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Search Results: 1 - 10 of 202045 matches for " Jonathan D Todd "
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Projecting Invasion Risk of Non-Native Watersnakes (Nerodia fasciata and Nerodia sipedon) in the Western United States
Jonathan P. Rose, Brian D. Todd
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0100277
Abstract: Species distribution models (SDMs) are increasingly used to project the potential distribution of introduced species outside their native range. Such studies rarely explicitly evaluate potential conflicts with native species should the range of introduced species expand. Two snake species native to eastern North America, Nerodia fasciata and Nerodia sipedon, have been introduced to California where they represent a new stressor to declining native amphibians, fish, and reptiles. To project the potential distributions of these non-native watersnakes in western North America, we built ensemble SDMs using MaxEnt, Boosted Regression Trees, and Random Forests and habitat and climatic variables. We then compared the overlap between the projected distribution of invasive watersnakes and the distributions of imperiled native amphibians, fish, and reptiles that can serve as prey or competitors for the invaders, to estimate the risk to native species posed by non-native watersnakes. Large areas of western North America were projected to be climatically suitable for both species of Nerodia according to our ensemble SDMs, including much of central California. The potential distributions of both N. fasciata and N. sipedon overlap extensively with the federally threatened Giant Gartersnake, Thamnophis gigas, which inhabits a similar ecological niche. N. fasciata also poses risk to the federally threatened California Tiger Salamander, Ambystoma californiense, whereas N. sipedon poses risk to some amphibians of conservation concern, including the Foothill Yellow-legged Frog, Rana boylii. We conclude that non-native watersnakes in California can likely inhabit ranges of several native species of conservation concern that are expected to suffer as prey or competing species for these invaders. Action should be taken now to eradicate or control these invasions before detrimental impacts on native species are widespread. Our methods can be applied broadly to quantify the risk posed by incipient invasions to native biodiversity.
Crack-Tip Strain Field Mapping and the Toughness of Metallic Glasses
Todd C. Hufnagel, Uday K. Vempati, Jonathan D. Almer
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0083289
Abstract: We have used high-energy x-ray scattering to map the strain fields around crack tips in fracture specimens of a bulk metallic glass under load at room temperature and below. From the measured strain fields we can calculate the components of the stress tensor as a function of position and determine the size and shape of the plastic process zone around the crack tip. Specimens tested at room temperature develop substantial plastic zones and achieve high stress intensities () prior to fracture. Specimens tested at cryogenic temperatures fail at reduced but still substantial stress intensities () and show only limited evidence of crack-tip plasticity. We propose that the difference in behavior is associated with changes in the flow stress and elastic constants, which influence the number density of shear bands in the plastic zone and thus the strain required to initiate fracture on an individual band. A secondary effect is a change in the triaxial state of stress around the crack tip due to the temperature dependence of Poisson's ratio. It is likely that this ability to map elastic strains on the microscale will be useful in other contexts, although interpreting shifts in the position of the scattering peaks in amorphous materials in terms of elastic strains must be done with caution.
The Ruegeria pomeroyi acuI Gene Has a Role in DMSP Catabolism and Resembles yhdH of E. coli and Other Bacteria in Conferring Resistance to Acrylate
Jonathan D. Todd, Andrew R. J. Curson, Matthew J. Sullivan, Mark Kirkwood, Andrew W. B. Johnston
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035947
Abstract: The Escherichia coli YhdH polypeptide is in the MDR012 sub-group of medium chain reductase/dehydrogenases, but its biological function was unknown and no phenotypes of YhdH? mutants had been described. We found that an E. coli strain with an insertional mutation in yhdH was hyper-sensitive to inhibitory effects of acrylate, and, to a lesser extent, to those of 3-hydroxypropionate. Close homologues of YhdH occur in many Bacterial taxa and at least two animals. The acrylate sensitivity of YhdH? mutants was corrected by the corresponding, cloned homologues from several bacteria. One such homologue is acuI, which has a role in acrylate degradation in marine bacteria that catabolise dimethylsulfoniopropionate (DMSP) an abundant anti-stress compound made by marine phytoplankton. The acuI genes of such bacteria are often linked to ddd genes that encode enzymes that cleave DMSP into acrylate plus dimethyl sulfide (DMS), even though these are in different polypeptide families, in unrelated bacteria. Furthermore, most strains of Roseobacters, a clade of abundant marine bacteria, cleave DMSP into acrylate plus DMS, and can also demethylate it, using DMSP demethylase. In most Roseobacters, the corresponding gene, dmdA, lies immediately upstream of acuI and in the model Roseobacter strain Ruegeria pomeroyi DSS-3, dmdA-acuI were co-regulated in response to the co-inducer, acrylate. These observations, together with findings by others that AcuI has acryloyl-CoA reductase activity, lead us to suggest that YdhH/AcuI enzymes protect cells against damaging effects of intracellular acryloyl-CoA, formed endogenously, and/or via catabolising exogenous acrylate. To provide “added protection” for bacteria that form acrylate from DMSP, acuI was recruited into clusters of genes involved in this conversion and, in the case of acuI and dmdA in the Roseobacters, their co-expression may underpin an interaction between the two routes of DMSP catabolism, whereby the acrylate product of DMSP lyases is a co-inducer for the demethylation pathway.
The Function and Organization of Lateral Prefrontal Cortex: A Test of Competing Hypotheses
Jeremy R. Reynolds, Randall C. O'Reilly, Jonathan D. Cohen, Todd S. Braver
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030284
Abstract: The present experiment tested three hypotheses regarding the function and organization of lateral prefrontal cortex (PFC). The first account (the information cascade hypothesis) suggests that the anterior-posterior organization of lateral PFC is based on the timing with which cue stimuli reduce uncertainty in the action selection process. The second account (the levels-of-abstraction hypothesis) suggests that the anterior-posterior organization of lateral PFC is based on the degree of abstraction of the task goals. The current study began by investigating these two hypotheses, and identified several areas of lateral PFC that were predicted to be active by both the information cascade and levels-of-abstraction accounts. However, the pattern of activation across experimental conditions was inconsistent with both theoretical accounts. Specifically, an anterior area of mid-dorsolateral PFC exhibited sensitivity to experimental conditions that, according to both accounts, should have selectively engaged only posterior areas of PFC. We therefore investigated a third possible account (the adaptive context maintenance hypothesis) that postulates that both posterior and anterior regions of PFC are reliably engaged in task conditions requiring active maintenance of contextual information, with the temporal dynamics of activity in these regions flexibly tracking the duration of maintenance demands. Activity patterns in lateral PFC were consistent with this third hypothesis: regions across lateral PFC exhibited transient activation when contextual information had to be updated and maintained in a trial-by-trial manner, but sustained activation when contextual information had to be maintained over a series of trials. These findings prompt a reconceptualization of current views regarding the anterior-posterior organization of lateral PFC, but do support other findings regarding the active maintenance role of lateral PFC in sequential working memory paradigms.
Mediciones de potencial zeta de microespferas de vidrio en glicol de etileno y en soluciones tampón de fosfato
Juan E. Tibaquirá G.,Jeff Moran,Todd Otanicar,Jonathan D. Posner
Scientia Et Technica , 2007,
Abstract: Este artículo cubre el procedimiento y los resultados obtenidos midiendo potencial zeta (ζ) de microesferas de vidrio en glicol de etileno y en soluciones tampón (soluciones buffer) de fosfato. El potencial zeta fue medido usando el dispositivo NICOMP ZLS 388 el cual emplea el principio de dispersión electroforética de la luz. El potencial zeta de las microesferas en soluciones de agua y glicol de etileno fue medido entre -63 y -68 mV y en las soluciones tampón de fosfato varia entre -60 y -110 mV. Los resultados que fueron obtenidos son comparados con resultados publicados para las soluciones mencionadas. Finalmente son discutidas las dificultades asociadas con la medición del potencial zeta.
Existence and stability of hole solutions to complex Ginzburg-Landau equations
Todd Kapitula,Jonathan Rubin
Physics , 1999, DOI: 10.1088/0951-7715/13/1/305
Abstract: We consider the existence and stability of the hole, or dark soliton, solution to a Ginzburg-Landau perturbation of the defocusing nonlinear Schroedinger equation (NLS), and to the nearly real complex Ginzburg-Landau equation (CGL). By using dynamical systems techniques, it is shown that the dark soliton can persist as either a regular perturbation or a singular perturbation of that which exists for the NLS. When considering the stability of the soliton, a major difficulty which must be overcome is that eigenvalues may bifurcate out of the continuous spectrum, i.e., an edge bifurcation may occur. Since the continuous spectrum for the NLS covers the imaginary axis, and since for the CGL it touches the origin, such a bifurcation may lead to an unstable wave. An additional important consideration is that an edge bifurcation can happen even if there are no eigenvalues embedded in the continuous spectrum. Building on and refining ideas first presented in Kapitula and Sandstede (Physica D, 1998) and Kapitula (SIAM J. Math. Anal., 1999), we show that when the wave persists as a regular perturbation, at most three eigenvalues will bifurcate out of the continuous spectrum. Furthermore, we precisely track these bifurcating eigenvalues, and thus are able to give conditions for which the perturbed wave will be stable. For the NLS the results are an improvement and refinement of previous work, while the results for the CGL are new. The techniques presented are very general and are therefore applicable to a much larger class of problems than those considered here.
Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria
Dmitry A Rodionov ,Mikhail S Gelfand,Jonathan D Todd,Andrew R. J Curson,Andrew W. B Johnston
PLOS Computational Biology , 2006, DOI: 10.1371/journal.pcbi.0020163
Abstract: We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria. Combined with other computational approaches, this allowed us to reconstruct the metal regulatory network in more than three dozen species with available genome sequences. We identified several classes of cis-acting regulatory DNA motifs (Irr-boxes or ICEs, RirA-boxes, Iron-Rhodo-boxes, Fur-alpha-boxes, Mur-box or MRS, MntR-box, and IscR-boxes) in regulatory regions of various genes involved in iron and manganese uptake, Fe-S and heme biosynthesis, iron storage, and usage. Despite the different nature of the iron regulons in selected lineages of alpha-proteobacteria, the overall regulatory network is consistent with, and confirmed by, many experimental observations. This study expands the range of genes involved in iron homeostasis and demonstrates considerable interconnection between iron-responsive regulatory systems. The detailed comparative and phylogenetic analyses of the regulatory systems allowed us to propose a theory about the possible evolution of Fe and Mn regulons in alpha-proteobacteria. The main evolutionary event likely occurred in the common ancestor of the Rhizobiales and Rhodobacterales, where the Fur protein switched to regulating manganese transporters (and hence Fur had become Mur). In these lineages, the role of global iron homeostasis was taken by RirA and Irr, two transcriptional regulators that act by sensing the physiological consequence of the metal availability rather than its concentration per se, and thus provide for more flexible regulation.
Unusual Regulation of a Leaderless Operon Involved in the Catabolism of Dimethylsulfoniopropionate in Rhodobacter sphaeroides
Matthew J. Sullivan,Andrew R. J. Curson,Neil Shearer,Jonathan D. Todd,Robert T. Green,Andrew W. B. Johnston
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015972
Abstract: Rhodobacter sphaeroides strain 2.4.1 is a widely studied bacterium that has recently been shown to cleave the abundant marine anti-stress molecule dimethylsulfoniopropionate (DMSP) into acrylate plus gaseous dimethyl sulfide. It does so by using a lyase encoded by dddL, the promoter-distal gene of a three-gene operon, acuR-acuI-dddL. Transcription of the operon was enhanced when cells were pre-grown with the substrate DMSP, but this induction is indirect, and requires the conversion of DMSP to the product acrylate, the bona fide co-inducer. This regulation is mediated by the product of the promoter-proximal gene acuR, a transcriptional regulator in the TetR family. AcuR represses the operon in the absence of acrylate, but this is relieved by the presence of the co-inducer. Another unusual regulatory feature is that the acuR-acuI-dddL mRNA transcript is leaderless, such that acuR lacks a Shine-Dalgarno ribosomal binding site and 5′-UTR, and is translated at a lower level compared to the downstream genes. This regulatory unit may be quite widespread in bacteria, since several other taxonomically diverse lineages have adjacent acuR-like and acuI-like genes; these operons also have no 5′ leader sequences or ribosomal binding sites and their predicted cis-acting regulatory sequences resemble those of R. sphaeroides acuR-acuI-dddL.
Analysis of Venezuelan Equine Encephalitis Replicon Particles Packaged in Different Coats
Kurt I. Kamrud, Kim D. Alterson, Chasity Andrews, Laura O. Copp, Whitney C. Lewis, Bolyn Hubby, Deepa Patel, Jonathan O. Rayner, Todd Talarico, Jonathan F. Smith
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002709
Abstract: Background The Venezuelan equine encephalitis (VEE) virus replicon system was used to produce virus-like replicon particles (VRP) packaged with a number of different VEE-derived glycoprotein (GP) coats. The GP coat is believed to be responsible for the cellular tropism noted for VRP and it is possible that different VEE GP coats may have different affinities for cells. We examined VRP packaged in four different VEE GP coats for their ability to infect cells in vitro and to induce both humoral and cellular immune responses in vivo. Methodology/Principal Findings The VRP preparations were characterized to determine both infectious units (IU) and genome equivalents (GE) prior to in vivo analysis. VRP packaged with different VEE GP coats demonstrated widely varying GE/IU ratios based on Vero cell infectivity. BALB/c mice were immunized with the different VRP based on equal GE titers and the humoral and cellular responses to the expressed HIV gag gene measured. The magnitude of the immune responses measured in mice revealed small but significant differences between different GP coats when immunization was based on GE titers. Conclusions/Significance We suggest that care should be taken when alternative coat proteins are used to package vector-based systems as the titers determined by cell culture infection may not represent accurate particle numbers and in turn may not accurately represent actual in vivo dose.
A framework for the evaluation of turbulence closures used in mesoscale ocean large-eddy simulations
Jonathan Pietarila Graham,Todd Ringler
Physics , 2012, DOI: 10.1016/j.ocemod.2013.01.004
Abstract: We present a methodology to determine the best turbulence closure for an eddy-permitting ocean model through measurement of the error-landscape of the closure's subgrid spectral transfers and flux. We apply this method to 6 different closures for forced-dissipative simulations of the barotropic vorticity equation on a f-plane (2D Navier-Stokes equation). Using a high-resolution benchmark, we compare each closure's model of energy and enstrophy transfer to the actual transfer observed in the benchmark run. The error-landscape norms enable us to both make objective comparisons between the closures and to optimize each closure's free parameter for a fair comparison. The hyper-viscous closure most closely reproduces the enstrophy cascade, especially at larger scales due to the concentration of its dissipative effects to the very smallest scales. The viscous and Leith closures perform nearly as well, especially at smaller scales where all three models were dissipative. The Smagorinsky closure dissipates enstrophy at the wrong scales. The anticipated potential vorticity closure was the only model to reproduce the upscale transfer of kinetic energy from the unresolved scales, but would require high-order Laplacian corrections in order to concentrate dissipation at the smallest scales. The Lagrangian-averaged alpha-model closure did not perform successfully for forced 2D isotropic Navier-Stokes: small-scale filamentation is only slightly reduced by the model while small-scale roll-up is prevented. Together, this reduces the effects of diffusion.
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