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Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals.

Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet would bring fully hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses ( 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. At the initial experiments at the AMO beamline using 6.9- Å wavelength, Bragg peaks were recorded to 8.5- Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage. Recently, femtosecond X-ray protein nanocrystallography experiments were done at the CXI beamline of the LCLS using 1.3- Å wavelength, and Bragg reflections were recorded to 3- Å resolution; the data are currently being processed. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
ContributorsHunter, Mark (Author) / Fromme, Petra (Thesis advisor) / Wolf, George (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Molybdenum (Mo) is a key trace nutrient for biological assimilation of nitrogen, either as nitrogen gas (N2) or nitrate (NO3-). Although Mo is the most abundant metal in seawater (105 nM), its concentration is low (<5 nM) in most freshwaters today, and it was scarce in the ocean before 600

Molybdenum (Mo) is a key trace nutrient for biological assimilation of nitrogen, either as nitrogen gas (N2) or nitrate (NO3-). Although Mo is the most abundant metal in seawater (105 nM), its concentration is low (<5 nM) in most freshwaters today, and it was scarce in the ocean before 600 million years ago. The use of Mo for nitrogen assimilation can be understood in terms of the changing Mo availability through time; for instance, the higher Mo content of eukaryotic vs. prokaryotic nitrate reductase may have stalled proliferation of eukaryotes in low-Mo Proterozoic oceans. Field and laboratory experiments were performed to study Mo requirements for NO3- assimilation and N2 fixation, respectively. Molybdenum-nitrate addition experiments at Castle Lake, California revealed interannual and depth variability in plankton community response, perhaps resulting from differences in species composition and/or ammonium availability. Furthermore, lake sediments were elevated in Mo compared to soils and bedrock in the watershed. Box modeling suggested that the largest source of Mo to the lake was particulate matter from the watershed. Month-long laboratory experiments with heterocystous cyanobacteria (HC) showed that <1 nM Mo led to low N2 fixation rates, while 10 nM Mo was sufficient for optimal rates. At 1500 nM Mo, freshwater HC hyperaccumulated Mo intercellularly, whereas coastal HC did not. These differences in storage capacity were likely due to the presence in freshwater HC of the small molybdate-binding protein, Mop, and its absence in coastal and marine cyanobacterial species. Expression of the mop gene was regulated by Mo availability in the freshwater HC species Nostoc sp. PCC 7120. Under low Mo (<1 nM) conditions, mop gene expression was up-regulated compared to higher Mo (150 and 3000 nM) treatments, but the subunit composition of the Mop protein changed, suggesting that Mop does not bind Mo in the same manner at <1 nM Mo that it can at higher Mo concentrations. These findings support a role for Mop as a Mo storage protein in HC and suggest that freshwater HC control Mo cellular homeostasis at the post-translational level. Mop's widespread distribution in prokaryotes lends support to the theory that it may be an ancient protein inherited from low-Mo Precambrian oceans.
ContributorsGlass, Jennifer (Author) / Anbar, Ariel D (Thesis advisor) / Shock, Everett L (Committee member) / Jones, Anne K (Committee member) / Hartnett, Hilairy E (Committee member) / Elser, James J (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Anti-retroviral drugs and AIDS prevention programs have helped to decrease the rate of new HIV-1 infections in some communities, however, a prophylactic vaccine is still needed to control the epidemic world-wide. Despite over two decades of research, a vaccine against HIV-1 remains elusive, although recent clinical trials have shown promising

Anti-retroviral drugs and AIDS prevention programs have helped to decrease the rate of new HIV-1 infections in some communities, however, a prophylactic vaccine is still needed to control the epidemic world-wide. Despite over two decades of research, a vaccine against HIV-1 remains elusive, although recent clinical trials have shown promising results. Recent successes have focused on highly conserved, mucosally-targeted antigens within HIV-1 such as the membrane proximal external region (MPER) of the envelope protein, gp41. MPER has been shown to play critical roles in the viral mucosal transmission, though this peptide is not immunogenic on its own. Gag is a structural protein configuring the enveloped virus particles, and has been suggested to constitute a target of the cellular immunity potentially controlling the viral load. It was hypothesized that HIV-1 enveloped virus-like particles (VLPs) consisting of Gag and a deconstructed form of gp41 comprising the MPER, transmembrane, and cytoplasmic domains (dgp41) could be expressed in plants. Plant-optimized HIV-1 genes were constructed and expressed in Nicotiana benthamiana by stable transformation, or transiently using a tobacco mosaic virus-based expression system or a combination of both. Results of biophysical, biochemical and electron microscopy characterization demonstrated that plant cells could support not only the formation of HIV-1 Gag VLPs, but also the accumulation of VLPs that incorporated dgp41. These particles were purified and utilized in mice immunization experiments. Prime-boost strategies combining systemic and mucosal priming with systemic boosting using two different vaccine candidates (VLPs and CTB-MPR - a fusion of MPER and the B-subunit of cholera toxin) were administered to BALB/c mice. Serum antibody responses against both the Gag and gp41 antigens could be elicited in mice systemically primed with VLPs and these responses could be recalled following systemic boosting with VLPs. In addition, mucosal priming with VLPs allowed for a robust boosting response against Gag and gp41 when boosted with either candidate. Functional assays of these antibodies are in progress to test the antibodies' effectiveness in neutralizing and preventing mucosal transmission of HIV-1. This immunogenicity of plant-based Gag/dgp41 VLPs represents an important milestone on the road towards a broadly-efficacious and inexpensive subunit vaccine against HIV-1.
ContributorsKessans, Sarah (Author) / Mor, Tsafrir S (Thesis advisor) / Matoba, Nobuyuki (Committee member) / Mason, Hugh (Committee member) / Hogue, Brenda (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Semiconductor nanowires are featured by their unique one-dimensional structure which makes them promising for small scale electronic and photonic device applications. Among them, III-V material nanowires are particularly outstanding due to their good electronic properties. In bulk, these materials reveal electron mobility much higher than conventional silicon based devices, for

Semiconductor nanowires are featured by their unique one-dimensional structure which makes them promising for small scale electronic and photonic device applications. Among them, III-V material nanowires are particularly outstanding due to their good electronic properties. In bulk, these materials reveal electron mobility much higher than conventional silicon based devices, for example at room temperature, InAs field effect transistor (FET) has electron mobility of 40,000 cm2/Vs more than 10 times of Si FET. This makes such materials promising for high speed nanowire FETs. With small bandgap, such as 0.354 eV for InAs and 1.52 eV for GaAs, it does not need high voltage to turn on such devices which leads to low power consumption devices. Another feature of direct bandgap allows their applications of optoelectronic devices such as avalanche photodiodes. However, there are challenges to face up. Due to their large surface to volume ratio, nanowire devices typically are strongly affected by the surface states. Although nanowires can be grown into single crystal structure, people observe crystal defects along the wires which can significantly affect the performance of devices. In this work, FETs made of two types of III-V nanowire, GaAs and InAs, are demonstrated. These nanowires are grown by catalyst-free MOCVD growth method. Vertically nanowires are transferred onto patterned substrates for coordinate calibration. Then electrodes are defined by e-beam lithography followed by deposition of contact metals. Prior to metal deposition, however, the substrates are dipped in ammonium hydroxide solution to remove native oxide layer formed on nanowire surface. Current vs. source-drain voltage with different gate bias are measured at room temperature. GaAs nanowire FETs show photo response while InAs nanowire FETs do not show that. Surface passivation is performed on GaAs FETs by using ammonium surfide solution. The best results on current increase is observed with around 20-30 minutes chemical treatment time. Gate response measurements are performed at room temperature, from which field effect mobility as high as 1490 cm2/Vs is extracted for InAs FETs. One major contributor for this is stacking faults defect existing along nanowires. For InAs FETs, thermal excitations observed from temperature dependent results which leads us to investigate potential barriers.
ContributorsLiang, Hanshuang (Author) / Yu, Hongbin (Thesis advisor) / Ferry, David (Committee member) / Tracy, Clarence (Committee member) / Arizona State University (Publisher)
Created2011
Description

Consider Steven Cryos’ words, “When disaster strikes, the time to prepare has passed.” Witnessing domestic water insecurity in events such as Hurricane Katrina, the instability in Flint, Michigan, and most recently the winter storms affecting millions across Texas, we decided to take action. The period between a water supply’s disruption

Consider Steven Cryos’ words, “When disaster strikes, the time to prepare has passed.” Witnessing domestic water insecurity in events such as Hurricane Katrina, the instability in Flint, Michigan, and most recently the winter storms affecting millions across Texas, we decided to take action. The period between a water supply’s disruption and restoration is filled with anxiety, uncertainty, and distress -- particularly since there is no clear indication of when, exactly, restoration comes. It is for this reason that Water Works now exists. As a team of students from diverse backgrounds, what started as an honors project with the Founders Lab at Arizona State University became the seed that will continue to mature into an economically sustainable business model supporting the optimistic visions and tenants of humanitarianism. By having conversations with community members, conducting market research, competing for funding and fostering progress amid the COVID-19 pandemic, our team’s problem-solving traverses the disciplines. The purpose of this paper is to educate our readers about a unique solution to emerging issues of water insecurity that are nested across and within systems who could benefit from the introduction of a personal water reclamation system, showcase our team’s entrepreneurial journey, and propose future directions that will this once pedagogical exercise to continue fulfilling its mission: To heal, to hydrate and to help bring safe water to everyone.

ContributorsReitzel, Gage Alexander (Co-author) / Filipek, Marina (Co-author) / Sadiasa, Aira (Co-author) / Byrne, Jared (Thesis director) / Sebold, Brent (Committee member) / Historical, Philosophical & Religious Studies (Contributor) / School of Human Evolution & Social Change (Contributor, Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Animals encounter information from different resources simultaneously, integrating input from multiple sensory systems before responding behaviorally. When different cues interact with one another, they may enhance, diminish, or have no impact on their responses. In this project, we test how the presence of chemical cues affect the perception of visual

Animals encounter information from different resources simultaneously, integrating input from multiple sensory systems before responding behaviorally. When different cues interact with one another, they may enhance, diminish, or have no impact on their responses. In this project, we test how the presence of chemical cues affect the perception of visual cues. Zebrafish (Danio rerio) often use both chemical cues and visual cues to communicate with shoal mates, to assess predation risk, and to locate food. For example, zebrafish rely on both olfactory cues and visual cues for kin recognition, and they frequently use both chemical and visual cues to search for and to capture prey. In zebrafish, the terminal nerve (TN) constitutes the olfacto-visual centrifugal pathway and connects the olfactory bulb with the retina, thus allowing olfactory perception also to activate visual receptors. Past studies have found that the presence of an olfactory cue can modulate visual sensitivity in zebrafish through the terminal nerve pathway. Alternatively, given that zebrafish are highly social, the presence of social chemical cues may distract individuals from responding to other visual cues, such as food and predator visual cues. Foraging and predator chemical cues, including chemical food cues and alarm cues, may also distract individuals from responding to non-essential visual cues. Here, we test whether the response to a visual cue either increases or decreases when presented in concert with alanine, an amino acid that represents the olfactory cues of zebrafish prey. We found that the presence of chemical cues did not affect whether zebrafish responded to visual cues, but that the fish took longer to respond to visual cues when chemical cues were also present. These findings suggest that different aspects of behavior could be affected by the interaction between sensory modalities. We also found that this impact of delayed response was significant only when the visual cue<br/>was weak compared to the strength of the chemical cue, suggesting that the salience of interacting cues may also have an influence on determining the outcomes of the interactions. Overall, the interactive effects of chemicals on an animal’s response to visual cues may also have wide-ranging impacts on behavior including foraging, mating, and evading predators, and the interaction of cues may affect different aspects of the same behavior.

ContributorsPuffer, Georgie Delilah (Author) / Martins, Emilia (Thesis director) / Suriyampola, Piyumika (Committee member) / Gerkin, Richard (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Exploratory Play is a universal experience that occurs throughout different kinds of childhoods. This study investigates how children’s vocabulary and exploratory play are influenced by how the caregiver responds to the child’s communicative bids. We hypothesize that if caregivers use more open-ended questions in response to their child’s communicative bids,

Exploratory Play is a universal experience that occurs throughout different kinds of childhoods. This study investigates how children’s vocabulary and exploratory play are influenced by how the caregiver responds to the child’s communicative bids. We hypothesize that if caregivers use more open-ended questions in response to their child’s communicative bids, children will show higher rates of exploration during free play.

ContributorsMccollum, Shani Monifa (Author) / Lucca, Kelsey (Thesis director) / Spinrad, Tracy (Committee member) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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In this thesis I will explore deficits in Theory of Mind (ToM) in autistic people due to new evidence that they do not completely lack a ToM. A new theory is proposed, claiming that autistic people use a Hyper Theory of Mind (HyperToM) which has some application and processing differences

In this thesis I will explore deficits in Theory of Mind (ToM) in autistic people due to new evidence that they do not completely lack a ToM. A new theory is proposed, claiming that autistic people use a Hyper Theory of Mind (HyperToM) which has some application and processing differences from typical ToM. The HyperToM test will be administered as an online questionnaire that includes a self-reported Autism Quotient (AQ) section. The study is done in low support needs autistic (LSA) adults, which should have a developed ToM due to age and ability. Results showed some correlations with the AQ symptoms and HyperToM, but not enough diagnosed autistic people (9) participated in this study for significant results.

ContributorsMarkov, Vlada A (Author) / Fabricius, William (Thesis director) / Philips, Ben (Committee member) / Department of Psychology (Contributor) / Dean, W.P. Carey School of Business (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Appearance ideals are standards of beauty imposed by a culture or society, that are unrealistic and impossible to achieve. Research documents the existence of three appearance ideals, thin, muscular and hourglass ideals. The thin ideal is the pursuit of a very thin and low body weight. The muscular ideal is

Appearance ideals are standards of beauty imposed by a culture or society, that are unrealistic and impossible to achieve. Research documents the existence of three appearance ideals, thin, muscular and hourglass ideals. The thin ideal is the pursuit of a very thin and low body weight. The muscular ideal is the pursuit of a toned and fit body. The hourglass ideal is the pursuit of a shapely body with bigger breasts and hips/buttocks than waist. These ideals are associated with disordered eating. However, no current study has examined the prevalence of all three ideals, or how the combination of ideals relates to dietary restraint, one example of a disordered eating behavior. This study was conducted on 505 undergraduate women at Arizona State University, who were completing research credit for a psychology course. The women participated in an online survey that assessed their demographics, each ideal, and dietary restraint. Results show that all combinations of ideals exist. Specifically, 41.5% of the sample endorse high levels of all three ideals, while 12.5% report thin and muscular ideals, 9.5% report thin and hourglass ideals, 9.9% report hourglass and muscular ideals, 8.4% report low levels of all three ideals, 6.4% report muscular ideal only, 6.4% report hourglass ideal only, and 5.6% report thin ideal only. Endorsing more than one ideal significantly associated with dietary restraint. Findings fulfill an important gap in the literature, suggest future directions for research, and have important clinical implications.

ContributorsByrd, Jordyn (Author) / Perez, Marisol (Thesis director) / Hernández, Juan (Committee member) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Mayer-Rokitansky-Küster-Hauser (MRKH) is a rare Disorder of Sexual Development (DSD) that results in the lack of a uterus and vagina in women. Receiving this diagnosis during adolescence can cause various forms of psychological distress in patients and families.<br/>Specifically, this condition could affect a women’s gender identity, body image, romantic relationships,

Mayer-Rokitansky-Küster-Hauser (MRKH) is a rare Disorder of Sexual Development (DSD) that results in the lack of a uterus and vagina in women. Receiving this diagnosis during adolescence can cause various forms of psychological distress in patients and families.<br/>Specifically, this condition could affect a women’s gender identity, body image, romantic relationships, family relationships, and psychological wellbeing. Parents are also put in a stressful<br/>position as they now have to navigate the healthcare system, disclosure, and the relationship with their child. This study aims to expand the knowledge of psychosocial adjustment by studying body<br/>image, gender identity, and mental health in individuals living with MRKH as well as parental disclosure, parental support systems, and parental perceptions of their child’s mental health.

ContributorsLaloudakis, Vasiliki (Author) / Wilson, Melissa (Thesis director) / Fontinha de Alcantara, Christiane (Committee member) / Baimbridge, Erica (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05