Faculty Scholarship

Showing 441 - 450 of 733 Items

Projecting global land-use change and its effect on ecosystem service provision and biodiversity with simple models

Date: 2010-12-01

Creator: Erik Nelson, Heather Sander, Peter Hawthorne, Marc Conte, Driss, Ennaanay, Stacie Wolny, Steven Manson, Stephen Polasky

Access: Open access

Background: As the global human population grows and its consumption patterns change, additional land will be needed for living space and agricultural production. A critical question facing global society is how to meet growing human demands for living space, food, fuel, and other materials while sustaining ecosystem services and biodiversity [1]. Methodology/Principal Findings: We spatially allocate two scenarios of 2000 to 2015 global areal change in urban land and cropland at the grid cell-level and measure the impact of this change on the provision of ecosystem services and biodiversity. The models and techniques used to spatially allocate land-use/land-cover (LULC) change and evaluate its impact on ecosystems are relatively simple and transparent [2]. The difference in the magnitude and pattern of cropland expansion across the two scenarios engenders different tradeoffs among crop production, provision of species habitat, and other important ecosystem services such as biomass carbon storage. For example, in one scenario, 5.2 grams of carbon stored in biomass is released for every additional calorie of crop produced across the globe; under the other scenario this tradeoff rate is 13.7. By comparing scenarios and their impacts we can begin to identify the global pattern of cropland and irrigation development that is significant enough to meet future food needs but has less of an impact on ecosystem service and habitat provision. Conclusions/Significance: Urban area and croplands will expand in the future to meet human needs for living space, livelihoods, and food. In order to jointly provide desired levels of urban land, food production, and ecosystem service and species habitat provision the global society will have to become much more strategic in its allocation of intensively managed land uses. Here we illustrate a method for quickly and transparently evaluating the performance of potential global futures.


Tame combing and almost convexity conditions

Date: 2011-12-01

Creator: Sean Cleary, Susan Hermiller, Melanie Stein, Jennifer Taback

Access: Open access

We give the first examples of groups which admit a tame combing with linear radial tameness function with respect to any choice of finite presentation, but which are not minimally almost convex on a standard generating set. Namely, we explicitly construct such combings for Thompson's group F and the Baumslag-Solitar groups BS(1, p) with p ≥ 3. In order to make this construction for Thompson's group F, we significantly expand the understanding of the Cayley complex of this group with respect to the standard finite presentation. In particular we describe a quasigeodesic set of normal forms and combinatorially classify the arrangements of 2-cells adjacent to edges that do not lie on normal form paths. © 2010 Springer-Verlag.


Wall-associated kinase 1 (WAK1) is crosslinked in endomembranes, and transport to the cell surface requires correct cell-wall synthesis

Date: 2006-06-01

Creator: Bruce D. Kohorn, Masaru Kobayashi, Sue Johansen, Henry Perry Friedman, Andy, Fischer, Nicole Byers

Access: Open access

The Arabidopsis thaliana wall-associated kinases (WAKs) bind to pectin with an extracellular domain and also contain a cytoplasmic protein kinase domain. WAKs are required for cell elongation and modulate sugar metabolism. This work shows that in leaf protoplasts a WAK1-GFP fusion protein accumulates in a cytoplasmic compartment that contains pectin. The WAK compartment contains markers for the Golgi, the site of pectin synthesis. The migration of WAK1-GFP to the cell surface is far slower than that of a cell surface receptor not associated with the cell wall, is influenced by the presence of fucose side chains on one or more unidentified molecules that might include pectin, and is dependent upon cellulose synthesis on the plasma membrane. WAK is crosslinked into a detergent-insoluble complex within the cytoplasmic compartment before it appears on the cell surface, and this is independent of fucose modification or cellulose synthesis. Thus, the assembly and crosslinking of WAKs may begin at an early stage within a cytoplasmic compartment rather than in the cell wall itself, and is coordinated with synthesis of surface cellulose.


An improved comparison of atmospheric Ar/N2 time series and paired ocean-atmosphere model predictions

Date: 2008-11-16

Creator: Nicolas Cassar, Galen A. McKinley, Michael L. Bender, Robert Mika, Mark, Battle

Access: Open access

Ar/N2 variations in the atmosphere reflect ocean heat fluxes, air-sea gas exchange, and atmospheric dynamics. Here atmospheric Ar/N2 time series are compared to paired ocean-atmosphere model predictions. Agreement between Ar/N2 observations and simulations has improved in comparison to a previous study because of longer time series and the introduction of automated samplers at several of the atmospheric stations, as well as the refinement of the paired ocean-atmosphere models by inclusion of Ar and N2 as active tracers in the ocean component. Although analytical uncertainties and collection artifacts are likely to be mainly responsible for observed Ar/N2 outliers, air parcel back-trajectory analysis suggests that some of the variability in Ar/N2 measurements could be due to the low-altitude history of the air mass collected and, by extension, the local oceanic Ar/N2 signal. Although the simulated climatological seasonal cycle can currently be evaluated with Ar/N2 observations, longer time series and additional improvements in the signal-to-noise ratio will be required to test other model predictions such as interannual variability, latitudinal gradients, and the secular increase in atmospheric Ar/N2 expected to result from ocean warming. Copyright 2008 by the American Geophysical Union.


Comparing enhancer action in cis and in trans

Date: 2012-08-01

Creator: Jack R. Bateman, Justine E. Johnson, Melissa N. Locke

Access: Open access

Studies from diverse systems have shown that distinct interchromosomal interactions are a central component of nuclear organization. In some cases, these interactions allow an enhancer to act in trans, modulating the expression of a gene encoded on a separate chromosome held in close proximity. Despite recent advances in uncovering such phenomena, our understanding of how a regulatory element acts on another chromosome remains incomplete. Here, we describe a transgenic approach to better understand enhancer action in trans in Drosophila melanogaster. Using phiC31-based recombinase-mediated cassette exchange (RMCE), we placed transgenes carrying combinations of the simple enhancer GMR, a minimal promoter, and different fluorescent reporters at equivalent positions on homologous chromosomes so that they would pair via the endogenous somatic pairing machinery of Drosophila. Our data demonstrate that the enhancer GMR is capable of activating a promoter in trans and does so in a variegated pattern, suggesting stochastic interactions between the enhancer and the promoter when they are carried on separate chromosomes. Furthermore, we quantitatively assessed the impact of two concurrent promoter targets in cis and in trans to GMR, demonstrating that each promoter is capable of competing for the enhancer's activity, with the presence of one negatively affecting expression from the other. Finally, the single-cell resolution afforded by our approach allowed us to show that promoters in cis and in trans to GMR can both be activated in the same nucleus, implying that a single enhancer can share its activity between multiple promoter targets carried on separate chromosomes. © 2012 by the Genetics Society of America.


Matrix-model description of N = 2 gauge theories with non-hyperelliptic Seiberg-Witten curves

Date: 2003-12-08

Creator: Stephen G. Naculich, Howard J. Schnitzer, Niclas Wyllard

Access: Open access

Using matrix-model methods we study three different N=2 models: U(N)×U(N) with matter in the bifundamental representation, U(N) with matter in the symmetric representation, and U(N) with matter in the antisymmetric representation. We find that the (singular) cubic Seiberg-Witten curves (and associated Seiberg-Witten differentials) implied by the matrix models, although of a different form from the ones previously proposed using M-theory, can be transformed into the latter and are thus physically equivalent. We also calculate the one-instanton corrections to the gauge-coupling matrix using the perturbative expansion of the matrix model. For the U(N) theories with symmetric or antisymmetric matter we use the modified matrix-model prescription for the gauge-coupling matrix discussed in our paper: Cubic curves from matrix models and generalized Konishi anomalies (hep-th/0303268). Moreover, in the matrix model for the U(N) theory with antisymmetric matter, one is required to expand around a different vacuum than one would naively have anticipated. With these modifications of the matrix-model prescription, the results of this paper are in complete agreement with those of Seiberg-Witten theory obtained using M-theory methods. © 2003 Elsevier B.V. All rights reserved.


Effects of stochasticity on the length and behaviour of ecological transients

Date: 2021-07-01

Creator: Alan Hastings, Karen C. Abbott, Kim Cuddington, Tessa B. Francis, Ying Cheng, Lai, Andrew Morozov

Access: Open access

There is a growing recognition that ecological systems can spend extended periods of time far away from an asymptotic state, and that ecological understanding will therefore require a deeper appreciation for how long ecological transients arise. Recent work has defined classes of deterministic mechanisms that can lead to long transients. Given the ubiquity of stochasticity in ecological systems, a similar systematic treatment of transients that includes the influence of stochasticity is important. Stochasticity can of course promote the appearance of transient dynamics by preventing systems from settling permanently near their asymptotic state, but stochasticity also interacts with deterministic features to create qualitatively new dynamics. As such, stochasticity may shorten, extend or fundamentally change a system's transient dynamics. Here, we describe a general framework that is developing for understanding the range of possible outcomes when random processes impact the dynamics of ecological systems over realistic time scales. We emphasize that we can understand the ways in which stochasticity can either extend or reduce the lifetime of transients by studying the interactions between the stochastic and deterministic processes present, and we summarize both the current state of knowledge and avenues for future advances.


The large-scale geometry of some metabelian groups

Date: 2003-01-01

Creator: Jennifer Taback, Kevin Whyte

Access: Open access



Direct selection for sequences encoding proteases of known specificity

Date: 1991-06-15

Creator: Tracy A. Smith, Bruce D. Kohorn

Access: Open access

We have developed a simple genetic selection that could be used to isolate eukaryotic cDNAs encoding proteases that cleave within a defined amino acid sequence. The selection was developed by using the transcription factor GAL4 from Saccharomyces cerevisiae as a selectable marker, a cloned protease from tobacco etch virus (TEV), and an 18-amino acid TEV protease target sequence. In yeast, TEV protease cleaves its target even when the target is fused to internal regions of the GAL4 protein. This cleavage separates the DNA binding domain from the transcription activation domain of GAL4, rendering it transcriptionally inactive. The proteolytic cleavage can be detected phenotypically by the inability of cells to metabolize galactose. Cells expressing the TEV protease can also be selected on the suicide substrate 2-deoxygalactose. DNA binding studies show that the TEV protease decreases the activity of the GAL4/target fusion protein. Because another protease target sequence of 55 amino acids can be inserted into GAL4 without any loss of transcriptional activity, this assay offers the opportunity to use high-efficiency cDNA cloning and expression vectors to select coding sequences of other proteases from various species. The assay could also be used to help define both target specificities and functional domains of proteases.


One-instanton predictions of Seiberg-Witten curves for product groups

Date: 1999-01-01

Creator: Isabel P. Ennes, Stephen G. Naculich, Henric Rhedin, Howard J. Schnitzer

Access: Open access

One-instanton predictions for the prepotential are obtained from the Seiberg-Witten curve for the Coulomb branch of script N sign = 2 supersymmetric gauge theory for the product group IIn=1m SU(Nn) with a massless matter hypermultiplet in the bifundamental representation (Nn,N̄n+1) of SU(Nn) × SU(Nn+1) for n = 1 to m - 1, together with N0 and Nm+1 matter hypermultiplets in the fundamental representations of SU(N1) and SU(Nm) respectively. The derivation uses a generalization of the systematic perturbation expansion about a hyperelliptic curve developed by us in earlier work. © 1999 Published by Elsevier Science B.V. All rights reserved.