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We sequenced and annotated genomes of two haloalkaliphilic Deltaproteobacteria, Geoalkalibacter ferrihydriticus Z-0531T (DSM 17813) and Geoalkalibacter subterraneus Red1T (DSM 23483). During assembly, we discovered that the DSMZ stock culture of G. subterraneus was contaminated. We reisolated G. subterraneus in axenic culture and redeposited it in DSMZ and JCM.

ContributorsBadalamenti, Jonathan P. (Author) / Krajmalnik-Brown, Rosa (Author) / Torres, Cesar (Author) / Bond, Daniel R. (Author) / Biodesign Institute (Contributor)
Created2015-03-12
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Attributing observed CO2 variations to human or natural cause is critical to deducing and tracking emissions from observations. We have used in situ CO2, CO, and planetary boundary layer height (PBLH) measurements recorded during the CalNex-LA (CARB et al., 2008) ground campaign of 15 May-15 June 2010, in Pasadena, CA,

Attributing observed CO2 variations to human or natural cause is critical to deducing and tracking emissions from observations. We have used in situ CO2, CO, and planetary boundary layer height (PBLH) measurements recorded during the CalNex-LA (CARB et al., 2008) ground campaign of 15 May-15 June 2010, in Pasadena, CA, to deduce the diurnally varying anthropogenic component of observed CO2 in the megacity of Los Angeles (LA). This affordable and simple technique, validated by carbon isotope observations and WRF-STILT (Weather Research and Forecasting model - Stochastic Time-Inverted Lagrangian Transport model) predictions, is shown to robustly attribute observed CO2 variation to anthropogenic or biogenic origin over the entire diurnal cycle. During CalNex-LA, local fossil fuel combustion contributed up to similar to 50% of the observed CO2 enhancement overnight, and similar to 100% of the enhancement near midday. This suggests that sufficiently accurate total column CO2 observations recorded near midday, such as those from the GOSAT or OCO-2 satellites, can potentially be used to track anthropogenic emissions from the LA megacity.

ContributorsNewman, S. (Author) / Jeong, S. (Author) / Fischer, M.L. (Author) / Xu, X. (Author) / Haman, C.L. (Author) / Lefer, B. (Author) / Alvarez, S. (Author) / Rappenglueck, B. (Author) / Kort, E.A. (Author) / Andrews, A. E. (Author) / Peischl, J. (Author) / Gurney, Kevin (Author) / Miller, C.E. (Author) / Yung, Y.L. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2013-04-26
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Description

Background: Continuous monitoring technologies such as accelerometers and pedometers are the gold standard for physical activity (PA) measurement. However, inconsistencies in use, analysis, and reporting limit the understanding of dose–response relationships involving PA and the ability to make comparisons across studies and population subgroups. These issues are particularly detrimental to

Background: Continuous monitoring technologies such as accelerometers and pedometers are the gold standard for physical activity (PA) measurement. However, inconsistencies in use, analysis, and reporting limit the understanding of dose–response relationships involving PA and the ability to make comparisons across studies and population subgroups. These issues are particularly detrimental to the study of PA across different ethnicities with different PA habits. This systematic review examined the inclusion of published guidelines involving data collection, processing, and reporting among articles using accelerometers or pedometers in Hispanic or Latino populations.

Methods: English (PubMed; EbscoHost) and Spanish (SCIELO; Biblioteca Virtual en Salud) articles published between 2000 and 2013 using accelerometers or pedometers to measure PA among Hispanics or Latinos were identified through systematic literature searches. Of the 253 abstracts which were initially reviewed, 57 met eligibility criteria (44 accelerometer, 13 pedometer). Articles were coded and reviewed to evaluate compliance with recommended guidelines (N = 20), and the percentage of accelerometer and pedometer articles following each guideline were computed and reported.

Results: On average, 57.1 % of accelerometer and 62.2 % of pedometer articles reported each recommended guideline for data collection. Device manufacturer and model were reported most frequently, and provision of instructions for device wear in Spanish was reported least frequently. On average, 29.6 % of accelerometer articles reported each guideline for data processing. Definitions of an acceptable day for inclusion in analyses were reported most frequently, and definitions of an acceptable hour for inclusion in analyses were reported least frequently. On average, 18.8 % of accelerometer and 85.7 % of pedometer articles included each guideline for data reporting. Accelerometer articles most frequently included average number of valid days and least frequently included percentage of wear time.

Discussion: Inclusion of standard collection and reporting procedures in studies using continuous monitoring devices in Hispanic or Latino population is generally low.

ContributorsLayne, Charles S. (Author) / Parker, Nathan H. (Author) / Soltero, Erica G. (Author) / Rosales Chavez, Jose (Author) / O'Connor, Daniel P. (Author) / Gallagher, Martina R. (Author) / Lee, Rebecca (Author) / College of Liberal Arts and Sciences (Contributor)
Created2015-09-18
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Description
Fossil fuel CO2 (FFCO2) emissions are recognized as the dominant greenhouse gas driving climate change (Enting et. al., 1995; Conway et al., 1994; Francey et al., 1995; Bousquet et. al., 1999). Transportation is a major component of FFCO2 emissions, especially in urban areas. An improved understanding of on-road FFCO2 emission

Fossil fuel CO2 (FFCO2) emissions are recognized as the dominant greenhouse gas driving climate change (Enting et. al., 1995; Conway et al., 1994; Francey et al., 1995; Bousquet et. al., 1999). Transportation is a major component of FFCO2 emissions, especially in urban areas. An improved understanding of on-road FFCO2 emission at high spatial resolution is essential to both carbon science and mitigation policy. Though considerable research has been accomplished within a few high-income portions of the planet such as the United States and Western Europe, little work has attempted to comprehensively quantify high-resolution on-road FFCO2 emissions globally. Key questions for such a global quantification are: (1) What are the driving factors for on-road FFCO2 emissions? (2) How robust are the relationships? and (3) How do on-road FFCO2 emissions vary with urban form at fine spatial scales?

This study used urban form/socio-economic data combined with self-reported on-road FFCO2 emissions for a sample of global cities to estimate relationships within a multivariate regression framework based on an adjusted STIRPAT model. The on-road high-resolution (whole-city) regression FFCO2 model robustness was evaluated by introducing artificial error, conducting cross-validation, and assessing relationship sensitivity under various model specifications. Results indicated that fuel economy, vehicle ownership, road density and population density were statistically significant factors that correlate with on-road FFCO2 emissions. Of these four variables, fuel economy and vehicle ownership had the most robust relationships.

A second regression model was constructed to examine the relationship between global on-road FFCO2 emissions and urban form factors (described by population

ii

density, road density, and distance to activity centers) at sub-city spatial scales (1 km2). Results showed that: 1) Road density is the most significant (p<2.66e-037) predictor of on-road FFCO2 emissions at the 1 km2 spatial scale; 2) The correlation between population density and on-road FFCO2 emissions for interstates/freeways varies little by city type. For arterials, on-road FFCO2 emissions show a stronger relationship to population density in clustered cities (slope = 0.24) than dispersed cities (slope = 0.13). FFCO2 3) The distance to activity centers has a significant positive relationship with on-road FFCO2 emission for the interstate and freeway toad types, but an insignificant relationship with the arterial road type.
ContributorsSong, Yang (Author) / Gurney, Kevin (Thesis advisor) / Kuby, Michael (Committee member) / Golub, Aaron (Committee member) / Chester, Mikhail (Committee member) / Selover, Nancy (Committee member) / Arizona State University (Publisher)
Created2018
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Description

The objective of the Indianapolis Flux Experiment (INFLUX) is to develop, evaluate and improve methods for measuring greenhouse gas (GHG) emissions from cities. INFLUX’s scientific objectives are to quantify CO2 and CH4 emission rates at 1 km2 resolution with a 10% or better accuracy and precision, to determine whole-city emissions

The objective of the Indianapolis Flux Experiment (INFLUX) is to develop, evaluate and improve methods for measuring greenhouse gas (GHG) emissions from cities. INFLUX’s scientific objectives are to quantify CO2 and CH4 emission rates at 1 km2 resolution with a 10% or better accuracy and precision, to determine whole-city emissions with similar skill, and to achieve high (weekly or finer) temporal resolution at both spatial resolutions. The experiment employs atmospheric GHG measurements from both towers and aircraft, atmospheric transport observations and models, and activity-based inventory products to quantify urban GHG emissions. Multiple, independent methods for estimating urban emissions are a central facet of our experimental design. INFLUX was initiated in 2010 and measurements and analyses are ongoing. To date we have quantified urban atmospheric GHG enhancements using aircraft and towers with measurements collected over multiple years, and have estimated whole-city CO2 and CH4 emissions using aircraft and tower GHG measurements, and inventory methods. Significant differences exist across methods; these differences have not yet been resolved; research to reduce uncertainties and reconcile these differences is underway. Sectorally- and spatially-resolved flux estimates, and detection of changes of fluxes over time, are also active research topics. Major challenges include developing methods for distinguishing anthropogenic from biogenic CO2 fluxes, improving our ability to interpret atmospheric GHG measurements close to urban GHG sources and across a broader range of atmospheric stability conditions, and quantifying uncertainties in inventory data products. INFLUX data and tools are intended to serve as an open resource and test bed for future investigations. Well-documented, public archival of data and methods is under development in support of this objective.

ContributorsDavis, Kenneth J. (Author) / Deng, Aijun (Author) / Lauvaux, Thomas (Author) / Miles, Natasha L. (Author) / Richardson, Scott J. (Author) / Sarmiento, Daniel P. (Author) / Gurney, Kevin (Author) / Hardesty, R. Michael (Author) / Bonin, Timothy A. (Author) / Brewer, W. Alan (Author) / Lamb, Brian K. (Author) / Shepson, Paul B. (Author) / Harvey, Rebecca M. (Author) / Cambaliza, Maria O. (Author) / Sweeney, Colm (Author) / Turnbull, Jocelyn C. (Author) / Whetstone, James (Author) / Karion, Anna (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-05-23
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Resource-poor social environments predict poor health, but the mechanisms and processes linking the social environment to psychological health and well-being remain unclear. This study explored psychosocial mediators of the association between the social environment and mental health in African American adults. African American men and women (n = 1467) completed

Resource-poor social environments predict poor health, but the mechanisms and processes linking the social environment to psychological health and well-being remain unclear. This study explored psychosocial mediators of the association between the social environment and mental health in African American adults. African American men and women (n = 1467) completed questionnaires on the social environment, psychosocial factors (stress, depressive symptoms, and racial discrimination), and mental health. Multiple-mediator models were used to assess direct and indirect effects of the social environment on mental health. Low social status in the community (p < .001) and U.S. (p < .001) and low social support (p < .001) were associated with poor mental health. Psychosocial factors significantly jointly mediated the relationship between the social environment and mental health in multiple-mediator models. Low social status and social support were associated with greater perceived stress, depressive symptoms, and perceived racial discrimination, which were associated with poor mental health. Results suggest the relationship between the social environment and mental health is mediated by psychosocial factors and revealed potential mechanisms through which social status and social support influence the mental health of African American men and women. Findings from this study provide insight into the differential effects of stress, depression and discrimination on mental health. Ecological approaches that aim to improve the social environment and psychosocial mediators may enhance health-related quality of life and reduce health disparities in African Americans.

Created2016-04-27
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Description

Background: Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 1013 bacteria in the human intestines, have been implicated because children

Background: Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 1013 bacteria in the human intestines, have been implicated because children with ASD often suffer gastrointestinal (GI) problems that correlate with ASD severity. Several previous studies have reported abnormal gut bacteria in children with ASD. The gut microbiome-ASD connection has been tested in a mouse model of ASD, where the microbiome was mechanistically linked to abnormal metabolites and behavior. Similarly, a study of children with ASD found that oral non-absorbable antibiotic treatment improved GI and ASD symptoms, albeit temporarily. Here, a small open-label clinical trial evaluated the impact of Microbiota Transfer Therapy (MTT) on gut microbiota composition and GI and ASD symptoms of 18 ASD-diagnosed children.

Results: MTT involved a 2-week antibiotic treatment, a bowel cleanse, and then an extended fecal microbiota transplant (FMT) using a high initial dose followed by daily and lower maintenance doses for 7–8 weeks. The Gastrointestinal Symptom Rating Scale revealed an approximately 80% reduction of GI symptoms at the end of treatment, including significant improvements in symptoms of constipation, diarrhea, indigestion, and abdominal pain. Improvements persisted 8 weeks after treatment. Similarly, clinical assessments showed that behavioral ASD symptoms improved significantly and remained improved 8 weeks after treatment ended. Bacterial and phage deep sequencing analyses revealed successful partial engraftment of donor microbiota and beneficial changes in the gut environment. Specifically, overall bacterial diversity and the abundance of Bifidobacterium, Prevotella, and Desulfovibrio among other taxa increased following MTT, and these changes persisted after treatment stopped (followed for 8 weeks).

Conclusions: This exploratory, extended-duration treatment protocol thus appears to be a promising approach to alter the gut microbiome and virome and improve GI and behavioral symptoms of ASD. Improvements in GI symptoms, ASD symptoms, and the microbiome all persisted for at least 8 weeks after treatment ended, suggesting a long-term impact.

ContributorsKang, Dae Wook (Author) / Adams, James (Author) / Gregory, Ann C. (Author) / Borody, Thomas (Author) / Chittick, Lauren (Author) / Fasano, Alessio (Author) / Khoruts, Alexander (Author) / Geis, Elizabeth (Author) / Maldonado Ortiz, Juan (Author) / McDonough-Means, Sharon (Author) / Pollard, Elena (Author) / Roux, Simon (Author) / Sadowsky, Michael J. (Author) / Schwarzberg Lipson, Karen (Author) / Sullivan, Matthew B. (Author) / Caporaso, J. Gregory (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor)
Created2017-01-23
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Description

High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are

High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. Therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. We recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, we compared gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.

ContributorsKang, Dae Wook (Author) / Park, Jin (Author) / Ilhan, Zehra (Author) / Wallstrom, Garrick (Author) / LaBaer, Joshua (Author) / Adams, James (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor)
Created2013-06-03
Description
Fumonisins are fungal metabolites found in corn and cereals. Fumonisins pose health risks, including suspected carcinogenicity, yet their mechanism of toxicity remains unclear. While modifications in the human gut microbiome can impact host health, the effects of fumonisins on the microbiome are not well understood. Thus, our study aimed to

Fumonisins are fungal metabolites found in corn and cereals. Fumonisins pose health risks, including suspected carcinogenicity, yet their mechanism of toxicity remains unclear. While modifications in the human gut microbiome can impact host health, the effects of fumonisins on the microbiome are not well understood. Thus, our study aimed to assess a possible dose-response relationship between fumonisin B1 (FB1) and the gut microbiome. We utilized in vitro anaerobic bioreactors with media simulating most of the nutrients in the human large intestine, inoculated them with fecal samples from 19 healthy adults and treated them with FB1 at concentrations of 0, 10, 100, and 1000 ppb. Analyses of bioreactor headspace revealed declining methane production over time, possibly influenced by the addition of dimethyl sulfoxide (DMSO). Significant differences in acetic acid production were observed in 10 ppb reactor (Day 2) and 100 ppb reactor (Day 8) when compared to 0 ppb control. Microbiome analysis showed minimal shifts in microbial relative abundances during FB1 treatment, except for Desulfovibrio desulfuricans C at Day 8 when compared between 0 ppb and 10 ppb as well as 10 ppb and 1000 ppb at Day 16. Alpha diversity analyses indicated significant differences in observed features within bioreactors of different treatments, with some variation in Faith’s Phylogenetic Diversity between the 0 ppb and 10 ppb bioreactors. Beta diversity analyses, however, revealed no significant differences between bioreactors. Overall, our findings suggest no clear dose-response relationship between FB1 treatment and gut microbiome composition/functions. The presence of DMSO may have obscured potential effects. This research will help contribute to our understanding of mycotoxicity influence on the human gut microbiome.
ContributorsSanchez Carreon, Aurely (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Cheng, Qiwen (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2024-05
Description
As obesity rates continue to rise in adolescents and young children, the concern for poor future health of the younger population grows. Physical activity and improving nutrition are two ways to combat obesity rates, and the Sustainability via Active Gardening Education (SAGE) project addresses this in underserved and low-income communities

As obesity rates continue to rise in adolescents and young children, the concern for poor future health of the younger population grows. Physical activity and improving nutrition are two ways to combat obesity rates, and the Sustainability via Active Gardening Education (SAGE) project addresses this in underserved and low-income communities in Maricopa County. This project employs a curriculum designed to promote physical activity and healthy eating for Early Care and Education (ECE) sites, most of which are daycares. Further, utilizing indicators of future health can also allow for us to understand and lower obesity rates. One indicator of future health is grip strength: greater grip strength is associated with healthier outcomes such as lower triglycerides, blood pressure, and body mass index. Grip strength has been observed in the older population; however, there are few studies looking at grip strength in younger children, namely preschoolers. As grip strength is a predictor of health, it follows that it should be observed in preschoolers, and improved, if possible, by factors such as physical activity, which would ultimately improve obesity rates. This study aimed to see if there was any relationship between physical activity and grip strength in preschoolers aged 3-5 years old. To do so, grip strength, hand length, height, weight, and information regarding physical activity of preschoolers enrolled in the SAGE project were collected. Physical activity and grip strength were not found to be significantly associated in this study; however, hand length and hand strength were associated. Among secondary outcomes, it was observed that males of ages 3 to 5-years-old may have greater hand grip strength than females of the same age group. Although this was not statistically significant, there was a trend toward statistical significance. Small sample size hampered observation of expected relationships between hand grip strength and dominant hand of the participants, and hand grip strength was not significantly related with BMI. Future directions would consist of collecting longitudinal data, as well as calling back previous years’ participants for additional data, so that there is a larger sample size for data analysis.
ContributorsAtluri, Haarika (Author) / Lee, Rebecca (Thesis director) / Tucker, Derek (Committee member) / Cantu Garcia, Lisbeth (Committee member) / De Mello, Gabrielli (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2024-05