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Description

Bacteriophages are ideal candidates for pathogen biocontrol to mitigate outbreaks of prevalent foodborne pathogens, such as Escherichia coli. We identified a bacteriophage (AAPEc6) from wastewater that infects E. coli O45:H10. The AAPEc6 genome sequence shares 93% identity (with 92% coverage) to enterobacterial phage K1E (Sp6likevirus) in the Autographivirinae subfamily (Podoviridae).

ContributorsNonis, Judith (Author) / Premaratne, Aruni (Author) / Billington, Craig (Author) / Varsani, Arvind (Author) / Biodesign Institute (Contributor)
Created2017-08-03
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This article focuses on the immigration-related demands currently being placed on local police in the United States and the emergence of what we call a “multilayered jurisdictional patchwork” (MJP) of immigration enforcement. We report results from nationwide surveys of city police chiefs and county sheriffs and intensive fieldwork in three

This article focuses on the immigration-related demands currently being placed on local police in the United States and the emergence of what we call a “multilayered jurisdictional patchwork” (MJP) of immigration enforcement. We report results from nationwide surveys of city police chiefs and county sheriffs and intensive fieldwork in three jurisdictions. The enforcement landscape we describe is complicated by the varying and overlapping responsibilities of sheriffs and city police, and by the tendency for sheriffs to maintain closer relationships with federal Immigration and Customs Enforcement (ICE) authorities. We conclude by reflecting on the implications of the MJP—for immigrants, for their communities, and for the evolving relationship between levels of government in the federal system.

ContributorsVarsanyi, Monica W. (Author) / Lewis, Paul (Author) / Provine, Doris (Author) / Decker, Scott (Author) / College of Liberal Arts and Sciences (Contributor)
Created2011-12-22
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Nominally anhydrous minerals formed deep in the mantle and transported to the Earth’s surface contain tens to hundreds of ppm wt H2O, providing evidence for the presence of dissolved water in the Earth’s interior. Even at these low concentrations, H2O greatly affects the physico-chemical properties of mantle materials, governing planetary

Nominally anhydrous minerals formed deep in the mantle and transported to the Earth’s surface contain tens to hundreds of ppm wt H2O, providing evidence for the presence of dissolved water in the Earth’s interior. Even at these low concentrations, H2O greatly affects the physico-chemical properties of mantle materials, governing planetary dynamics and evolution. The diffusion of hydrogen (H) controls the transport of H2O in the Earth’s upper mantle, but is not fully understood for olivine ((Mg, Fe)2SiO4) the most abundant mineral in this region. Here we present new hydrogen self-diffusion coefficients in natural olivine single crystals that were determined at upper mantle conditions (2 GPa and 750–900 °C). Hydrogen self-diffusion is highly anisotropic, with values at 900 °C of 10-10.9, 10-12.8 and 10-11.9 m2/s along [100], [010] and [001] directions, respectively. Combined with the Nernst-Einstein relation, these diffusion results constrain the contribution of H to the electrical conductivity of olivine to be σH = 102.12S/m·CH20·exp−187kJ/mol/(RT). Comparisons between the model presented in this study and magnetotelluric measurements suggest that plausible H2O concentrations in the upper mantle (≤250 ppm wt) can account for high electrical conductivity values (10-2–10-1 S/m) observed in the asthenosphere.

ContributorsNovella, Davide (Author) / Jacobsen, Benjamin (Author) / Weber, Peter K. (Author) / Tyburczy, James (Author) / Ryerson, Frederick J. (Author) / Du Frane, Wyatt L. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-07-13
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Description

Establishing the in vivo diagnosis of Alzheimer’s disease (AD) or other dementias relies on clinical criteria; however, the accuracy of these criteria can be limited. The diagnostic accuracy is 77% for a clinical diagnosis of AD, even among experts. We performed a review through PubMed of articles related to specific

Establishing the in vivo diagnosis of Alzheimer’s disease (AD) or other dementias relies on clinical criteria; however, the accuracy of these criteria can be limited. The diagnostic accuracy is 77% for a clinical diagnosis of AD, even among experts. We performed a review through PubMed of articles related to specific diagnostic modalities, including APOE genotyping, cerebrospinal fluid (CSF) testing, fludeoxyglucose F 18 positron emission tomography (PET), amyloid PET, tau PET, computed tomography (CT), single-photon emission CT, magnetic resonance imaging (MRI), and B12 and thyroid-stimulating hormone screening, to determine the specificity and sensitivity of each test used in the clinical diagnosis of AD. We added a novel immunomagnetic reduction assay that provides ultrasensitivity for analyzing the levels of plasma tau and beta amyloid 42 (Aβ42). The sensitivity and specificity of the current diagnostic approach (structural CT or MRI with screening labs) remain low for clinical detection of AD and are primarily used to exclude other conditions. Because of limited diagnostic capabilities, physicians do not feel comfortable or skilled in rendering a clinical diagnosis of AD. Compounding this problem is the fact that inexpensive, minimally invasive diagnostic tests do not yet exist. Biomarkers (obtained through CSF testing or PET imaging), which are not routinely incorporated in clinical practice, correlate well with pathologic changes. While PET is particularly costly and difficult to assess, CSF measures of tau and beta amyloid are not costly, and these tests may be worthwhile when the tiered approach proposed here warrants further testing. There is a need for developing bloodborne biomarkers that can aid in the clinical diagnosis of AD. Here we present a streamlined questionnaire-enriched, biomarker-enriched approach that is more cost-effective than the current diagnosis of exclusion and is designed to increase clinical confidence for a diagnosis of dementia due to AD.

ContributorsSabbagh, Marwan N. (Author) / Lue, Lih-Fen (Author) / Fayard, Daniel (Author) / Shi, Jiong (Author)
Created2017-07-21
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Description

Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H2 production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible

Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H2 production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH2). High-throughput sequencing and metagenome functional prediction from 16S rRNA data showed that butyrate production pathways and microbial communities were different during batch (closed) and continuous-mode operation. Lactobacillaceae, Lachnospiraceae, and Enterococcaceae were the most abundant phylotypes in the closed system without PH2 control, whereas Prevotellaceae, Ruminococcaceae, and Actinomycetaceae were the most abundant phylotypes under continuous operation at low PH2. Putative butyrate producers identified in our system were from Prevotellaceae, Clostridiaceae, Ruminococcaceae, and Lactobacillaceae. Metagenome prediction analysis suggests that nonbutyrogenic microorganisms influenced butyrate production by generating butyrate precursors such as acetate, lactate, and succinate. 16S rRNA gene analysis suggested that, in the reactor, a partnership between identified butyrogenic microorganisms and succinate (i.e., Actinomycetaceae), acetate (i.e., Ruminococcaceae and Actinomycetaceae), and lactate producers (i.e., Ruminococcaceae and Lactobacillaceae) took place under continuous-flow operation at low PH2.

ContributorsEsquivel Elizondo, Sofia (Author) / Ilhan, Zehra (Author) / Garcia-Pena, E. I. (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor)
Created2017-07-18
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Description

We described newly discovered baenid specimens from the Uintan North American Land Mammal Age (NALMA), in the Uinta Formation, Uinta Basin, Utah. These specimens include a partial skull and several previously undescribed postcranial elements of Baena arenosa, and numerous well-preserved shells of B. arenosa and Chisternon undatum. Baenids from the

We described newly discovered baenid specimens from the Uintan North American Land Mammal Age (NALMA), in the Uinta Formation, Uinta Basin, Utah. These specimens include a partial skull and several previously undescribed postcranial elements of Baena arenosa, and numerous well-preserved shells of B. arenosa and Chisternon undatum. Baenids from the Uintan NALMA (46.5–40 Ma) are critical in that they provide valuable insight into the morphology and evolution of the diverse and speciose baenid family near the end of its extensive radiation, just prior to the disappearance of this clade from the fossil record. These Uintan specimens greatly increase the known variation in these late-surviving taxa and indicate that several characters thought to define these species should be reassessed. The partial cranium of B. arenosa, including portions of the basicranium, neurocranium, face, and lower jaw, was recently recovered from Uinta B sediments. While its morphology is consistent with known specimens of B. arenosa, we observed several distinct differences: a crescent-shaped condylus occipitalis that is concave dorsally, tuberculum basioccipitale that flare out laterally, and a distinct frontal-nasal suture. The current sample of plastral and carapacial morphology considerably expands the documented variation in the hypodigms of B. arenosa and C. undatum. Novel shell characters observed include sigmoidal extragular-humeral sulci, and small, subtriangular gular scutes. Subadult specimens reveal ontogenetic processes in both taxa, and demonstrate that diagnostic morphological differences between them were present from an early developmental age.

ContributorsSmith, Heather (Author) / Hutchison, J. Howard (Author) / Townsend, K. E. Beth (Author) / Adrian, Brent (Author) / Jager, Daniel (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-07-07
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Description

Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane

Background: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses.

Methods: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3.

Results: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion.

Conclusions: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

ContributorsBoukari, Wardatou (Author) / Alcala-Briseno, Ricardo I. (Author) / Kraberger, Simona Joop (Author) / Fernandez, Emmanuel (Author) / Filloux, Denis (Author) / Daugrois, Jean-Heinrich (Author) / Comstock, Jack C. (Author) / Lett, Jean-Michel (Author) / Martin, Darren P. (Author) / Varsani, Arvind (Author) / Roumagnac, Philippe (Author) / Polston, Jane E. (Author) / Rott, Philippe C. (Author) / Biodesign Institute (Contributor)
Created2017-07-28
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Background: An online version of the Microscale Audit of Pedestrian Streetscapes (Abbreviated) tool was adapted to virtually audit built environment features supportive of physical activity. The current study assessed inter-rater reliability of MAPS Online between in-person raters and online raters unfamiliar with the regions.

Methods: In-person and online audits were conducted for a

Background: An online version of the Microscale Audit of Pedestrian Streetscapes (Abbreviated) tool was adapted to virtually audit built environment features supportive of physical activity. The current study assessed inter-rater reliability of MAPS Online between in-person raters and online raters unfamiliar with the regions.

Methods: In-person and online audits were conducted for a total of 120 quarter-mile routes (60 per site) in Phoenix, AZ and San Diego, CA. Routes in each city included 40 residential origins stratified by walkability and SES, and 20 commercial centers. In-person audits were conducted by raters residing in their region. Online audits were conducted by raters in the alternate location using Google Maps (Aerial and Street View) images. The MAPS Abbreviated Online tool consisted of four sections: overall route, street segments, crossings and cul-de-sacs. Items within each section were grouped into subscales, and inter-rater reliability (ICCs) was assessed for subscales at multiple levels of aggregation.

Results: Online and in-person audits showed excellent agreement for overall positive microscale (ICC = 0.86, 95% CI [0.80, 0.90]) and grand scores (ICC = 0.93, 95% CI [0.89, 0.95]). Substantial to near-perfect agreement was found for 21 of 30 (70%) subscales, valence, and subsection scores, with ICCs ranging from 0.62, 95% CI [0.50, 0.72] to 0.95, 95% CI [0.93, 0.97]. Lowest agreement was found for the aesthetics and social characteristics scores, with ICCs ranging from 0.07, 95% CI [−0.12, 0.24] to 0.27, 95% CI [0.10, 0.43].

Conclusions: Results support use of the MAPS Abbreviated Online tool to reliably assess microscale neighborhood features that support physical activity and may be used by raters residing in different geographic regions and unfamiliar with the audit areas.

ContributorsPhillips, Christine (Author) / Engelberg, Jessa K. (Author) / Geremia, Carrie M. (Author) / Zhu, Wenfei (Author) / Kurka, Jonathan (Author) / Cain, Kelli L. (Author) / Sallis, James F. (Author) / Conway, Terry L. (Author) / Adams, Marc (Author) / College of Health Solutions (Contributor)
Created2017-08-04
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The risk of developing cancer should theoretically increase with both the number of cells and the lifespan of an organism. However, gigantic animals do not get more cancer than humans, suggesting that super-human cancer suppression has evolved numerous times across the tree of life. This is the essence and promise

The risk of developing cancer should theoretically increase with both the number of cells and the lifespan of an organism. However, gigantic animals do not get more cancer than humans, suggesting that super-human cancer suppression has evolved numerous times across the tree of life. This is the essence and promise of Peto’s Paradox. We discuss what is known about Peto’s Paradox and provide hints of what is yet to be discovered.

ContributorsTollis, Marc (Author) / Boddy, Amy (Author) / Maley, Carlo (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-07-13
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Description

Salmonella enterica serovar Typhimurium strains belonging to sequence type ST313 are a major cause of fatal bacteremia among HIV-infected adults and children in sub-Saharan Africa. Unlike “classical” non-typhoidal Salmonella (NTS), gastroenteritis is often absent during ST313 infections and isolates are most commonly recovered from blood, rather than from stool. This

Salmonella enterica serovar Typhimurium strains belonging to sequence type ST313 are a major cause of fatal bacteremia among HIV-infected adults and children in sub-Saharan Africa. Unlike “classical” non-typhoidal Salmonella (NTS), gastroenteritis is often absent during ST313 infections and isolates are most commonly recovered from blood, rather than from stool. This is consistent with observations in animals, in which ST313 strains displayed lower levels of intestinal colonization and higher recovery from deeper tissues relative to classic NTS isolates. A better understanding of the key environmental factors regulating these systemic infections is urgently needed. Our previous studies using dynamic Rotating Wall Vessel (RWV) bioreactor technology demonstrated that physiological levels of fluid shear regulate virulence, gene expression, and stress response profiles of classic S. Typhimurium. Here we provide the first demonstration that fluid shear alters the virulence potential and pathogenesis-related stress responses of ST313 strain D23580 in a manner that differs from classic NTS.

ContributorsYang, Jiseon (Author) / Barrila, Jennifer (Author) / Roland, Kenneth (Author) / Ott, C. Mark (Author) / Nickerson, Cheryl (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Biodesign Institute (Contributor)
Created2016-06-09