Showing 651 - 660 of 733 Items
Replacement of histidines of light harvesting chlorophyll a/b binding protein II disrupts chlorophyll-Protein complex assembly
Date: 1990-01-01
Creator: Bruce D. Kohorn
Access: Open access
- Eukaryotic light harvesting proteins (LHCPs) bind pigments and assemble into complexes (LHCs) that channel light energy into photosynthetic reaction centers. The structures of several prokaryotic LHCPs are known and histidines are important for the binding of the associated pigments. It has been difficult to predict how the eukaryotic LHCPs associate with pigments as the structure of the major LHCP of photosystem II is not yet known. While each LHCPII binds approximately 13 chlorophylls the protein contains only three histidines, one in each putative transmembrane helix. Experiments that use isolated pea (Pisum sativum L.) chloroplasts and mutant LHCPII synthesized in vitro show that the substitution of either an alanine or an arginine for each histidine residue inhibits some aspect of LHCII assembly. The histidine of the first membrane helix, but not the second or third, may be involved in the transport across the chloroplast envelope. No histidine alone is essential for the insertion of LHCP into thylakoid membranes, yet arginine substitutions are more inhibitory than those of alanine. The histidine replacements have their most pronounced effect on the assembly of LHCP into LHCII.
Breathers and other time-periodic solutions in an array of cantilevers decorated with magnetsy
Date: 2019-01-01
Creator: Christopher Chong, Andre Foehr, Efstathios G. Charalampidis, Panayotis G. Kevrekidis, Chiara, Daraio
Access: Open access
- In this article, the existence, stability and bifurcation structure of time-periodic solutions (including ones that also have the property of spatial localization, i.e., breathers) are studied in an array of cantilevers that have magnetic tips. The repelling magnetic tips are responsible for the intersite nonlinearity of the system, whereas the cantilevers are responsible for the onsite (potentially nonlinear) force. The relevant model is of the mixed Fermi-Pasta-Ulam-Tsingou and Klein-Gordon type with both damping and driving. In the case of base excitation, we provide experimental results to validate the model. In particular, we identify regions of bistability in the model and in the experiment, which agree with minimal tuning of the system parameters. We carry out additional numerical explorations in order to contrast the base excitation problem with the boundary excitation problem and the problem with a single mass defect. We find that the base excitation problem is more stable than the boundary excitation problem and that breathers are possible in the defect system. The effect of an onsite nonlinearity is also considered, where it is shown that bistability is possible for both softening and hardening cubic nonlinearities.
Bounding right-arm rotation distances
Date: 2007-03-01
Creator: Sean Cleary, Jennifer Taback
Access: Open access
- Rotation distance measures the difference in shape between binary trees of the same size by counting the minimum number of rotations needed to transform one tree to the other. We describe several types of rotation distance where restrictions are put on the locations where rotations are permitted, and provide upper bounds on distances between trees with a fixed number of nodes with respect to several families of these restrictions. These bounds are sharp in a certain asymptotic sense and are obtained by relating each restricted rotation distance to the word length of elements of Thompson's group F with respect to different generating sets, including both finite and infinite generating sets. © World Scientific Publishing Company.
Simplified insertion of transgenes onto balancer chromosomes via recombinase-mediated cassette exchange
Date: 2012-05-01
Creator: Florence F. Sun, Justine E. Johnson, Martin P. Zeidler, Jack R. Bateman
Access: Open access
- Balancer chromosomes are critical tools for Drosophila genetics. Many useful transgenes are inserted onto balancers using a random and inefficient process. Here we describe balancer chromosomes that can be directly targeted with transgenes of interest via recombinase-mediated cassette exchange (RMCE). ©2012 Sun et al.
Maximal stomatal conductance to water and plasticity in stomatal traits differ between native and invasive introduced lineages of Phragmites australis in North America
Date: 2016-01-27
Creator: V. Douhovnikoff, S. H. Taylor, E. L.G. Hazelton, C. M. Smith, J., O'Brien
Access: Open access
- The fitness costs of reproduction by clonal growth can include a limited ability to adapt to environmental and temporal heterogeneity. Paradoxically, some facultatively clonal species are not only able to survive, but colonize, thrive and expand in heterogeneous environments. This is likely due to the capacity for acclimation (sensu stricto) that compensates for the fitness costs and complements the ecological advantages of clonality. Introduced Phragmites australis demonstrates great phenotypic plasticity in response to temperature, nutrient availability, geographic gradient, water depths, habitat fertility, atmospheric CO2, interspecific competition and intraspecific competition for light. However, no in situ comparative subspecies studies have explored the difference in plasticity between the non-invasive native lineage and the highly invasive introduced lineage. Clonality of the native and introduced lineages makes it possible to control for genetic variation, making P. australis a unique system for the comparative study of plasticity. Using previously identified clonal genotypes, we investigated differences in their phenotypic plasticity through measurements of the lengths and densities of stomata on both the abaxial (lower) and adaxial (upper) surfaces of leaves, and synthesized these measurements to estimate impacts on maximum stomatal conductance to water (gwmax). Results demonstrated that at three marsh sites, invasive lineages have consistently greater gwmax than their native congeners, as a result of greater stomatal densities and smaller stomata. Our analysis also suggests that phenotypic plasticity, determined as within-genotype variation in gwmax, of the invasive lineage is similar to, or exceeds, that shown by the native lineage.
Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis
Date: 2011-08-01
Creator: Kimberly A. Tice, D. B. Carlon
Access: Open access
- Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium (LD) and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, whereas no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error using multiple outlier detection approaches, multitest corrections and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.
Schwarzschild-de Sitter spacetimes, McVittie coordinates, and trumpet geometries
Date: 2017-12-15
Creator: Kenneth A. Dennison, Thomas W. Baumgarte
Access: Open access
- Trumpet geometries play an important role in numerical simulations of black hole spacetimes, which are usually performed under the assumption of asymptotic flatness. Our Universe is not asymptotically flat, however, which has motivated numerical studies of black holes in asymptotically de Sitter spacetimes. We derive analytical expressions for trumpet geometries in Schwarzschild-de Sitter spacetimes by first generalizing the static maximal trumpet slicing of the Schwarzschild spacetime to static constant mean curvature trumpet slicings of Schwarzschild-de Sitter spacetimes. We then switch to a comoving isotropic radial coordinate which results in a coordinate system analogous to McVittie coordinates. At large distances from the black hole the resulting metric asymptotes to a Friedmann-Lemaître-Robertson-Walker metric with an exponentially-expanding scale factor. While McVittie coordinates have another asymptotically de Sitter end as the radial coordinate goes to zero, so that they generalize the notion of a "wormhole" geometry, our new coordinates approach a horizon-penetrating trumpet geometry in the same limit. Our analytical expressions clarify the role of time-dependence, boundary conditions and coordinate conditions for trumpet slices in a cosmological context, and provide a useful test for black hole simulations in asymptotically de Sitter spacetimes.
“Fanny Buitrago: La magia de contar historias”. A Body of One’s Own: Conversations with Caribbean and Latina Writers
Date: 2007-01-01
Creator: Nadia V. Celis Salgado, Fanny Buitrago
Access: Open access
Captured segment exchange: A strategy for custom engineering large genomic regions in Drosophila melanogaster
Date: 2013-04-24
Creator: Jack R. Bateman, Michael F. Palopoli, Sarah T. Dale, Jennifer E. Stauffer, Anita L., Shah, Justine E. Johnson, Conor W. Walsh, Hanna Flaten, Christine M. Parsons
Access: Open access
- Site-specific recombinases (SSRs) are valuable tools for manipulating genomes. In Drosophila, thousands of transgenic insertions carrying SSR recognition sites have been distributed throughout the genome by several large-scale projects. Here we describe a method with the potential to use these insertions to make custom alterations to the Drosophila genome in vivo. Specifically, by employing recombineering techniques and a dual recombinase-mediated cassette exchange strategy based on the phiC31 integrase and FLP recombinase, we show that a large genomic segment that lies between two SSR recognition-site insertions can be "captured" as a target cassette and exchanged for a sequence that was engineered in bacterial cells. We demonstrate this approach by targeting a 50-kb segment spanning the tsh gene, replacing the existing segment with corresponding recombineered sequences through simple and efficient manipulations. Given the high density of SSR recognition-site insertions in Drosophila, our method affords a straightforward and highly efficient approach to explore gene function in situ for a substantial portion of the Drosophila genome. © 2013 by the Genetics Society of America.