Matching Items (291)
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Description
Premise of the study: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.
Methods: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear

Premise of the study: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.
Methods: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).
Key results: The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.
Conclusions: The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.
ContributorsSanderson, Michael J. (Author) / Copetti, Dario (Author) / Burquez, Alberto (Author) / Bustamante, Enriquena (Author) / Charboneau, Joseph L. M. (Author) / Eguiarte, Luis E. (Author) / Kumar, Sudhir (Author) / Lee, Hyun Oh (Author) / Lee, Junki (Author) / McMahon, Michelle (Author) / Steele, Kelly (Author) / Wing, Rod (Author) / Yang, Tae-Jin (Author) / Zwickl, Derrick (Author) / Wojciechowski, Martin (Author) / College of Integrative Sciences and Arts (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2015-07-01
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Description

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.

ContributorsOberthuer, Dominik (Author) / Knoska, Juraj (Author) / Wiedorn, Max O. (Author) / Beyerlein, Kenneth R. (Author) / Bushnell, David A. (Author) / Kovaleva, Elena G. (Author) / Heymann, Michael (Author) / Gumprecht, Lars (Author) / Kirian, Richard (Author) / Barty, Anton (Author) / Mariani, Valerio (Author) / Tolstikova, Aleksandra (Author) / Adriano, Luigi (Author) / Awel, Salah (Author) / Barthelmess, Miriam (Author) / Dorner, Katerina (Author) / Xavier, P. Lourdu (Author) / Yefanov, Oleksandr (Author) / James, Daniel (Author) / Nelson, Garrett (Author) / Wang, Dingjie (Author) / Calvey, George (Author) / Chen, Yujie (Author) / Schmidt, Andrea (Author) / Szczepek, Michael (Author) / Frielingsdorf, Stefan (Author) / Lenz, Oliver (Author) / Snell, Edward (Author) / Robinson, Philip J. (Author) / Sarler, Bozidar (Author) / Belsak, Grega (Author) / Macek, Marjan (Author) / Wilde, Fabian (Author) / Aquila, Andrew (Author) / Boutet, Sebastien (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Scheerer, Patrick (Author) / Lipscomb, John D. (Author) / Weierstall, Uwe (Author) / Kornberg, Roger D. (Author) / Spence, John (Author) / Pollack, Lois (Author) / Chapman, Henry N. (Author) / Bajt, Sasa (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-03-16
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Description

X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a

X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.

ContributorsLi, Xuanxuan (Author) / Chiu, Chun-Ya (Author) / Wang, Hsiang-Ju (Author) / Kassemeyer, Stephan (Author) / Botha, Sabine (Author) / Shoeman, Robert L. (Author) / Lawrence, Robert (Author) / Kupitz, Christopher (Author) / Kirian, Richard (Author) / James, Daniel (Author) / Wang, Dingjie (Author) / Nelson, Garrett (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Hartman, Elisabeth (Author) / Jafarpour, Aliakbar (Author) / Foucar, Lutz M. (Author) / Barty, Anton (Author) / Chapman, Henry (Author) / Liang, Mengning (Author) / Menzel, Andreas (Author) / Wang, Fenglin (Author) / Basu, Shibom (Author) / Fromme, Raimund (Author) / Doak, R. Bruce (Author) / Fromme, Petra (Author) / Weierstall, Uwe (Author) / Huang, Michael H. (Author) / Spence, John (Author) / Schlichting, Ilme (Author) / Hogue, Brenda (Author) / Liu, Haiguang (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / School of Life Sciences (Contributor)
Created2017-04-11
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Description

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

ContributorsMunke, Anna (Author) / Andreasson, Jakob (Author) / Aquila, Andrew (Author) / Awel, Salah (Author) / Ayyer, Kartik (Author) / Barty, Anton (Author) / Bean, Richard J. (Author) / Berntsen, Peter (Author) / Bielecki, Johan (Author) / Boutet, Sebastien (Author) / Bucher, Maximilian (Author) / Chapman, Henry N. (Author) / Daurer, Benedikt J. (Author) / DeMirci, Hasan (Author) / Elser, Veit (Author) / Fromme, Petra (Author) / Hajdu, Janos (Author) / Hantke, Max F. (Author) / Higashiura, Akifumi (Author) / Hogue, Brenda (Author) / Hosseinizadeh, Ahmad (Author) / Kim, Yoonhee (Author) / Kirian, Richard (Author) / Reddy, Hemanth K. N. (Author) / Lan, Ti-Yen (Author) / Larsson, Daniel S. D. (Author) / Liu, Haiguang (Author) / Loh, N. Duane (Author) / Maia, Filipe R. N. C. (Author) / Mancuso, Adrian P. (Author) / Muhlig, Kerstin (Author) / Nakagawa, Atsushi (Author) / Nam, Daewoong (Author) / Nelson, Garrett (Author) / Nettelblad, Carl (Author) / Okamoto, Kenta (Author) / Ourmazd, Abbas (Author) / Rose, Max (Author) / van der Schot, Gijs (Author) / Schwander, Peter (Author) / Seibert, M. Marvin (Author) / Sellberg, Jonas A. (Author) / Sierra, Raymond G. (Author) / Song, Changyong (Author) / Svenda, Martin (Author) / Timneanu, Nicusor (Author) / Vartanyants, Ivan A. (Author) / Westphal, Daniel (Author) / Wiedom, Max O. (Author) / Williams, Garth J. (Author) / Xavier, Paulraj Lourdu (Author) / Soon, Chun Hong (Author) / Zook, James (Author) / College of Liberal Arts and Sciences (Contributor, Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Life Sciences (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Department of Physics (Contributor)
Created2016-08-01
Description
This survey was used to identify the concerns of the public. There are many population techniques that the public feels are harmful to the behavior and nature of the horses. This research defined the different techniques and history of the situation to then analyze the public's opinion of the topic.

This survey was used to identify the concerns of the public. There are many population techniques that the public feels are harmful to the behavior and nature of the horses. This research defined the different techniques and history of the situation to then analyze the public's opinion of the topic. The survey was trying to determine if any of the techniques could be accepted by the public to control the population of the horses that won’t put the forest, other species, and the herds themselves in danger of possible overpopulation effects.

The data collected from this research showed conflict for the subject. Some of the data was skewed due to conflicting viewpoints on the topic. Analyzing the other aspects of the data we saw noticed that 73% of the servers felt the horses were wild. A majority agreed that the horses should stay there and not be relocated. Some individuals who took the survey were interested in adopting out the horses to help manage horses, there were some concerns with background checks for these adopters since slaughter houses and poor living conditions is a concern.
ContributorsPadayachee, Brittany (Co-author) / Hoover, Sierra (Co-author) / Roen, Duane (Thesis director) / Murphree, Julie (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
This survey was used to identify the concerns of the public. There are many population techniques that the public feels are harmful to the behavior and nature of the horses. This research defined the different techniques and history of the situation to then analyze the public's opinion of the topic.

This survey was used to identify the concerns of the public. There are many population techniques that the public feels are harmful to the behavior and nature of the horses. This research defined the different techniques and history of the situation to then analyze the public's opinion of the topic. The survey was trying to determine if any of the techniques could be accepted by the public to control the population of the horses that won’t put the forest, other species, and the herds themselves in danger of possible overpopulation effects.

The data collected from this research showed conflict for the subject. Some of the data was skewed due to conflicting viewpoints on the topic. Analyzing the other aspects of the data we saw noticed that 73% of the servers felt the horses were wild. A majority agreed that the horses should stay there and not be relocated. Some individuals who took the survey were interested in adopting out the horses to help manage horses, there were some concerns with background checks for these adopters since slaughter houses and poor living conditions is a concern.
ContributorsHoover, Sierra Nicole (Co-author) / Padayachee, Brittany (Co-author) / Roen, Duane (Thesis director) / Murphree, Julie (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
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Description
The purpose of this project was to create a workshop for adults without dance experience to immerse them in dance as a form of therapy. The goals of this workshop are to foster physical awareness and physical creativity. There are four main areas the participants would get experience in from

The purpose of this project was to create a workshop for adults without dance experience to immerse them in dance as a form of therapy. The goals of this workshop are to foster physical awareness and physical creativity. There are four main areas the participants would get experience in from this workshop including self-care/awareness, expression, gesture and choreography. These four areas are the ways that the two main goals manifest themselves. For this project I reviewed research by many different professionals from the therapy, psychology, self-care, dance, and dance therapy fields. Their studies as well as my own experience aided in putting together my themes for the workshop and class activities. I include my methodology, lesson plans, a workbook, and my reflection on the process.
ContributorsWilson, Deepika (Author) / Roses-Thema, Cynthia (Thesis director) / Giorgis, Cyndi (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
Particulate matter (PM) air pollution is a known factor to exacerbate cardiopulmonary diseases. We previously demonstrated that PM mediated endothelial injury and barrier disruption via modulation of the endothelial cytoskeleton and cell-cell junctions, while the effects of PM exposure on cell-cell communication and gap junction activity are still unknown. This

Particulate matter (PM) air pollution is a known factor to exacerbate cardiopulmonary diseases. We previously demonstrated that PM mediated endothelial injury and barrier disruption via modulation of the endothelial cytoskeleton and cell-cell junctions, while the effects of PM exposure on cell-cell communication and gap junction activity are still unknown. This study is focused on the characterization of PM-mediated endothelial dysfunction via Connexin 43 (Cx43), the most abundant Gap junction protein expressed in lung endothelial cells (ECs). PM exposure induces a time-dependent elevation of Cx43 in human lung ECs, at both mRNA and protein levels. N-acetyl-cysteine (NAC), an ROS scavenger, significantly suppresses PM-induced Cx43 expression. Membrane-associated and ER/ Golgi apparatus Cx43 protein are elevated upon PM challenge. In addition, PM also activates the gap junction activity, indicated by the transportation of green fluorescence dye between two adjacent ECs. Moreover, GAP27, a selective Cx43 channel inhibitor, attenuates PM-reduced human lung EC barrier disruption, measured by trans-endothelial electrical resistance (TER) with an electric cell-substrate impedance sensing system. Moreover, knock-down the expression of Cx43 by its selective siRNA alleviates PM-induced MLC phosphorylation. These results highly suggest that Cx43 plays a key role in PM-mediated endothelial barrier disruption and signal transduction. Cx43 may deputy as a therapeutic target in PM-mediated cardiopulmonary disorders.
ContributorsKheshtchin-Kamel, Nabia (Author) / Welcome, Natalie (Thesis director) / Wang, Ting (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
“Sam’s Emotional Day: A Child’s Guide to Recognizing and Handling Emotions” is a creative project that fulfills the thesis requirement for Barrett, The Honors College at Arizona State University. It is an illustrated children’s book meant to help children ages 4-7 identify, understand, and manage the six basic emotions. The

“Sam’s Emotional Day: A Child’s Guide to Recognizing and Handling Emotions” is a creative project that fulfills the thesis requirement for Barrett, The Honors College at Arizona State University. It is an illustrated children’s book meant to help children ages 4-7 identify, understand, and manage the six basic emotions. The illustrations of the main character throughout the book display clear facial expressions associated with each emotion, which were designed for children to easily identify them. The text in the story portion will prompt children to understand the feelings behind each emotion in a simple matter, and the end of the book provides techniques for them to manage emotions. Research on the importance of teaching children emotions, how to teach them, and similar children’s literature are discussed. Facial expressions and feelings while experiencing an emotion was also researched, which is presented in the creative process. An analysis of the text and illustrations is provided as well.
ContributorsMartinson, Hannah Marie (Author) / Jimenez-Arista, Laura (Thesis director) / Pereira, Jennifer (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
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Description
Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.
ContributorsZhou, X. Edward (Author) / Gao, Xiang (Author) / Barty, Anton (Author) / Kang, Yanyong (Author) / He, Yuanzheng (Author) / Liu, Wei (Author) / Ishchenko, Andrii (Author) / White, Thomas A. (Author) / Yefanov, Oleksandr (Author) / Han, Gye Won (Author) / Xu, Qingping (Author) / de Waal, Parker W. (Author) / Suino-Powell, Kelly M. (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Wang, Meitian (Author) / Li, Dianfan (Author) / Caffrey, Martin (Author) / Chapman, Henry N. (Author) / Spence, John (Author) / Fromme, Petra (Author) / Weierstall, Uwe (Author) / Stevens, Raymond C. (Author) / Cherezov, Vadim (Author) / Melcher, Karsten (Author) / Xu, H. Eric (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2016-04-12