Showing 501 - 550 of 733 Items

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.


Developmental genetic mechanisms of evolutionary tooth loss in cypriniform fishes

Date: 2006-08-01

Creator: David W. Stock, William R. Jackman, Josh Trapani

Access: Open access

The fossil record indicates that cypriniform fishes, a group including the zebrafish, lost oral teeth over 50 million years ago. Despite subsequent diversification of feeding modes, no cypriniform has regained oral teeth, suggesting the zebrafish as a model for studying the developmental genetic basis of evolutionary constraint. To investigate the mechanism of cypriniform tooth loss, we compared the oral expression of seven genes whose mammalian orthologs are involved in tooth initiation in the zebrafish and the Mexican tetra, Astyanax mexicanus, a related species retaining oral teeth. The most significant difference we found was an absence in zebrafish oral epithelium of expression of dlx2a and dlx2b, transcription factors that are expressed in early Astyanax odontogenic epithelium. Analysis of orthologous genes in the Japanese medaka (Oryzias latipes) and a catfish (Synodontis multipunctatus) suggests that expression was lost in cypriniforms, rather than gained in Astyanax. Treatment of Astyanaxwith an inhibitor of Fibroblast growth factor (Fgf) signaling produced a partial phenocopy of the zebrafish oral region, in that oral teeth, and expression of d1x2a and d1x2b, were lost, whereas shh and pitx2, genes whose expression is present in zebrafish oral epithelium, were unaffected. We hypothesize that a loss of Fgf signaling to oral epithelium was associated with cypriniform tooth loss.


Efficient and rapid identification of Candida albicans allelic status using SNP-RFLP

Date: 2009-11-01

Creator: Anja Forche, Musetta Steinbach, Judith Berman

Access: Open access

Candida albicans is the most prevalent opportunistic fungal pathogen in the clinical setting, causing a wide spectrum of diseases ranging from superficial mucosal lesions to life-threatening deep-tissue infections. Recent studies provide strong evidence that C. albicans possesses an arsenal of genetic mechanisms promoting genome plasticity and that it uses these mechanisms under conditions of nutritional or antifungal drug stress. Two microarray-based methods, single nucleotide polymorphism (SNP) and comparative genome hybridization arrays, have been developed to study genome changes in C. albicans. However, array technologies can be relatively expensive and are not available to every laboratory. In addition, they often generate more data than needed to analyze specific genomic loci or regions. Here, we have developed a set of SNP-restriction fragment length polymorphism (RFLP) (or PCR-RFLP) markers, two per chromosome arm, for C. albicans. These markers can be used to rapidly and accurately detect large-scale changes in the C. albicans genome including loss of heterozygosity (LOH) at single loci, across chromosome arms or across whole chromosomes. Furthermore, skewed SNP-RFLP allelic ratios are indicative of trisomy at heterozygous loci. While less comprehensive than array-based approaches, we propose SNP-RFLP as an inexpensive, rapid, and reliable method to screen strains of interest for possible genome changes. © 2009 Federation of European Microbiological Societies.


Transgenic analysis of Dlx regulation in fish tooth development reveals evolutionary retention of enhancer function despite organ loss

Date: 2006-12-19

Creator: William R. Jackman, David W. Stock

Access: Open access

It has been considered a "law" that a lost structure cannot reappear in evolution. The common explanation, that genes required for the development of the lost structure degrade by mutation, remains largely theoretical, however. Additionally, the extent to which this mechanism applies to systems of repeated parts, where individual modules are likely to exhibit few unique aspects of genetic control, is unclear. We investigated reversibility of evolution in one such system, the vertebrate dentition, using as a model loss of oral teeth in cypriniform fishes, which include the zebra fish. This evolutionary event, which occurred >50 million years ago, has not been reversed despite subsequent diversification of feeding modes and retention of pharyngeal teeth. We asked whether the cis-regulatory region of a gene whose expression loss parallels cypriniform tooth loss, Dlx2b, retains the capacity for expression in oral teeth. We first created a zebrafish reporter transgenic line that recapitulates endogenous dlx2b expression. We then showed that this zebrafish construct drives reporter expression in oral teeth of the related characiform Astyanax mexicanus. This result, along with our finding that Dlx genes are required for normal tooth development, suggests that changes in trans-acting regulators of these genes were responsible for loss of cypriniform oral teeth. Preservation of oral enhancer function unused for >50 million years could be the result of pleiotropic function in the pharyngeal dentition. If enhancers of other genes in the tooth developmental pathway are similarly preserved, teeth lost from specific regions may be relatively easy to reacquire in evolution. © 2006 by The National Academy of Sciences of the USA.


Time-Periodic Solutions of Driven-Damped Trimer Granular Crystals

Date: 2015-01-01

Creator: E. G. Charalampidis, F. Li, C. Chong, J. Yang, P. G., Kevrekidis

Access: Open access

We consider time-periodic structures of granular crystals consisting of alternate chrome steel (S) and tungsten carbide (W) spherical particles where each unit cell follows the pattern of a 2: 1 trimer: S-W-S. The configuration at the left boundary is driven by a harmonic in-time actuation with given amplitude and frequency while the right one is a fixed wall. Similar to the case of a dimer chain, the combination of dissipation, driving of the boundary, and intrinsic nonlinearity leads to complex dynamics. For fixed driving frequencies in each of the spectral gaps, we find that the nonlinear surface modes and the states dictated by the linear drive collide in a saddle-node bifurcation as the driving amplitude is increased, beyond which the dynamics of the system becomes chaotic. While the bifurcation structure is similar for solutions within the first and second gap, those in the first gap appear to be less robust. We also conduct a continuation in driving frequency, where it is apparent that the nonlinearity of the system results in a complex bifurcation diagram, involving an intricate set of loops of branches, especially within the spectral gap. The theoretical findings are qualitatively corroborated by the experimental full-field visualization of the time-periodic structures.


Institutions and democratic invention in 19th-century America: Evidence from "great inventors," 1790-1930

Date: 2004-05-01

Creator: B. Zorina Khan, Kenneth L. Sokoloff

Access: Open access



"Not for ornament": Patenting activity by nineteenth-century women inventors

Date: 2000-01-01

Creator: B. Zorina Khan

Access: Open access



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.


Fighting for Every Inch of Land: Greed and Grievance in Petition Mobilization in Zhejiang

Date: 2020-07-01

Creator: Christopher Heurlin

Access: Open access

Despite a proliferation of studies of the micro-level dynamics of protests and petitions against land takings in China, we know very little about how meso-level factors, such as the local economy, influence petitions to Beijing and provincial governments. Drawing upon the economic approach to civil war, this article examines the roles played by grievances and greed in determining the scale of mobilization at the county level in Zhejiang province. Through archival evidence and interviews in Ningbo and Lishui, as well as an original dataset of petitions, this article suggests that both grievances and greed influence petitioning. Mobilization is especially high in Ningbo, where valuable real estate markets have prompted landless farmers to compete with local governments over control of the rents from land. The article proposes the concept of resource value activation as a cognitive mechanism that has contributed to this process of mobilization.


Inventing Prizes: A Historical Perspective on Innovation Awards and Technology Policy

Date: 2015-01-01

Creator: B. Zorina Khan

Access: Open access

Prizes for innovations are currently experiencing a renaissance, following their marked decline during the nineteenth century. Debates about such incentive mechanisms tend to employ canonical historical anecdotes to motivate and support the analysis and policy proposals. Daguerre's "patent buyout," the Longitude Prize, inducement prizes for butter substitutes and billiard balls, the activities of the Royal Society of Arts and other "encouragement" institutions-all comprise potentially misleading case studies. The article surveys and summarizes extensive empirical research using samples drawn from Britain, France, and the United States, including "great inventors" and their ordinary counterparts, and prizes at industrial exhibitions. The results suggest that administered systems of rewards to innovators suffered from a number of disadvantages in design and practice, which might be inherent to their nonmarket orientation.


Conservation as if people also mattered: Policy and practice of community-based conservation

Date: 2013-01-01

Creator: Ashish Kothari, Philip Camill, Jessica Brown

Access: Open access

Community-based conservation is being increasingly recognised as a major global force in the protection and sustainable management of ecosystems and species. Yet documentation of its main achievements and shortcomings, and the key issues it faces, is still at a nascent stage. This paper introduces the concept and experience of two forms of community-based conservation: Collaborative Management of Protected Areas (CMPA), and Indigenous Peoples' and Local Community Conserved Territories and Areas (ICCAs). It explores the emergence of these approaches in the context of global international conservation policy. Reviewing four case studies that were presented at a symposium convened at the Bowdoin College (Maine, USA, in November 2008), and drawing from the discussion during that session, it identifies some key lessons and principles that are likely to be applicable to community-based conservation across the world.


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.


A cell wall-associated, receptor-like protein kinase

Date: 1996-09-05

Creator: Zheng Hui He, Masaaki Fujiki, Bruce D. Kohorn

Access: Open access

Physical connections between higher plant cell walls and the plasma membrane have been identified visually, but the molecules involved in the contact are unknown. We describe here an Arabidopsis thaliana protein kinase, designated Wak1 for wall-associated kinase, whose predicted extracytoplasmic domain contains several epidermal growth factor repeats and identity with a viral movement protein. Wak1 fractionates with insoluble material when plant tissue is ground in a variety of buffers and detergents, suggesting a tight association with the plant extracellular matrix. Immunocytochemistry confirms that Wak1 is associated with the cell wall. Enzymatic digestion of the cell wall allows the release of Wak1 from the insoluble cell wall fraction, and protease experiments indicate that Wak1 likely has a cytoplasmic kinase domain, and the EGF containing domain is extracellular. Wak1 is found in all vegetative tissues of Arabidopsis, and has relatives in other angiosperms, but not Chlamydomonas. We suggest that Wak1 is a good candidate for a physical continuum between the cell wall and the cytoplasm, and since the kinase is cytoplasmic, it also has the potential to mediate signals to the cytoplasm from the cell wall.


Functional and mutational analysis of the light-harvesting chlorophyll a/b protein of thylakoid membranes.

Date: 1986-01-01

Creator: B. D. Kohorn, E. Harel, P. R. Chitnis, J. P. Thornber, E. M., Tobin

Access: Open access

The precursor for a Lemna light-harvesting chlorophyll a/b protein (pLHCP) has been synthesized in vitro from a single member of the nuclear LHCP multigene family. We report the sequence of this gene. When incubated with Lemna chloroplasts, the pLHCP is imported and processed into several polypeptides, and the mature form is assembled into the light-harvesting complex of photosystem II (LHC II). The accumulation of the processed LHCP is enhanced by the addition to the chloroplasts of a precursor and a co-factor for chlorophyll biosynthesis. Using a model for the arrangement of the mature polypeptide in the thylakoid membrane as a guide, we have created mutations that lie within the mature coding region. We have studied the processing, the integration into thylakoid membranes, and the assembly into light-harvesting complexes of six of these deletions. Four different mutant LHCPs are found as processed proteins in the thylakoid membrane, but only one appears to have an orientation in the membrane that is similar to that of the wild type. No mutant LHCP appears in LHC II. The other two mutant LHCPs cannot be detected within the chloroplasts. We conclude that stable complex formation is not required for the processing and insertion of altered LHCPs into the thylakoid membrane. We discuss the results in light of our model.


Risks of multimodal signaling: Bat predators attend to dynamic motion in frog sexual displays

Date: 2014-09-01

Creator: Wouter Halfwerk, Marjorie M. Dixon, Kristina J. Ottens, Ryan C. Taylor, Michael J., Ryan, Rachel A. Page, Patricia L. Jones

Access: Open access

Many sexual displays contain multiple components that are received through a variety of sensory modalities. Primary and secondary signal components can interact to induce novel receiver responses and become targets of sexual selection as complex signals. However, predators can also use these complex signals for prey assessment, which may limit the evolution of elaborate sexual signals. We tested whether a multimodal sexual display of the male túngara frog (Physalaemus pustulosus) increases predation risk from the fringe-lipped bat (Trachops cirrhosus) when compared with a unimodal display. We gave bats a choice to attack one of two frog models: a model with a vocal sac moving in synchrony with a mating call (multisensory cue), or a control model with the call but no vocal sac movement (unimodal cue). Bats preferred to attack the model associated with the multimodal display. Furthermore, we determined that bats perceive the vocal sac using echolocation rather than visual cues. Our data illustrate the costs associated with multimodal signaling and that sexual and natural selection pressures on the same trait are not always mediated through the same sensory modalities. These data are important when considering the role of environmental fluctuations on signal evolution as different sensory modalities will be differentially affected.


Bounding the number of cycles of O.D.E.S in Rn

Date: 2001-01-01

Creator: M. Farkas, P. Van Den Driessche, M. L. Zeeman

Access: Open access

Criteria are given under which the boundary of an oriented surface does not consist entirely of trajectories of the C1 differential equation ẋ = f(x) in Rn. The special case of an annulus is further considered, and the criteria are used to deduce sufficient conditions for the differential equation to have at most one cycle. A bound on the number of cycles on surfaces of higher connectivity is given by similar conditions. ©2000 American Mathematical Society.


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.


An Arabidopsis serine/threonine kinase homologue with an epidermal growth factor repeat selected in yeast for its specificity for a thylakoid membrane protein

Date: 1992-01-01

Creator: Bruce D. Kohorn, Steven Lane, Tracy A. Smith

Access: Open access

A number of molecules have recently been described that effect the correct transport and assembly of cytoplasmically synthesized proteins to cellular membranes. To identify proteins that bind or modify other proteins during the process of membrane translocation, we developed a yeast selection scheme that employs the yeast transcriptional activator GAL4. This selection facilitates the isolation of cDNAs that encode proteases and binding proteins for known target peptide sequences. We report the isolation of an Arabidopsis cDNA encoding a polypeptide that can interact with the amino terminus of a light-harvesting chlorophyll a/b-binding protein (LHCP), a cytoplasmically synthesized protein that is integral to the chloroplast thylakoid membrane. The cDNA was selected in yeast from an Arabidopsis expression library for its ability to inhibit a transcriptional activator GAL4-LHCP fusion protein, but not inhibit native GAL4 protein. The LHCP aminoterminal sequences included in the fusion protein are known to regulate LHCP biogenesis and function. The Arabidopsis cDNA encodes a 595-amino acid protein with at least two functional domains, one with similarity to the family of proteinserine/threonine kinases and another that contains an epidermal growth factor repeat. The identification of an EGF repeat in Arabidopsis indicates that the motif is conserved between the plant and animal kingdoms. Hybridization studies indicate that this gene is likely to be present in other genera of plants. Its mRNA is detected in green leaves but not in other plant tissues or in etiolated plants. The specificity in yeast and the expression pattern in plants together are suggestive of a role for this protein kinase in the assembly or regulation of LHCP.


Combinatorial properties of Thompson's group F

Date: 2004-07-01

Creator: Sean Cleary, Jennifer Taback

Access: Open access

We study some combinatorial consequences of Blake Fordham's theorems on the word metric of Thompson's group F in the standard two generator presentation. We explore connections between the tree pair diagram representing an element w of F, its normal form in the infinite presentation, its word length, and minimal length representatives of it. We estimate word length in terms of the number and type of carets in the tree pair diagram and show sharpness of those estimates. In addition we explore some properties of the Cayley graph of F with respect to the two generator finite presentation. Namely, we exhibit the form of "dead end" elements in this Cayley graph, and show that it has no "deep pockets". Finally, we discuss a simple method for constructing minimal length representatives for strictly positive or negative words.


Consequences of toxic secondary compounds in nectar for mutualist bees and antagonist butterflies

Date: 2016-10-01

Creator: Patricia L. Jones, Anurag A. Agrawal

Access: Open access

Attraction of mutualists and defense against antagonists are critical challenges for most organisms and can be especially acute for plants with pollinating and non-pollinating flower visitors. Secondary compounds in flowers have been hypothesized to adaptively mediate attraction of mutualists and defense against antagonists, but this hypothesis has rarely been tested. The tissues of milkweeds (Asclepias spp.) contain toxic cardenolides that have long been studied as chemical defenses against herbivores. Milkweed nectar also contains cardenolides, and we have examined the impact of manipulating cardenolides in nectar on the foraging choices of two flower visitors: generalist bumble bees, Bombus impatiens, which are mutualistic pollinators, and specialist monarch butterflies, Danaus plexippus, which are herbivores as larvae and ineffective pollinators as adults. Although individual bumble bees in single foraging bouts showed no avoidance of cardenolides at the highest natural concentrations reported for milkweeds, a pattern of deterrence did arise when entire colonies were allowed to forage for several days. Monarch butterflies were not deterred by the presence of cardenolides in nectar when foraging from flowers, but laid fewer eggs on plants paired with cardenolide-laced flowers compared to controls. Thus, although deterrence of bumble bees by cardenolides may only occur after extensive foraging, a primary effect of nectar cardenolides appears to be reduction of monarch butterfly oviposition.


Surface symmetries and PSL2(p)

Date: 2007-05-01

Creator: Murad Özaydin, Charlotte Simmons, Jennifer Taback

Access: Open access

We classify, up to conjugacy, all orientation-preserving actions of PSL2(p) on closed connected orientable surfaces with spherical quotients. This classification is valid in the topological, PL, smooth, conformal, geometric and algebraic categories and is related to the Inverse Galois Problem. © 2006 American Mathematical Society.


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.


Erratum: Context-dependent protein stabilization by methionine-to- leucine substitution shown in T4 lysozyme (Protein Science (November 3, 1998) 7:3 (772))

Date: 1998-01-01

Creator: L. A. Lipscomb, N. C. Gassner, S. D. Snow, A. M. Eldridge, W. A., Baase, D. L. Drew, B. W. Matthews

Access: Open access



Mitochondrial genotype influences the response to cold stress in the European green crab, Carcinus maenas

Date: 2019-01-01

Creator: Aidan F. Coyle, Erin R. Voss, Carolyn K. Tepolt, David B. Carlon

Access: Open access

Hybrid zones provide natural experiments in recombination within and between genomes that may have strong effects on organismal fitness. On the East Coast of North America, two distinct lineages of the European green crab (Carcinus maenas) have been introduced in the last two centuries. These two lineages with putatively different adaptive properties have hybridized along the coast of the eastern Gulf of Maine, producing new nuclear and mitochondrial combinations that show clinal variation correlated with water temperature. To test the hypothesis that mitochondrial or nuclear genes have effects on thermal tolerance, we first measured the response to cold stress in crabs collected throughout the hybrid zone, then sequenced the mitochondrial CO1 gene and two nuclear single nucleotide polymorphisms (SNPs) representative of nuclear genetic lineage. Mitochondrial haplotype had a strong association with the ability of crabs to right themselves at 4.5°C that was sex specific: haplotypes originally from northern Europe gave male crabs an advantage while there was no haplotype effect on righting in female crabs. By contrast, the two nuclear SNPs that were significant outliers in a comparison between northern and southern C. maenas populations had no effect on righting response at low temperature. These results add C. maenas to the shortlist of ectotherms in which mitochondrial variation has been shown to affect thermal tolerance, and suggest that natural selection is shaping the structure of the hybrid zone across the Gulf of Maine. Our limited genomic sampling does not eliminate the strong possibility that mito-nuclear co-adaptation may play a role in the differences in thermal phenotypes documented here. Linkage between mitochondrial genotype and thermal tolerance suggests a role for local adaptation in promoting the spread of invasive populations of C. maenas around the world.


Isolation of nine microsatellite loci in Dolichogenidea homoeosomae (Hymenoptera) a parasitoid of the sunflower moth Homoeosoma electellum (Lepidoptera)

Date: 2006-03-01

Creator: Vladimir Douhovnikoff, Caterina Nerney, George K. Roderick, Craig H. Newton, Stephen C., Welter

Access: Open access

Nine microsatellite loci were isolated from the insect Dolichogenidea homoeosomae (Hymenoptera: Braconidae), an important parasitoid of the sunflower moth Homosoeosoma electellum (Lepidoptera: Pyralidae), and assayed for polymorphism. All nine loci were polymorphic within the five populations tested, with two to 14 alleles per locus. Expected and observed heterozygosities ranged from 0.39 to 0.90 and 0.25 to 0.72 respectively. These are the first microsatellite primers developed for D. homeosomae and will be useful for studies of population dynamics and connectivity. © 2006 Blackwell Publishing Ltd.


Erratum: The 'obligate diploid' Candida albicans forms mating-competent haploids (Nature (2013) 494 (55-59) DOI: 10.1038/nature11865)

Date: 2016-02-11

Creator: Meleah A. Hickman, Guisheng Zeng, Anja Forche, Matthew P. Hirakawa, Darren, Abbey, Benjamin D. Harrison, Yan Ming Wang, Ching Hua Su, Richard J. Bennett, Yue Wang, Judith Berman

Access: Open access



C-graph automatic groups

Date: 2014-09-01

Creator: Murray Elder, Jennifer Taback

Access: Open access

We generalize the notion of a graph automatic group introduced by Kharlampovich, Khoussainov and Miasnikov by replacing the regular languages in their definition with more powerful language classes. For a fixed language class C, we call the resulting groups C-graph automatic. We prove that the class of C-graph automatic groups is closed under change of generating set, direct and free product for certain classes C. We show that for quasi-realtime counter-graph automatic groups where normal forms have length that is linear in the geodesic length, there is an algorithm to compute normal forms (and therefore solve the word problem) in polynomial time. The class of quasi-realtime counter-graph automatic groups includes all Baumslag-Solitar groups, and the free group of countably infinite rank. Context-sensitive-graph automatic groups are shown to be a very large class, which encompasses, for example, groups with unsolvable conjugacy problem, the Grigorchuk group, and Thompson's groups F, T and V. © 2014 Elsevier Inc.


Assessment and Treatment of Pathological Skin Picking

Date: 2012-09-18

Creator: Jedidiah Siev, Hannah E. Reese, Kiara Timpano, Sabine Wilhelm

Access: Open access

Pathological skin picking (PSP) refers to chronic skin picking or scratching that causes tissue damage and distress. It is a heterogeneous category of behaviors and may be manifest in the context of various psychological disorders. This chapter presents an overview of the empirical literature on the assessment and treatment of PSP, including (1) a cognitive-behavioral model as heuristic for conceptualizing treatment, (2) assessment tools, (3) a review of the pharmacological and psychosocial treatment outcome literatures, (4) cognitive-behavioral treatment techniques, and (5) future directions. The chapter is intended to introduce the clinician to the assessment and psychological tools used to treat PSP, as well as to provide impetus to advance research in this understudied domain.


Thompson's group F is 1-counter graph automatic

Date: 2016-05-01

Creator: Murray Elder, Jennifer Taback

Access: Open access

It is not known whether Thompson's group F is automatic. With the recent extensions of the notion of an automatic group to graph automatic by Kharlampovich, Khoussainov and Miasnikov and then to C-graph automatic by the authors, a compelling question is whether F is graph automatic or C-graph automatic for an appropriate language class C. The extended definitions allow the use of a symbol alphabet for the normal form language, replacing the dependence on generating set. In this paper we construct a 1-counter graph automatic structure for F based on the standard infinite normal form for group elements.


Ploidy variation in fungi: Polyploidy, aneuploidy, and genome evolution

Date: 2017-07-01

Creator: Robert T. Todd, Anja Forche, Anna Selmecki

Access: Open access

The ability of an organism to replicate and segregate its genome with high fidelity is vital to its survival and for the production of future generations. Errors in either of these steps (replication or segregation) can lead to a change in ploidy or chromosome number. While these drastic genome changes can be detrimental to the organism, resulting in decreased fitness, they can also provide increased fitness during periods of stress. A change in ploidy or chromosome number can fundamentally change how a cell senses and responds to its environment. Here, we discuss current ideas in fungal biology that illuminate how eukaryotic genome size variation can impact the organism at a cellular and evolutionary level. One of the most fascinating observations from the past 2 decades of research is that some fungi have evolved the ability to tolerate large genome size changes and generate vast genomic heterogeneity without undergoing canonical meiosis.


Separation of internal and interaction dynamics for NLS-described wave packets with different carrier waves

Date: 2008-11-01

Creator: Martina Chirilus-Bruckner, Christopher Chong, Guido Schneider, Hannes Uecker

Access: Open access

We give a detailed analysis of the interaction of two NLS-described wave packets with different carrier waves for a nonlinear wave equation. By separating the internal dynamics of each wave packet from the dynamics caused by the interaction we prove that there is almost no interaction of such wave packets. We also prove the validity of a formula for the envelope shift caused by the interaction of the wave packets. © 2008 Elsevier Inc. All rights reserved.


Seasonal acclimatization of antioxidants and photosynthesis in Chondrus crispus and Mastocarpus stellatus, two co-occurring red algae with differing stress tolerances

Date: 2004-01-01

Creator: Nissa L. Lohrmann, Barry A. Logan, Amy S. Johnson

Access: Open access

Mastocarpus stellatus and Chondrus crispus are red macroalgae that co-dominate the lower rocky intertidal zones of the northern Atlantic coast. M. stellatus is more tolerant than C. crispus of environmental stresses, particularly those experienced during winter. This difference in tolerance has been attributed, in part, to greater contents or activities of certain antioxidants in M. stellatus. We compared the photosynthetic capacities and activities of three antioxidant enzymes - superoxide dismutase (SOD), ascorbate peroxidase (APX), and glutathione reductase (GR) - as well as the contents of ascorbate from fronds of M. stellatus and C. crispus collected over a year. Photosynthetic capacity increased in winter, but did not differ between species in any season. The activities of the three antioxidant enzymes and the contents of ascorbate were significantly greater in tissues collected during months with mean air and water temperatures below 7.5°C ("cold" months; December, February, March, April) than in months with mean air temperatures above 11°C ("warm" months; June, July, August, October). Overall, C. crispus had significantly greater SOD and APX activities, while M. stellatus had higher ascorbate contents. Species-specific differences in GR activity depended upon mean monthly temperatures at the time of tissue collection; C. crispus had higher activities during cold months, whereas M. stellatus had higher activities during warm months. Taken together, these data indicate that increased ROS scavenging capacity is a part of winter acclimatization; however, only trends in ascorbate content support the hypothesis that greater levels of antioxidants underlie the relatively greater winter tolerance of M. stellatus in comparison to C. crispus.


Resistance to dislodgement: habitat and size-specific differences in morphology and tenacity in an intertidal snail

Date: 1993-01-01

Creator: G. C. Trussell, A. S. Johnson, S. G. Rudolph, E. S. Gilfillan

Access: Open access

The authors quantified 1) shell size (defined as the maximum projected surface area, MPSA); 2) shell shape; 3) foot area; 4) maximum force to dislodge a snail in shear; and 5) tenacity (force per foot area required to dislodge) of the herbivorous Littorina obtusata. Wave-exposed snails were smaller (lower average MPSA), and were shorter and had larger foot area and greater dislodgement force than did protected snails of similar MPSA. The greater dislodgement force at the exposed site was due to larger foot area, not to greater tenacity. -from Authors


Origami-based impact mitigation via rarefaction solitary wave creation

Date: 2019-01-01

Creator: Hiromi Yasuda, Yasuhiro Miyazawa, Efstathios G. Charalampidis, Christopher Chong, Panayotis G., Kevrekidis, Jinkyu Yang

Access: Open access

The principles underlying the art of origami paper folding can be applied to design sophisticated metamaterials with unique mechanical properties. By exploiting the flat crease patterns that determine the dynamic folding and unfolding motion of origami, we are able to design an origami-based metamaterial that can form rarefaction solitary waves. Our analytical, numerical, and experimental results demonstrate that this rarefaction solitary wave overtakes initial compressive strain waves, thereby causing the latter part of the origami structure to feel tension first instead of compression under impact. This counterintuitive dynamic mechanism can be used to create a highly efficient-yet reusable-impact mitigating system without relying on material damping, plasticity, or fracture.


Inbreeding shapes the evolution of marine invertebrates

Date: 2020-05-01

Creator: Kevin C. Olsen, Will H. Ryan, Alice A. Winn, Ellen T. Kosman, Jose A., Moscoso, Stacy A. Krueger-Hadfield, Scott C. Burgess, David B. Carlon, Richard K. Grosberg, Susan Kalisz, Don R. Levitan

Access: Open access

Inbreeding is a potent evolutionary force shaping the distribution of genetic variation within and among populations of plants and animals. Yet, our understanding of the forces shaping the expression and evolution of nonrandom mating in general, and inbreeding in particular, remains remarkably incomplete. Most research on plant mating systems focuses on self-fertilization and its consequences for automatic selection, inbreeding depression, purging, and reproductive assurance, whereas studies of animal mating systems have often assumed that inbreeding is rare, and that natural selection favors traits that promote outbreeding. Given that many sessile and sedentary marine invertebrates and marine macroalgae share key life history features with seed plants (e.g., low mobility, modular construction, and the release of gametes into the environment), their mating systems may be similar. Here, we show that published estimates of inbreeding coefficients (FIS) for sessile and sedentary marine organisms are similar and at least as high as noted in terrestrial seed plants. We also found that variation in FIS within invertebrates is related to the potential to self-fertilize, disperse, and choose mates. The similarity of FIS for these organismal groups suggests that inbreeding could play a larger role in the evolution of sessile and sedentary marine organisms than is currently recognized. Specifically, associations between traits of marine invertebrates and FIS suggest that inbreeding could drive evolutionary transitions between hermaphroditism and separate sexes, direct development and multiphasic life cycles, and external and internal fertilization.


Increasing forest loss worldwide from invasive pests requires new trade regulations

Date: 2014-10-01

Creator: Bitty A. Roy, Helen M. Alexander, Jennifer Davidson, Faith T. Campbell, Jeremy J., Burdon, Richard Sniezko, Clive Brasier

Access: Open access

Loss of forests due to non-native invasive pests (including insects, nematodes, and pathogens) is a global phenomenon with profound population, community, ecosystem, and economic impacts. We review the magnitude of pest-associated forest loss worldwide and discuss the major ecological and evolutionary causes and consequences of these invasions. After compiling and analyzing a dataset of pest invasions from 21 countries, we show that the number of forest pest invasions recorded for a given country has a significant positive relationship with trade (as indicated by gross domestic product) and is not associated with the amount of forested land within that country. We recommend revisions to existing international protocols for preventing pest entry and proliferation, including prohibiting shipments of non-essential plants and plant products unless quarantined. Because invasions often originate from taxa that are scientifically described only after their introduction, current phytosanitary regulations - which target specific, already named organisms - Are ineffective.


A simple polymerase chain reaction-based method for the construction of recombinase-mediated cassette exchange donor vectors

Date: 2008-11-01

Creator: Jack R. Bateman, C. Ting Wu

Access: Open access

Here we describe a simple method for generating donor vectors suitable for targeted transgenesis via recombinase-mediated cassette exchange (RMCE) using the ΦC31 integrase. This PCR-based strategy employs small attB "tails" on the primers used to amplify a sequence of interest, permitting the rapid creation of transgenes for in vivo analysis. Copyright © 2008 by the Genetics Society of America.


FMRF-NH2-related neuropeptides in Biomphalaria spp., intermediate hosts for schistosomiasis: Precursor organization and immunohistochemical localization

Date: 2021-09-01

Creator: Solymar Rolón-Martínez, Mohamed R. Habib, Tamer A. Mansour, Manuel Díaz-Ríos, Joshua J.C., Rosenthal, Xiao Nong Zhou, Roger P. Croll, Mark W. Miller

Access: Open access

Freshwater snails of the genus Biomphalaria serve as intermediate hosts for the digenetic trematode Schistosoma mansoni, the etiological agent for the most widespread form of intestinal schistosomiasis. As neuropeptide signaling in host snails can be altered by trematode infection, a neural transcriptomics approach was undertaken to identify peptide precursors in Biomphalaria glabrata, the major intermediate host for S. mansoni in the Western Hemisphere. Three transcripts that encode peptides belonging to the FMRF-NH2-related peptide (FaRP) family were identified in B. glabrata. One transcript encoded a precursor polypeptide (Bgl-FaRP1; 292 amino acids) that included eight copies of the tetrapeptide FMRF-NH2 and single copies of FIRF-NH2, FLRF-NH2, and pQFYRI-NH2. The second transcript encoded a precursor (Bgl-FaRP2; 347 amino acids) that comprised 14 copies of the heptapeptide GDPFLRF-NH2 and 1 copy of SKPYMRF-NH2. The precursor encoded by the third transcript (Bgl-FaRP3; 287 amino acids) recapitulated Bgl-FaRP2 but lacked the full SKPYMRF-NH2 peptide. The three precursors shared a common signal peptide, suggesting a genomic organization described previously in gastropods. Immunohistochemical studies were performed on the nervous systems of B. glabrata and B. alexandrina, a major intermediate host for S. mansoni in Egypt. FMRF-NH2-like immunoreactive (FMRF-NH2-li) neurons were located in regions of the central nervous system associated with reproduction, feeding, and cardiorespiration. Antisera raised against non-FMRF-NH2 peptides present in the tetrapeptide and heptapeptide precursors labeled independent subsets of the FMRF-NH2-li neurons. This study supports the participation of FMRF-NH2-related neuropeptides in the regulation of vital physiological and behavioral systems that are altered by parasitism in Biomphalaria.


Molecules and fossils reveal punctuated diversification in Caribbean "faviid" corals

Date: 2012-08-27

Creator: Sonja A. Schwartz, Ann F. Budd, David B. Carlon

Access: Open access

Background: Even with well-known sampling biases, the fossil record is key to understanding macro-evolutionary patterns. During the Miocene to Pleistocene in the Caribbean Sea, the fossil record of scleractinian corals shows a remarkable period of rapid diversification followed by massive extinction. Here we combine a time-calibrated molecular phylogeny based on three nuclear introns with an updated fossil stratigraphy to examine patterns of radiation and extinction in Caribbean corals within the traditional family Faviidae. Results: Concatenated phylogenetic analysis showed most species of Caribbean faviids were monophyletic, with the exception of two Manicina species. The time-calibrated tree revealed the stem group originated around the closure of the Tethys Sea (17.0 Ma), while the genus Manicina diversified during the Late Miocene (8.20 Ma), when increased sedimentation and productivity may have favored free-living, heterotrophic species. Reef and shallow water specialists, represented by Diploria and Favia, originate at the beginning of the Pliocene (5 - 6 Ma) as the Isthmus of Panama shoaled and regional productivity declined. Conclusions: Later origination of the stem group than predicted from the fossil record corroborates the hypothesis of morphological convergence in Diploria and Favia genera. Our data support the rapid evolution of morphological and life-history traits among faviid corals that can be linked to Mio-Pliocene environmental changes. © 2012 Schwartz et al.; licensee BioMed Central Ltd.


Non-amidated and amidated members of the C-type allatostatin (AST-C) family are differentially distributed in the stomatogastric nervous system of the American lobster, Homarus americanus

Date: 2018-03-01

Creator: Andrew E. Christie, Alexandra Miller, Rebecca Fernandez, Evyn S. Dickinson, Audrey, Jordan, Jessica Kohn, Mina C. Youn, Patsy S. Dickinson

Access: Open access

The crustacean stomatogastric nervous system (STNS) is a well-known model for investigating neuropeptidergic control of rhythmic behavior. Among the peptides known to modulate the STNS are the C-type allatostatins (AST-Cs). In the lobster, Homarus americanus, three AST-Cs are known. Two of these, pQIRYHQCYFNPISCF (AST-C I) and GNGDGRLYWRCYFNAVSCF (AST-C III), have non-amidated C-termini, while the third, SYWKQCAFNAVSCFamide (AST-C II), is C-terminally amidated. Here, antibodies were generated against one of the non-amidated peptides (AST-C I) and against the amidated isoform (AST-C II). Specificity tests show that the AST-C I antibody cross-reacts with both AST-C I and AST-C III, but not AST-C II; the AST-C II antibody does not cross-react with either non-amidated peptide. Wholemount immunohistochemistry shows that both subclasses (non-amidated and amidated) of AST-C are distributed throughout the lobster STNS. Specifically, the antibody that cross-reacts with the two non-amidated peptides labels neuropil in the CoGs and the stomatogastric ganglion (STG), axons in the superior esophageal (son) and stomatogastric (stn) nerves, and ~ 14 somata in each commissural ganglion (CoG). The AST-C II-specific antibody labels neuropil in the CoGs, STG and at the junction of the sons and stn, axons in the sons and stn, ~ 42 somata in each CoG, and two somata in the STG. Double immunolabeling shows that, except for one soma in each CoG, the non-amidated and amidated peptides are present in distinct sets of neuronal profiles. The differential distributions of the two AST-C subclasses suggest that the two peptide groups are likely to serve different modulatory roles in the lobster STNS.


Inter-animal variability in the effects of C-type allatostatin on the cardiac neuromuscular system in the lobster Homarus americanus

Date: 2012-07-01

Creator: Teerawat Wiwatpanit, Brian Powers, Patsy S. Dickinson

Access: Open access

Although the global effects of many modulators on pattern generators are relatively consistent among preparations, modulators can induce different alterations in different preparations. We examined the mechanisms that underlie such variability in the modulatory effects of the peptide C-type allatostatin (C-AST; pQIRYHQCYFNPISCF) on the cardiac neuromuscular system of the lobster Homarus americanus. Perfusion of C-AST through the semi-intact heart consistently decreased the frequency of ongoing contractions. However, the effect of C-AST on contraction amplitude varied between preparations, decreasing in some preparations and increasing in others. To investigate this variable effect, we examined the effects of C-AST both peripherally and centrally. When contractions of the myocardium were elicited by controlled stimuli, C-AST did not alter heart contraction at the periphery (myocardium or neuromuscular junction) in any hearts. However, when applied either to the semi-intact heart or to the cardiac ganglion (CG) isolated from hearts that responded to C-AST with increased contraction force, C-AST increased both motor neuron burst duration and the number of spikes per burst by about 25%. In contrast, CG output was increased only marginally in hearts that responded to C-AST with a decrease in contraction amplitude, suggesting that the decrease in amplitude in those preparations resulted from decreased peripheral facilitation. Our data suggest that the differential effects of a single peptide on the cardiac neuromuscular system are due solely to differential effects of the peptide on the pattern generator; the extent to which the peptide induces increased burst duration is crucial in determining its overall effect on the system. © 2012. Published by The Company of Biologists Ltd.


The contributions of motor neuronal and muscle modulation to behavioral flexibility in the stomatogastric system

Date: 1995-12-01

Creator: Patsy S. Dickinson

Access: Open access

The stomatogastric nervous system of crustaceans, which controls the four parts ofthe foregut, is subject to modulation at all levels, sensory, central and motor. Modulation of the central pattern generators, which are themselves made up largely of motor neurons, providesfor increased behavioral flexibility in a variety of ways. First, each of the pattern generators can be reconfigured to give multiple outputs. Second, the "boundaries" of the different pattern generators are in fact somewhat fluid, so that the neuronal composition of the pattern generators can be altered. For example, neurons can switch from one pattern generator toanother, or two or more pattern generators can fuse to generate an entirely new pattern and thereby produce a new behavior. The mechanisms responsible for many of these modulations include alterations of both intrinsic properties and synaptic interactions between neurons. In addition, the alteration of membrane properties contributes more directly to the behavioral output by changing action potential frequency. Finally, the muscles of the stomatogastric system can themselves be modulated, with the cpvl muscle, for example, becoming an endogenous oscillator in the presence of either dopamine or the peptide FMRFamide. © 1995 by the American Society of Zoologists.


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.


Neuropeptide modulation of pattern-generating systems in crustaceans: comparative studies and approaches

Date: 2016-12-01

Creator: Patsy S. Dickinson, Xuan Qu, Meredith E. Stanhope

Access: Open access

Central pattern generators are subject to modulation by peptides, allowing for flexibility in patterned output. Current techniques used to characterize peptides include mass spectrometry and transcriptomics. In recent years, hundreds of neuropeptides have been sequenced from crustaceans; mass spectrometry has been used to identify peptides and to determine their levels and locations, setting the stage for comparative studies investigating the physiological roles of peptides. Such studies suggest that there is some evolutionary conservation of function, but also divergence of function even within a species. With current baseline data, it should be possible to begin using comparative approaches to ask fundamental questions about why peptides are encoded the way that they are and how this affects nervous system function.


Managing server clusters on intermittent power

Date: 2015-01-01

Creator: Navin Sharma, Dilip Krishnappa, Sean Barker, David Irwin, Prashant, Shenoy

Access: Open access

Reducing the energy footprint of data centers continues to receive significant attention due to both its financial and environmental impact. There are numerous methods that limit the impact of both factors, such as expanding the use of renewable energy or participating in automated demand-response programs. To take advantage of these methods, servers and applications must gracefully handle intermittent constraints in their power supply. In this paper, we propose blinking-metered transitions between a high-power active state and a low-power inactive state-as the primary abstraction for conforming to intermittent power constraints. We design Blink, an application-independent hardware-software platform for developing and evaluating blinking applications, and define multiple types of blinking policies.We then use Blink to design both a blinking version of memcached (BlinkCache) and a multimedia cache (GreenCache) to demonstrate how application characteristics affect the design of blink-aware distributed applications. Our results show that for BlinkCache, a load-proportional blinking policy combines the advantages of both activation and synchronous blinking for realistic Zipf-like popularity distributions and wind/solar power signals by achieving near optimal hit rates (within 15% of an activation policy), while also providing fairer access to the cache (within 2% of a synchronous policy) for equally popular objects. In contrast, for GreenCache, due to multimedia workload patterns, we find that a staggered load proportional blinking policy with replication of the first chunk of each video reduces the buffering time at all power levels, as compared to activation or load-proportional blinking policies.


Targeted identification of glycosylated proteins in the gastric pathogen helicobacter pylori (Hp)

Date: 2013-09-01

Creator: Kanokwan Champasa, Scott A. Longwell, Aimee M. Eldridge, Elizabeth A. Stemmler, Danielle H., Dube

Access: Open access

Virulence of the gastric pathogen Helicobacter pylori (Hp) is directly linked to the pathogen's ability to glycosylate proteins; for example, Hp flagellin proteins are heavily glycosylated with the unusual nine-carbon sugar pseudaminic acid, and this modification is absolutely essential for Hp to synthesize functional flagella and colonize the host's stomach. Although Hp's glycans are linked to pathogenesis, Hp's glycome remains poorly understood; only the two flagellin glycoproteins have been firmly characterized in Hp. Evidence from our laboratory suggests that Hp synthesizes a large number of as-yet unidentified glycoproteins. Here we set out to discover Hp's glycoproteins by coupling glycan metabolic labeling with mass spectrometry analysis. An assessment of the subcellular distribution of azide-labeled proteins by Western blot analysis indicated that glycoproteins are present throughout Hp and may therefore serve diverse functions. To identify these species, Hp's azide-labeled glycoproteins were tagged via Staudinger ligation, enriched by tandem affinity chromatography, and analyzed by multidimensional protein identification technology. Direct comparison of enriched azide-labeled glycoproteins with a mock-enriched control by both SDS-PAGE and mass spectrometry-based analyses confirmed the selective enrichment of azide-labeled glycoproteins. We identified 125 candidate glycoproteins with diverse biological functions, including those linked with pathogenesis. Mass spectrometry analyses of enriched azide-labeled glycoproteins before and after cleavage of O-linked glycans revealed the presence of Staudinger ligation-glycan adducts in samples only after beta-elimination, confirming the synthesis of O-linked glycoproteins in Hp. Finally, the secreted colonization factors urease alpha and urease beta were biochemically validated as glycosylated proteins via Western blot analysis as well as by mass spectrometry analysis of cleaved glycan products. These data set the stage for the development of glycosylation-based therapeutic strategies, such as new vaccines based on natively glycosylated Hp proteins, to eradicate Hp infection. Broadly, this report validates metabolic labeling as an effective and efficient approach for the identification of bacterial glycoproteins. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.


Identification of SYWKQCAFNAVSCFamide: A broadly conserved crustacean C-type allatostatin-like peptide with both neuromodulatory and cardioactive properties

Date: 2009-04-15

Creator: Patsy S. Dickinson, Teerawat Wiwatpanit, Emily R. Gabranski, Rachel J. Ackerman, Jake S., Stevens, Christopher R. Cashman, Elizabeth A. Stemmler, Andrew E. Christie

Access: Open access

The allatostatins comprise three structurally distinct peptide families that regulate juvenile hormone production by the insect corpora allata. A-type family members contain the C-terminal motif -YXFGLamide and have been found in species from numerous arthropod taxa. Members of the B-type family exhibit a -WX6Wamide C-terminus and, like the A-type peptides, appear to be broadly conserved within the Arthropoda. By contrast, members of the C-type family, typified by the unblocked C-terminus -PISCF, a pyroglutamine blocked N-terminus, and a disulfide bridge between two internal Cys residues, have only been found in holometabolous insects, i.e. lepidopterans and dipterans. Here, using transcriptomics, we have identified SYWKQCAFNAVSCFamide (disulfide bridging predicted between the two Cys residues), a known honeybee and water flea C-typelike peptide, from the American lobster Homarus americanus (infraorder Astacidea). Using matrix assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS), a mass corresponding to that of SYWKQCAFNAVSCFamide was detected in the H. americanus brain, supporting the existence of this peptide and its theorized structure. Furthermore, SYWKQCAFNAVSCFamide was detected by MALDI-FTMS in neural tissues from five additional astacideans as well as 19 members of four other decapod infraorders (i.e. Achelata, Anomura, Brachyura and Thalassinidea), suggesting that it is a broadly conserved decapod peptide. In H. americanus, SYWKQCAFNAVSCFamide is capable of modulating the output of both the pyloric circuit of the stomatogastric nervous system and the heart. This is the first demonstration of bioactivity for this peptide in any species.


Seeking shear waves in liquids with picosecond ultrasonics

Date: 2007-12-01

Creator: M. E. Msall, O. B. Wright, O. Matsuda

Access: Open access

Picosecond shear acoustic pulses can be generated in solids using ultrashort optical pulses. Here we use this technique to seek high frequency shear waves in water, ethylene glycol and glycerol while simultaneously measuring high frequency longitudinal wave velocity and attenuation. We use a silica thin film on (114) GaAs to generate shear and longitudinal acoustic pulses at frequencies up to ∼50 GHz by ultrashort pulsed optical excitation. The acoustic pulses are transmitted into adjacent liquids, and are detected through variations in the optical reflectivity. Although we could not detect shear waves in these liquids, we did detect gigahertz longitudinal elastic stiffening. © 2007 IOP Publishing Ltd.


One-armed spiral instability in differentially rotating stars

Date: 2003-01-01

Creator: M. Saijo, T.W. Baumgarte, S.L. Shapiro

Access: Open access



Search for τ-→γμ-: A test of lepton number conservation

Date: 1993-01-01

Creator: A. Bean, J. Gronberg, R. Kutschke, S. Menary, R. J., Morrison, H. Nelson, J. Richman, H. Tajima, D. Schmidt, D. Sperka, M. Witherell, M. Procario, S. Yang, M. Daoudi, W. T. Ford, D. R. Johnson, K. Lingel, M. Lohner, P. Rankin, J. G. Smith, J. P. Alexander, C. Bebek, K. Berkelman, D. Besson, T. E. Browder, D. G. Cassel, D. M. Coffman, P. S. Drell, R. Ehrlich, R. S. Galik, M. Garcia-Sciveres

Access: Open access

A search for the lepton mumber violating decay of the τ lepton to the γμ final state has been performed with the CLEO II detector at the Cornell e+e- storage ring CESR. In a data sample that corresponds to an integrated luminosity of 1.55 fb-1, we observe no candidates in the signal region. We thus determine an upper limit of B(τ-→γμ-)<4. 2×10-6 at 90% confidence level. © 1993 The American Physical Society.