ASU Regents' Professors Open Access Works
The title “Regents’ Professor” is the highest faculty honor awarded at Arizona State University. It is conferred on ASU faculty who have made pioneering contributions in their areas of expertise, who have achieved a sustained level of distinction, and who enjoy national and international recognition for these accomplishments. This collection contains primarily open access works by ASU Regents' Professors.
Displaying 41 - 50 of 211
Description
Anaerobic oxidation of methane (AOM) is an important process for understanding the global flux of methane and its relation to the global carbon cycle. Although AOM is known to be coupled to reductions of sulfate, nitrite, and nitrate, evidence that AOM is coupled with extracellular electron transfer (EET) to conductive solids is relatively insufficient. Here, we demonstrate EET-dependent AOM in a biofilm anode dominated by Geobacter spp. and Methanobacterium spp. using carbon-fiber electrodes as the terminal electron sink. The steady-state current density was kept at 11.0 ± 1.3 mA/m[superscript 2] in a microbial electrochemical cell, and isotopic experiments supported AOM-EET to the anode. Fluorescence in situ hybridization images and metagenome results suggest that Methanobacterium spp. may work synergistically with Geobacter spp. to allow AOM, likely by employing intermediate (formate or H[subscript 2])-dependent inter-species electron transport. Since metal oxides are widely present in sedimentary and terrestrial environments, an AOM-EET niche would have implications for minimizing the net global emissions of methane.
ContributorsGao, Yaohuan (Author) / Lee, Jangho (Author) / Neufeld, Josh D. (Author) / Park, Joonhong (Author) / Rittmann, Bruce (Author) / Lee, Hyung-Sool (Author) / Biodesign Institute (Contributor) / Swette Center for Environmental Biotechnology (Contributor)
Created2017-07-11
Description
Surveys of carbon:nitrogen:phosphorus ratios are available now for major groups of biota and for various aquatic and terrestrial biomes. However, while fungi play an important role in nutrient cycling in ecosystems, relatively little is known about their C:N:P stoichiometry and how it varies across taxonomic groups, functional guilds, and environmental conditions. Here we present the first systematic compilation of C:N:P data for fungi including four phyla (Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota). The C, N, and P contents (percent of dry mass) of fungal biomass varied from 38 to 57%, 0.23 to 15%, and 0.040 to 5.5%, respectively. Median C:N:P stoichiometry for fungi was 250:16:1 (molar), remarkably similar to the canonical Redfield values. However, we found extremely broad variation in fungal C:N:P ratios around the central tendencies in C:N:P ratios. Lower C:P and N:P ratios were found in Ascomycota fungi than in Basidiomycota fungi while significantly lower C:N ratios (p < 0.05) and higher N:P ratios (p < 0.01) were found in ectomycorrhizal fungi than in saprotrophs. Furthermore, several fungal stoichiometric ratios were strongly correlated with geographic and abiotic environmental factors, especially latitude, precipitation, and temperature. The results have implications for understanding the roles that fungi play in function in symbioses and in soil nutrient cycling. Further work is needed on the effects of actual in situ growth conditions of fungal growth on stoichiometry in the mycelium.
ContributorsZhang, Ji (Author) / Elser, James (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2017-07-14
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
Gene expression patterns assayed across development can offer key clues about a gene’s function and regulatory role. Drosophila melanogaster is ideal for such investigations as multiple individual and high-throughput efforts have captured the spatiotemporal patterns of thousands of embryonic expressed genes in the form of in situ images. FlyExpress (www.flyexpress.net), a knowledgebase based on a massive and unique digital library of standardized images and a simple search engine to find coexpressed genes, was created to facilitate the analytical and visual mining of these patterns. Here, we introduce the next generation of FlyExpress resources to facilitate the integrative analysis of sequence data and spatiotemporal patterns of expression from images. FlyExpress 7 now includes over 100,000 standardized in situ images and implements a more efficient, user-defined search algorithm to identify coexpressed genes via Genomewide Expression Maps (GEMs). Shared motifs found in the upstream 5′ regions of any pair of coexpressed genes can be visualized in an interactive dotplot. Additional webtools and link-outs to assist in the downstream validation of candidate motifs are also provided. Together, FlyExpress 7 represents our largest effort yet to accelerate discovery via the development and dispersal of new webtools that allow researchers to perform data-driven analyses of coexpression (image) and genomic (sequence) data.
ContributorsKumar, Sudhir (Author) / Konikoff, Charlotte (Author) / Sanderford, Maxwell (Author) / Liu, Li (Author) / Newfeld, Stuart (Author) / Ye, Jieping (Author) / Kulathinal, Rob J. (Author) / College of Health Solutions (Contributor) / Department of Biomedical Informatics (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2017-06-30
Description
For many species, migration evolves to allow organisms to access better resources. However, the proximate factors that trigger these developmental changes, and how and why these vary across species, remain poorly understood. One prominent hypothesis is that poor-quality food promotes development of migratory phenotypes and this has been clearly shown for some polyphenic insects. In other animals, particularly long-distance bird migrants, it is clear that high-quality food is required to prepare animals for a successful migration. We tested the effect of diet quality on the flight behaviour and morphology of the Mongolian locust, Oedaleus asiaticus. Locusts reared at high population density and fed low-N grass (performance-enhancing for this species) had enhanced migratory morphology relative to locusts fed high-N grass. Furthermore, locusts fed synthetic diets with an optimal 1 : 2 protein : carbohydrate ratio flew for longer times than locusts fed diets with lower or higher protein : carbohydrate ratios. In contrast to the hypothesis that performance-degrading food should enhance migration, our results support the more nuanced hypothesis that high-quality diets promote development of migratory characteristics when migration is physiologically challenging.
ContributorsCease, Arianne (Author) / Harrison, Jon (Author) / Hao, Shuguang (Author) / Niren, Danielle (Author) / Zhang, Guangming (Author) / Kang, Le (Author) / Elser, James (Author) / Julie Ann Wrigley Global Institute of Sustainability (Contributor) / School of Sustainability (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2017-06-07
Description
Aim
The aim of this study was to investigate the potential associations of reallocating 30 minutes sedentary time in long bouts (>60 min) to sedentary time in non-bouts, light intensity physical activity (LPA) and moderate- to vigorous physical activity (MVPA) with cardiometabolic risk factors in a population diagnosed with prediabetes or type 2 diabetes.
Methods
Participants diagnosed with prediabetes and type 2 diabetes (n = 124, 50% men, mean [SD] age = 63.8 [7.5] years) were recruited to the physical activity intervention Sophia Step Study. For this study baseline data was used with a cross-sectional design. Time spent in sedentary behaviors in bouts (>60 min) and non-bouts (accrued in <60 min bouts) and physical activity was measured using the ActiGraph GT1M. Associations of reallocating bouted sedentary time to non-bouted sedentary time, LPA and MVPA with cardiometabolic risk factors were examined using an isotemporal substitution framework with linear regression models.
Results
Reallocating 30 minutes sedentary time in bouts to MVPA was associated with lower waist circumference (b = -4.30 95% CI:-7.23, -1.38 cm), lower BMI (b = -1.46 95% CI:-2.60, -0.33 kg/m2) and higher HDL cholesterol levels (b = 0.11 95% CI: 0.02, 0.21 kg/m[superscript 2]. Similar associations were seen for reallocation of sedentary time in non-bouts to MVPA. Reallocating sedentary time in bouts to LPA was associated only with lower waist circumference.
Conclusion
Reallocation of sedentary time in bouts as well as non-bouts to MVPA, but not to LPA, was beneficially associated with waist circumference, BMI and HDL cholesterol in individuals with prediabetes and type 2 diabetes. The results of this study confirm the importance of reallocation sedentary time to MVPA.
The aim of this study was to investigate the potential associations of reallocating 30 minutes sedentary time in long bouts (>60 min) to sedentary time in non-bouts, light intensity physical activity (LPA) and moderate- to vigorous physical activity (MVPA) with cardiometabolic risk factors in a population diagnosed with prediabetes or type 2 diabetes.
Methods
Participants diagnosed with prediabetes and type 2 diabetes (n = 124, 50% men, mean [SD] age = 63.8 [7.5] years) were recruited to the physical activity intervention Sophia Step Study. For this study baseline data was used with a cross-sectional design. Time spent in sedentary behaviors in bouts (>60 min) and non-bouts (accrued in <60 min bouts) and physical activity was measured using the ActiGraph GT1M. Associations of reallocating bouted sedentary time to non-bouted sedentary time, LPA and MVPA with cardiometabolic risk factors were examined using an isotemporal substitution framework with linear regression models.
Results
Reallocating 30 minutes sedentary time in bouts to MVPA was associated with lower waist circumference (b = -4.30 95% CI:-7.23, -1.38 cm), lower BMI (b = -1.46 95% CI:-2.60, -0.33 kg/m2) and higher HDL cholesterol levels (b = 0.11 95% CI: 0.02, 0.21 kg/m[superscript 2]. Similar associations were seen for reallocation of sedentary time in non-bouts to MVPA. Reallocating sedentary time in bouts to LPA was associated only with lower waist circumference.
Conclusion
Reallocation of sedentary time in bouts as well as non-bouts to MVPA, but not to LPA, was beneficially associated with waist circumference, BMI and HDL cholesterol in individuals with prediabetes and type 2 diabetes. The results of this study confirm the importance of reallocation sedentary time to MVPA.
ContributorsRossen, Jenny (Author) / Buman, Matthew (Author) / Johansson, Unn-Britt (Author) / Yngve, Agneta (Author) / Ainsworth, Barbara (Author) / Brismar, Kerstin (Author) / Hagstromer, Maria (Author) / College of Health Solutions (Contributor) / School of Nutrition and Health Promotion (Contributor)
Created2017-07-28
Description
X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
ContributorsFrank, Matthias (Author) / Carlson, David B. (Author) / Hunter, Mark S. (Author) / Williams, Garth J. (Author) / Messerschmidt, Marc (Author) / Zatsepin, Nadia (Author) / Barty, Anton (Author) / Benner, W. Henry (Author) / Chu, Kaiqin (Author) / Graf, Alexander T. (Author) / Hau-Riege, Stefan P. (Author) / Kirian, Richard A. (Author) / Padeste, Celestino (Author) / Pardini, Tommaso (Author) / Pedrini, Bill (Author) / Segelke, Brent (Author) / Seibert, M. Marvin (Author) / Spence, John (Author) / Tsai, Ching-Ju (Author) / Lane, Stephen M. (Author) / Li, Xiao-Dan (Author) / Schertler, Gebhard (Author) / Boutet, Sebastien (Author) / Coleman, Matthew (Author) / Evans, James E. (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-02-28
Description
The invention of the laser in the 1950 s for visible light and microwaves, and the slow but steady recognition of its manifold uses, is a truly remarkable story in the history of science. But the severe λ[superscript 3] dependence of the ratio of stimulated (mostly coherent) to spontaneous (incoherent) emission meant that efforts to build an X-ray laser seemed hopeless for decades. As so often happens in the history of science, the breakthrough eventually occurred at the interface of several fields – synchrotron science (and especially their insertion devices), laser physics, and work on microwave tubes for radar, emerging from the second world war. Synchrotrons themselves were an outgrowth of the particle accelerators of nuclear physics, whose X-ray radiation was considered a nuisance. All of this culminated recently in the construction of the first hard-X-ray laser, the US Department of Energy's Linac Coherent Light Source (LCLS), at their SLAC laboratory near Stanford. The first X-ray lasing occurred in that two-mile long tunnel on April 21, 2009, at about 2 kV, in an all-or-nothing moment of intense excitement, as theoretical predictions proved spot-on. The new laser principle needed for hard-X-ray lasing, the free-electron laser (FEL), was first demonstrated in the infra-red region at Stanford in 1975 in John Madey's group, following earlier theoretical work by Motz and Phillips on microwave tubes. Other FELs soon followed, in the microwave and visible region, leading to the LCLS. The XFEL method provides brief pulses of X-ray laser radiation by the SASE (self-amplified spontaneous emission) process, using a resonant undulator driven by a LINAC electron accelerator. Each LCLS pulse, of 10 fs duration (repeated 120 times a second) contains about 10[superscript 12] hard-X-ray photons, about the same number that a synchrotron might generate in a second.
ContributorsSpence, John (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2014-04-30
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