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- Creators: Ira A. Fulton Schools of Engineering
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Description
Peter was 12 years old when he heard gunshots and bombing at his village.
“Lost Boys Found” is an ongoing, interdisciplinary project that is collecting, recording and archiving the oral histories of the Lost Boys/Girls of Sudan. The collection is a work-in-progress, seeking to record the oral history of as many Lost Boys/Girls as are willing, and will be used in a future book.
“Lost Boys Found” is an ongoing, interdisciplinary project that is collecting, recording and archiving the oral histories of the Lost Boys/Girls of Sudan. The collection is a work-in-progress, seeking to record the oral history of as many Lost Boys/Girls as are willing, and will be used in a future book.
ContributorsMach, Peter (Author)
Description
We studied left ventricular flow patterns for a range of rotational orientations of a bileaflet mechanical heart valve (MHV) implanted in the mitral position of an elastic model of a beating left ventricle (LV). The valve was rotated through 3 angular positions (0, 45, and 90 degrees) about the LV long axis. Ultrasound scans of the elastic LV were obtained in four apical 2-dimensional (2D) imaging projections, each with 45 degrees of separation. Particle imaging velocimetry was performed during the diastolic period to quantify the in-plane velocity field obtained by computer tracking of diluted microbubbles in the acquired ultrasound projections. The resulting velocity field, vorticity, and shear stresses were statistically significantly altered by angular positioning of the mechanical valve, although the results did not show any specific trend with the valve angular position and were highly dependent on the orientation of the imaging plane with respect to the valve. We conclude that bileaflet MHV orientation influences hemodynamics of LV filling. However, determination of ‘optimal’ valve orientation cannot be made without measurement techniques that account for the highly 3-dimensional (3D) intraventricular flow.
ContributorsWesterdale, John (Author) / Adrian, Ronald (Author) / Squires, Kyle (Author) / Chaliki, Hari (Author) / Belohlavek, Marek (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School for the Engineering of Matter, Transport and Energy (Contributor)
Created2015-06-26
Description
The advent and application of the X-ray free-electron laser (XFEL) has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors) lead to the requirement of large data sets (and thus 10–100 mg of protein) for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also permit an analysis of the dependence of crystal quality on crystal size.
ContributorsAbdallah, Bahige (Author) / Zatsepin, Nadia (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Conrad, Chelsie (Author) / Dorner, Katerina (Author) / Sierra, Raymond G. (Author) / Stevenson, Hilary P. (Author) / Camacho Alanis, Fernanda (Author) / Grant, Thomas D. (Author) / Nelson, Garrett (Author) / James, Daniel (Author) / Calero, Guillermo (Author) / Wachter, Rebekka (Author) / Spence, John (Author) / Weierstall, Uwe (Author) / Fromme, Petra (Author) / Ros, Alexandra (Author) / Department of Chemistry and Biochemistry (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2015-08-19
Description
pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or 6.9 and 10 mM glucose, fructose, or cellobiose as the carbon substrate. We analyzed 16S rRNA gene sequences and fermentation products. Microbial diversity was driven by both pH and substrate type. Due to insufficient alkalinity, a drop in pH from 6.0 to ~4.5 clustered pH 6.0 cultures together and distant from pH 6.5 and 6.9 cultures, which experienced only small pH drops. Cellobiose yielded more acidity than alkalinity due to the amount of fermentable carbon, which moved cellobiose pH 6.5 cultures away from other pH 6.5 cultures. The impact of pH on microbial community structure was reflected by fermentative metabolism. Lactate accumulation occurred in pH 6.0 cultures, whereas propionate and acetate accumulations were observed in pH 6.5 and 6.9 cultures and independently from the type of substrate provided. Finally, pH had an impact on the interactions between lactate-producing and -consuming communities. Lactate-producing Streptococcus dominated pH 6.0 cultures, and acetate- and propionate-producing Veillonella, Bacteroides, and Escherichia dominated the cultures started at pH 6.5 and 6.9. Acid inhibition on lactate-consuming species led to lactate accumulation. Our results provide insights into pH-derived changes in fermenting microbiota and metabolisms in the human gut.
ContributorsIlhan, Zehra (Author) / Marcus, Andrew (Author) / Kang, Dae-Wook (Author) / Rittmann, Bruce (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Fundamental and Applied Microbiomics (Contributor) / Ira A. Fulton Schools of Engineering (Contributor) / School of Sustainable Engineering and the Built Environment (Contributor)
Created2017-05-03
Description
The occurrence of nonliquid and liquid physical states of submicron atmospheric particulate matter (PM) downwind of an urban region in central Amazonia was investigated. Measurements were conducted during two intensive operating periods (IOP1 and IOP2) that took place during the wet and dry seasons of the GoAmazon2014/5 campaign. Air masses representing variable influences of background conditions, urban pollution, and regional- and continental-scale biomass burning passed over the research site. As the air masses varied, particle rebound fraction, an indicator of physical state, was measured in real time at ground level using an impactor apparatus. Micrographs collected by transmission electron microscopy confirmed that liquid particles adhered, while nonliquid particles rebounded. Relative humidity (RH) was scanned to collect rebound curves.
When the apparatus RH matched ambient RH, 95 % of the particles adhered as a campaign average. Secondary organic material, produced for the most part by the oxidation of volatile organic compounds emitted from the forest, produces liquid PM over this tropical forest. During periods of anthropogenic influence, by comparison, the rebound fraction dropped to as low as 60 % at 95 % RH. Analyses of the mass spectra of the atmospheric PM by positive-matrix factorization (PMF) and of concentrations of carbon monoxide, total particle number, and oxides of nitrogen were used to identify time periods affected by anthropogenic influences, including both urban pollution and biomass burning. The occurrence of nonliquid PM at high RH correlated with these indicators of anthropogenic influence. A linear model having as output the rebound fraction and as input the PMF factor loadings explained up to 70 % of the variance in the observed rebound fractions. Anthropogenic influences can contribute to the presence of nonliquid PM in the atmospheric particle population through the combined effects of molecular species that increase viscosity when internally mixed with background PM and increased concentrations of nonliquid anthropogenic particles in external mixtures of anthropogenic and biogenic PM.
ContributorsBateman, Adam P. (Author) / Gong, Zhaoheng (Author) / Harder, Tristan H. (Author) / de Sa, Suzane S. (Author) / Wang, Bingbing (Author) / Castillo, Paulo (Author) / China, Swarup (Author) / Liu, Yingjun (Author) / O'Brien, Rachel E. (Author) / Palm, Brett B. (Author) / Shiu, Hung-Wei (Author) / Cirino, Glauber G. (Author) / Thalman, Ryan (Author) / Adachi, Kouji (Author) / Alexander, M. Lizabeth (Author) / Artaxo, Paulo (Author) / Bertram, Allan K. (Author) / Buseck, Peter (Author) / Gilles, Mary K. (Author) / Jimenez, Jose L. (Author) / Laskin, Alexander (Author) / Manzi, Antonio O. (Author) / Sedlacek, Arthur (Author) / Souza, Rodrigo A. F. (Author) / Wang, Jian (Author) / Zaveri, Rahul (Author) / Martin, Scot T. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Earth and Space Exploration (Contributor) / School of Molecular Sciences (Contributor)
Created2017-02-06
Description
Carbohydrates are one of the four main building blocks of life, and are categorized as monosaccharides (sugars), oligosaccharides and polysaccharides. Each sugar can exist in two alternative anomers (in which a hydroxy group at C-1 takes different orientations) and each pair of sugars can form different epimers (isomers around the stereocentres connecting the sugars). This leads to a vast combinatorial complexity, intractable to mass spectrometry and requiring large amounts of sample for NMR characterization. Combining measurements of collision cross section with mass spectrometry (IM–MS) helps, but many isomers are still difficult to separate. Here, we show that recognition tunnelling (RT) can classify many anomers and epimers via the current fluctuations they produce when captured in a tunnel junction functionalized with recognition molecules. Most importantly, RT is a nanoscale technique utilizing sub-picomole quantities of analyte. If integrated into a nanopore, RT would provide a unique approach to sequencing linear polysaccharides.
ContributorsIm, Jong One (Author) / Biswas, Sovan (Author) / Liu, Hao (Author) / Zhao, Yanan (Author) / Sen, Suman (Author) / Biswas, Sudipta (Author) / Ashcroft, Brian (Author) / Borges, Chad (Author) / Wang, Xu (Author) / Lindsay, Stuart (Author) / Zhang, Peiming (Author) / Biodesign Institute (Contributor) / Single Molecule Biophysics (Contributor) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / School of Molecular Sciences (Contributor)
Created2016-12-21
Description
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A[subscript 2A] adenosine receptor (A[subscript 2A]AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A[subscript 2A]AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A[subscript 2A]AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
ContributorsMartin Garcia, Jose Manuel (Author) / Conrad, Chelsie (Author) / Nelson, Garrett (Author) / Stander, Natasha (Author) / Zatsepin, Nadia (Author) / Zook, James (Author) / Zhu, Lan (Author) / Geiger, James (Author) / Chun, Eugene (Author) / Kissick, David (Author) / Hilgart, Mark C. (Author) / Ogata, Craig (Author) / Ishchenko, Andrii (Author) / Nagaratnam, Nirupa (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Subramanian, Ganesh (Author) / Schaffer, Alexander (Author) / James, Daniel (Author) / Ketwala, Gihan (Author) / Venugopalan, Nagarajan (Author) / Xu, Shenglan (Author) / Corcoran, Stephen (Author) / Ferguson, Dale (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Cherezov, Vadim (Author) / Fromme, Petra (Author) / Fischetti, Robert F. (Author) / Liu, Wei (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2017-05-24
Description
Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.
ContributorsReddy, Hemanth K. N. (Author) / Yoon, Chun Hong (Author) / Aquila, Andrew (Author) / Awel, Salah (Author) / Ayyer, Kartik (Author) / Barty, Anton (Author) / Berntsen, Peter (Author) / Bielecki, Johan (Author) / Bobkov, Sergey (Author) / Bucher, Maximilian (Author) / Carini, Gabriella A. (Author) / Carron, Sebastian (Author) / Chapman, Henry (Author) / Daurer, Benedikt (Author) / DeMirci, Hasan (Author) / Ekeberg, Tomas (Author) / Fromme, Petra (Author) / Hajdu, Janos (Author) / Hanke, Max Felix (Author) / Hart, Philip (Author) / Hogue, Brenda (Author) / Hasseinizadeh, Ahmad (Author) / Kim, Yoonhee (Author) / Kirian, Richard (Author) / Kurta, Ruslan P. (Author) / Larsson, Daniel S. D. (Author) / Loh, N. Duane (Author) / Maia, Filipe R. N. C. (Author) / Mancuso, Adrian P. (Author) / Muhlig, Kerstin (Author) / Munke, Anna (Author) / Nam, Daewoong (Author) / Nettelblad, Carl (Author) / Ourmazd, Abbas (Author) / Rose, Max (Author) / Schwander, Peter (Author) / Seibert, Marvin (Author) / Sellberg, Jonas A. (Author) / Song, Changyong (Author) / Spence, John (Author) / Svenda, Martin (Author) / van der Schot, Gijs (Author) / Vartanyants, Ivan A. (Author) / Williams, Garth J. (Author) / Xavier, P. Lourdu (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) / School of Life Sciences (Contributor) / Department of Physics (Contributor)
Created2017-06-27
Description
Purpose: To evaluate a new method of measuring ocular exposure in the context of a natural blink pattern through analysis of the variables tear film breakup time (TFBUT), interblink interval (IBI), and tear film breakup area (BUA).
Methods: The traditional methodology (Forced-Stare [FS]) measures TFBUT and IBI separately. TFBUT is measured under forced-stare conditions by an examiner using a stopwatch, while IBI is measured as the subject watches television. The new methodology (video capture manual analysis [VCMA]) involves retrospective analysis of video data of fluorescein-stained eyes taken through a slit lamp while the subject watches television, and provides TFBUT and BUA for each IBI during the 1-minute video under natural blink conditions. The FS and VCMA methods were directly compared in the same set of dry-eye subjects. The VCMA method was evaluated for the ability to discriminate between dry-eye subjects and normal subjects. The VCMA method was further evaluated in the dry eye subjects for the ability to detect a treatment effect before, and 10 minutes after, bilateral instillation of an artificial tear solution.
Results: Ten normal subjects and 17 dry-eye subjects were studied. In the dry-eye subjects, the two methods differed with respect to mean TFBUTs (5.82 seconds, FS; 3.98 seconds, VCMA; P = 0.002). The FS variables alone (TFBUT, IBI) were not able to successfully distinguish between the dry-eye and normal subjects, whereas the additional VCMA variables, both derived and observed (BUA, BUA/IBI, breakup rate), were able to successfully distinguish between the dry-eye and normal subjects in a statistically significant fashion. TFBUT (P = 0.034) and BUA/IBI (P = 0.001) were able to distinguish the treatment effect of artificial tears in dry-eye subjects.
Conclusion: The VCMA methodology provides a clinically relevant analysis of tear film stability measured in the context of a natural blink pattern.
Methods: The traditional methodology (Forced-Stare [FS]) measures TFBUT and IBI separately. TFBUT is measured under forced-stare conditions by an examiner using a stopwatch, while IBI is measured as the subject watches television. The new methodology (video capture manual analysis [VCMA]) involves retrospective analysis of video data of fluorescein-stained eyes taken through a slit lamp while the subject watches television, and provides TFBUT and BUA for each IBI during the 1-minute video under natural blink conditions. The FS and VCMA methods were directly compared in the same set of dry-eye subjects. The VCMA method was evaluated for the ability to discriminate between dry-eye subjects and normal subjects. The VCMA method was further evaluated in the dry eye subjects for the ability to detect a treatment effect before, and 10 minutes after, bilateral instillation of an artificial tear solution.
Results: Ten normal subjects and 17 dry-eye subjects were studied. In the dry-eye subjects, the two methods differed with respect to mean TFBUTs (5.82 seconds, FS; 3.98 seconds, VCMA; P = 0.002). The FS variables alone (TFBUT, IBI) were not able to successfully distinguish between the dry-eye and normal subjects, whereas the additional VCMA variables, both derived and observed (BUA, BUA/IBI, breakup rate), were able to successfully distinguish between the dry-eye and normal subjects in a statistically significant fashion. TFBUT (P = 0.034) and BUA/IBI (P = 0.001) were able to distinguish the treatment effect of artificial tears in dry-eye subjects.
Conclusion: The VCMA methodology provides a clinically relevant analysis of tear film stability measured in the context of a natural blink pattern.
ContributorsAbelson, Richard (Author) / Lane, Keith J. (Author) / Angjeli, Endri (Author) / Johnston, Patrick (Author) / Ousler, George (Author) / Montgomery, Douglas (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Computing, Informatics and Decision Systems Engineering (Contributor)
Created2011-09-21
Description
Purpose: To investigate use of an improved ocular tear film analysis protocol (OPI 2.0) in the Controlled Adverse Environment (CAE[superscript SM]) model of dry eye disease, and to examine the utility of new metrics in the identification of subpopulations of dry eye patients.
Methods: Thirty-three dry eye subjects completed a single-center, single-visit, pilot CAE study. The primary endpoint was mean break-up area (MBA) as assessed by the OPI 2.0 system. Secondary endpoints included corneal fluorescein staining, tear film break-up time, and OPI 2.0 system measurements. Subjects were also asked to rate their ocular discomfort throughout the CAE. Dry eye endpoints were measured at baseline, immediately following a 90-minute CAE exposure, and again 30 minutes after exposure.
Results: The post-CAE measurements of MBA showed a statistically significant decrease from the baseline measurements. The decrease was relatively specific to those patients with moderate to severe dry eye, as measured by baseline MBA. Secondary endpoints including palpebral fissure size, corneal staining, and redness, also showed significant changes when pre- and post-CAE measurements were compared. A correlation analysis identified specific associations between MBA, blink rate, and palpebral fissure size. Comparison of MBA responses allowed us to identify subpopulations of subjects who exhibited different compensatory mechanisms in response to CAE challenge. Of note, none of the measures of tear film break-up time showed statistically significant changes or correlations in pre-, versus post-CAE measures.
Conclusion: This pilot study confirms that the tear film metric MBA can detect changes in the ocular surface induced by a CAE, and that these changes are correlated with other, established measures of dry eye disease. The observed decrease in MBA following CAE exposure demonstrates that compensatory mechanisms are initiated during the CAE exposure, and that this compensation may provide the means to identify and characterize clinically relevant subpopulations of dry eye patients.
Methods: Thirty-three dry eye subjects completed a single-center, single-visit, pilot CAE study. The primary endpoint was mean break-up area (MBA) as assessed by the OPI 2.0 system. Secondary endpoints included corneal fluorescein staining, tear film break-up time, and OPI 2.0 system measurements. Subjects were also asked to rate their ocular discomfort throughout the CAE. Dry eye endpoints were measured at baseline, immediately following a 90-minute CAE exposure, and again 30 minutes after exposure.
Results: The post-CAE measurements of MBA showed a statistically significant decrease from the baseline measurements. The decrease was relatively specific to those patients with moderate to severe dry eye, as measured by baseline MBA. Secondary endpoints including palpebral fissure size, corneal staining, and redness, also showed significant changes when pre- and post-CAE measurements were compared. A correlation analysis identified specific associations between MBA, blink rate, and palpebral fissure size. Comparison of MBA responses allowed us to identify subpopulations of subjects who exhibited different compensatory mechanisms in response to CAE challenge. Of note, none of the measures of tear film break-up time showed statistically significant changes or correlations in pre-, versus post-CAE measures.
Conclusion: This pilot study confirms that the tear film metric MBA can detect changes in the ocular surface induced by a CAE, and that these changes are correlated with other, established measures of dry eye disease. The observed decrease in MBA following CAE exposure demonstrates that compensatory mechanisms are initiated during the CAE exposure, and that this compensation may provide the means to identify and characterize clinically relevant subpopulations of dry eye patients.
ContributorsAbelson, Richard (Author) / Lane, Keith J. (Author) / Rodriguez, John (Author) / Johnston, Patrick (Author) / Angjeli, Endri (Author) / Ousler, George (Author) / Montgomery, Douglas (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Computing, Informatics and Decision Systems Engineering (Contributor)
Created2012-11-12