Matching Items (161)
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 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
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
Description
Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.
ContributorsLi, Dianfan (Author) / Stansfeld, Phillip J. (Author) / Sansom, Mark S. P. (Author) / Keogh, Aaron (Author) / Vogeley, Lutz (Author) / Howe, Nicole (Author) / Lyons, Joseph A. (Author) / Aragao, David (Author) / Fromme, Petra (Author) / Fromme, Raimund (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Kupitz, Christopher (Author) / Rendek, Kimberley (Author) / Weierstall, Uwe (Author) / Zatsepin, Nadia (Author) / Cherezov, Vadim (Author) / Liu, Wei (Author) / Bandaru, Sateesh (Author) / English, Niall J. (Author) / Gati, Cornelius (Author) / Barty, Anton (Author) / Yefanov, Oleksandr (Author) / Chapman, Henry N. (Author) / Diederichs, Kay (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Seibert, M. Marvin (Author) / Caffrey, Martin (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-12-17
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 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
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. 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
Background: National and international strategies to increase physical activity emphasize environmental and policy changes that can have widespread and long-lasting impact. Evidence from multiple countries using comparable methods is required to strengthen the evidence base for such initiatives. Because some environment and policy changes could have generalizable effects and others may depend on each country's context, only international studies using comparable methods can identify the relevant differences. Methods: Currently 12 countries are participating in the International Physical Activity and the Environment Network (IPEN) study. The IPEN Adult study design involves recruiting adult participants from neighborhoods with wide variations in environmental walkability attributes and socioeconomic status (SES). Results: Eleven of twelve countries are providing accelerometer data and 11 are providing GIS data. Current projections indicate that 14,119 participants will provide survey data on built environments and physical activity and 7145 are likely to provide objective data on both the independent and dependent variables. Though studies are highly comparable, some adaptations are required based on the local context. Conclusions: This study was designed to inform evidence-based international and country-specific physical activity policies and interventions to help prevent obesity and other chronic diseases that are high in developed countries and growing rapidly in developing countries.
ContributorsKerr, Jacqueline (Author) / Sallis, James F. (Author) / Owen, Neville (Author) / De Bourdeaudhuij, Ilse (Author) / Cerin, Ester (Author) / Sugiyama, Takemi (Author) / Reis, Rodrigo (Author) / Sarmiento, Olga (Author) / Froemel, Karel (Author) / Mitas, Josef (Author) / Troelsen, Jens (Author) / Christiansen, Lars Breum (Author) / Macfarlane, Duncan (Author) / Salvo, Deborah (Author) / Schofield, Grant (Author) / Badland, Hannah (Author) / Guillen-Grima, Francisco (Author) / Aguinaga-Ontoso, Ines (Author) / Davey, Rachel (Author) / Bauman, Adrian (Author) / Saelens, Brian (Author) / Riddoch, Chris (Author) / Ainsworth, Barbara (Author) / Pratt, Michael (Author) / Schmidt, Tom (Author) / Frank, Lawrence (Author) / Adams, Marc (Author) / Conway, Terry (Author) / Cain, Kelli (Author) / Van Dyck, Delfien (Author) / Bracy, Nicole (Author) / College of Health Solutions (Contributor) / School of Nutrition and Health Promotion (Contributor)
Created2013
Description
The development of stab-resistant Kevlar armor has been an ongoing field of research
since the late 1990s, with the ultimate goal of improving the multi-threat capabilities of
traditional soft-body armor while significantly improving its protective efficiency - the amount
of layers of armor material required to defeat threats. To create a novel, superior materials
system to reinforce Kevlar armor for the Norica Capstone project, this thesis set out to
synthesize, recover, and characterize zinc oxide nanowire colloids.
The materials synthesized were successfully utilized in the wider Capstone effort to
dramatically enhance the protective abilities of Kevlar, while the data obtained on the 14
hydrothermal synthesis attempts and numerous challenges at recovery provided critical
information on the synthesis parameters involved in the reliable, scalable mass production of the
nanomaterial additive. Additionally, recovery was unconventionally facilitated in the absence of
a vacuum filtration apparatus with nanoscale filters by intentionally inducing electrostatic
agglomeration of the nanowires during standard gravity filtration. The subsequent application of
these nanowires constituted a pioneering use in the production of nanowire-reinforced
STF-based Kevlar coatings, and support the future development and, ultimately, the
commercialization of lighter and more-protective soft armor systems.
since the late 1990s, with the ultimate goal of improving the multi-threat capabilities of
traditional soft-body armor while significantly improving its protective efficiency - the amount
of layers of armor material required to defeat threats. To create a novel, superior materials
system to reinforce Kevlar armor for the Norica Capstone project, this thesis set out to
synthesize, recover, and characterize zinc oxide nanowire colloids.
The materials synthesized were successfully utilized in the wider Capstone effort to
dramatically enhance the protective abilities of Kevlar, while the data obtained on the 14
hydrothermal synthesis attempts and numerous challenges at recovery provided critical
information on the synthesis parameters involved in the reliable, scalable mass production of the
nanomaterial additive. Additionally, recovery was unconventionally facilitated in the absence of
a vacuum filtration apparatus with nanoscale filters by intentionally inducing electrostatic
agglomeration of the nanowires during standard gravity filtration. The subsequent application of
these nanowires constituted a pioneering use in the production of nanowire-reinforced
STF-based Kevlar coatings, and support the future development and, ultimately, the
commercialization of lighter and more-protective soft armor systems.
ContributorsDurso, Michael Nathan (Author) / Tongay, Sefaattin (Thesis director) / Zhuang, Houlong (Committee member) / Materials Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Cell viability is an important assessment in cell culture to characterize the health of the cell population and confirm if cells are alive. Morphology or end-line assays are used to determine cell viability of entire populations. Intracellular pO2 levels is indicative of cell health and metabolism that can be used as a factor to asses cell viability in an in-line assay. Siloxane based pO2 sensing nanoprobes present a modality to visualize intracellular pO2. Using fluorescent lifetime imaging microscopy (FLIM), pO2 levels can be mapped intracellular as a highly functional in-line assay for cell viability. FLIM is an imaging modality that reconstructs an image based of its fluorescent lifetime. Nanoprobes were synthesized in different manufacturing/storage conditions. The nanoprobes for both long- and short-term storage were characterized in a cell free environment testing for changes in fluorescent intensity, average and maximum nanoprobe diameter. The nanoprobes were validated in two different culture systems, 2D and microcarrier culture systems, for human derived neural progenitor cells (NPCs) and neurons. Long- and short-term storage nanoprobes were used to label different neuronal based culture systems to asses labeling efficiency through fluorescent microscopy and flow cytometry. NPCs and neurons in each culture system was tested to see if nanoprobe labeling effected cellular phenotype for traits such as: cell proliferation, gene expression, and calcium imaging. Long-term and short-term storage nanoprobes were successfully validated for both NPCs and neurons in all culture systems. Assessments of the pO2 sensing nanoprobes will be further developed to create a highly functional and efficient in-line test for cell viability.
ContributorsLeyasi, Salma (Author) / Brafman, David (Thesis director) / Kodibagkar, Vikram (Committee member) / Harrington Bioengineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
With the development of technology, using photographs to measure plate waste is an increasing
trend. These photographs are later analyzed when the data is being entered into a form or
system. Previously, these forms or systems have not been assessed for usability. This research
study looks at three iterations of a digital plate waste observation system developed for the
School Lunch Study at Arizona State University. The System Usability Scale was used to
understand the functionality of the digital plate waste observation system. An area for free
responses was used to understand aspects of the system that were liked by research assistants
and what technical difficulties the research assistants encountered. These responses were used to
develop the next version of the digital plate waste observation system. Time to complete a task
was calculated to see the trends across all versions of the system. With each version, the System
Usability Scale scores increased along with the time to complete a task. This study found that
following the workflow of research assistants, being able to manipulate a photograph, having
menu items populated, and decreasing the amount of typing performed by adding selections to be
useful design aspects. Future digital plate waste observation systems can implement the
successful design aspects of this system, be aware of errors experienced, and implement helpful
features not found in this system. Future studies can look at the effect proctored training sessions
have on the time to complete a task and the relation of System Usability Scale scores with the
success of data entry.
trend. These photographs are later analyzed when the data is being entered into a form or
system. Previously, these forms or systems have not been assessed for usability. This research
study looks at three iterations of a digital plate waste observation system developed for the
School Lunch Study at Arizona State University. The System Usability Scale was used to
understand the functionality of the digital plate waste observation system. An area for free
responses was used to understand aspects of the system that were liked by research assistants
and what technical difficulties the research assistants encountered. These responses were used to
develop the next version of the digital plate waste observation system. Time to complete a task
was calculated to see the trends across all versions of the system. With each version, the System
Usability Scale scores increased along with the time to complete a task. This study found that
following the workflow of research assistants, being able to manipulate a photograph, having
menu items populated, and decreasing the amount of typing performed by adding selections to be
useful design aspects. Future digital plate waste observation systems can implement the
successful design aspects of this system, be aware of errors experienced, and implement helpful
features not found in this system. Future studies can look at the effect proctored training sessions
have on the time to complete a task and the relation of System Usability Scale scores with the
success of data entry.
ContributorsStott, Dahlia (Author) / Adams, Marc (Thesis director) / Barto, Henry (Committee member) / College of Health Solutions (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12
Description
Over 5.8 million people are currently living with Alzheimer’s disease (AD), with the sixth highest mortality rate in the United States. No known cure or substantially life-extending treatment exists. With the growing aging population these numbers are only expected to increase to about 13.8 million by the year 2050. Alzheimer’s is a multifactorial disease, giving rise to two main types: familial AD (FAD) and sporadic AD (SAD). Although there are different factors associated with each type of the disease, both FAD and SAD result in neuronal and synaptic loss and remain difficult to model in-vitro and treat overall.
Current advances in cellular models of neurodegenerative diseases overcome a variety of limitations possessed in animal and post-mortem human models. Human-induced pluripotent stem cells (hiPSCs) provide a platform with cells that can self-renew and differentiate into mature and functional cell types. HiPSCs are at the forefront of neurodegenerative disease research because of their ability to differentiate into neural cell types. Apolipoprotein E (ApoE) is a protein encoded by the APOE gene found on chromosome 19 of the human genome. There are three common polymorphisms in the APOE gene, resulting from a single amino acid change in the protein. The presence of these polymorphisms are studied as associated risk factors of developing AD. Different combinations of these alleles closely relate to the risk a patient has in developing Alzheimer’s disease. The risk associated effects of this gene are primarily investigated, however the protective effects are not examined to the same extent.
This research aims to overcome the existing limitations in cell differentiations and improve cell population purity that limits the variables present in the culture. To do this, this study optimized a differentiation protocol by separating and purifying neuronal cell populations to study the potential protective effects associated with ApoE, a risk factor seen in SAD. This platform aims to use a purified cell population to effectively analyze cell type specific affects of the ApoE risk factor, specifically in neurons.
Current advances in cellular models of neurodegenerative diseases overcome a variety of limitations possessed in animal and post-mortem human models. Human-induced pluripotent stem cells (hiPSCs) provide a platform with cells that can self-renew and differentiate into mature and functional cell types. HiPSCs are at the forefront of neurodegenerative disease research because of their ability to differentiate into neural cell types. Apolipoprotein E (ApoE) is a protein encoded by the APOE gene found on chromosome 19 of the human genome. There are three common polymorphisms in the APOE gene, resulting from a single amino acid change in the protein. The presence of these polymorphisms are studied as associated risk factors of developing AD. Different combinations of these alleles closely relate to the risk a patient has in developing Alzheimer’s disease. The risk associated effects of this gene are primarily investigated, however the protective effects are not examined to the same extent.
This research aims to overcome the existing limitations in cell differentiations and improve cell population purity that limits the variables present in the culture. To do this, this study optimized a differentiation protocol by separating and purifying neuronal cell populations to study the potential protective effects associated with ApoE, a risk factor seen in SAD. This platform aims to use a purified cell population to effectively analyze cell type specific affects of the ApoE risk factor, specifically in neurons.
ContributorsFrisch, Carlye Arin (Author) / Brafman, David (Thesis director) / Tian, Xiaojun (Committee member) / Harrington Bioengineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05