out-of-school contexts. The bulk of this dissertation is written as a series of three interconnected papers from a single qualitative study where I explored activities of a working group I facilitated to support prospective K-8 teachers to notice children's mathematical practices in out-of-school contexts. A primary thread across this work involves blurring boundaries within mathematics education. In my first article (pp. 51-76), I provided an overview of boundary blurring that prospective teachers in this study engaged--between mathematics and people as well as between mathematics and other disciplines--through early field experiences in out-of-school contexts. I zoomed in to examine a specific boundary, women and mathematics, in my second article (pp. 83-105) and explored intersections of gender, age, and elementary mathematics during an interaction at a science museum site visit. Then, in my third article (pp. 110-133), I zoomed out to focus on broader discourses within mathematics education to challenge overly simplistic allor-nothing type stories about mathematics and people (e.g., 'being a math person'). Across my three articles, I engage an overarching question: What stories do prospective teachers tell about themselves, about children, and about mathematics? This study contributes to a collection of stories about prospective teachers' learning to notice children and their mathematical practices with implications for supporting mathematics teacher education, particularly in contexts outside of school. In closing, I share how my work connects to a broader project in mathematics education, blurring boundaries. I pose an underlying question for my continued work: What would it take to decolonize mathematics education?"--Pages ii-iii.
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Title: Polycrystalline diamond based neural interface for optogenetics and neurotransmitter detection
Creator: Fan, Bin (Electronics engineer)
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Neural interface forms a communication bridge between a human brain and external circuitries, which enables promising bioelectronics medicines for diseases treatments, such as inflammatory bowel disease, Alzheimer's disease, and restore sensorimotor function lost due to traumatic brain, spinal cord injury, and amputations. Neurons in the central nervous systems communicate with each other electrically along the axon from soma to dendrite and chemically between neuron to neuron in the synapses...
Show moreNeural interface forms a communication bridge between a human brain and external circuitries, which enables promising bioelectronics medicines for diseases treatments, such as inflammatory bowel disease, Alzheimer's disease, and restore sensorimotor function lost due to traumatic brain, spinal cord injury, and amputations. Neurons in the central nervous systems communicate with each other electrically along the axon from soma to dendrite and chemically between neuron to neuron in the synapses through release and uptake of neurotransmitters. In particular, dopamine (DA) is one of the most important neurotransmitters, which associates with many aspects of the neurophysiological processing, such as stress, memory, and addiction. External stimulation is desired to study the dynamics of DA release and uptake and its correlation to the animal behavioral changes. Previously, electrical stimulation was used as a neuromodulation technique for such purpose, which can cause a significant amount of nondopaminergic system activation and result in consequential neurological activities or dynamics not related to DA release[1]. Recent advances in optogenetics provide a unique neuromodulation technique, allowing optical control of genetically targeted specific neurons that express light-sensitive opsin proteins with sub-millisecond temporal precision. Utilizing the cell-type specificity of Optogenetics, researchers can have a more controlled manipulation of the dopaminergic system and have an unbiased study on DA related neurological diseases. The current engineering tools for Optogenetics use laser and micro light emitting diodes (μLEDs) as the light sources, where μLEDs show great promises with respect to device miniaturization, simplicity, low power and low cost of system implementation. However, using μLEDs as a light source can cause potential thermally-induced tissue damage due to μLED Joule heating. To address the localized Joule heating issue, a μLED based optrode was developed in this thesis using polycrystalline diamond as a heat spreader due to its very high thermal conductivity. Compared with an SU8 probe with the same dimensions, a diamond probe can reduce the maximum temperature variations by ~90% at 3.6V 100ms duration pulses. The functionality of the probe was tested in vivo, where light-evoked action potentials were successfully detected. Besides the very high thermal conductivity, diamond has unique features for neurotransmitter sensing, such as a larger potential window, low background current and resistance to surface fouling. In addition, diamond is a biocompatible and chemically inert material, which enables long-term device implantation. Therefore, above mentioned properties make diamond a promising candidate for Optogenetics and neurotransmitter detection. However, diamond is a rigid material and the micromotion-induced strain has been hypothesized to be the main cause of harmful immune responses and even irreversible tissue damage. Due to the process temperature intolerant, diamond cannot synthesis onto polymer substrates directly. To address this issue, a wafer-level substrate transfer process is first time proposed to transfer all diamond macro/micro patterns from a diamond growth substrate, silicon, onto a flexible Parylene substrate. The electrochemical properties of the transferred diamond-polymer electrodes were evaluated (i) using an outer sphere redox couple to study the electron transfer process and (ii) quantitative and qualitative studies of a neurotransmitter redox dopamine/dopamine-o-quinone. A linear response of the BDD sensor to dopamine concentrations of 0.5 μM to 100 μM was observed (R2 = 0.999) with a sensitivity of 0.21 μA/cm2·μM.
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Title: Compliance to prenatal supplement use in relation to low birth weight in Malawi
Creator: Chikakuda, Aaron Thokozani
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Background: Prenatal iron and folic acid (IFA) supplements are offered free to pregnant women in Malawi to reduce maternal anemia and improve birth outcomes. We investigated the association between self-reported compliance to IFA intake and risk of low birth weight (LBW). Methods: Pregnant women who attended Bwaila Maternity Wing of Lilongwe District Hospital for delivery were recruited (n=220). We used questionnaire to collect self-reported information on IFA use and maternal...
Show more"Background: Prenatal iron and folic acid (IFA) supplements are offered free to pregnant women in Malawi to reduce maternal anemia and improve birth outcomes. We investigated the association between self-reported compliance to IFA intake and risk of low birth weight (LBW). Methods: Pregnant women who attended Bwaila Maternity Wing of Lilongwe District Hospital for delivery were recruited (n=220). We used questionnaire to collect self-reported information on IFA use and maternal sociodemographic data. Before delivery blood samples for maternal hemoglobin (Hb) and folate status, and upon delivery, birth weight, and other newborn anthropometrics were measured. We used multivariate logistic regression to determine risk of LBW by prenatal IFA intake. Results: The self-reported number of IFA pills taken during pregnancy was positively associated with Hb, but not serum and RBC folate concentration: 90 pills taken corresponded with mean (SD) Hb 10.7 (1.6), 11.3 (1.8), and 11.7 (1.6) g/dl respectively (P= 0.006). The prevalence of LBW was 20.1%, 13.5% and 5.6% for those who reported taken IFA pills < 45 , 45 - 89, and 2265 90 pills, respectively (P = 0.027). Taking > 60 IFA pills reduced risk of LBW delivery (OR (95% CI)= 0.11 (0.02-0.056), P = 0.008) than taking 2264 30 pills. Conclusion: Self-reported compliance to IFA is valid for assessing prenatal supplement program in Malawi, especially Hb status, can improve adherence and reduce LBW."--Page ii.
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Title: Characterization of axenic immune deficiency in arabidopsis thaliana
Creator: Kremer, James Michael
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Evolution of land plants began and has since occurred, in concert with complex communities of microorganisms, giving rise to a vast spectrum of plant-microbe relationships. Over the past decade, plant molecular biologists and microbial ecologists have worked together to identify drivers of microbiome composition that inspire hypotheses about microbiome functional potential, but many fall short of offering empirical evidence of microbiome-mediated influence on host phenotypes. Herein, I...
Show moreEvolution of land plants began and has since occurred, in concert with complex communities of microorganisms, giving rise to a vast spectrum of plant-microbe relationships. Over the past decade, plant molecular biologists and microbial ecologists have worked together to identify drivers of microbiome composition that inspire hypotheses about microbiome functional potential, but many fall short of offering empirical evidence of microbiome-mediated influence on host phenotypes. Herein, I introduce a new suite of tools to explore microbiome function and report that many facets of plant immunocompetence are microbiome-dependent.Chapter One summarizes the current understanding of plant innate immunity and notable progress of plant microbiome research, including: (1) detection and response to microbe-associated molecular patterns, (2) hormone signaling during biotic interactions, (3) technology for exploration of plant microbiome ecology, (4) factors that influence microbiome community structure, and (5) a review of relevant model systems and gnotobiotic growth platforms. Chapter Two describes the development of a novel “FlowPot” growth system: a peat-based platform conducive to axenic (microbe-free), gnotobiotic (defined microbiota), and holoxenic (undefined, complex microbiota) Arabidopsis thaliana growth. This system provides the ability to maintain control of abiotic parameters and exogenous microbiota, thus providing a valuable platform for discovery for plant microbiome research. The FlowPot system and offers a substantial improvement over alternative growth systems regarding plant health, tractability to greenhouse conditions, and maintenance of bacterial alpha diversity upon inoculation with soil-derived microbiota. An implementation of the growth system is detailed in Chapter Three, featuring a comparative analysis of the axenic vs. holoxenic Arabidopsis transcriptome, metabolome, and immunocompetence. Axenic Arabidopsis has a reduced level of defense- and immunity-associated gene expression and the defense hormone salicylic acid (SA). We report that axenic Arabidopsis is compromised in defense against the foliar pathogen Pseudomonas syringae pv. tomato DC3000 (Pst). Immune elicitation experiments revealed that axenic Arabidopsis is also compromised in the ability to recognize and/or mount normal defense responses to the microbe-associated molecular pattern flg22. Axenic susceptibility to Pst is partially explained by defective innate immunity. Finally, we report the identity of differentially abundant metabolites and transcripts in axenic and holoxenic Arabidopsis that may be involved in microbiome-influenced host phenotypes. Collectively, research described in this dissertation provides new tools and a discovery platform to empirically characterize the function of plant microbiota, as well as detailed characterization of axenic phenotypes and axenic immune deficiency.
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Title: The search for "self" : cultural identity through representations of parent-child relationships in "Instructions Not Included" (2013) and "Under the Same Moon" (2007)
Creator: Moulding, Charles
Date: 2017
Collection: Electronic Theses & Dissertations
Description: This thesis analyzes the films Instructions Not Included (2013), a fish-out-of-water comedy drama about a single father from Mexico raising his daughter in the United States, and Under the Same Moon (2007), a melodrama which shows the quest of a young boy trying to arrive in California from Mexico in less than a week so that he can be reunited with his mother. Focusing on the representations of the parent-child relationship in the context of immigration that are presented in these films, this...
Show moreThis thesis analyzes the films Instructions Not Included (2013), a fish-out-of-water comedy drama about a single father from Mexico raising his daughter in the United States, and Under the Same Moon (2007), a melodrama which shows the quest of a young boy trying to arrive in California from Mexico in less than a week so that he can be reunited with his mother. Focusing on the representations of the parent-child relationship in the context of immigration that are presented in these films, this thesis addresses the debate between globalization and nationalism. The thesis analyses the films' representations of globalization, using the theoretical framework of Arjun Appadurai's "scapes" which postulates that there are five flows which enable people, ideas, and finances to cross political and ideological boundaries. Specifically, this thesis analyzes the implications of these representations for transnational communities and the development of cultural identity. Accordingly, this thesis also demonstrates how the representations of the parent-child relationship are effectively used to illuminate several aspects of immigrant and diaspora cultural identity using the theory of cultural identity of Stuart Hall to support this perspective. Finally, this thesis concludes by applying this analysis to demonstrate what role nationalist ideologies and politics play in the fracture of families, and to demonstrate the ineffectiveness of institutional attempts to curb or control forces of globalization based on the representations in the films.
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Title: Freezing and thawing of frost-susceptible soils : (development of a reliable predictive model)
Creator: Rajaei, Pegah
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Frost depth is an important factor that affects the design of various transportation infrastructures including pavements, retaining structures, bridge foundations, utility lines, and so forth. Soil freezing can lead to frost heave and heave pressure, which may cause serious stability issues. On the other hand, at the beginning of spring season, the ice starts to thaw from the top down and to a lesser extend from the bottom up. The melted water below the pavement surface is trapped (setting on...
Show moreFrost depth is an important factor that affects the design of various transportation infrastructures including pavements, retaining structures, bridge foundations, utility lines, and so forth. Soil freezing can lead to frost heave and heave pressure, which may cause serious stability issues. On the other hand, at the beginning of spring season, the ice starts to thaw from the top down and to a lesser extend from the bottom up. The melted water below the pavement surface is trapped (setting on impermeable frozen materials). It saturates the top part of the upper pavement layer. Consequently, the stiffness of the saturated layer decreases causing substantial decrease in its load bearing capacity and high deformations, which lead to premature and localized failure. To decrease the spring thaw damage, Spring Load Restrictions (SLR) signs are usually placed along the roads. The objectives of this study are to develop accurate and reliable frost and thaw depth and frost heave prediction models, estimate heave pressure and develop a reliable SLR policy. After extensive literature review, various existing frost depth models were identified and tested. These include the finite difference UNSAT-H, the Stefan, the Modified Berggren, and the Chisholm and Phang models. Unfortunately, some of these models require substantial input data that are not available and all models yielded inaccurate results. Therefore, statistical frost depth models were developed using frost depth and air temperature data collected by Michigan Department of Transportation (MDOT); one for clayey soils and one for sandy soil. The two models were then combined using the measured thermal conductivity of clayey and sandy soils. The combined statistical model was then verified using frost depth and air temperature data collected by Minnesota Department of Transportation (MnDOT). Additionally, The Gilpin's mechanistic-empirical model was employed to predict frost heave. The model produced inaccurate and counterintuitive results in some cases. Therefore, the model was modified and the empirical frost depth model developed in this study was incorporated into the model. The resulting model was then simplified to replace some of the required of input data that are not available. The modified model accuracy was assessed using the frost heave data measured at 5 sites in Oakland County, Michigan. Further, the relationship between frost heave and heave pressures were established for four soil types.Moreover, a new statistical model was developed for calculating the cumulative thaw degree-day (CTDD) using pavement surface temperature and air temperate data collected by MDOT. Then, the thaw depth data measured in the state of Michigan were used to assess Nixon and McRoberts thaw depth predictions model. Since the model did not produce accurate and acceptable results, statistical thaw depth models were developed using the calculated CTDD values and thaw depth data collected by MDOT and MnDOT; one for clayey soils and one for sandy soils. The models were then verified using the calculated CTDD values and thaw depth data collected by MnDOT. Finally, based on the results of thaw depth model a new SLR policy was proposed.
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Title: Mechanistic connections between the proton motive force and ATP homeostasis in higher plant photosynthesis under dynamic environmental conditions
Creator: Carrillo, Leticia Ruby
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Through photosynthesis, plants can capture light energy from the sun for the conversion to a more stable high-energy form, ATP and NADPH. These products are then used to fuel an array of metabolic processes including the biosynthesis of sugars and complex carbohydrates. Yet, the abundant source of solar energy used in the process is highly varied and fluctuates throughout the day, directly impacting the photosynthetic apparatus and carbon assimilation. This dissertation focuses on several...
Show moreThrough photosynthesis, plants can capture light energy from the sun for the conversion to a more stable high-energy form, ATP and NADPH. These products are then used to fuel an array of metabolic processes including the biosynthesis of sugars and complex carbohydrates. Yet, the abundant source of solar energy used in the process is highly varied and fluctuates throughout the day, directly impacting the photosynthetic apparatus and carbon assimilation. This dissertation focuses on several mechanisms by which plants are able to respond to the dynamic environmental pressures through modulation of the proton motive force (pmf) and ATP homeostasis.ATP is the primary energy currency in cells and is synthesized in plastids by the chloroplast ATP synthase. However, unlike other stromal thiol-regulated enzymes that incrementally become redox-activated in response to light, chloroplast ATP synthase acts more like an on-off switch, only requiring minimal irradiance to become fully active. Previous work suggested that the rapid sensitivity to light could be explained by the relative redox potentials of the regulatory thiols on the γ-subunit of ATP synthase. This work uncovered a new, unexpected component, NADPH thioredoxin reductase C (NTRC) that controls thiol regulation specifically under low light intensities. Mutants lacking NTRC show strong photosynthetic phenotypes, e.g., increased nonphotochemical quenching and inhibition of linear electron flow, at low irradiances, consistent with an inability to activate ATP synthase resulting in a buildup of the thylakoid pmf. We predict both NTRC and the canonical ferredoxin-thioredoxin reductase system co-regulate the thiol state of ATP synthase at specific light intensities using different reducing potentials (NADPH versus ferredoxin) that allow for added flexibility.Photosynthesis copes with, and adapts to, fluctuating environments using a wide range of mechanisms. While most of the research has been devoted to the processes occurring inside the plastid, work described here on the nucleotide triphosphate transporter (NTT) illuminates an additional mechanism of augmenting and balancing ATP. Previous work suggested that the chloroplast transporter, NTT, acted primarily as an importer of ATP during the night cycle, presumably under non-photosynthesizing conditions. However, isolated intact chloroplasts from both spinach and Arabidopsis thaliana export ATP at rapid rates that can constitute a large fraction of that generated by the light reactions. Furthermore, these findings suggest that earlier results of minimal rates of ATP transport were based on suboptimal assay conditions and incorrect characterization of T-DNA knockout lines, rendering NTT essential for seed germination. Work on double NTT knock-down lines (NTTdKD) have decreased gene expression levels of ntt1 and ntt2 and show strong photosynthetic responses, particularly in the pH and energy-dependent quenching response (qE) with related accumulation of the pmf under fluctuating light and/or decreased CO2 levels. These results indicate a greater role for NTT in balancing ATP levels between the stromal and cytosolic pools than previously thought.
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Title: The experiences and decision making processes of couples with a child with a childhood genetic disorder
Creator: McKee, Kate Szubeczak
Date: 2017
Collection: Electronic Theses & Dissertations
Description: There is a disparity in the research between the individual's and the family as a whole's interactional processes in the collection and dissemination of genetic information. There is a gap in our understanding of how couples deal with genetic information, especially when a child is diagnosed with an inherited genetic condition. Also, there is a lack of understanding of the decision-making processes regarding genetic testing. Furthermore, medical professionals and family therapists are...
Show moreThere is a disparity in the research between the individual's and the family as a whole's interactional processes in the collection and dissemination of genetic information. There is a gap in our understanding of how couples deal with genetic information, especially when a child is diagnosed with an inherited genetic condition. Also, there is a lack of understanding of the decision-making processes regarding genetic testing. Furthermore, medical professionals and family therapists are becoming more aware of the effect these tests will have on family systems and on the health beliefs of the family. Once a diagnosis has been received, families now have the task of making sense of the diagnosis and deciding on how the family system needs to change or adapt in order to accommodate the genetic disorder. The purpose of this qualitative study was to understand the lived experiences of couples who have a child suffering from a genetic disorder (affected child) and to understand the couple's experiences of receiving the diagnosis of an inherited genetic disorder in a child, and how they as a couple, and by extension, their family, adapted to that diagnosis. Nine couples from the Midwestern United States were interviewed using a semi-structured, joint interview process. Using thematic analysis and the couples' own words, two studies emerged from the data. The focus of study 1 was on the decision-making processes about genetic testing and the decision to have future children of couples who have a child with an inherited genetic disorder. The focus of study 2 was on how the family adapted after receiving the diagnosis for their child. Implications and further considerations for family therapists are addressed.
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Title: Real Fantasies in Mathematics Education : numeracy, Quantitative Reasoners, and Transdisciplinary Wicked Problems
Creator: Craig, Jeffrey Carl
Date: 2017
Collection: Electronic Theses & Dissertations
Description: This dissertation has seven chapters. In chapter one, I discuss through why I am doing this dissertation, my positionality, and how I learned from and with all of my committee members.Chapter two is where I situate my dissertation study through developing a social theory of quantitative literacy by translating a social theory of literacy (Barton & Hamilton, 2000). I also describe my epistemological stance towards research as a creative act, my theoretical commitments to critical postmodernism...
Show moreThis dissertation has seven chapters. In chapter one, I discuss through why I am doing this dissertation, my positionality, and how I learned from and with all of my committee members.Chapter two is where I situate my dissertation study through developing a social theory of quantitative literacy by translating a social theory of literacy (Barton & Hamilton, 2000). I also describe my epistemological stance towards research as a creative act, my theoretical commitments to critical postmodernism, and summarize my methodologies and methods for each of the three articles. Chapter three is my first article. In this article, I historicize the numeracy discourse by writing a genealogy that traces how statements about numeracy emerge in scholarship, with a focus on the United States. Scholars’ statements about numeracy form a discourse that pressures mathematics education to reform. These pressures are sustained when scholars connect numeracy to historically powerful justifications for reform. I name these as three promises embedded in the discourse: (1) numeracy promises to reflect modern reality, (2) numeracy promises to empower, and (3) innumeracy promises to have social costs. I conclude with a discussion of the literacy myth and its implications for mathematics education. Chapter four is my second article. In this article, I take the quantitative reasoner to be a persona embodying the goals mathematics educators describe for who our students should become. The quantitative reasoner has both cognitive and affective dimensions; they know and feel particular things about mathematics and statistics. As a member of a curriculum design team, I invoked the value of students becoming quantitative reasoners to defend new courses existing. My students helped me see that the quantitative reasoner is an incomplete person who is a fantasy of mathematics educators, including myself. Together, we re-humanized the quantitative reasoner and each other. Chapter five is my third article. This article describes findings from a study on students’ projects during a mathematics course in quantitative literacy. The issues students chose to research turned out to be connected to a particular class of problems. Across places and disciplines, people are working on these wicked problems which are messy, global, connected, responsive, and unavoidable. Wicked problems are in contrast to curricula that may center tame problems. This apparent mismatch provided the impetus to consider education for wicked problems. After coding students’ projects using the Rittel & Weber’s (1973/1984) ten characteristics of wicked problems, I found three themes: complexity, transdisciplinarity, and openness. Chapter six is my conclusion. In the chapter I synthesize what I have done in my dissertation and revisit some of my theoretical work – most notably my social theory of quantitative literacy. I also use my dissertation to revisit mathematics education as a whole, including research, and try to make some new connections and trouble my conclusions. Chapter seven is my parting thoughts. In it, I return to my positionality by discussing an aesthetic choice I have engaged during this dissertation. That aesthetic is the metamodern aesthetic and it involves the juxtaposition of incredible seriousness with playful detachment. I think about the metamodern aesthetic and my millennial identity in order to reframe doing education research.
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Title: Deep sequencing driven protein engineering : new methods and applications in studying the constraints of functional enzyme evolution
Creator: Wrenbeck, Emily Elizabeth
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "Chemical engineers have long sought enzymes as alternatives to traditional chemocatalytic routes as they are highly selective and have evolved to function under mild conditions (physiological temperature, neutral pH, and atmospheric pressure). Enzymes, the workhorses of biological chemistry, represent a vast catalogue of chemical transformations. This feature lends their use in a variety of industrial applications including food processing, biofuels, engineered biosynthetic pathways, and as...
Show more"Chemical engineers have long sought enzymes as alternatives to traditional chemocatalytic routes as they are highly selective and have evolved to function under mild conditions (physiological temperature, neutral pH, and atmospheric pressure). Enzymes, the workhorses of biological chemistry, represent a vast catalogue of chemical transformations. This feature lends their use in a variety of industrial applications including food processing, biofuels, engineered biosynthetic pathways, and as biocatalysts for preparing specialty chemicals (e.g. pharmaceutical building blocks). The totality of an enzymatic bioprocess is a function of its catalytic efficiency (specificity and turnover), product profile (i.e. regio- and enantio-selectivity), and thermodynamic and kinetic stability. For native enzymes, these parameters are seldom optimal. Importantly, they can be modified using protein engineering techniques, which generally involves introducing mutation(s) to a protein sequence and screening for beneficial effects. However, robust enzyme engineering and design based on first principles is extremely challenging, as mutations that improve one parameter often yield undesired tradeoffs with one or more other parameters. In this thesis, deep mutational scanning - the testing of all possible single-amino acid substitutions of a protein sequence using high-throughput screens/selections and DNA counting via deep sequencing - was used to address two fundamental constraints on functional enzyme evolution. First, how do enzymes encode substrate specificity? To address this question, deep mutational scanning of an amidase on multiple substrates was performed using growth-based selections. Comparison of the resulting datasets revealed that mutations benefiting function on a given substrate were globally distributed in both protein sequence and structure. Additionally, our massive datasets permitted the most rigorous testing to date of theoretical models of adaptive molecular evolution. These results have implications for both design of biocatalysts and in understanding how natural enzymes function and evolve. Another fundamental constraint of enzyme engineering is that mutations improving stability (folding probability) of an enzyme are often inactivating for catalytic function, and vice versa. Towards overcoming this activity-stability constraint, I sought to improve the heterologous expression and maintain the catalytic function of a Type III polyketide synthase from Atropa belladonna. This was accomplished using deep mutational scanning and high-throughput GFP-fusion stability screening, followed by novel filtering methods to only accept beneficial mutations with high probability for maintaining function. Lastly, deep mutational scanning relies on the construction of user-defined DNA libraries, however current available techniques are limited by accessibility or poor coverage. To address these limitations, I will present the development of Nicking Mutagenesis, a new method for the construction of comprehensive single-site saturation mutagenesis libraries that requires only double-stranded plasmid DNA as input substrate. This method has been validated on several gene targets and plasmids and is currently being used in academic, government, and industry laboratories worldwide."--Pages ii-iii.
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