Matching Items (169)
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Description
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.
ContributorsEdlund, Petra (Author) / Takala, Heikki (Author) / Claesson, Elin (Author) / Henry, Leocadie (Author) / Dods, Robert (Author) / Lehtivuori, Heli (Author) / Panman, Matthijs (Author) / Pande, Kanupriya (Author) / White, Thomas (Author) / Nakane, Takanori (Author) / Berntsson, Oskar (Author) / Gustavsson, Emil (Author) / Bath, Petra (Author) / Modi, Vaibhav (Author) / Roy Chowdhury, Shatabdi (Author) / Zook, James (Author) / Berntsen, Peter (Author) / Pandey, Suraj (Author) / Poudyal, Ishwor (Author) / Tenboer, Jason (Author) / Kupitz, Christopher (Author) / Barty, Anton (Author) / Fromme, Petra (Author) / Koralek, Jake D. (Author) / Tanaka, Tomoyuki (Author) / Spence, John (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Boutet, Sebastien (Author) / Nango, Eriko (Author) / Moffat, Keith (Author) / Groenhof, Gerrit (Author) / Ihalainen, Janne (Author) / Stojkovic, Emina A. (Author) / Schmidt, Marius (Author) / Westenhoff, Sebastian (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-10-19
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Description
Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone

Antibodies are essential for structural determinations and functional studies of membrane proteins, but antibody generation is limited by the availability of properly-folded and purified antigen. We describe the first application of genetic immunization to a structurally diverse set of membrane proteins to show that immunization of mice with DNA alone produced antibodies against 71% (n = 17) of the bacterial and viral targets. Antibody production correlated with prior reports of target immunogenicity in host organisms, underscoring the efficiency of this DNA-gold micronanoplex approach. To generate each antigen for antibody characterization, we also developed a simple in vitro membrane protein expression and capture method. Antibody specificity was demonstrated upon identifying, for the first time, membrane-directed heterologous expression of the native sequences of the FopA and FTT1525 virulence determinants from the select agent Francisella tularensis SCHU S4. These approaches will accelerate future structural and functional investigations of therapeutically-relevant membrane proteins.
ContributorsHansen, Debra (Author) / Robida, Mark (Author) / Craciunescu, Felicia (Author) / Loskutov, Andrey (Author) / Dorner, Katerina (Author) / Rodenberry, John-Charles (Author) / Wang, Xiao (Author) / Olson, Tien (Author) / Patel, Hetal (Author) / Fromme, Petra (Author) / Sykes, Kathryn (Author) / Biodesign Institute (Contributor) / Innovations in Medicine (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor)
Created2016-02-24
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Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement.

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description
Personal experiences with body image dysmorphia and an eating disorder necessitated that I do a thorough investigation into why they happened and why I felt this way about my body. For this project, not only was I motivated by my own struggles, but I noticed that these experiences were shared

Personal experiences with body image dysmorphia and an eating disorder necessitated that I do a thorough investigation into why they happened and why I felt this way about my body. For this project, not only was I motivated by my own struggles, but I noticed that these experiences were shared among my family, my friends, and my fellow peers in the dance community. We had been struggling since childhood. I began to realize that these behaviors and thought patterns were manifestations of apology, an apology that women have been learning, living, and spreading since our beginnings. Why do women apologize? How does this apology affect how we view, treat, and navigate our bodies in space? In what ways can dance be the mechanism by which we remove apology and individually and collectively find joy, freedom, and liberation? Not only was I interested in understanding the ‘why’, but I was deeply interested in finding a solution. Research for this thesis came from written materials, stories that the dancers and I shared, and choreographic research in the body. The final goal was to create a community-based performance of dance, spoken word, and storytelling that demonstrated the findings from each of those questions and catalyzed a conversation about how we can liberate ourselves. We used rehearsals to explore our own experiences within apology and shame, while also exploring how the ways in which we practice being unapologetic in the dance space can translate to how we move through the world on a daily basis.

Through a deep analysis and application of Sonya Renee Taylor’s book The Body Is Not An Apology, I discovered that apology is learned. We learn how to apologize through body shame, the media, family/generational trauma, and government/law/policy. This apology is embodied through gestures, movement patterns, and postures, such as bowing the head, hunching the shoulders, and walking around others. Apology causes us to view our bodies as things to be manipulated, discarded, and embarrassed by. After recognizing why we apologize and how it affects our bodies, we can then begin to think of how to remove it. Because the body the site of the problem, it is also the site of the solution. Dance gives us an opportunity to deeply learn our bodies, to cultivate their power, and to heal from their traumas. By being together in community as women, we are able to feel seen and supported as we work through uncharted territory of being free from apology in these bodies. By dancing in ways that allow us to take up space, to be free, to be unapologetic, we use dance as a practice for life. Through transforming ourselves, we begin to transform the world and rewrite the narrative of how we exist in and move through our bodies as women.
ContributorsWaller, Marguerite Lilith (Author) / Fitzgerald, Mary (Thesis director) / Britt, Melissa (Committee member) / Lerman, Liz (Committee member) / Dean, Herberger Institute for Design and the Arts (Contributor) / School of Film, Dance and Theatre (Contributor, Contributor) / School of Social Transformation (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Description
The arts benefit society through positively affecting an individual's physical, emotional, cognitive, and social development. The arts are comprised of many genres. The four genres of art this thesis researched includes: dance, theatre, music, and the visual arts. These four genres aid the four areas of human development. The research

The arts benefit society through positively affecting an individual's physical, emotional, cognitive, and social development. The arts are comprised of many genres. The four genres of art this thesis researched includes: dance, theatre, music, and the visual arts. These four genres aid the four areas of human development. The research present in this thesis demonstrates a variety of developmental benefits from participation in the arts. While the benefits of participating in the arts exist, there is not equal accessibility to the arts. People are prevented from participating in the arts mainly due to cost. Four art specialists, one for each genre of the arts were anonymously interviewed to provide real life examples of participating in the arts. These findings informed a business plan for a non-profit arts center, Arts Center for Expression. This center is based off the beliefs that there is an artistic experience for everyone and that anyone who wants to should have access. Following the research in this thesis is a business plan for Arts Center for Expression. It details the operating plan, funding, future/harvest, competition, market, marketing plan, and potential impact. The benefits of the arts are numerous and undeniable.
ContributorsMcHugh, Colleen Godfrey (Author) / Fitzgerald, Mary (Thesis director) / Schupp, Karen (Committee member) / School of Film, Dance and Theatre (Contributor) / Department of Management and Entrepreneurship (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
The purpose of this study is to examine the effect of an existing medication management program in Hispanic individuals with diabetes, focusing on overall management and perceived quality of life (QOL). Diseases such as diabetes affect an individual's physical health, mental health, and social life. The degree to which these

The purpose of this study is to examine the effect of an existing medication management program in Hispanic individuals with diabetes, focusing on overall management and perceived quality of life (QOL). Diseases such as diabetes affect an individual's physical health, mental health, and social life. The degree to which these diseases affect an individual's life depend on how well they control and self-manage care needs. It has been found that Hispanic patients report and demonstrate inadequacy with controlling their diabetes compared to other ethnicities, making this an important public health topic (Schneiderman eta al., 2014). One of the greatest issues the Hispanic population reports as causing most concern is medication management and compliance. Poor medication adherence can increase complications of diabetes and depression, thus increasing poor overall health status and perception. Medication therapy management (MTM) programs run by clinical pharmacists are available to help with medication adherence, aiding in developing a tailored plan to help individuals manage the disease. This study is a cross-sectional study which assess reported QOL and functionality of diabetics enrolled in an MTM program. Participants were recruited from a clinic in Phoenix, Az. Patients completed a questionnaire that included demographics, a QOL questionnaire and a health belief questionnaire. A total of sixteen participants completed the study. The association between time in the medication therapy management program and its effect on general health, social functioning, emotional well-being, and hemoglobin A1C were reviewed. Though no significance was found, means were similar in all groups indicating functionality and A1C control through the diabetes support program may exist.
Created2016-05
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Description
Objectives: Although childhood obesity has received growing attention, parents still fail to recognize overweight and obesity in their children. Accurate identification of overweight or obesity in their child is associated with the parent's responsiveness to interventions aimed at preventing weight-related health issues. Recent research shows that a child's age and

Objectives: Although childhood obesity has received growing attention, parents still fail to recognize overweight and obesity in their children. Accurate identification of overweight or obesity in their child is associated with the parent's responsiveness to interventions aimed at preventing weight-related health issues. Recent research shows that a child's age and gender are associated with parental misperception of their child's weight status, but little is known about the interaction of these factors across various age groups. This study examined the association between a wide range of parent, child, and household factors and the accuracy of parental perception of their child's body weight status compared to parent-measured body weight status. Methods: Data were collected from a random-digit-dial telephone survey of 1708 households located in five low-income New Jersey cities with large minority populations. A subset of 548 children whose parents completed the survey and returned a worksheet of parent-measured heights and weights were the focus of the analysis. Bivariate and multivariate analyses were performed to determine the factors significantly associated with parental perception of their child's body weight status. Results: Based on parent-measure heights and weights, 36% of the children were overweight or obese (OWOB). Only 21% of OWOB children were perceived by their parents as OWOB. Child gender, child body mass index (BMI) and parent BMI were significant independent predictors of parents' accuracy at perceiving their child's body weight status. Conclusion: Boys, OWOB children, and children of OWOB parents had significantly greater odds of parental underestimation of their body weight status. Parents had better recognition of OWOB in their daughters, especially older daughters, than in their sons, suggesting parental gender bias in identifying OWOB in children. Further research is needed regarding parental gender bias and its implications in OWOB identification in children.
ContributorsBader, Wendy (Author) / Ohri-Vachaspati, Punam (Thesis advisor) / Lloyd, Kristen (Committee member) / Crespo, Noe (Committee member) / Arizona State University (Publisher)
Created2013
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Description

This study aims to examine children’s fruit, vegetable, and added sugar consumption relative to the Dietary Guidelines for Americans and the American Heart Association’s recommendations, as well as to compare children’s reported consumption with parental perception of the child’s overall diet quality. Data were drawn from 2 independent, cross sectional

This study aims to examine children’s fruit, vegetable, and added sugar consumption relative to the Dietary Guidelines for Americans and the American Heart Association’s recommendations, as well as to compare children’s reported consumption with parental perception of the child’s overall diet quality. Data were drawn from 2 independent, cross sectional panels (2009–10 and 2014–15) of the New Jersey Child Health Study. The analytical sample included 2229 households located in five New Jersey cities. Daily consumption of fruit (cups), vegetables (cups), and added sugars (teaspoons) for all children (3–18 years old) were based on parent reports. Multivariate linear regression analyses estimated children’s adjusted fruit, vegetable, and added sugar consumption across parents’ perception categories (Disagree; Somewhat Agree; and Strongly Agree that their child eats healthy). Although only a small proportion of children meet recommendations, the majority of parents strongly agreed that their child ate healthy. Nonetheless, significant differences, in the expected direction, were observed in vegetable and fruit consumption (but not sugar) across parental perceptional categories for most age/sex groups. Dietary interventions tailored to parents should include specific quantity and serving-size information for fruit and vegetable recommendations, based on their child’s age/sex, and highlight sources of added sugar and their sugar content.

ContributorsEliason, Jessica (Author) / Acciai, Francesco (Author) / DeWeese, Robin (Author) / Vega-Lopez, Sonia (Author) / Ohri-Vachaspati, Punam (Author)
Created2020-08-03
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Description

Disparities in healthy food access are well documented in cross-sectional studies in communities across the United States. However, longitudinal studies examining changes in food environments within various neighborhood contexts are scarce. In a sample of 142 census tracts in four low-income, high-minority cities in New Jersey, United States, we examined

Disparities in healthy food access are well documented in cross-sectional studies in communities across the United States. However, longitudinal studies examining changes in food environments within various neighborhood contexts are scarce. In a sample of 142 census tracts in four low-income, high-minority cities in New Jersey, United States, we examined the availability of different types of food stores by census tract characteristics over time (2009–2017). Outlets were classified as supermarkets, small grocery stores, convenience stores, and pharmacies using multiple sources of data and a rigorous protocol. Census tracts were categorized by median household income and race/ethnicity of the population each year. Significant declines were observed in convenience store prevalence in lower- and medium-income and majority black tracts (p for trend: 0.004, 0.031, and 0.006 respectively), while a slight increase was observed in the prevalence of supermarkets in medium-income tracts (p for trend: 0.059). The decline in prevalence of convenience stores in lower-income and minority neighborhoods is likely attributable to declining incomes in these already poor communities. Compared to non-Hispanic neighborhoods, Hispanic communities had a higher prevalence of small groceries and convenience stores. This higher prevalence of smaller stores, coupled with shopping practices of Hispanic consumers, suggests that efforts to upgrade smaller stores in Hispanic communities may be more sustainable.

ContributorsOhri-Vachaspati, Punam (Author) / DeWeese, Robin (Author) / Acciai, Francesco (Author) / DeLia, Derek Michael, 1969- (Author) / Tulloch, David (Author) / Tong, Daoqin (Author) / Lorts, Cori (Author) / Yedidia, Michael J., 1946- (Author)
Created2019-07-03
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Description

Objective

In response to recent national efforts to increase the availability of healthy food in small stores, we sought to understand the extent to which small food stores could implement the newly published Healthy Small Store Minimum Stocking Recommendations and reflect on the new US Department of Agriculture Food and

Objective

In response to recent national efforts to increase the availability of healthy food in small stores, we sought to understand the extent to which small food stores could implement the newly published Healthy Small Store Minimum Stocking Recommendations and reflect on the new US Department of Agriculture Food and Nutrition Service's final rule for stocking of staple foods for Supplemental Nutrition Assistance Program–approved retailers.

Design

We collected qualitative and quantitative data from 57 small stores in four states (Arizona, Delaware, Minnesota, and North Carolina) that accepted Supplemental Nutrition Assistance Program but not Special Supplemental Nutrition Assistance Program for Women, Infants, and Children benefits. Data from semistructured, in-depth interviews with managers/owners were transcribed, coded, and analyzed. We collected quantitative store inventory data onsite and later performed descriptive analyses.

Results

Store interviews revealed a reluctant willingness to stock healthy food and meet new recommendations. No stores met recommended fruit and vegetable stocking, although 79% carried at least one qualifying fruit and 74% carried at least one qualifying vegetable. Few stores met requirements for other food categories (ie, whole grains and low-fat dairy) with the exception of lean proteins, where stores carrying nuts or nut butter were more likely to meet the protein recommendation. Water and 100% juice were widely available and 68% met basic healthy beverage criteria.

Conclusions

In contrast to the inventory observed, most owners believed store stock met basic recommendations. Further, findings indicate that small stores are capable of stocking healthy products; however, technical and infrastructure support, as well as incentives, would facilitate shifts from staple to healthier staple foods. Retailers may need support to understand healthier product criteria and to drive consumer demand for new products.

ContributorsKarpyn, Allison (Author) / DeWeese, Robin (Author) / Pelletier, Jennifer (Author) / Laska, Melissa (Author) / Ohri-Vachaspati, Punam (Author) / Deahl-Greenlaw, Amy (Author) / Ughwanogho, Ogheneruona (Author) / Jilcott Pitts, Stephanie Bell (Author)
Created2018-04-09