Faculty Scholarship
Showing 511 - 520 of 733 Items
Developmental Gene Discovery in a Hemimetabolous Insect: De Novo Assembly and Annotation of a Transcriptome for the Cricket Gryllus bimaculatus
Date: 2013-05-06
Creator: Victor Zeng, Ben Ewen-Campen, Hadley W. Horch, Siegfried Roth, Taro, Mito, Cassandra G. Extavour
Access: Open access
- Most genomic resources available for insects represent the Holometabola, which are insects that undergo complete metamorphosis like beetles and flies. In contrast, the Hemimetabola (direct developing insects), representing the basal branches of the insect tree, have very few genomic resources. We have therefore created a large and publicly available transcriptome for the hemimetabolous insect Gryllus bimaculatus (cricket), a well-developed laboratory model organism whose potential for functional genetic experiments is currently limited by the absence of genomic resources. cDNA was prepared using mRNA obtained from adult ovaries containing all stages of oogenesis, and from embryo samples on each day of embryogenesis. Using 454 Titanium pyrosequencing, we sequenced over four million raw reads, and assembled them into 21,512 isotigs (predicted transcripts) and 120,805 singletons with an average coverage per base pair of 51.3. We annotated the transcriptome manually for over 400 conserved genes involved in embryonic patterning, gametogenesis, and signaling pathways. BLAST comparison of the transcriptome against the NCBI non-redundant protein database (nr) identified significant similarity to nr sequences for 55.5% of transcriptome sequences, and suggested that the transcriptome may contain 19,874 unique transcripts. For predicted transcripts without significant similarity to known sequences, we assessed their similarity to other orthopteran sequences, and determined that these transcripts contain recognizable protein domains, largely of unknown function. We created a searchable, web-based database to allow public access to all raw, assembled and annotated data. This database is to our knowledge the largest de novo assembled and annotated transcriptome resource available for any hemimetabolous insect. We therefore anticipate that these data will contribute significantly to more effective and higher-throughput deployment of molecular analysis tools in Gryllus. © 2013 Zeng et al.
Elliptic models and M-theory
Date: 2000-06-12
Creator: Isabel P. Ennes, Carlos Lozano, Stephen G. Naculich, Howard J. Schnitzer
Access: Open access
- We give a unified analysis of four-dimensional elliptic models with N = 2 supersymmetry and a simple gauge group, and their relation to M-theory. Explicit calculations of the Seiberg-Witten curves and the resulting one-instanton prepotential are presented. The remarkable regularities that emerge are emphasized. In addition, we calculate the prepotential in the Coulomb phase of the (asymptotically-free) Sp(2N) gauge theory with Nf fundamental hypermultiplets of arbitrary mass. © 2000 Elsevier Science B.V. All rights reserved.
Social Learning Strategies: Bridge-Building between Fields
Date: 2018-07-01
Creator: Rachel L. Kendal, Neeltje J. Boogert, Luke Rendell, Kevin N. Laland, Mike, Webster, Patricia L. Jones
Access: Open access
- While social learning is widespread, indiscriminate copying of others is rarely beneficial. Theory suggests that individuals should be selective in what, when, and whom they copy, by following 'social learning strategies’ (SLSs). The SLS concept has stimulated extensive experimental work, integrated theory, and empirical findings, and created impetus to the social learning and cultural evolution fields. However, the SLS concept needs updating to accommodate recent findings that individuals switch between strategies flexibly, that multiple strategies are deployed simultaneously, and that there is no one-to-one correspondence between psychological heuristics deployed and resulting population-level patterns. The field would also benefit from the simultaneous study of mechanism and function. SLSs provide a useful vehicle for bridge-building between cognitive psychology, neuroscience, and evolutionary biology.
Wall-associated kinases are expressed throughout plant development and are required for cell expansion
Date: 2001-01-01
Creator: T. A. Wagner, B. D. Kohorn
Access: Open access
- The mechanism by which events in the angiosperm cell wall are communicated to the cytoplasm is not well characterized. A family of five Arabidopsis wall-associated kinases (WAKs) have the potential to provide a physical and signaling continuum between the cell wall and the cytoplasm. The WAKs have an active cytoplasmic protein kinase domain, span the plasma membrane, and contain an N terminus that binds the cell wall. We show here that WAKs are expressed at organ junctions, in shoot and root apical meristems, in expanding leaves, and in response to wall disturbances. Leaves expressing an antisense WAK gene have reduced WAK protein levels and exhibit a loss of cell expansion. WAKs are covalently bound to pectin in the cell wall, providing evidence that the binding of a structural carbohydrate by a receptor-like kinase may have significance in the control of cell expansion.
Hydrophobic core but not amino-terminal charged residues are required for translocation of an integral thylakoid membrane protein in vivo
Date: 1996-10-07
Creator: Benoit Baillet, Bruce D. Kohorn
Access: Open access
- The integral membrane protein cytochrome f contains an amino-terminal signal sequence that is required for translocation into the thylakoid membrane. The signal sequence contains a hydrophobic core neighbored by an amino-terminal charged residue. Mutations that introduce charged amino acids into the hydrophobic core are inhibitory to cytochrome f translocation, and thus render cells non-photosynthetic. We have isolated both nuclear and chloroplast suppressors of these mutations by selecting for restoration of photosynthetic growth of Chlamydomonas. Here we describe the characterization of two chloroplast, second site suppressor mutations. Both suppressors remove the positively charged amino acid that borders the amino terminus of the hydrophobic core, and replace this arginine with either a cysteine or a leucine. The existence of these suppressors suggests that the hydrophobic core can be shifted in position within the signal sequence, and analysis of triple mutants in the signal confirms this hypothesis. Thus this signal that mediates translocation into the thylakoid membrane is characterized by a hydrophobic region whose exact amino acid content is not critical, and that need not be flanked on its amino terminus by a charged residue.
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.
The Importance of What We Care About: A Solidarity Approach to Resource Allocation
Date: 2020-01-01
Creator: Kristi A. Olson
Access: Open access
- At some point in your life, you will need to allocate resources among individuals, but how should you do so? One prominent suggestion is the envy test: the envy test is satisfied when and only when no one prefers someone else’s bundle. In Part I, I explain and then reject Tom Parr’s recent attempt to justify the envy test. Yet, like Parr, I believe the envy test captures something important. Thus, in Part II, I distinguish two approaches to resource allocation. Parr’s defense of the envy test assumes what I will call an individualist approach: what matters are each individual’s preferences. In lieu of the individualist approach, I endorse the solidarity approach: what matters are everyone’s preferences. After explaining the distinction, I show that the envy test—or at least something like it—can be defended using the solidarity approach even if it cannot be defended using the individualist approach.
Anthropogenic Impacts on Atmospheric Carbonyl Sulfide Since the 19th Century Inferred From Polar Firn Air and Ice Core Measurements
Date: 2020-08-27
Creator: M. Aydin, G. L. Britten, S. A. Montzka, C. Buizert, F., Primeau, V. Petrenko, M. B. Battle, M. R. Nicewonger, J. Patterson, B. Hmiel, E. S. Saltzman
Access: Open access
- Carbonyl sulfide (COS) was measured in firn air collected during seven different field campaigns carried out at four different sites in Greenland and Antarctica between 2001 and 2015. A Bayesian probabilistic statistical model is used to conduct multisite inversions and to reconstruct separate atmospheric histories for Greenland and Antarctica. The firn air inversions cover most of the 20th century over Greenland and extend back to the 19th century over Antarctica. The derived atmospheric histories are consistent with independent surface air time series data from the corresponding sites and the Antarctic ice core COS records during periods of overlap. Atmospheric COS levels began to increase over preindustrial levels starting in the 19th century, and the increase continued for much of the 20th century. Atmospheric COS peaked at higher than present-day levels around 1975 CE over Greenland and around 1987 CE over Antarctica. An atmosphere/surface ocean box model is used to investigate the possible causes of observed variability. The results suggest that changes in the magnitude and location of anthropogenic sources have had a strong influence on the observed atmospheric COS variability.
Formation of rarefaction waves in origami-based metamaterials
Date: 2016-04-15
Creator: H. Yasuda, C. Chong, E. G. Charalampidis, P. G. Kevrekidis, J., Yang
Access: Open access
- We investigate the nonlinear wave dynamics of origami-based metamaterials composed of Tachi-Miura polyhedron (TMP) unit cells. These cells exhibit strain softening behavior under compression, which can be tuned by modifying their geometrical configurations or initial folded conditions. We assemble these TMP cells into a cluster of origami-based metamaterials, and we theoretically model and numerically analyze their wave transmission mechanism under external impact. Numerical simulations show that origami-based metamaterials can provide a prototypical platform for the formation of nonlinear coherent structures in the form of rarefaction waves, which feature a tensile wavefront upon the application of compression to the system. We also demonstrate the existence of numerically exact traveling rarefaction waves in an effective lumped-mass model. Origami-based metamaterials can be highly useful for mitigating shock waves, potentially enabling a wide variety of engineering applications.
Discrete breathers in a mass-in-mass chain with Hertzian local resonators
Date: 2017-02-22
Creator: S. P. Wallen, J. Lee, D. Mei, C. Chong, P. G., Kevrekidis, N. Boechler
Access: Open access
- We report on the existence of discrete breathers in a one-dimensional, mass-in-mass chain with linear intersite coupling and nonlinear, precompressed Hertzian local resonators, which is motivated by recent studies of the dynamics of microspheres adhered to elastic substrates. After predicting theoretically the existence of discrete breathers in the continuum and anticontinuum limits of intersite coupling, we use numerical continuation to compute a family of breathers interpolating between the two regimes in a finite chain, where the displacement profiles of the breathers are localized around one lattice site. We then analyze the frequency-amplitude dependence of the breathers by performing numerical continuation on a linear eigenmode (vanishing amplitude) solution of the system near the upper band gap edge. Finally, we use direct numerical integration of the equations of motion to demonstrate the formation and evolution of the identified localized modes in energy-conserving and dissipative scenarios, including within settings that may be relevant to future experimental studies.