University of Delaware Open Access Articles
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The University of Delaware Open Access Articles collection consists of scholarly articles written by University of Delaware-affiliated authors. These articles were added in compliance with the University of Delaware Open Access policy passed unanimously by the Faculty Senate April 6, 2015. Digital images are available via Artstor Digital Library and Artstor Commons. Artstor Digital Library is a digital image library for education and scholarship available to the University of Delaware community containing both restricted and open access material. Artstor Commons contains open access content freely available to the public made available by the University of Delaware and other participating institutions.
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- ItemCatalytic Hydrodeoxygenation of High Carbon Furylmethanes to Renewable Jet-fuel Ranged Alkanes over a Rhenium Modified Iridium Catalyst(Wiley-Blackwell, 2017-07-07) Saha, Basudeb; Liu, Sibao; Dutta, Saikat; Zheng, Weiqing; Gould, Nicholas S.; Cheng, Ziwei; Xu, Bingjun; Vlachos, Dionisios G.; Sibao Liu, Saikat Dutta, Weiqing Zheng, Nicholas S. Gould, Ziwei Cheng, Bingjun Xu, Basudeb Saha, and Dionisios G. Vlachos; Saha, Basudeb; Liu, Sibao; Dutta, Saikat; Zheng, Weiqing; Gould, Nicholas S.; Cheng, Ziwei; Xu, Bingjun; Vlachos, Dionisios G.Renewable jet-fuel ranged alkanes are synthesized by hydrodeoxygenation of lignocellulose derived high carbon furylmethanes over ReOx modified Ir/SiO2 catalysts under mild reaction conditions. Ir-ReOx/SiO2 with a Re/Ir molar ratio of 2 exhibits the best performance, achieving a combined alkanes yield of 82-99% from C12-C15 furylmethanes. Catalyst can be regenerated in three consecutive cycles with only ~12% loss in the combined alkanes yield. Mechanistically, the furan moieties of furylmethanes undergo simultaneous ring saturation and ring opening to form a mixture of complex oxygenates consisting of saturated furan rings, mono-keto groups, and mono-hydroxy groups. Then, these oxygenates undergo a cascade of hydrogenolysis reactions to alkanes. The high yield of Ir-ReOx/SiO2 arises from a synergy between Ir and ReOx. The acidic sites of partially reduced ReOx activate the C-O bonds of the saturated furans and alcoholic groups, while the Ir sites are responsible for hydrogenation with H2.
- ItemPhloem unloading in Arabidopsis roots is convective and regulated by the phloem- pole pericycle(eLIFE Sciences Publications, 2017-02-23) Ross-Elliott, Timothy J.; Jensen, Kaare H.; Haaning, Katrine S.; Wager, Brittney M.; Knoblauch, Jan; Howell, Alexander H.; Mullendore, Daniel L.; Monteith, Alexander G.; Paultre, Danae; Yan, Dawei; Otero, Sofia; Bourdon, Matthieu; Sager, Ross; Lee, Jung-Youn; Helariutta, Yka¨; Knoblauch, Michael; Oparka, Karl J.; Timothy J Ross-Elliott, Kaare H Jensen, Katrine S Haaning, Brittney M Wager, Jan Knoblauch, Alexander H Howell, Daniel L Mullendore, Alexander G Monteith, Danae Paultre, Dawei Yan, Sofia Otero, Matthieu Bourdon, Ross Sager, Jung-Youn Lee, Yka¨ Helariutta, Michael Knoblauch, Karl J Oparka; Sager, Ross; Lee, Jung-YounIn plants, a complex mixture of solutes and macromolecules is transported by the phloem. Here, we examined how solutes and macromolecules are separated when they exit the phloem during the unloading process. We used a combination of approaches (non-invasive imaging, 3D-electron microscopy, and mathematical modelling) to show that phloem unloading of solutes in Arabidopsis roots occurs through plasmodesmata by a combination of mass flow and diffusion (convective phloem unloading). During unloading, solutes and proteins are diverted into the phloem-pole pericycle, a tissue connected to the protophloem by a unique class of ‘funnel plasmodesmata’. While solutes are unloaded without restriction, large proteins are released through funnel plasmodesmata in discrete pulses, a phenomenon we refer to as ‘batch unloading’. Unlike solutes, these proteins remain restricted to the phloem-pole pericycle. Our data demonstrate a major role for the phloem-pole pericycle in regulating phloem unloading in roots.
- ItemViscous anisotropy of textured olivine aggregates: 2. Micromechanical model(American Geophysical Union, 2016-09-27) Hansen, Lars N.; Conrad, Clinton P.; Boneh, Yuval; Skemer, Philip; Warren, Jessica M.; Kohlstedt, David L.; Lars N. Hansen, Clinton P. Conrad, Yuval Boneh, Philip Skemer, Jessica M. Warren, and David L. Kohlstedt; Warren, Jessica M.The significant viscous anisotropy that results from crystallographic alignment (texture) of olivine grains in deformed upper mantle rocks strongly influences a large variety of geodynamic processes. Our ability to explore the effects of anisotropic viscosity in simulations of these processes requires a mechanical model that can predict the magnitude of anisotropy and its evolution. Unfortunately, existing models of olivine textural evolution and viscous anisotropy are calibrated for relatively small deformations and simple strain paths, making them less general than desired for many large-scale geodynamic scenarios. Here we develop a new set of micromechanical models to describe the mechanical behavior and textural evolution of olivine through a large range of strains and complex strain histories. For the mechanical behavior, we explore two extreme scenarios, one in which each grain experiences the same stress tensor (Sachs model) and one in which each grain undergoes a strain rate as close as possible to the macroscopic strain rate (pseudo-Taylor model). For the textural evolution, we develop a new model in which the director method is used to control the rate of grain rotation and the available slip systems in olivine are used to control the axis of rotation. Only recently has enough laboratory data on the deformation of olivine become available to calibrate these models. We use these new data to conduct inversions for the best parameters to characterize both the mechanical and textural evolution models. These inversions demonstrate that the calibrated pseudo-Taylor model best reproduces the mechanical observations. Additionally, the pseudo-Taylor textural evolution model can reasonably reproduce the observed texture strength, shape, and orientation after large and complex deformations. A quantitative comparison between our calibrated models and previously published models reveals that our new models excel in predicting the magnitude of viscous anisotropy and the details of the textural evolution. In addition, we demonstrate that the mechanical and textural evolution models can be coupled and used to reproduce mechanical evolution during large-strain torsion tests. This set of models therefore provides a new geodynamic tool for incorporating viscous anisotropy into large-scale numerical simulations.
- ItemQuorum sensing regulators are required for metabolic fitness in Vibrio parahaemolyticus(American Society for Microbiology Journals, 2017-01-09) Kalburge, Sai Siddarth; Carpenter, Megan R.; Rozovsky, Sharon; Boyd, E. Fidelma; Sai Siddarth Kalburge, Megan R. Carpenter, Sharon Rozovsky, E. Fidelma Boyd; Kalburge, Sai Siddarth; Carpenter, Megan R.; Rozovsky, Sharon; Boyd, E. FidelmaQuorum sensing (QS) is a process by which bacteria alter gene expression in response to cell density changes. In Vibrio species, at low cell density, the sigma 54-dependent response regulator LuxO, is active, and regulates the two QS master regulators AphA, which is induced and OpaR, which is repressed. At high cell density the opposite occurs, LuxO is inactive, therefore OpaR is induced and AphA is repressed. In V. parahaemolyticus, a significant enteric pathogen of humans, the role of these regulators in pathogenesis is less known. We examined deletion mutants of luxO, opaR and aphA for in vivo fitness using an adult mouse model. We found that the luxO and aphA mutants were defective in colonization compared to wild-type. The opaR mutant did not show any defect in vivo. Colonization was restored to wild-type levels in a luxO/opaR double mutant and was also increased in an opaR/aphA double mutant. These data suggest that AphA is important and that overexpression of opaR is detrimental to in vivo fitness. RNA-seq analysis of the wild-type and luxO mutant grown in mouse intestinal mucus showed that 60% of the genes that were downregulated in the luxO mutant were involved in amino acid and sugar transport and metabolism. These data suggest that the luxO mutant has a metabolic disadvantage, which was confirmed by growth pattern analysis using phenotype microarrays. Bioinformatics analysis revealed OpaR binding sites in the regulatory region of 55 carbon transporter and metabolism genes. Biochemical analysis of five representatives of these regulatory regions demonstrated direct binding of OpaR in all five tested. These data demonstrate the role of OpaR in carbon utilization and metabolic fitness, an overlooked role in the QS regulon.
- ItemMegacity pumping and preferential flow threaten groundwater quality(Nature Publishing Group, 2016-09-27) Khan, Mahfuzur R.; Koneshloo, Mohammad; Knappett, Peter S.K.; Ahmed, Kazi M.; Bostick, Benjamin C.; Mailloux, Brian J.; Mozumder, Rajib H.; Zahid, Anwar; Harvey, Charles F.; van Geen, Alexander; Michael, Holly A.; Mahfuzur R. Khan, Mohammad Koneshloo, Peter S.K. Knappett, Kazi M. Ahmed, Benjamin C. Bostick, Brian J. Mailloux, Rajib H. Mozumder, Anwar Zahid, Charles F. Harvey, Alexander van Geen & Holly A. Michael; Khan, Mahfuzur R.; Koneshloo, Mohammad; Michael, Holly A.Many of the world’s megacities depend on groundwater from geologically complex aquifers that are over-exploited and threatened by contamination. Here, using the example of Dhaka, Bangladesh, we illustrate how interactions between aquifer heterogeneity and groundwater exploitation jeopardize groundwater resources regionally. Groundwater pumping in Dhaka has caused large-scale drawdown that extends into outlying areas where arseniccontaminated shallow groundwater is pervasive and has potential to migrate downward. We evaluate the vulnerability of deep, low-arsenic groundwater with groundwater models that incorporate geostatistical simulations of aquifer heterogeneity. Simulations show that preferential flow through stratigraphy typical of fluvio-deltaic aquifers could contaminate deep (4150 m) groundwater within a decade, nearly a century faster than predicted through homogeneous models calibrated to the same data. The most critical fast flowpaths cannot be predicted by simplified models or identified by standard measurements. Such complex vulnerability beyond city limits could become a limiting factor for megacity groundwater supplies in aquifers worldwide.